Starting phenix.real_space_refine on Sun Oct 25 01:50:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y70_72637/10_2026/9y70_72637.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y70_72637/10_2026/9y70_72637.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9y70_72637/10_2026/9y70_72637.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y70_72637/10_2026/9y70_72637.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9y70_72637/10_2026/9y70_72637.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y70_72637/10_2026/9y70_72637.map" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.072 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 9820 2.51 5 N 2380 2.21 5 O 2652 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14948 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3710 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 6, 'TRANS': 446} Chain breaks: 3 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'AQV': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D Time building chain proxies: 3.59, per 1000 atoms: 0.24 Number of scatterers: 14948 At special positions: 0 Unit cell: (107.167, 107.167, 120.157, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 2652 8.00 N 2380 7.00 C 9820 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.18 Conformation dependent library (CDL) restraints added in 562.9 milliseconds 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3464 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 8 sheets defined 70.9% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 39 through 49 Processing helix chain 'A' and resid 51 through 59 Processing helix chain 'A' and resid 63 through 106 removed outlier: 3.564A pdb=" N GLY A 67 " --> pdb=" O PRO A 63 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN A 69 " --> pdb=" O LYS A 65 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 140 Processing helix chain 'A' and resid 140 through 145 Processing helix chain 'A' and resid 194 through 201 removed outlier: 4.622A pdb=" N GLU A 201 " --> pdb=" O VAL A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 207 Processing helix chain 'A' and resid 208 through 212 removed outlier: 3.575A pdb=" N ARG A 212 " --> pdb=" O SER A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 236 removed outlier: 3.602A pdb=" N VAL A 235 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 330 removed outlier: 3.627A pdb=" N TYR A 330 " --> pdb=" O PHE A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.679A pdb=" N PHE A 342 " --> pdb=" O ASP A 338 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N VAL A 343 " --> pdb=" O GLN A 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 338 through 343' Processing helix chain 'A' and resid 344 through 370 removed outlier: 3.824A pdb=" N VAL A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU A 349 " --> pdb=" O GLY A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 398 removed outlier: 3.560A pdb=" N TRP A 390 " --> pdb=" O THR A 386 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 413 Processing helix chain 'A' and resid 413 through 440 removed outlier: 3.522A pdb=" N GLY A 440 " --> pdb=" O TRP A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 447 removed outlier: 3.940A pdb=" N GLU A 447 " --> pdb=" O GLU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 461 Processing helix chain 'A' and resid 464 through 471 Processing helix chain 'A' and resid 476 through 497 Processing helix chain 'A' and resid 497 through 519 removed outlier: 3.513A pdb=" N LYS A 515 " --> pdb=" O HIS A 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 49 Processing helix chain 'B' and resid 51 through 59 Processing helix chain 'B' and resid 63 through 106 removed outlier: 3.564A pdb=" N GLY B 67 " --> pdb=" O PRO B 63 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN B 69 " --> pdb=" O LYS B 65 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 140 Processing helix chain 'B' and resid 140 through 145 Processing helix chain 'B' and resid 194 through 201 removed outlier: 4.622A pdb=" N GLU B 201 " --> pdb=" O VAL B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 207 Processing helix chain 'B' and resid 208 through 212 removed outlier: 3.575A pdb=" N ARG B 212 " --> pdb=" O SER B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 236 removed outlier: 3.602A pdb=" N VAL B 235 " --> pdb=" O LEU B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 330 removed outlier: 3.627A pdb=" N TYR B 330 " --> pdb=" O PHE B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.680A pdb=" N PHE B 342 " --> pdb=" O ASP B 338 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N VAL B 343 " --> pdb=" O GLN B 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 338 through 343' Processing helix chain 'B' and resid 344 through 370 removed outlier: 3.824A pdb=" N VAL B 348 " --> pdb=" O ASN B 344 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU B 349 " --> pdb=" O GLY B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 398 removed outlier: 3.560A pdb=" N TRP B 390 " --> pdb=" O THR B 386 