Starting phenix.real_space_refine on Fri Jul 3 19:07:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ei0_48072/07_2026/9ei0_48072.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ei0_48072/07_2026/9ei0_48072.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ei0_48072/07_2026/9ei0_48072.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ei0_48072/07_2026/9ei0_48072.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ei0_48072/07_2026/9ei0_48072.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ei0_48072/07_2026/9ei0_48072.map" } resolution = 2.91 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= 0.001 sd= 0.033 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: 5 Type Number sf(0) Gaussians K 4 8.98 5 S 60 5.16 5 C 9912 2.51 5 N 2568 2.21 5 O 2708 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15252 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2919 Classifications: {'peptide': 358} Link IDs: {'PTRANS': 20, 'TRANS': 337} Chain breaks: 2 Chain: "E" Number of atoms: 893 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 115, 885 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Conformer: "B" Number of residues, atoms: 115, 885 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} bond proxies already assigned to first conformer: 894 Chain: "F" Number of atoms: 893 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 115, 885 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Conformer: "B" Number of residues, atoms: 115, 885 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} bond proxies already assigned to first conformer: 894 Chain: "G" Number of atoms: 893 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 115, 885 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Conformer: "B" Number of residues, atoms: 115, 885 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} bond proxies already assigned to first conformer: 894 Chain: "H" Number of atoms: 893 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 115, 885 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Conformer: "B" Number of residues, atoms: 115, 885 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} bond proxies already assigned to first conformer: 894 Chain: "B" Number of atoms: 2919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2919 Classifications: {'peptide': 358} Link IDs: {'PTRANS': 20, 'TRANS': 337} Chain breaks: 2 Chain: "C" Number of atoms: 2919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2919 Classifications: {'peptide': 358} Link IDs: {'PTRANS': 20, 'TRANS': 337} Chain breaks: 2 Chain: "D" Number of atoms: 2919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2919 Classifications: {'peptide': 358} Link IDs: {'PTRANS': 20, 'TRANS': 337} Chain breaks: 2 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 0 Ad-hoc single atom residues: {' K': 4} Chain breaks: 4 Time building chain proxies: 4.66, per 1000 atoms: 0.31 Number of scatterers: 15252 At special positions: 0 Unit cell: (100.43, 100.43, 149.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 4 19.00 S 60 16.00 O 2708 8.00 N 2568 7.00 C 9912 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 96 " distance=2.03 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 705.2 milliseconds 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3512 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 20 sheets defined 50.5% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 119 through 123 Processing helix chain 'A' and resid 154 through 165 removed outlier: 4.299A pdb=" N ALA A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 188 Processing helix chain 'A' and resid 190 through 202 removed outlier: 3.504A pdb=" N MET A 194 " --> pdb=" O GLY A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 226 Processing helix chain 'A' and resid 231 through 254 Processing helix chain 'A' and resid 293 through 317 removed outlier: 3.557A pdb=" N VAL A 298 " --> pdb=" O PRO A 294 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG A 313 " --> pdb=" O GLU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 324 removed outlier: 3.534A pdb=" N PHE A 323 " --> pdb=" O SER A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 335 removed outlier: 3.957A pdb=" N ASP A 332 " --> pdb=" O MET A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 347 removed outlier: 3.510A pdb=" N PHE A 340 " --> pdb=" O ILE A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 370 Processing helix chain 'A' and resid 371 through 378 removed outlier: 3.679A pdb=" N PHE A 375 " --> pdb=" O PHE A 372 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS A 376 " --> pdb=" O ARG A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 394 Processing helix chain 'A' and resid 394 through 419 Processing helix chain 'A' and resid 434 through 443 Processing helix chain 'A' and resid 454 through 474 removed outlier: 3.586A pdb=" N ALA A 465 " --> pdb=" O GLY A 461 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 489 Processing helix chain 'E' and resid 29 through 33 Processing helix chain 'F' and resid 29 through 33 Processing helix chain 'G' and resid 29 through 33 Processing helix chain 'H' and resid 29 through 33 Processing helix chain 'B' and resid 119 through 123 Processing helix chain 'B' and resid 154 through 165 removed outlier: 4.299A pdb=" N ALA B 158 " --> pdb=" O PRO B 154 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 188 Processing helix chain 'B' and resid 190 through 202 removed outlier: 3.503A pdb=" N MET B 194 " --> pdb=" O GLY B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 226 Processing helix chain 'B' and resid 231 through 254 Processing helix chain 'B' and resid 293 through 317 removed outlier: 3.557A pdb=" N VAL B 298 " --> pdb=" O PRO B 294 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG B 313 " --> pdb=" O GLU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 324 removed outlier: 3.534A pdb=" N PHE B 323 " --> pdb=" O SER B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 335 removed outlier: 3.957A pdb=" N ASP B 332 " --> pdb=" O MET B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 347 removed outlier: 3.510A pdb=" N PHE B 340 " --> pdb=" O ILE B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 370 Processing helix chain 