*******************************************************************
*-----------------------------------------------------------------*
*-------------------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 - 2015.----------------*
* 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.................................................... : TET-SLD_b.pdb
Number of chains read............................................ : 1
Number of atoms read............................................. : 3829
====================Analysing input PDB data=====================
Geometric center at.............................................. : [3.50555 A, -1.79169 A, -3.59255 A]
Radius of gyration............................................... : 33.4787 A
Maximum extention from the center................................ : 57.1699 A
Number of residues............................................... : 464
Molecular weight................................................. : 54.5286 kDa
==================Computing the hydration layer==================
Number of points in the hydration shell.......................... : 367
Radius of gyration of the hydration shell........................ : 38.646 A
Radius of gyration of the envelope............................... : 36.7736 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..................................... : TET-SLD_merge_003.dat
New angular units................................................ : 1/nm, q = 4pi sin(theta)/lambda
Number of experimental points.................................... : 1014
Minimum angle in the data file................................... : 0.0169353
Maximum angle in the data file................................... : 0.4946
Angular units multiplied by...................................... : 0.1
Estimated resolution............................................. : 12.7036 A
===================Adaptive memory allocation====================
Estimated minimal expansion order of spherical harmonics......... : 19
Actually used order of spherical harmonics....................... : 19
====================Initializing form factors====================
Number of atom groups used....................................... : 35
==========Computing amplitudes for the hydration shell===========
=========Computing atomic and excluded volume amplitudes=========
Number of atomic groups.......................................... : 3829
Average radius of the atomic group............................... : 1.60646 A
Total number of electrons........................................ : 29110
Displaced Volume................................................. : 66494.3 A^3
======================Computing intensities======================
================Fitting to the experimental curve================
Number of search points in r0.................................... : 100
Minimum r0....................................................... : 1.44581 e/A^3
Maximum r0....................................................... : 1.92775 e/A^3
Number of search points in d_rho................................. : 100
Minimum d_rho.................................................... : -0.015 e/A^3
Maximum d_rho.................................................... : 0.06 e/A^3
Best d_rho found................................................. : -0.00075 e/A^3
Best r0 found.................................................... : 1.81209 e/A^3
Chi.............................................................. : 2.47419
Chi^2............................................................ : 6.12163
=====================Writing the output file=====================
Output file name................................................. : TET-SLD_b.fit
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=========================== Timing : ============================
=================================================================
Parsing arguments................................................ : 0.000272427 s
Reading PDB file................................................. : 0.00476062 s
Analysing input PDB data......................................... : 0.000875961 s
Computing the hydration layer.................................... : 0.00127804 s
Initialization................................................... : 3.1141e-05 s
Reading experimental curve....................................... : 0.00258967 s
Adaptive memory allocation....................................... : 0.000153221 s
Initializing form factors........................................ : 0.00214814 s
Computing amplitudes for the hydration shell..................... : 0.00377761 s
Computing atomic and excluded volume amplitudes.................. : 0.0456915 s
Computing intensities............................................ : 0.000158705 s
Fitting to the experimental curve................................ : 0.0364309 s
Writing the output file.......................................... : 0.0009025 s
.................................................................
Total time : .................................................... : 0.0990706 s
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