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 413 Processing helix chain 'B' and resid 413 through 440 removed outlier: 3.522A pdb=" N GLY B 440 " --> pdb=" O TRP B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 447 removed outlier: 3.941A pdb=" N GLU B 447 " --> pdb=" O GLU B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 461 Processing helix chain 'B' and resid 464 through 471 Processing helix chain 'B' and resid 476 through 497 Processing helix chain 'B' and resid 497 through 519 removed outlier: 3.513A pdb=" N LYS B 515 " --> pdb=" O HIS B 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 49 Processing helix chain 'C' and resid 51 through 59 Processing helix chain 'C' and resid 63 through 106 removed outlier: 3.564A pdb=" N GLY C 67 " --> pdb=" O PRO C 63 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN C 69 " --> pdb=" O LYS C 65 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE C 70 " --> pdb=" O LEU C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 140 Processing helix chain 'C' and resid 140 through 145 Processing helix chain 'C' and resid 194 through 201 removed outlier: 4.622A pdb=" N GLU C 201 " --> pdb=" O VAL C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 207 Processing helix chain 'C' and resid 208 through 212 removed outlier: 3.575A pdb=" N ARG C 212 " --> pdb=" O SER C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 236 removed outlier: 3.602A pdb=" N VAL C 235 " --> pdb=" O LEU C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 330 removed outlier: 3.628A pdb=" N TYR C 330 " --> pdb=" O PHE C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.678A pdb=" N PHE C 342 " --> pdb=" O ASP C 338 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL C 343 " --> pdb=" O GLN C 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 338 through 343' Processing helix chain 'C' and resid 344 through 370 removed outlier: 3.824A pdb=" N VAL C 348 " --> pdb=" O ASN C 344 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU C 349 " --> pdb=" O GLY C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 398 removed outlier: 3.560A pdb=" N TRP C 390 " --> pdb=" O THR C 386 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL C 391 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 413 Processing helix chain 'C' and resid 413 through 440 removed outlier: 3.522A pdb=" N GLY C 440 " --> pdb=" O TRP C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 447 removed outlier: 3.940A pdb=" N GLU C 447 " --> pdb=" O GLU C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 461 Processing helix chain 'C' and resid 464 through 471 Processing helix chain 'C' and resid 476 through 497 Processing helix chain 'C' and resid 497 through 519 removed outlier: 3.512A pdb=" N LYS C 515 " --> pdb=" O HIS C 511 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 49 Processing helix chain 'D' and resid 51 through 59 Processing helix chain 'D' and resid 63 through 106 removed outlier: 3.563A pdb=" N GLY D 67 " --> pdb=" O PRO D 63 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN D 69 " --> pdb=" O LYS D 65 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE D 70 " --> pdb=" O LEU D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 140 Processing helix chain 'D' and resid 140 through 145 Processing helix chain 'D' and resid 194 through 201 removed outlier: 4.622A pdb=" N GLU D 201 " --> pdb=" O VAL D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 207 Processing helix chain 'D' and resid 208 through 212 removed outlier: 3.576A pdb=" N ARG D 212 " --> pdb=" O SER D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 236 removed outlier: 3.602A pdb=" N VAL D 235 " --> pdb=" O LEU D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 330 removed outlier: 3.626A pdb=" N TYR D 330 " --> pdb=" O PHE D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 343 removed outlier: 3.679A pdb=" N PHE D 342 " --> pdb=" O ASP D 338 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL D 343 " --> pdb=" O GLN D 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 338 through 343' Processing helix chain 'D' and resid 344 through 370 removed outlier: 3.824A pdb=" N VAL D 348 " --> pdb=" O ASN D 344 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU D 349 " --> pdb=" O GLY D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 398 removed outlier: 3.560A pdb=" N TRP D 390 " --> pdb=" O THR D 386 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL D 391 " --> pdb=" O LEU D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 413 Processing helix chain 'D' and resid 413 through 440 removed outlier: 3.522A pdb=" N GLY D 440 " --> pdb=" O TRP D 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 443 through 447 removed outlier: 3.941A pdb=" N GLU D 447 " --> pdb=" O GLU D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 461 Processing helix chain 'D' and resid 464 through 471 Processing helix chain 'D' and resid 476 through 497 Processing helix chain 'D' and resid 497 through 519 removed outlier: 3.512A pdb=" N LYS D 515 " --> pdb=" O HIS D 511 