'B' and resid 371 through 378 removed outlier: 3.679A pdb=" N PHE B 375 " --> pdb=" O PHE B 372 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS B 376 " --> pdb=" O ARG B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 394 Processing helix chain 'B' and resid 394 through 419 Processing helix chain 'B' and resid 434 through 443 Processing helix chain 'B' and resid 454 through 474 removed outlier: 3.587A pdb=" N ALA B 465 " --> pdb=" O GLY B 461 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE B 466 " --> pdb=" O SER B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 489 Processing helix chain 'C' and resid 119 through 123 Processing helix chain 'C' and resid 154 through 165 removed outlier: 4.299A pdb=" N ALA C 158 " --> pdb=" O PRO C 154 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR C 163 " --> pdb=" O ILE C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 188 Processing helix chain 'C' and resid 190 through 202 removed outlier: 3.504A pdb=" N MET C 194 " --> pdb=" O GLY C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 226 Processing helix chain 'C' and resid 231 through 254 Processing helix chain 'C' and resid 293 through 317 removed outlier: 3.556A pdb=" N VAL C 298 " --> pdb=" O PRO C 294 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG C 313 " --> pdb=" O GLU C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 324 removed outlier: 3.534A pdb=" N PHE C 323 " --> pdb=" O SER C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 335 removed outlier: 3.958A pdb=" N ASP C 332 " --> pdb=" O MET C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 347 removed outlier: 3.510A pdb=" N PHE C 340 " --> pdb=" O ILE C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 370 Processing helix chain 'C' and resid 371 through 378 removed outlier: 3.678A pdb=" N PHE C 375 " --> pdb=" O PHE C 372 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS C 376 " --> pdb=" O ARG C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 394 Processing helix chain 'C' and resid 394 through 419 Processing helix chain 'C' and resid 434 through 443 Processing helix chain 'C' and resid 454 through 474 removed outlier: 3.586A pdb=" N ALA C 465 " --> pdb=" O GLY C 461 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE C 466 " --> pdb=" O SER C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 489 Processing helix chain 'D' and resid 119 through 123 Processing helix chain 'D' and resid 154 through 165 removed outlier: 4.299A pdb=" N ALA D 158 " --> pdb=" O PRO D 154 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR D 163 " --> pdb=" O ILE D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 188 Processing helix chain 'D' and resid 190 through 202 removed outlier: 3.504A pdb=" N MET D 194 " --> pdb=" O GLY D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 226 Processing helix chain 'D' and resid 231 through 254 Processing helix chain 'D' and resid 293 through 317 removed outlier: 3.557A pdb=" N VAL D 298 " --> pdb=" O PRO D 294 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG D 313 " --> pdb=" O GLU D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 324 removed outlier: 3.534A pdb=" N PHE D 323 " --> pdb=" O SER D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 335 removed outlier: 3.957A pdb=" N ASP D 332 " --> pdb=" O MET D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 347 removed outlier: 3.510A pdb=" N PHE D 340 " --> pdb=" O ILE D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 370 Processing helix chain 'D' and resid 371 through 378 removed outlier: 3.679A pdb=" N PHE D 375 " --> pdb=" O PHE D 372 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS D 376 " --> pdb=" O ARG D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 394 Processing helix chain 'D' and resid 394 through 419 Processing helix chain 'D' and resid 434 through 443 Processing helix chain 'D' and resid 454 through 474 removed outlier: 3.587A pdb=" N ALA D 465 " --> pdb=" O GLY D 461 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE D 466 " --> pdb=" O SER D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 489 Processing sheet with id=AA1, first strand: chain 'A' and resid 113 through 118 removed outlier: 8.622A pdb=" N TYR A 147 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N VAL A 107 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N PHE A 149 " --> pdb=" O VAL A 107 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ASN A 109 " --> pdb=" O PHE A 149 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 4 through 8 removed outlier: 3.671A pdb=" N GLN E 4 " --> pdb=" O SER E 26 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER E 22 " --> pdb=" O SER E 8 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER E 71 " --> pdb=" O TYR E 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 47 through 48 Processing sheet with id=AA4, first strand: chain 'E' and resid 47 through 48 Processing sheet with id=AA5, first strand: chain 'E' and resid 50 through 51 Processing sheet with id=AA6, first strand: chain 'F' and resid 4 through 8 removed outlier: 3.671A pdb=" N GLN F 4 " --> pdb=" O SER F 26 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER F 22 " --> pdb=" O SER F 8 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER F 71 " --> pdb=" O TYR F 80 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 47 through 48 Processing sheet with id=AA8, first strand: chain 'F' and resid 47 through 48 Processing sheet with id=AA9, first strand: chain 'F' and resid 50 through 51 Processing sheet with id=AB1, first strand: chain 'G' and resid 4 through 8 removed outlier: 3.670A pdb=" N GLN G 4 " --> pdb=" O SER G 26 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER G 22 " --> pdb=" O SER G 8 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER G 71 " --> pdb=" O TYR G 80 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 47 through 48 Processing sheet with id=AB3, first strand: chain 'G' and resid 47 through 48 Processing sheet with id=AB4, first strand: chain 'G' and resid 50 through 51 Processing sheet with id=AB5, first strand: chain 'H' and resid 4 through 8 removed outlier: 3.671A pdb=" N GLN H 4 " --> pdb=" O SER H 26 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER H 22 " --> pdb=" O