*******************************************************************
*-----------------------------------------------------------------*
*-------------------Pepsi-SAXS, a small angle --------------------*
*------- adaptive X-ray scattering reconstruction algorithm-------*
*--- that uses polynomial expansions of scattering amplitudes.----*
*---------- Authors: Sergei Grudinin & Maria Garkavenko.----------*
* Reference: Sergei Grudinin, Maria Garkavenko & Andrei Kazennov,-*
*----- Pepsi-SAXS : an adaptive method for rapid and accurate-----*
*------computation of small angle X-ray scattering profiles.------*
*--- Copyright (c): Nano-D team, Inria/CNRS Grenoble, France &----*
*----- Laboratoty of Advanced Studies of Membrane Proteins, ------*
*----------------MIPT Moscow, Russia, 2012 - 2018.----------------*
* Available at : http://team.inria.fr/nano-d/software/pepsi-saxs -*
*-------------------- For academic use only! ---------------------*
*--------------- e-mail: sergei.grudinin@inria.fr ----------------*
*-----------------------------------------------------------------*
*******************************************************************
Version.......................................................... : 3.0 from May 2020
Run at........................................................... : lpct-ic-e-tm on Sun Dec  1 00:45:08 2024
Command-line arguments........................................... : /home/terez/progs/Pepsi-SAXS/Pepsi-SAXS --angular_units 1 last_cyana_67.pdb S7_pH68_M08-lq_M20-hq_smooth3.dat -o logs/S7_pH68_M08-lq_M20-hq_smooth3_last_cyana_67.fit 
========================Reading PDB file=========================
PDB filename..................................................... : last_cyana_67.pdb
Number of chains read............................................ : 1
Number of atoms read............................................. : 508
====================Analysing input PDB data=====================
Geometric center at.............................................. : [-16.4355 A, 17.472 A, 9.52815 A]
Radius of gyration............................................... : 25.5713 A
Maximum extension from the center................................ : 52.5287 A
Number of residues............................................... : 62
Chemical formula................................................. : C299H536N106O99S4
Expected formula................................................. : C299H536N106O99S4 (different by 0.00%)
Total molecular weight........................................... : 7.31836 kDa
Molecular concentration.......................................... : 1 mg/mL
Intensity scaling................................................ : 6.53433e-09
==================Computing the hydration layer==================
Accessible solvent radius........................................ : 3 A
Width of the hydration shell..................................... : 5 A
Number of points in the hydration shell.......................... : 580
Radius of gyration of the hydration shell........................ : 30.896 A
Radius of gyration of the envelope............................... : 29.4478 A
=========================Initialization==========================
Angular units.................................................... : 1/A, q = 4pi sin(theta)/lambda
Maximum number of processors..................................... : 4
Number of processors online...................................... : 4
Number of processors used........................................ : 4
===================Reading experimental curve====================
Experimental curve read from..................................... : S7_pH68_M08-lq_M20-hq_smooth3.dat
Data smearing.................................................... : off
Number of experimental points.................................... : 288
Minimum angle in the data file................................... : 0.008326
Maximum angle in the data file................................... : 0.3501
Angular units multiplied by...................................... : 1
Estimated resolution............................................. : 17.9468 A
===================Computing Rg from the curve===================
Experimental Rg.................................................. : 26.5664 A
===================Adaptive memory allocation====================
Estimated minimal expansion order of spherical harmonics......... : 11
Actually used order of spherical harmonics....................... : 11
====================Initializing form factors====================
Number of X-ray atom groups used................................. : 69
==========Computing amplitudes for the hydration shell===========
=========Computing atomic and excluded volume amplitudes=========
Number of atomic groups.......................................... : 508
Average radius of the atomic group............................... : 1.61584 A
Total number of electrons........................................ : 3909.68
Displaced (Dry) Volume........................................... : 8977.31 A^3
======================Computing intensities======================
Bulk SLD......................................................... : 3.33986 x10e-6/A^2
================Fitting to the experimental curve================
Number of search points in r0.................................... : 100
Minimum r0....................................................... : 1.53505 A
Maximum r0....................................................... : 1.69663 A
Number of search points in d_rho................................. : 100
Minimum d_rho.................................................... : 0 e/A^3
Maximum d_rho.................................................... : 0.0334 e/A^3
Best d_rho found................................................. : 0.016032 e/A^3
Best r0 found.................................................... : 1.68694 A^3
Chi.............................................................. : 0.859325
Chi^2............................................................ : 0.738439
Scaling factor between the intensities........................... : 3.76286
Displaced Volume................................................. : 10215.2 A^3
I(0)............................................................. : 0.0117262
=====================Writing the output file=====================
Output file name................................................. : logs/S7_pH68_M08-lq_M20-hq_smooth3_last_cyana_67.fit
Log file name.................................................... : logs/S7_pH68_M08-lq_M20-hq_smooth3_last_cyana_67.log
=================================================================
=========================== Timing : ============================
=================================================================
Parsing arguments................................................ : 0.000344303 s
Reading PDB file................................................. : 0.00119144 s
Analysing input PDB data......................................... : 0.000300361 s
Computing the hydration layer.................................... : 0.000858585 s
Initialization................................................... : 8.534e-06 s
Reading experimental curve....................................... : 0.000962911 s
Computing Rg from the curve...................................... : 0.000344562 s
Adaptive memory allocation....................................... : 4.1175e-05 s
Initializing form factors........................................ : 0.00102632 s
Computing amplitudes for the hydration shell..................... : 0.00206079 s
Computing atomic and excluded volume amplitudes.................. : 0.00295352 s
Computing intensities............................................ : 7.4478e-05 s
Fitting to the experimental curve................................ : 0.00309709 s
Writing the output file.......................................... : 0.000380017 s
.................................................................
Total time : .................................................... : 0.0136442 s
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