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 121 Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 121 removed outlier: 6.884A pdb=" N LEU A 218 " --> pdb=" O TYR A 168 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N TYR A 168 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN A 220 " --> pdb=" O GLN A 166 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 119 through 121 Processing sheet with id=AA4, first strand: chain 'B' and resid 119 through 121 removed outlier: 6.885A pdb=" N LEU B 218 " --> pdb=" O TYR B 168 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N TYR B 168 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN B 220 " --> pdb=" O GLN B 166 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 119 through 121 Processing sheet with id=AA6, first strand: chain 'C' and resid 119 through 121 removed outlier: 6.885A pdb=" N LEU C 218 " --> pdb=" O TYR C 168 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N TYR C 168 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN C 220 " --> pdb=" O GLN C 166 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 119 through 121 Processing sheet with id=AA8, first strand: chain 'D' and resid 119 through 121 removed outlier: 6.884A pdb=" N LEU D 218 " --> pdb=" O TYR D 168 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N TYR D 168 " --> pdb=" O LEU D 218 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN D 220 " --> pdb=" O GLN D 166 " (cutoff:3.500A) 1165 hydrogen bonds defined for protein. 3399 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.46 Time building geometry restraints manager: 1.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2336 1.31 - 1.43: 4255 1.43 - 1.56: 8565 1.56 - 1.68: 4 1.68 - 1.81: 132 Bond restraints: 15292 Sorted by residual: bond pdb=" CA SER B 311 " pdb=" CB SER B 311 " ideal model delta sigma weight residual 1.528 1.437 0.091 1.56e-02 4.11e+03 3.42e+01 bond pdb=" CA SER D 311 " pdb=" CB SER D 311 " ideal model delta sigma weight residual 1.528 1.437 0.091 1.56e-02 4.11e+03 3.42e+01 bond pdb=" CA SER A 311 " pdb=" CB SER A 311 " ideal model delta sigma weight residual 1.528 1.438 0.091 1.56e-02 4.11e+03 3.40e+01 bond pdb=" CA SER C 311 " pdb=" CB SER C 311 " ideal model delta sigma weight residual 1.528 1.438 0.091 1.56e-02 4.11e+03 3.38e+01 bond pdb=" C ARG D 310 " pdb=" O ARG D 310 " ideal model delta sigma weight residual 1.236 1.180 0.057 1.15e-02 7.56e+03 2.44e+01 ... (remaining 15287 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 20328 2.22 - 4.44: 279 4.44 - 6.66: 53 6.66 - 8.88: 32 8.88 - 11.09: 12 Bond angle restraints: 20704 Sorted by residual: angle pdb=" N PHE D 322 " pdb=" CA PHE D 322 " pdb=" C PHE D 322 " ideal model delta sigma weight residual 111.14 118.46 -7.32 1.08e+00 8.57e-01 4.59e+01 angle pdb=" N PHE C 322 " pdb=" CA PHE C 322 " pdb=" C PHE C 322 " ideal model delta sigma weight residual 111.14 118.45 -7.31 1.08e+00 8.57e-01 4.59e+01 angle pdb=" N PHE B 322 " pdb=" CA PHE B 322 " pdb=" C PHE B 322 " ideal model delta sigma weight residual 111.14 118.43 -7.29 1.08e+00 8.57e-01 4.55e+01 angle pdb=" N PHE A 322 " pdb=" CA PHE A 322 " pdb=" C PHE A 322 " ideal model delta sigma weight residual 111.14 118.42 -7.28 1.08e+00 8.57e-01 4.55e+01 angle pdb=" C THR B 309 " pdb=" CA THR B 309 " pdb=" CB THR B 309 " ideal model delta sigma weight residual 110.85 121.94 -11.09 1.70e+00 3.46e-01 4.26e+01 ... (remaining 20699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.01: 8339 23.01 - 46.02: 505 46.02 - 69.03: 104 69.03 - 92.04: 32 92.04 - 115.04: 12 Dihedral angle restraints: 8992 sinusoidal: 3632 harmonic: 5360 Sorted by residual: dihedral pdb=" C THR C 309 " pdb=" N THR C 309 " pdb=" CA THR C 309 " pdb=" CB THR C 309 " ideal model delta harmonic sigma weight residual -122.00 -135.17 13.17 0 2.50e+00 1.60e-01 2.78e+01 dihedral pdb=" C THR B 309 " pdb=" N THR B 309 " pdb=" CA THR B 309 " pdb=" CB THR B 309 " ideal model delta harmonic sigma weight residual -122.00 -135.14 13.14 0 2.50e+00 1.60e-01 2.76e+01 dihedral pdb=" C THR A 309 " pdb=" N THR A 309 " pdb=" CA THR A 309 " pdb=" CB THR A 309 " ideal model delta harmonic sigma weight residual -122.00 -135.14 13.14 0 2.50e+00 1.60e-01 2.76e+01 ... (remaining 8989 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2137 0.073 - 0.146: 171 0.146 - 0.220: 24 0.220 - 0.293: 12 0.293 - 0.366: 8 Chirality restraints: 2352 Sorted by residual: chirality pdb=" CA THR C 309 " pdb=" N THR C 309 " pdb=" C THR C 309 " pdb=" CB THR C 309 " both_signs ideal model delta sigma weight residual False 2.53 2.16 0.37 2.00e-01 2.50e+01 3.35e+00 chirality pdb=" CA THR A 309 " pdb=" N THR A 309 " pdb=" C THR A 309 " pdb=" CB THR A 309 " both_signs ideal model delta sigma weight residual False 2.53 2.16 0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" CA THR D 309 " pdb=" N THR D 309 " pdb=" C THR D 309 " pdb=" CB THR D 309 " both_signs ideal model delta sigma weight residual False 2.53 2.16 0.36 2.00e-01 2.50e+01 3.27e+00 ... (remaining 2349 not shown) Planarity restraints: 2524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE D 312 " 0.012 2.00e-02 2.50e+03 2.35e-02 5.54e+00 pdb=" C ILE D 312 " -0.041 2.00e-02 2.50e+03 pdb=" O ILE D 312 " 0.015 2.00e-02 2.50e+03 pdb=" N VAL D 313 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 312 " -0.012 2.00e-02 2.50e+03 2.35e-02 5.50e+00 pdb=" C ILE B 312 " 0.041 2.00e-02 2.50e+03 pdb=" O ILE B 312 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL B 313 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 312 " -0.012 2.00e-02 2.50e+03 2.33e-02 5.41e+00 pdb=" C ILE A 312 " 0.040 2.00e-02 2.50e+03 pdb=" O ILE A 312 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL A 313 " -0.014 2.00e-02 2.50e+03 ... (remaining 2521 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2582 2.77 - 3.30: 13662 3.30 - 3.83: 24018 3.83 - 4.37: 28520 4.37 - 4.90: 50643 Nonbonded interactions: 119425 Sorted by model distance: nonbonded pdb=" OH TYR C 428 " pdb=" O ALA C 453 " model vdw 2.234 3.040 nonbonded pdb=" OH TYR A 428 " pdb=" O ALA A 453 " model vdw 2.234 3.040 nonbonded pdb=" OH TYR D 428 " pdb=" O ALA D 453 " model vdw 2.234 3.040 nonbonded pdb=" OH TYR B 428 " pdb=" O ALA B 453 " model vdw 2.234 3.040 nonbonded pdb=" N VAL C 334 " pdb=" OD2 ASP C 338 " model vdw 2.371 3.120 ... (remaining 119420 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.950 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 15292 Z= 0.306 Angle : 0.705 11.094 20704 Z= 0.464 Chirality : 0.051 0.366 2352 Planarity : 0.003 0.037 2524 Dihedral : 17.032 115.045 5528 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.70 % Allowed : 0.24 % Favored : 98.06 % Cbeta Deviations : 0.69 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.20), residues: 1780 helix: 1.61 (0.15), residues: 1144 sheet: 0.78 (0.36), residues: 220 loop : -1.92 (0.27), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 139 TYR 0.014 0.001 TYR B 486 PHE 0.033 0.001 PHE A 322 TRP 0.013 0.002 TRP B 205 HIS 0.002 0.001 HIS D 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.31 (15292) covalent geometry : angle 0.70480 / 0.46 (20704) hydrogen bonds : bond 0.18955 / 12.12 ( 1069) hydrogen bonds : angle 7.07712 / 5.15 ( 3399) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 188 time to evaluate : 0.545 Fit side-chains REVERT: A 322 PHE cc_start: 0.7354 (OUTLIER) cc_final: 0.6731 (t80) REVERT: A 323 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.7071 (mp) REVERT: A 356 MET cc_start: 0.8642 (mtp) cc_final: 0.8418 (mtp) REVERT: B 322 PHE cc_start: 0.7387 (OUTLIER) cc_final: 0.6761 (t80) REVERT: B 323 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7127 (mp) REVERT: B 356 MET cc_start: 0.8841 (mtp) cc_final: 0.8633 (mtp) REVERT: C 244 TYR cc_start: 0.8667 (m-80) cc_final: 0.8460 (m-80) REVERT: C 322 PHE cc_start: 0.7511 (OUTLIER) cc_final: 0.7052 (t80) REVERT: C 323 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7174 (mp) REVERT: D 244 TYR cc_start: 0.8605 (m-80) cc_final: 0.8297 (m-80) REVERT: D 322 PHE cc_start: 0.7483 (OUTLIER) cc_final: 0.6975 (t80) REVERT: D 323 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.7083 (mp) REVERT: D 351 THR cc_start: 0.8743 (m) cc_final: 0.8403 (p) REVERT: D 476 SER cc_start: 0.8480 (p) cc_final: 0.8209 (p) outliers start: 28 outliers final: 6 residues processed: 212 average time/residue: 0.1024 time to fit residues: 34.1198 Evaluate side-chains 172 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 158 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 322 PHE Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 322 PHE Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 322 PHE Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain D residue 311 SER Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 322 PHE Chi-restraints excluded: chain D residue 323 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 511 HIS B 450 ASN B 511 HIS C 511 HIS D 511 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.147039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.106417 restraints weight = 15587.576| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.52 r_work: 0.2909 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15292 Z= 0.158 Angle : 0.517 7.200 20704 Z= 0.280 Chirality : 0.039 0.136 2352 Planarity : 0.004 0.038 2524 Dihedral : 14.969 116.431 2078 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.67 % Allowed : 6.67 % Favored : 92.