SER H 8 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER H 71 " --> pdb=" O TYR H 80 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 47 through 48 Processing sheet with id=AB7, first strand: chain 'H' and resid 47 through 48 Processing sheet with id=AB8, first strand: chain 'H' and resid 50 through 51 Processing sheet with id=AB9, first strand: chain 'B' and resid 113 through 118 removed outlier: 8.622A pdb=" N TYR B 147 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N VAL B 107 " --> pdb=" O TYR B 147 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N PHE B 149 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ASN B 109 " --> pdb=" O PHE B 149 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 113 through 118 removed outlier: 8.622A pdb=" N TYR C 147 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N VAL C 107 " --> pdb=" O TYR C 147 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N PHE C 149 " --> pdb=" O VAL C 107 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ASN C 109 " --> pdb=" O PHE C 149 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 113 through 118 removed outlier: 8.623A pdb=" N TYR D 147 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N VAL D 107 " --> pdb=" O TYR D 147 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N PHE D 149 " --> pdb=" O VAL D 107 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ASN D 109 " --> pdb=" O PHE D 149 " (cutoff:3.500A) 816 hydrogen bonds defined for protein. 2268 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: 2.23 Time building geometry restraints manager: 1.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2396 1.32 - 1.44: 4496 1.44 - 1.56: 8644 1.56 - 1.68: 0 1.68 - 1.81: 92 Bond restraints: 15628 Sorted by residual: bond pdb=" CA ALA B 465 " pdb=" CB ALA B 465 " ideal model delta sigma weight residual 1.528 1.457 0.071 1.59e-02 3.96e+03 2.01e+01 bond pdb=" CA ALA A 465 " pdb=" CB ALA A 465 " ideal model delta sigma weight residual 1.528 1.458 0.071 1.59e-02 3.96e+03 1.98e+01 bond pdb=" CA ALA C 465 " pdb=" CB ALA C 465 " ideal model delta sigma weight residual 1.528 1.458 0.071 1.59e-02 3.96e+03 1.98e+01 bond pdb=" CA ALA D 465 " pdb=" CB ALA D 465 " ideal model delta sigma weight residual 1.528 1.458 0.071 1.59e-02 3.96e+03 1.98e+01 bond pdb=" CA ALA C 438 " pdb=" CB ALA C 438 " ideal model delta sigma weight residual 1.528 1.464 0.064 1.59e-02 3.96e+03 1.64e+01 ... (remaining 15623 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 20212 1.65 - 3.30: 707 3.30 - 4.95: 204 4.95 - 6.59: 33 6.59 - 8.24: 8 Bond angle restraints: 21164 Sorted by residual: angle pdb=" CA HIS B 451 " pdb=" C HIS B 451 " pdb=" N PRO B 452 " ideal model delta sigma weight residual 117.95 122.22 -4.27 7.70e-01 1.69e+00 3.07e+01 angle pdb=" CA HIS A 451 " pdb=" C HIS A 451 " pdb=" N PRO A 452 " ideal model delta sigma weight residual 117.95 122.22 -4.27 7.70e-01 1.69e+00 3.07e+01 angle pdb=" CA HIS C 451 " pdb=" C HIS C 451 " pdb=" N PRO C 452 " ideal model delta sigma weight residual 117.95 122.22 -4.27 7.70e-01 1.69e+00 3.07e+01 angle pdb=" CA HIS D 451 " pdb=" C HIS D 451 " pdb=" N PRO D 452 " ideal model delta sigma weight residual 117.95 122.22 -4.27 7.70e-01 1.69e+00 3.07e+01 angle pdb=" N LEU C 463 " pdb=" CA LEU C 463 " pdb=" CB LEU C 463 " ideal model delta sigma weight residual 110.40 102.38 8.02 1.63e+00 3.76e-01 2.42e+01 ... (remaining 21159 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 8463 17.14 - 34.28: 609 34.28 - 51.42: 132 51.42 - 68.56: 12 68.56 - 85.70: 8 Dihedral angle restraints: 9224 sinusoidal: 3748 harmonic: 5476 Sorted by residual: dihedral pdb=" N LEU B 463 " pdb=" C LEU B 463 " pdb=" CA LEU B 463 " pdb=" CB LEU B 463 " ideal model delta harmonic sigma weight residual 122.80 113.37 9.43 0 2.50e+00 1.60e-01 1.42e+01 dihedral pdb=" N LEU C 463 " pdb=" C LEU C 463 " pdb=" CA LEU C 463 " pdb=" CB LEU C 463 " ideal model delta harmonic sigma weight residual 122.80 113.38 9.42 0 2.50e+00 1.60e-01 1.42e+01 dihedral pdb=" N LEU A 463 " pdb=" C LEU A 463 " pdb=" CA LEU A 463 " pdb=" CB LEU A 463 " ideal model delta harmonic sigma weight residual 122.80 113.38 9.42 0 2.50e+00 1.60e-01 1.42e+01 ... (remaining 9221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1607 0.047 - 0.094: 546 0.094 - 0.140: 135 0.140 - 0.187: 16 0.187 - 0.234: 20 Chirality restraints: 2324 Sorted by residual: chirality pdb=" CB VAL C 440 " pdb=" CA VAL C 440 " pdb=" CG1 VAL C 440 " pdb=" CG2 VAL C 440 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CB VAL B 440 " pdb=" CA VAL B 440 " pdb=" CG1 VAL B 440 " pdb=" CG2 VAL B 440 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CB VAL A 440 " pdb=" CA VAL A 440 " pdb=" CG1 VAL A 440 " pdb=" CG2 VAL A 440 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 2321 not shown) Planarity restraints: 2696 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 445 " -0.014 2.00e-02 2.50e+03 2.81e-02 7.89e+00 pdb=" C VAL B 445 " 0.049 2.00e-02 2.50e+03 pdb=" O VAL B 445 " -0.018 2.00e-02 2.50e+03 pdb=" N GLY B 446 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 445 " 0.014 2.00e-02 2.50e+03 2.81e-02 7.89e+00 pdb=" C VAL A 445 " -0.049 2.00e-02 2.50e+03 pdb=" O VAL A 445 " 0.018 2.00e-02 2.50e+03 pdb=" N GLY A 446 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 445 " 0.014 2.00e-02 2.50e+03 2.81e-02 7.89e+00 pdb=" C VAL D 445 " -0.049 2.00e-02 2.50e+03 pdb=" O VAL D 445 " 0.018 2.00e-02 2.50e+03 pdb=" N GLY D 446 " 0.016 2.00e-02 2.50e+03 ... (remaining 2693 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.79: 3884 2.79 - 3.38: 16783 3.38 - 3.97: 28711 3.97 - 4.55: 42070 4.55 - 5.14: 61819 Nonbonded interactions: 153267 Sorted by model distance: nonbonded pdb=" OD1 ASN G 33 " pdb=" OH TYR G 104 " model vdw 2.209 3.040 nonbonded pdb=" OD1 ASN F 33 " pdb=" OH TYR F 104 " model vdw 2.209 3.040 nonbonded pdb=" OD1 ASN H 33 " pdb=" OH TYR H 104 " model vdw 2.209 3.040 nonbonded pdb=" OD1 ASN E 33 " pdb=" OH TYR E 104 " model vdw 2.209 3.040 nonbonded pdb=" O VAL C 409 " pdb=" OG SER C 413 " model vdw 2.258 3.040 ... (remaining 153262 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 103 through 490) selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = (chain 'E' and (resid 2 through 31 or resid 33 through 116)) selection = (chain 'F' and (resid 2 through 31 or resid 33 through 116)) selection = (chain 'G' and (resid 2 through 31 or resid 33 through 116)) selection = (chain 'H' and (resid 2 through 31 or resid 33 through 116)) } 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=0.35 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: 7.380 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: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 15.390 Find NCS groups from input model: 0.180 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:6.