*******************************************************************
*-----------------------------------------------------------------*
*-------------------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 - 2016.----------------*
* Available at : http://team.inria.fr/nano-d/software/pepsi-saxs -*
*-------------------- For academic use only! ---------------------*
*--------------- e-mail: sergei.grudinin@inria.fr ----------------*
*-----------------------------------------------------------------*
*******************************************************************
========================Reading PDB file=========================
Read PDB file.................................................... : FINALRBCC.pdb
Number of chains read............................................ : 4
Number of atoms read............................................. : 6437
====================Analysing input PDB data=====================
Geometric center at.............................................. : [126.608 A, -24.7416 A, 1198.25 A]
Radius of gyration............................................... : 75.7921 A
Maximum extention from the center................................ : 193.245 A
Number of residues............................................... : 845
Molecular weight................................................. : 92.6551 kDa
==================Computing the hydration layer==================
Accessable solvent radius........................................ : 3 A
Width of the hydration shell..................................... : 5 A
Number of points in the hydration shell.......................... : 3719
Radius of gyration of the hydration shell........................ : 89.024 A
Radius of gyration of the envelope............................... : 83.3637 A
=========================Initialization==========================
Angular units.................................................... : 1/A, q = 4pi sin(theta)/lambda
Maximum number of processors..................................... : 8
Number of processors online...................................... : 8
Number of processors used........................................ : 8
===================Reading experimental curve====================
Experimental curve read from..................................... : RBCC_cut_3_600_NM.dat
New angular units................................................ : 1/nm, q = 4pi sin(theta)/lambda
Number of experimental points.................................... : 598
Minimum angle in the data file................................... : 0.00457362
Maximum angle in the data file................................... : 0.285473
Angular units multiplied by...................................... : 0.1
Estimated resolution............................................. : 22.0098 A
===================Adaptive memory allocation====================
Estimated minimal expansion order of spherical harmonics......... : 25
Actually used order of spherical harmonics....................... : 25
====================Initializing form factors====================
Number of atom groups used....................................... : 36
==========Computing amplitudes for the hydration shell===========
=========Computing atomic and excluded volume amplitudes=========
Number of atomic groups.......................................... : 6437
Average radius of the atomic group............................... : 1.60979 A
Total number of electrons........................................ : 49309.6
Displaced Volume................................................. : 112482 A^3
======================Computing intensities======================
================Fitting to the experimental curve================
Number of search points in r0.................................... : 100
Minimum r0....................................................... : 1.5293 e/A^3
Maximum r0....................................................... : 1.69028 e/A^3
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................................................. : 0.02171 e/A^3
Best r0 found.................................................... : 1.68867 e/A^3
Chi.............................................................. : 0.959224
Chi^2............................................................ : 0.920111
Displaced Volume................................................. : 129840 A^3
=====================Writing the output file=====================
Output file name................................................. : logs/RBCC_cut_3_600_NM_FINALRBCC.fit
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=========================== Timing : ============================
=================================================================
Parsing arguments................................................ : 0.004946 s
Reading PDB file................................................. : 0.00706 s
Analysing input PDB data......................................... : 0.003399 s
Computing the hydration layer.................................... : 0.01308 s
Initialization................................................... : 3.6e-05 s
Reading experimental curve....................................... : 0.00381 s
Adaptive memory allocation....................................... : 0.000629 s
Initializing form factors........................................ : 0.003852 s
Computing amplitudes for the hydration shell..................... : 0.053862 s
Computing atomic and excluded volume amplitudes.................. : 0.115128 s
Computing intensities............................................ : 0.000252 s
Fitting to the experimental curve................................ : 0.020128 s
Writing the output file.......................................... : 0.00091 s
.................................................................
Total time : .................................................... : 0.227097 s
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