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.20), residues: 1780 helix: 1.91 (0.15), residues: 1164 sheet: 1.20 (0.34), residues: 220 loop : -1.78 (0.27), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 319 TYR 0.018 0.001 TYR A 428 PHE 0.013 0.001 PHE C 494 TRP 0.014 0.001 TRP D 205 HIS 0.002 0.001 HIS B 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (15292) covalent geometry : angle 0.51735 / 0.28 (20704) hydrogen bonds : bond 0.06203 / 4.07 ( 1069) hydrogen bonds : angle 4.49630 / 3.27 ( 3399) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 174 time to evaluate : 0.565 Fit side-chains REVERT: A 96 ASP cc_start: 0.7757 (m-30) cc_final: 0.7480 (m-30) REVERT: A 244 TYR cc_start: 0.8991 (m-80) cc_final: 0.8769 (m-80) REVERT: A 476 SER cc_start: 0.8350 (p) cc_final: 0.8146 (t) REVERT: C 96 ASP cc_start: 0.7793 (m-30) cc_final: 0.7463 (m-30) REVERT: C 244 TYR cc_start: 0.8985 (m-80) cc_final: 0.8615 (m-80) REVERT: D 96 ASP cc_start: 0.7774 (m-30) cc_final: 0.7477 (m-30) REVERT: D 244 TYR cc_start: 0.9026 (m-80) cc_final: 0.8682 (m-80) outliers start: 11 outliers final: 7 residues processed: 178 average time/residue: 0.1007 time to fit residues: 28.5105 Evaluate side-chains 168 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 161 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 351 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [137, 139, 138, 75, 143, 110, 144, 63, 17, 120, 21] chunk 137 optimal weight: 0.9980 chunk 139 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 144 optimal weight: 0.5980 chunk 63 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 120 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 450 ASN A 511 HIS B 511 HIS C 450 ASN C 511 HIS D 192 HIS D 450 ASN D 511 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.142746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.100730 restraints weight = 15992.699| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 1.56 r_work: 0.2822 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 15292 Z= 0.216 Angle : 0.550 7.302 20704 Z= 0.297 Chirality : 0.041 0.132 2352 Planarity : 0.003 0.035 2524 Dihedral : 14.826 110.836 2056 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.91 % Allowed : 8.86 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.20), residues: 1780 helix: 1.86 (0.15), residues: 1168 sheet: 1.11 (0.32), residues: 228 loop : -1.77 (0.28), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 395 TYR 0.018 0.002 TYR D 428 PHE 0.012 0.002 PHE B 494 TRP 0.013 0.002 TRP C 205 HIS 0.003 0.001 HIS D 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.22 (15292) covalent geometry : angle 0.55017 / 0.30 (20704) hydrogen bonds : bond 0.07078 / 4.64 ( 1069) hydrogen bonds : angle 4.47584 / 3.25 ( 3399) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 164 time to evaluate : 0.591 Fit side-chains REVERT: A 244 TYR cc_start: 0.9001 (m-80) cc_final: 0.8770 (m-80) REVERT: A 354 ASP cc_start: 0.8447 (m-30) cc_final: 0.8247 (m-30) REVERT: A 476 SER cc_start: 0.8409 (p) cc_final: 0.8208 (t) REVERT: C 96 ASP cc_start: 0.8020 (m-30) cc_final: 0.7800 (m-30) REVERT: C 244 TYR cc_start: 0.9043 (m-80) cc_final: 0.8719 (m-80) REVERT: D 244 TYR cc_start: 0.9036 (m-80) cc_final: 0.8700 (m-80) REVERT: D 368 LYS cc_start: 0.7756 (tptp) cc_final: 0.7523 (tptt) outliers start: 15 outliers final: 14 residues processed: 167 average time/residue: 0.1040 time to fit residues: 27.4357 Evaluate side-chains 170 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 156 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 476 SER Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 318 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [32, 161, 130, 166, 149, 150, 170, 11, 169, 43, 175] chunk 32 optimal weight: 0.6980 chunk 161 optimal weight: 10.0000 chunk 130 optimal weight: 0.9980 chunk 166 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 chunk 170 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 169 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 175 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 511 HIS B 511 HIS C 511 HIS D 511 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.147458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.106324 restraints weight = 15791.811| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.53 r_work: 0.2913 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15292 Z= 0.136 Angle : 0.470 7.352 20704 Z= 0.254 Chirality : 0.038 0.131 2352 Planarity : 0.003 0.036 2524 Dihedral : 14.842 116.781 2056 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.97 % Allowed : 10.98 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.20), residues: 1780 helix: 2.16 (0.15), residues: 1164 sheet: 1.13 (0.32), residues: 220 loop : -1.82 (0.27), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 212 TYR 0.016 0.001 TYR B 486 PHE 0.008 0.001 PHE A 420 TRP 0.012 0.001 TRP C 205 HIS 0.002 0.001 HIS D 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (15292) covalent geometry : angle 0.46969 / 0.25 (20704) hydrogen bonds : bond 0.05650 / 3.71 ( 1069) hydrogen bonds : angle 4.12396 / 2.99 ( 3399) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 0.598 Fit side-chains REVERT: A 96 ASP cc_start: 0.7997 (m-30) cc_final: 0.7790 (m-30) REVERT: A 244 TYR cc_start: 0.8995 (m-80) cc_final: 0.8677 (m-80) REVERT: B 48 TYR cc_start: 0.8281 (t80) cc_final: 0.7897 (t80) REVERT: C 96 ASP cc_start: 0.7907 (m-30) cc_final: 0.7683 (m-30) REVERT: C 244 TYR cc_start: 0.9018 (m-80) cc_final: 0.8647 (m-80) REVERT: D 244 TYR cc_start: 0.9007 (m-80) cc_final: 0.8635 (m-80) REVERT: D 368 LYS cc_start: 0.7740 (tptp) cc_final: 0.7513 (tptt) outliers start: 16 outliers final: 16 residues processed: 161 average time/residue: 0.1022 time to fit residues: 26.1500 Evaluate side-chains 169 