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 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 : 0.007 0.071 15632 Z= 0.357 Angle : 0.776 8.243 21172 Z= 0.493 Chirality : 0.052 0.234 2324 Planarity : 0.006 0.059 2696 Dihedral : 12.329 85.698 5700 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.94 % Allowed : 7.83 % 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: -0.53 (0.21), residues: 1864 helix: 0.17 (0.18), residues: 924 sheet: -2.14 (0.36), residues: 212 loop : -0.22 (0.26), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 370 TYR 0.027 0.002 TYR D 447 PHE 0.018 0.002 PHE B 406 TRP 0.014 0.002 TRP B 437 HIS 0.010 0.002 HIS B 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00678 / 0.36 (15628) covalent geometry : angle 0.77599 / 0.49 (21164) SS BOND : bond 0.00071 / 0.04 ( 4) SS BOND : angle 0.35288 / 0.20 ( 8) hydrogen bonds : bond 0.17420 / 11.68 ( 784) hydrogen bonds : angle 7.03299 / 5.05 ( 2268) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 183 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 TYR cc_start: 0.7957 (t80) cc_final: 0.7757 (t80) REVERT: A 212 PRO cc_start: 0.7505 (Cg_exo) cc_final: 0.7186 (Cg_endo) REVERT: A 262 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7844 (mm-30) REVERT: F 77 ASN cc_start: 0.7885 (t0) cc_final: 0.7668 (t0) REVERT: G 77 ASN cc_start: 0.7869 (t0) cc_final: 0.7647 (t0) REVERT: H 53 ARG cc_start: 0.8061 (mtp85) cc_final: 0.7807 (mtm180) REVERT: H 77 ASN cc_start: 0.7883 (t0) cc_final: 0.7674 (t0) REVERT: B 212 PRO cc_start: 0.7518 (Cg_exo) cc_final: 0.7201 (Cg_endo) REVERT: B 261 ASP cc_start: 0.7182 (t70) cc_final: 0.6941 (t0) REVERT: B 262 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7829 (mm-30) REVERT: C 162 TYR cc_start: 0.7953 (t80) cc_final: 0.7753 (t80) REVERT: C 212 PRO cc_start: 0.7515 (Cg_exo) cc_final: 0.7198 (Cg_endo) REVERT: C 261 ASP cc_start: 0.7183 (t70) cc_final: 0.6942 (t0) REVERT: C 262 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7814 (mm-30) REVERT: D 162 TYR cc_start: 0.7950 (t80) cc_final: 0.7735 (t80) REVERT: D 212 PRO cc_start: 0.7515 (Cg_exo) cc_final: 0.7195 (Cg_endo) REVERT: D 261 ASP cc_start: 0.7181 (t70) cc_final: 0.6942 (t0) REVERT: D 262 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7828 (mm-30) outliers start: 32 outliers final: 24 residues processed: 211 average time/residue: 0.3378 time to fit residues: 83.2721 Evaluate side-chains 191 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 167 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 394 SER Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 394 SER Chi-restraints excluded: chain D residue 416 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.0970 chunk 10 optimal weight: 0.0570 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.0170 chunk 149 optimal weight: 0.9980 overall best weight: 0.3734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 40 GLN F 40 GLN G 40 GLN H 40 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.217977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.139277 restraints weight = 21823.078| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.74 r_work: 0.3244 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3253 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3253 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15632 Z= 0.120 Angle : 0.550 5.894 21172 Z= 0.288 Chirality : 0.042 0.140 2324 Planarity : 0.005 0.047 2696 Dihedral : 4.431 26.240 2144 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.43 % Allowed : 12.56 % Favored : 85.01 % 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: 0.37 (0.21), residues: 1864 helix: 0.90 (0.18), residues: 940 sheet: -1.70 (0.37), residues: 212 loop : 0.21 (0.26), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 209 TYR 0.009 0.001 TYR H 38 PHE 0.016 0.001 PHE C 186 TRP 0.011 0.001 TRP C 436 HIS 0.003 0.001 HIS D 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (15628) covalent geometry : angle 0.55023 / 0.29 (21164) SS BOND : bond 0.00358 / 0.22 ( 4) SS BOND : angle 0.54902 / 0.31 ( 8) hydrogen bonds : bond 0.04397 / 2.88 ( 784) hydrogen bonds : angle 4.71520 / 3.35 ( 2268) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 178 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 PRO cc_start: 0.7397 (Cg_exo) cc_final: 0.7040 (Cg_endo) REVERT: A 262 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7816 (mm-30) REVERT: A 466 ILE cc_start: 0.8254 (mt) cc_final: 0.7908 (mp) REVERT: F 39 ARG cc_start: 0.6998 (ptp90) cc_final: 0.6768 (ptp-170) REVERT: G 39 ARG cc_start: 0.7027 (ptp90) cc_final: 0.6798 (ptp-170) REVERT: H 39 ARG cc_start: 0.7035 (ptp90) cc_final: 0.6801 (ptp-170) REVERT: B 212 PRO cc_start: 0.7416 (Cg_exo) cc_final: 0.7072 (Cg_endo) REVERT: B 466 ILE cc_start: 0.8249 (mt) cc_final: 0.7904 (mp) REVERT: C 212 PRO cc_start: 0.7413 (Cg_exo) cc_final: 0.7068 (Cg_endo) REVERT: C 466 ILE cc_start: 0.8249 (mt) cc_final: 0.7905 (mp) REVERT: D 212 PRO cc_start: 0.7404 (Cg_exo) cc_final: 0.7049 (Cg_endo) REVERT: D 466 ILE cc_start: 0.8255 (mt) cc_final: 0.7910 (mp) outliers start: 40 outliers final: 24 residues processed: 198 average time/residue: 0.4399 time to fit residues: 99.2769 Evaluate side-chains 183 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 395 MET Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 395 MET Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 395 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 108 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 chunk 76 optimal weight: 8.9990 chunk 6 optimal weight: 0.8980 chunk 150 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 148 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.214736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.140335 