*******************************************************************
*-----------------------------------------------------------------*
*-------------------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 ----------------*
*-----------------------------------------------------------------*
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========================Reading PDB file=========================
Read PDB file.................................................... : Centroid_17_closeConf.pdb
Number of chains read............................................ : 2
Number of atoms read............................................. : 12791
====================Analysing input PDB data=====================
Geometric center at.............................................. : [-15.0934 A, -34.5806 A, -31.9895 A]
Radius of gyration............................................... : 90.8688 A
Maximum extention from the center................................ : 243.058 A
Number of residues............................................... : 1736
Molecular weight................................................. : 183.732 kDa
==================Computing the hydration layer==================
Accessable solvent radius........................................ : 3 A
Width of the hydration shell..................................... : 5 A
Number of points in the hydration shell.......................... : 7365
Radius of gyration of the hydration shell........................ : 104.161 A
Radius of gyration of the envelope............................... : 98.4246 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..................................... : FL_6_600.dat
New angular units................................................ : 1/nm, q = 4pi sin(theta)/lambda
Number of experimental points.................................... : 595
Minimum angle in the data file................................... : 0.00598517
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......... : 30
Actually used order of spherical harmonics....................... : 30
====================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.......................................... : 12791
Average radius of the atomic group............................... : 1.6118 A
Total number of electrons........................................ : 97804
Displaced Volume................................................. : 224351 A^3
======================Computing intensities======================
================Fitting to the experimental curve================
Number of search points in r0.................................... : 100
Minimum r0....................................................... : 1.53121 e/A^3
Maximum r0....................................................... : 1.69239 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................................................. : 0.004008 e/A^3
Best r0 found.................................................... : 1.67305 e/A^3
Chi.............................................................. : 0.926673
Chi^2............................................................ : 0.858723
Displaced Volume................................................. : 250912 A^3
=====================Writing the output file=====================
Output file name................................................. : logs/FL_6_600_Centroid_17_closeConf.fit
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=========================== Timing : ============================
=================================================================
Parsing arguments................................................ : 0.005385 s
Reading PDB file................................................. : 0.012222 s
Analysing input PDB data......................................... : 0.005738 s
Computing the hydration layer.................................... : 0.039249 s
Initialization................................................... : 2.9e-05 s
Reading experimental curve....................................... : 0.004058 s
Adaptive memory allocation....................................... : 0.00078 s
Initializing form factors........................................ : 0.004449 s
Computing amplitudes for the hydration shell..................... : 0.150725 s
Computing atomic and excluded volume amplitudes.................. : 0.36835 s
Computing intensities............................................ : 0.00031 s
Fitting to the experimental curve................................ : 0.014277 s
Writing the output file.......................................... : 0.000775 s
.................................................................
Total time : .................................................... : 0.606352 s
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