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 153 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [35, 109, 106, 134, 153, 36, 46, 83, 89, 22, 32] chunk 35 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 153 optimal weight: 0.3980 chunk 36 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 511 HIS B 511 HIS C 511 HIS D 511 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.148435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.108077 restraints weight = 15728.175| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.50 r_work: 0.2929 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15292 Z= 0.131 Angle : 0.458 7.399 20704 Z= 0.246 Chirality : 0.038 0.126 2352 Planarity : 0.003 0.035 2524 Dihedral : 14.744 118.621 2056 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.52 % Allowed : 10.98 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.20), residues: 1780 helix: 2.26 (0.15), residues: 1164 sheet: 1.19 (0.32), residues: 220 loop : -1.83 (0.27), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 484 TYR 0.016 0.001 TYR D 486 PHE 0.008 0.001 PHE B 420 TRP 0.011 0.001 TRP C 205 HIS 0.002 0.001 HIS D 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (15292) covalent geometry : angle 0.45782 / 0.25 (20704) hydrogen bonds : bond 0.05446 / 3.58 ( 1069) hydrogen bonds : angle 4.00719 / 2.90 ( 3399) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 0.572 Fit side-chains REVERT: A 48 TYR cc_start: 0.8327 (t80) cc_final: 0.7900 (t80) REVERT: A 96 ASP cc_start: 0.7982 (m-30) cc_final: 0.7760 (m-30) REVERT: A 244 TYR cc_start: 0.8996 (m-80) cc_final: 0.8684 (m-80) REVERT: B 48 TYR cc_start: 0.8247 (t80) cc_final: 0.7808 (t80) REVERT: B 311 SER cc_start: 0.8207 (m) cc_final: 0.7820 (t) REVERT: C 96 ASP cc_start: 0.7927 (m-30) cc_final: 0.7684 (m-30) REVERT: C 244 TYR cc_start: 0.9017 (m-80) cc_final: 0.8641 (m-80) REVERT: D 244 TYR cc_start: 0.8998 (m-80) cc_final: 0.8622 (m-80) outliers start: 25 outliers final: 17 residues processed: 170 average time/residue: 0.1064 time to fit residues: 28.4351 Evaluate side-chains 173 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 156 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 351 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [96, 135, 57, 132, 12, 89, 19, 44, 103, 171, 5] chunk 96 optimal weight: 0.9990 chunk 135 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 chunk 132 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 511 HIS B 511 HIS C 511 HIS D 511 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.144996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.105613 restraints weight = 15826.031| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.58 r_work: 0.2870 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15292 Z= 0.171 Angle : 0.495 7.444 20704 Z= 0.267 Chirality : 0.039 0.129 2352 Planarity : 0.003 0.035 2524 Dihedral : 14.734 115.814 2056 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.58 % Allowed : 11.95 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.20), residues: 1780 helix: 2.18 (0.15), residues: 1168 sheet: 1.26 (0.32), residues: 220 loop : -1.83 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 484 TYR 0.017 0.001 TYR D 428 PHE 0.009 0.001 PHE A 494 TRP 0.008 0.001 TRP C 205 HIS 0.003 0.001 HIS C 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 (15292) covalent geometry : angle 0.49523 / 0.27 (20704) hydrogen bonds : bond 0.06222 / 4.08 ( 1069) hydrogen bonds : angle 4.14285 / 3.00 ( 3399) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 165 time to evaluate : 0.450 Fit side-chains REVERT: A 48 TYR cc_start: 0.8330 (t80) cc_final: 0.7864 (t80) REVERT: A 244 TYR cc_start: 0.9015 (m-80) cc_final: 0.8701 (m-80) REVERT: B 48 TYR cc_start: 0.8241 (t80) cc_final: 0.7789 (t80) REVERT: B 266 ASN cc_start: 0.7157 (m110) cc_final: 0.6844 (t0) REVERT: B 311 SER cc_start: 0.8252 (m) cc_final: 0.7862 (t) REVERT: B 465 MET cc_start: 0.8788 (mtt) cc_final: 0.8578 (mtt) REVERT: C 244 TYR cc_start: 0.9048 (m-80) cc_final: 0.8699 (m-80) REVERT: D 244 TYR cc_start: 0.9041 (m-80) cc_final: 0.8744 (m-80) REVERT: D 368 LYS cc_start: 0.7822 (tptp) cc_final: 0.7582 (tptt) outliers start: 26 outliers final: 22 residues processed: 176 average time/residue: 0.1029 time to fit residues: 28.8074 Evaluate side-chains 183 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 476 SER Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 318 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [139, 174, 145, 98, 177, 79, 86, 38, 151, 9, 97] chunk 139 optimal weight: 2.9990 chunk 174 optimal weight: 0.7980 chunk 145 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 177 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 chunk 86 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 151 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 511 HIS B 511 HIS C 511 HIS D 511 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.147612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.107152 restraints weight = 15651.239| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.50 r_work: 