restraints weight = 29781.049| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 3.16 r_work: 0.3164 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3174 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3174 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15632 Z= 0.197 Angle : 0.569 5.397 21172 Z= 0.298 Chirality : 0.044 0.141 2324 Planarity : 0.005 0.054 2696 Dihedral : 4.147 19.874 2132 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.67 % Allowed : 14.08 % Favored : 83.25 % 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: 0.36 (0.21), residues: 1864 helix: 0.90 (0.17), residues: 940 sheet: -1.75 (0.36), residues: 212 loop : 0.22 (0.27), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 209 TYR 0.017 0.001 TYR B 162 PHE 0.022 0.002 PHE C 186 TRP 0.008 0.001 TRP A 437 HIS 0.003 0.001 HIS D 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.20 (15628) covalent geometry : angle 0.56845 / 0.30 (21164) SS BOND : bond 0.00168 / 0.10 ( 4) SS BOND : angle 0.93744 / 0.52 ( 8) hydrogen bonds : bond 0.04788 / 3.13 ( 784) hydrogen bonds : angle 4.62072 / 3.29 ( 2268) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 170 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 PRO cc_start: 0.7436 (Cg_exo) cc_final: 0.7077 (Cg_endo) REVERT: A 262 GLU cc_start: 0.8354 (mt-10) cc_final: 0.7916 (mm-30) REVERT: A 466 ILE cc_start: 0.8451 (mt) cc_final: 0.8123 (mp) REVERT: F 39 ARG cc_start: 0.7127 (ptp90) cc_final: 0.6874 (ptp-170) REVERT: H 39 ARG cc_start: 0.7132 (ptp90) cc_final: 0.6860 (ptp-170) REVERT: B 212 PRO cc_start: 0.7446 (Cg_exo) cc_final: 0.7097 (Cg_endo) REVERT: B 466 ILE cc_start: 0.8445 (mt) cc_final: 0.8117 (mp) REVERT: C 212 PRO cc_start: 0.7448 (Cg_exo) cc_final: 0.7093 (Cg_endo) REVERT: C 466 ILE cc_start: 0.8442 (mt) cc_final: 0.8117 (mp) REVERT: D 212 PRO cc_start: 0.7440 (Cg_exo) cc_final: 0.7085 (Cg_endo) REVERT: D 466 ILE cc_start: 0.8446 (mt) cc_final: 0.8119 (mp) outliers start: 44 outliers final: 33 residues processed: 194 average time/residue: 0.3509 time to fit residues: 79.7209 Evaluate side-chains 198 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 165 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 395 MET Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 395 MET Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 395 MET Chi-restraints excluded: chain D residue 416 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 160 optimal weight: 0.0000 chunk 12 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 58 optimal weight: 9.9990 chunk 15 optimal weight: 0.6980 chunk 167 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 150 optimal weight: 0.9980 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.216155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.137460 restraints weight = 25771.953| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 3.07 r_work: 0.3134 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3141 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3141 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15632 Z= 0.121 Angle : 0.509 5.508 21172 Z= 0.265 Chirality : 0.041 0.132 2324 Planarity : 0.005 0.048 2696 Dihedral : 3.961 18.709 2132 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.18 % Allowed : 14.93 % Favored : 82.89 % 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: 0.68 (0.21), residues: 1864 helix: 1.24 (0.18), residues: 940 sheet: -1.61 (0.36), residues: 212 loop : 0.24 (0.26), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 209 TYR 0.013 0.001 TYR C 162 PHE 0.023 0.001 PHE A 186 TRP 0.008 0.001 TRP D 305 HIS 0.003 0.001 HIS B 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (15628) covalent geometry : angle 0.50862 / 0.27 (21164) SS BOND : bond 0.00139 / 0.08 ( 4) SS BOND : angle 0.72919 / 0.40 ( 8) hydrogen bonds : bond 0.04008 / 2.63 ( 784) hydrogen bonds : angle 4.33564 / 3.08 ( 2268) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 174 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 PRO cc_start: 0.7258 (Cg_exo) cc_final: 0.6908 (Cg_endo) REVERT: A 466 ILE cc_start: 0.8339 (mt) cc_final: 0.8094 (mp) REVERT: F 39 ARG cc_start: 0.6990 (ptp90) cc_final: 0.6773 (ptp90) REVERT: H 39 ARG cc_start: 0.6978 (ptp90) cc_final: 0.6766 (ptp90) REVERT: B 212 PRO cc_start: 0.7360 (Cg_exo) cc_final: 0.7002 (Cg_endo) REVERT: B 466 ILE cc_start: 0.8297 (mt) cc_final: 0.8079 (mp) REVERT: C 212 PRO cc_start: 0.7358 (Cg_exo) cc_final: 0.7000 (Cg_endo) REVERT: C 466 ILE cc_start: 0.8305 (mt) cc_final: 0.8085 (mp) REVERT: D 212 PRO cc_start: 0.7354 (Cg_exo) cc_final: 0.6988 (Cg_endo) REVERT: D 466 ILE cc_start: 0.8318 (mt) cc_final: 0.8094 (mp) outliers start: 36 outliers final: 30 residues processed: 194 average time/residue: 0.3653 time to fit residues: 82.0872 Evaluate side-chains 188 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 158 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 395 MET Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 328 MET Chi-restraints excluded: chain C residue 395 MET Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 395 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 102 optimal weight: 0.8980 chunk 156 optimal weight: 0.1980 chunk 106 optimal weight: 0.7980 chunk 41 optimal weight: 0.0670 chunk 153 optimal weight: 0.5980 chunk 58 optimal weight: 0.0980 chunk 25 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 overall best weight: 0.3518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.217504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.143731 restraints weight = 31239.502| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 4.02 r_work: 0.3112 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3105 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3105 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15632 Z= 0.102 Angle : 0.493 6.126 21172 Z= 0.255 Chirality : 0.040 0.129 2324 Planarity : 0.005 0.048 2696 Dihedral : 3.811 18.964 2132 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.18 % Allowed : 15.35 % Favored : 82.46 % 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: 0.78 (0.21), residues: 1864 helix: 1.44 (0.18), residues: 960 sheet: -1.63 (0.35), residues: 212 loop : 0.08 (0.27), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 209 TYR 0.013 0.001 TYR B 162 PHE 0.014 0.001 PHE A 406 TRP 0.008 0.001 TRP C 436 HIS 0.002 0.001 HIS B 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (15628) covalent geometry : angle 0.49293 / 0.25 (21164) SS BOND : bond 0.00104 / 0.06 ( 4) SS BOND : angle 0.71087 / 0.39 ( 8) hydrogen bonds : bond 0.03601 / 2.37 ( 784) hydrogen bonds : angle 4.13139 / 2.93 ( 2268) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 175 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 PRO cc_start: 0.7258 (Cg_exo) cc_final: 0.6907 (Cg_endo) REVERT: H 39 ARG cc_start: 0.6938 (ptp90) cc_final: 0.6651 (ttm170) REVERT: B 212 PRO cc_start: 0.7268 (Cg_exo) cc_final: 0.6929 (Cg_endo) REVERT: B 466 ILE cc_start: 0.8359 (mt) cc_final: 0.8108 (mp) REVERT: C 212 PRO cc_start: 0.7269 (Cg_exo) cc_final: 0.6927 (Cg_endo) REVERT: C 466 ILE cc_start: 0.8361 (mt) cc_final: 0.8106 (mp) REVERT: D 212 PRO cc_start: 0.7263 (Cg_exo) cc_final: 0.6919 (Cg_endo) REVERT: D 466 ILE cc_start: 0.8366 (mt) cc_final: 0.8114 (mp) outliers start: 36 outliers final: 23 residues processed: 199 average time/residue: 0.3402 time to fit residues: 79.1202 Evaluate side-chains 193 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 170 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 416 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 175 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 132 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 181 optimal weight: 0.0980 chunk 143 optimal weight: 0.5980 chunk 157 optimal weight: 6.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.216073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.145362 restraints weight = 35474.002| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 4.69 r_work: 0.3064 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3051 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3051 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15632 Z= 0.145 Angle : 0.526 6.352 21172 Z= 0.271 Chirality : 0.042 0.143 2324 Planarity : 0.005 0.048 2696 Dihedral : 3.863 19.781 2131 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.61 % Allowed : 16.02 % Favored : 81.37 % 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: 0.87 (0.21), residues: 1864 helix: 1.57 (0.18), residues: 924 sheet: -1.55 (0.35), residues: 212 loop : 0.10 (0.26), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 209 TYR 0.017 0.001 TYR C 162 PHE 0.026 0.001 PHE D 186 TRP 0.008 0.001 TRP A 221 HIS 0.002 0.001 HIS B 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.14 (15628) covalent geometry : angle 0.52600 / 0.27 (21164) SS BOND : bond 0.00070 / 0.04 ( 4) SS BOND : angle 0.80633 / 0.44 ( 8) hydrogen bonds : bond 0.04020 / 2.63 ( 784) hydrogen bonds : angle 4.15955 / 2.95 ( 2268) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 172 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 PRO cc_start: 0.7151 (Cg_exo) cc_final: 0.6789 (Cg_endo) REVERT: A 258 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6681 (pt0) REVERT: A 328 MET cc_start: 0.7801 (OUTLIER) cc_final: 0.7464 (mtm) REVERT: A 366 ILE cc_start: 0.6740 (OUTLIER) cc_final: 0.6493 (mt) REVERT: A 466 ILE cc_start: 0.8070 (mt) cc_final: 0.7797 (mp) REVERT: B 212 PRO cc_start: 0.7194 (Cg_exo) cc_final: 0.6841 (Cg_endo) REVERT: B 328 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.7452 (mtm) REVERT: B 366 ILE cc_start: 0.6745 (OUTLIER) cc_final: 0.6510 (mt) REVERT: B 466 ILE cc_start: 0.8057 (mt) cc_final: 0.7785 (mp) REVERT: C 212 PRO cc_start: 0.7190 (Cg_exo) cc_final: 0.6833 (Cg_endo) REVERT: C 328 MET cc_start: 0.7793 (OUTLIER) cc_final: 0.7452 (mtm) REVERT: C 366 ILE cc_start: 0.6779 (OUTLIER) cc_final: 0.6541 (mt) REVERT: C 466 ILE cc_start: 0.8068 (mt) cc_final: 0.7796 (mp) REVERT: D 212 PRO cc_start: 0.7184 (Cg_exo) cc_final: 0.6825 (Cg_endo) REVERT: D 328 MET cc_start: 0.7787 (OUTLIER) cc_final: 0.7446 (mtm) REVERT: D 366 ILE cc_start: 0.6760 (OUTLIER) cc_final: 0.6525 (mt) REVERT: D 466 ILE cc_start: 0.8077 (mt) cc_final: 0.7803 (mp) outliers start: 43 outliers final: 25 residues processed: 201 average time/residue: 0.3602 time to fit residues: 83.6735 Evaluate side-chains 192 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 158 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 328 MET Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 366 ILE Chi-restraints excluded: chain D residue 416 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 62 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 114 optimal weight: 4.9990 chunk 10 optimal weight: 0.0870 chunk 142 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 144 optimal weight: 0.4980 chunk 49 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 27 optimal weight: 0.5980 chunk 121 optimal weight: 0.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.218369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.144305 restraints weight = 29506.479| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 3.14 r_work: 0.3219 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3228 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3228 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15632 Z= 0.121 Angle : 0.506 6.758 21172 Z= 0.261 Chirality : 0.041 0.133 2324 Planarity : 0.005 0.048 2696 Dihedral : 3.819 19.323 2130 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.91 % Allowed : 16.44 % Favored : 80.64 % 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: 0.94 (0.21), residues: 1864 helix: 1.62 (0.18), residues: 928 sheet: -1.48 (0.35), residues: 212 loop : 0.13 (0.26), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 144 TYR 0.018 0.001 TYR B 162 PHE 0.016 0.001 PHE B 406 TRP 0.007 0.001 TRP D 436 HIS 0.002 0.001 HIS D 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (15628) covalent geometry : angle 0.50543 / 0.26 (21164) SS BOND : bond 0.00048 / 0.03 ( 4) SS BOND : angle 0.73403 / 0.40 ( 8) hydrogen bonds : bond 0.03813 / 2.50 ( 784) hydrogen bonds : angle 3.99434 / 2.85 ( 2268) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 158 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 PRO cc_start: 0.7284 (Cg_exo) cc_final: 0.6952 (Cg_endo) REVERT: A 366 ILE cc_start: 0.7289 (OUTLIER) cc_final: 0.7015 (mt) REVERT: A 466 ILE cc_start: 0.8404 (mt) cc_final: 0.8179 (mp) REVERT: B 212 PRO cc_start: 0.7304 (Cg_exo) cc_final: 0.6977 (Cg_endo) REVERT: B 258 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6811 (pt0) REVERT: B 328 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7915 (mtm) REVERT: B 366 ILE cc_start: 0.7295 (OUTLIER) cc_final: 0.7030 (mt) REVERT: B 466 ILE cc_start: 0.8398 (mt) cc_final: 0.8173 (mp) REVERT: C 137 MET cc_start: 0.8085 (tpp) cc_final: 0.7879 (tpp) REVERT: C 212 PRO cc_start: 0.7309 (Cg_exo) cc_final: 0.6983 (Cg_endo) REVERT: C 258 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6795 (pt0) REVERT: C 328 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.7903 (mtm) REVERT: C 366 ILE cc_start: 0.7291 (OUTLIER) cc_final: 0.7019 (mt) REVERT: C 466 ILE cc_start: 0.8404 (mt) cc_final: 0.8177 (mp) REVERT: D 212 PRO cc_start: 0.7298 (Cg_exo) cc_final: 0.6969 (Cg_endo) REVERT: D 258 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6809 (pt0) REVERT: D 328 MET cc_start: 0.8221 (OUTLIER) cc_final: 0.7904 (mtm) REVERT: D 366 ILE cc_start: 0.7317 (OUTLIER) cc_final: 0.7051 (mt) REVERT: D 466 ILE cc_start: 0.8409 (mt) cc_final: 0.8183 (mp) outliers start: 48 outliers final: 27 residues processed: 188 average time/residue: 0.3177 time to fit residues: 69.8314 Evaluate side-chains 192 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 155 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 328 MET Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 366 ILE Chi-restraints excluded: chain D residue 416 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 95 optimal weight: 0.0030 chunk 65 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 56 optimal weight: 0.1980 chunk 175 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 158 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.218630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.150595 restraints weight = 37668.281| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 4.20 r_work: 0.3145 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3161 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3161 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15632 Z= 0.116 Angle : 0.501 6.309 21172 Z= 0.259 Chirality : 0.041 0.122 2324 Planarity : 0.005 0.048 2696 Dihedral : 3.739 19.500 2129 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.79 % Allowed : 16.44 % Favored : 80.76 % 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: 1.01 (0.21), residues: 1864 helix: 1.67 (0.18), residues: 928 sheet: -1.31 (0.36), residues: 212 loop : 0.13 (0.26), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 209 TYR 0.020 0.001 TYR A 162 PHE 0.030 0.001 PHE D 186 TRP 0.007 0.001 TRP D 436 HIS 0.002 0.001 HIS B 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (15628) covalent geometry : angle 0.50090 / 0.26 (21164) SS BOND : bond 0.00024 / 0.01 ( 4) SS BOND : angle 0.67514 / 0.37 ( 8) hydrogen bonds : bond 0.03740 / 2.45 ( 784) hydrogen bonds : angle 3.93952 / 2.81 ( 2268) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 158 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 PRO cc_start: 0.7305 (Cg_exo) cc_final: 0.6963 (Cg_endo) REVERT: A 366 ILE cc_start: 0.7327 (OUTLIER) cc_final: 0.7052 (mt) REVERT: A 466 ILE cc_start: 0.8443 (mt) cc_final: 0.8206 (mp) REVERT: B 212 PRO cc_start: 0.7315 (Cg_exo) cc_final: 0.6977 (Cg_endo) REVERT: B 258 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.6866 (pt0) REVERT: B 328 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.7940 (mtm) REVERT: B 366 ILE cc_start: 0.7334 (OUTLIER) cc_final: 0.7073 (mt) REVERT: B 466 ILE cc_start: 0.8430 (mt) cc_final: 0.8191 (mp) REVERT: C 212 PRO cc_start: 0.7315 (Cg_exo) cc_final: 0.6975 (Cg_endo) REVERT: C 258 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6852 (pt0) REVERT: C 328 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.7933 (mtm) REVERT: C 366 ILE cc_start: 0.7324 (OUTLIER) cc_final: 0.7062 (mt) REVERT: C 466 ILE cc_start: 0.8439 (mt) cc_final: 0.8199 (mp) REVERT: D 212 PRO cc_start: 0.7310 (Cg_exo) cc_final: 0.6968 (Cg_endo) REVERT: D 258 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.6869 (pt0) REVERT: D 328 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.7933 (mtm) REVERT: D 366 ILE cc_start: 0.7361 (OUTLIER) cc_final: 0.7094 (mt) REVERT: D 466 ILE cc_start: 0.8450 (mt) cc_final: 0.8212 (mp) outliers start: 46 outliers final: 27 residues processed: 186 average time/residue: 0.3520 time to fit residues: 76.6163 Evaluate side-chains 194 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 157 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 328 MET Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 366 ILE Chi-restraints excluded: chain D residue 416 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 145 optimal weight: 0.4980 chunk 72 optimal weight: 4.9990 chunk 123 optimal weight: 7.9990 chunk 98 optimal weight: 0.9980 chunk 58 optimal weight: 0.0970 chunk 101 optimal weight: 7.9990 chunk 120 optimal weight: 0.9990 chunk 136 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 168 optimal weight: 3.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.216161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.138283 restraints weight = 27801.912| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.99 r_work: 0.3189 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3207 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3207 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15632 Z= 0.191 Angle : 0.547 5.988 21172 Z= 0.285 Chirality : 0.044 0.146 2324 Planarity : 0.005 0.049 2696 Dihedral : 3.900 20.080 2129 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.09 % Allowed : 16.38 % Favored : 80.52 % 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: 0.72 (0.21), residues: 1864 helix: 1.35 (0.18), residues: 928 sheet: -1.36 (0.36), residues: 212 loop : 0.08 (0.26), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 209 TYR 0.019 0.001 TYR A 162 PHE 0.018 0.002 PHE A 406 TRP 0.006 0.001 TRP D 437 HIS 0.003 0.001 HIS C 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.19 (15628) covalent geometry : angle 0.54680 / 0.29 (21164) SS BOND : bond 0.00016 / 0.01 ( 4) SS BOND : angle 0.81801 / 0.44 ( 8) hydrogen bonds : bond 0.04372 / 2.86 ( 784) hydrogen bonds : angle 4.07805 / 2.91 ( 2268) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 157 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 PRO cc_start: 0.7356 (Cg_exo) cc_final: 0.7028 (Cg_endo) REVERT: A 258 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6822 (pt0) REVERT: A 366 ILE cc_start: 0.7297 (OUTLIER) cc_final: 0.7046 (mt) REVERT: A 466 ILE cc_start: 0.8402 (mt) cc_final: 0.8193 (mp) REVERT: B 212 PRO cc_start: 0.7363 (Cg_exo) cc_final: 0.7038 (Cg_endo) REVERT: B 258 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6796 (pt0) REVERT: B 366 ILE cc_start: 0.7312 (OUTLIER) cc_final: 0.7059 (mt) REVERT: B 466 ILE cc_start: 0.8401 (mt) cc_final: 0.8191 (mp) REVERT: C 212 PRO cc_start: 0.7366 (Cg_exo) cc_final: 0.7043 (Cg_endo) REVERT: C 258 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6777 (pt0) REVERT: C 366 ILE cc_start: 0.7305 (OUTLIER) cc_final: 0.7054 (mt) REVERT: C 466 ILE cc_start: 0.8397 (mt) cc_final: 0.8187 (mp) REVERT: D 137 MET cc_start: 0.8071 (tpp) cc_final: 0.7855 (tpp) REVERT: D 212 PRO cc_start: 0.7349 (Cg_exo) cc_final: 0.7019 (Cg_endo) REVERT: D 258 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.6794 (pt0) REVERT: D 366 ILE cc_start: 0.7317 (OUTLIER) cc_final: 0.7061 (mt) REVERT: D 466 ILE cc_start: 0.8406 (mt) cc_final: 0.8198 (mp) outliers start: 51 outliers final: 31 residues processed: 187 average time/residue: 0.3595 time to fit residues: 78.6507 Evaluate side-chains 192 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 153 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 366 ILE Chi-restraints excluded: chain D residue 416 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 115 optimal weight: 0.8980 chunk 36 optimal weight: 0.0370 chunk 50 optimal weight: 0.1980 chunk 153 optimal weight: 0.4980 chunk 101 optimal weight: 7.9990 chunk 165 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 97 optimal weight: 0.5980 chunk 147 optimal weight: 0.8980 overall best weight: 0.3858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.219471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.149579 restraints weight = 36168.070| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 3.98 r_work: 0.3155 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3168 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3168 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15632 Z= 0.104 Angle : 0.499 6.086 21172 Z= 0.259 Chirality : 0.041 0.122 2324 Planarity : 0.005 0.048 2696 Dihedral : 3.744 18.859 2129 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.31 % Allowed : 17.42 % Favored : 80.28 % 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: 1.07 (0.21), residues: 1864 helix: 1.67 (0.18), residues: 924 sheet: -1.26 (0.36), residues: 212 loop : 0.22 (0.26), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 209 TYR 0.020 0.001 TYR D 162 PHE 0.033 0.001 PHE C 186 TRP 0.009 0.001 TRP A 305 HIS 0.002 0.001 HIS C 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (15628) covalent geometry : angle 0.49875 / 0.26 (21164) SS BOND : bond 0.00006 / 0.00 ( 4) SS BOND : angle 0.68612 / 0.37 ( 8) hydrogen bonds : bond 0.03662 / 2.40 ( 784) hydrogen bonds : angle 3.91437 / 2.78 ( 2268) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 159 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 PRO cc_start: 0.7315 (Cg_exo) cc_final: 0.6978 (Cg_endo) REVERT: A 366 ILE cc_start: 0.7299 (OUTLIER) cc_final: 0.7024 (mt) REVERT: A 466 ILE cc_start: 0.8454 (mt) cc_final: 0.8234 (mp) REVERT: B 137 MET cc_start: 0.8042 (tpp) cc_final: 0.7824 (tpp) REVERT: B 212 PRO cc_start: 0.7313 (Cg_exo) cc_final: 0.6978 (Cg_endo) REVERT: B 366 ILE cc_start: 0.7312 (OUTLIER) cc_final: 0.7047 (mt) REVERT: B 466 ILE cc_start: 0.8445 (mt) cc_final: 0.8226 (mp) REVERT: C 137 MET cc_start: 0.8057 (tpp) cc_final: 0.7843 (tpp) REVERT: C 212 PRO cc_start: 0.7310 (Cg_exo) cc_final: 0.6973 (Cg_endo) REVERT: C 366 ILE cc_start: 0.7297 (OUTLIER) cc_final: 0.7036 (mt) REVERT: C 466 ILE cc_start: 0.8452 (mt) cc_final: 0.8231 (mp) REVERT: D 137 MET cc_start: 0.8097 (tpp) cc_final: 0.7884 (tpp) REVERT: D 212 PRO cc_start: 0.7401 (Cg_exo) cc_final: 0.7062 (Cg_endo) REVERT: D 366 ILE cc_start: 0.7330 (OUTLIER) cc_final: 0.7063 (mt) REVERT: D 466 ILE cc_start: 0.8455 (mt) cc_final: 0.8235 (mp) outliers start: 38 outliers final: 25 residues processed: 189 average time/residue: 0.3415 time to fit residues: 75.1668 Evaluate side-chains 187 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 158 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 366 ILE Chi-restraints excluded: chain D residue 416 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 25 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 75 optimal weight: 0.3980 chunk 103 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 172 optimal weight: 1.9990 chunk 163 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 20 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.218547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.144047 restraints weight = 28624.176| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 3.00 r_work: 0.3216 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3222 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3222 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15632 Z= 0.121 Angle : 0.505 5.942 21172 Z= 0.263 Chirality : 0.041 0.122 2324 Planarity : 0.005 0.048 2696 Dihedral : 3.712 18.577 2128 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.06 % Allowed : 17.66 % Favored : 80.28 % 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: 0.98 (0.21), residues: 1864 helix: 1.52 (0.18), residues: 944 sheet: -1.10 (0.34), residues: 240 loop : 0.26 (0.27), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 209 TYR 0.017 0.001 TYR A 162 PHE 0.017 0.001 PHE B 406 TRP 0.007 0.001 TRP D 436 HIS 0.002 0.001 HIS C 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (15628) covalent geometry : angle 0.50461 / 0.26 (21164) SS BOND : bond 0.00015 / 0.01 ( 4) SS BOND : angle 0.71278 / 0.39 ( 8) hydrogen bonds : bond 0.03775 / 2.47 ( 784) hydrogen bonds : angle 3.91289 / 2.78 ( 2268) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5000.72 seconds wall clock time: 85 minutes 50.73 seconds (5150.73 seconds total)