0.2921 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15292 Z= 0.135 Angle : 0.469 7.383 20704 Z= 0.251 Chirality : 0.038 0.171 2352 Planarity : 0.003 0.035 2524 Dihedral : 14.738 118.544 2056 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.64 % Allowed : 12.26 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.20), residues: 1780 helix: 2.31 (0.15), residues: 1164 sheet: 1.32 (0.32), residues: 220 loop : -1.79 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 484 TYR 0.016 0.001 TYR B 486 PHE 0.009 0.001 PHE B 420 TRP 0.012 0.001 TRP B 390 HIS 0.002 0.001 HIS D 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 (15292) covalent geometry : angle 0.46923 / 0.25 (20704) hydrogen bonds : bond 0.05507 / 3.62 ( 1069) hydrogen bonds : angle 4.01778 / 2.91 ( 3399) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 159 time to evaluate : 0.583 Fit side-chains REVERT: A 48 TYR cc_start: 0.8216 (t80) cc_final: 0.7780 (t80) REVERT: A 244 TYR cc_start: 0.9000 (m-80) cc_final: 0.8692 (m-80) REVERT: A 311 SER cc_start: 0.8228 (m) cc_final: 0.7838 (t) REVERT: B 48 TYR cc_start: 0.8230 (t80) cc_final: 0.7780 (t80) REVERT: B 311 SER cc_start: 0.8250 (m) cc_final: 0.7849 (t) REVERT: C 244 TYR cc_start: 0.9021 (m-80) cc_final: 0.8695 (m-80) REVERT: D 244 TYR cc_start: 0.9022 (m-80) cc_final: 0.8693 (m-80) REVERT: D 368 LYS cc_start: 0.7773 (tptp) cc_final: 0.7534 (tptt) outliers start: 27 outliers final: 24 residues processed: 171 average time/residue: 0.1027 time to fit residues: 27.6427 Evaluate side-chains 181 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 476 SER Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 377 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [5, 63, 114, 137, 147, 116, 29, 170, 144, 16, 81] chunk 5 optimal weight: 0.7980 chunk 63 optimal weight: 0.0040 chunk 114 optimal weight: 0.9980 chunk 137 optimal weight: 10.0000 chunk 147 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 chunk 144 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 511 HIS B 511 HIS C 511 HIS D 511 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.146306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.105512 restraints weight = 15781.749| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.51 r_work: 0.2893 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15292 Z= 0.153 Angle : 0.486 7.416 20704 Z= 0.260 Chirality : 0.039 0.133 2352 Planarity : 0.003 0.035 2524 Dihedral : 14.706 117.206 2056 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.00 % Allowed : 12.32 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.20), residues: 1780 helix: 2.29 (0.15), residues: 1164 sheet: 1.38 (0.32), residues: 220 loop : -1.77 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 395 TYR 0.016 0.001 TYR B 486 PHE 0.008 0.001 PHE A 420 TRP 0.009 0.001 TRP B 390 HIS 0.003 0.001 HIS C 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (15292) covalent geometry : angle 0.48584 / 0.26 (20704) hydrogen bonds : bond 0.05889 / 3.87 ( 1069) hydrogen bonds : angle 4.08717 / 2.96 ( 3399) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 159 time to evaluate : 0.530 Fit side-chains REVERT: A 48 TYR cc_start: 0.8230 (t80) cc_final: 0.7796 (t80) REVERT: A 244 TYR cc_start: 0.9024 (m-80) cc_final: 0.8714 (m-80) REVERT: A 311 SER cc_start: 0.8252 (m) cc_final: 0.7859 (t) REVERT: B 48 TYR cc_start: 0.8239 (t80) cc_final: 0.7819 (t80) REVERT: B 266 ASN cc_start: 0.7102 (m110) cc_final: 0.6795 (t0) REVERT: B 311 SER cc_start: 0.8298 (m) cc_final: 0.7855 (t) REVERT: C 244 TYR cc_start: 0.9041 (m-80) cc_final: 0.8701 (m-80) REVERT: C 266 ASN cc_start: 0.7157 (m110) cc_final: 0.6831 (t0) REVERT: D 244 TYR cc_start: 0.9026 (m-80) cc_final: 0.8676 (m-80) REVERT: D 266 ASN cc_start: 0.7142 (m110) cc_final: 0.6814 (t0) REVERT: D 368 LYS cc_start: 0.7804 (tptp) cc_final: 0.7550 (tptt) outliers start: 33 outliers final: 29 residues processed: 178 average time/residue: 0.0968 time to fit residues: 27.3818 Evaluate side-chains 185 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 156 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 476 SER Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 377 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [22, 36, 14, 51, 86, 169, 156, 99, 125, 41, 55] chunk 22 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 169 optimal weight: 0.7980 chunk 156 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 125 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 511 HIS B 511 HIS C 511 HIS D 511 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.147669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.107076 restraints weight = 15709.766| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.51 r_work: 0.2920 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15292 Z= 0.137 Angle : 0.470 7.386 20704 Z= 0.252 Chirality : 0.038 0.160 2352 Planarity : 0.003 0.035 2524 Dihedral : 14.707 118.484 2056 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.82 % Allowed : 12.62 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.20), residues: 1780 helix: 2.34 (0.15), residues: 1164 sheet: 1.44 (0.32), residues: 220 loop : -1.77 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 484 TYR 0.016 0.001 TYR D 486 PHE 0.008 0.001 PHE B 420 TRP 0.011 0.001 TRP D 390 HIS 0.002 0.001 HIS A 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (15292) covalent geometry : angle 0.47044 / 0.25 (20704) hydrogen bonds : bond 0.05533 / 3.64 ( 1069) hydrogen bonds : angle 4.02611 / 2.91 ( 3399) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 154 time to evaluate : 0.571 Fit side-chains REVERT: A 244 TYR cc_start: 0.9007 (m-80) cc_final: 0.8697 (m-80) REVERT: A 311 SER cc_start: 0.8284 (m) cc_final: 0.7845 (t) REVERT: B 311 SER cc_start: 0.8300 (m) cc_final: 0.7853 (t) REVERT: C 244 TYR cc_start: 0.9030 (m-80) cc_final: 0.8700 (m-80) REVERT: C 266 ASN cc_start: 0.7109 (m110) cc_final: 0.6799 (t0) REVERT: D 244 TYR cc_start: 0.9032 (m-80) cc_final: 0.8704 (m-80) REVERT: D 368 LYS cc_start: 0.7782 (tptp) cc_final: 0.7528 (tptt) outliers start: 30 outliers final: 29 residues processed: 169 average time/residue: 0.1002 time to fit residues: 27.1272 Evaluate side-chains 181 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 152 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 476 SER Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 377 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [150, 44, 105, 20, 9, 106, 177, 2, 136, 87, 77] chunk 150 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 105 optimal weight: 0.3980 chunk 20 optimal weight: 0.4980 chunk 9 optimal weight: 0.7980 chunk 106 optimal weight: 0.8980 chunk 177 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 136 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 77 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 511 HIS B 511 HIS C 511 HIS D 192 HIS D 511 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.150748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.110878 restraints weight = 15605.513| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.50 r_work: 0.2973 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15292 Z= 0.120 Angle : 0.451 7.329 20704 Z= 0.240 Chirality : 0.038 0.130 2352 Planarity : 0.003 0.035 2524 Dihedral : 14.658 120.017 2056 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.58 % Allowed : 12.80 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.20), residues: 1780 helix: 2.42 (0.15), residues: 1164 sheet: 1.53 (0.32), residues: 220 loop : -1.75 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 484 TYR 0.015 0.001 TYR D 486 PHE 0.008 0.001 PHE A 225 TRP 0.012 0.001 TRP B 390 HIS 0.002 0.001 HIS A 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 (15292) covalent geometry : angle 0.45082 / 0.24 (20704) hydrogen bonds : bond 0.05043 / 3.32 ( 1069) hydrogen bonds : angle 3.91536 / 2.83 ( 3399) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 0.444 Fit side-chains REVERT: A 244 TYR cc_start: 0.8955 (m-80) cc_final: 0.8621 (m-80) REVERT: A 311 SER cc_start: 0.8287 (m) cc_final: 0.7876 (t) REVERT: B 311 SER cc_start: 0.8290 (m) cc_final: 0.7868 (t) REVERT: C 244 TYR cc_start: 0.8986 (m-80) cc_final: 0.8616 (m-80) REVERT: C 410 MET cc_start: 0.9131 (mmp) cc_final: 0.8705 (mmt) REVERT: D 244 TYR cc_start: 0.8991 (m-80) cc_final: 0.8626 (m-80) outliers start: 26 outliers final: 26 residues processed: 164 average time/residue: 0.0961 time to fit residues: 25.4441 Evaluate side-chains 175 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 377 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: [60, 50, 146, 69, 100, 101, 178, 109, 96, 131, 117] chunk 60 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 146 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 178 optimal weight: 0.6980 chunk 109 optimal weight: 3.9990 chunk 96 optimal weight: 0.5980 chunk 131 optimal weight: 0.5980 chunk 117 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 401 GLN A 511 HIS B 511 HIS C 61 GLN C 511 HIS D 511 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.149625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.110498 restraints weight = 15672.988| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.66 r_work: 0.2959 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15292 Z= 0.128 Angle : 0.459 7.355 20704 Z= 0.245 Chirality : 0.038 0.131 2352 Planarity : 0.003 0.035 2524 Dihedral : 14.650 119.062 2056 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.64 % Allowed : 12.86 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.20), residues: 1780 helix: 2.42 (0.15), residues: 1164 sheet: 1.52 (0.31), residues: 220 loop : -1.73 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 484 TYR 0.015 0.001 TYR D 486 PHE 0.008 0.001 PHE A 420 TRP 0.010 0.001 TRP C 390 HIS 0.002 0.001 HIS D 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 (15292) covalent geometry : angle 0.45949 / 0.25 (20704) hydrogen bonds : bond 0.05274 / 3.47 ( 1069) hydrogen bonds : angle 3.93362 / 2.84 ( 3399) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3458.06 seconds wall clock time: 59 minutes 58.28 seconds (3598.28 seconds total)