Starting phenix.real_space_refine on Thu May 15 12:31:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c0h_45084/05_2025/9c0h_45084.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c0h_45084/05_2025/9c0h_45084.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c0h_45084/05_2025/9c0h_45084.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c0h_45084/05_2025/9c0h_45084.map" model { file = "/net/cci-nas-00/data/ceres_data/9c0h_45084/05_2025/9c0h_45084.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c0h_45084/05_2025/9c0h_45084.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.032 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: 8 Type Number sf(0) Gaussians K 2 8.98 5 P 4 5.49 5 S 78 5.16 5 Cl 2 4.86 5 Na 2 4.78 5 C 8572 2.51 5 N 2210 2.21 5 O 2256 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 13126 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 876, 6535 Classifications: {'peptide': 876} Incomplete info: {'backbone_only': 24, 'truncation_to_alanine': 77} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 844} Chain breaks: 3 Unresolved non-hydrogen bonds: 355 Unresolved non-hydrogen angles: 460 Unresolved non-hydrogen dihedrals: 254 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLN:plan1': 4, 'TPO:plan-1': 2, 'ASN:plan1': 9, 'ASP:plan': 16, 'PHE:plan': 2, 'GLU:plan': 21, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 204 Chain: "B" Number of atoms: 6535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 876, 6535 Classifications: {'peptide': 876} Incomplete info: {'backbone_only': 24, 'truncation_to_alanine': 77} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 844} Chain breaks: 3 Unresolved non-hydrogen bonds: 355 Unresolved non-hydrogen angles: 460 Unresolved non-hydrogen dihedrals: 254 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLN:plan1': 4, 'TPO:plan-1': 2, 'ASN:plan1': 9, 'ASP:plan': 16, 'PHE:plan': 2, 'GLU:plan': 21, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 204 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 28 Unusual residues: {' K': 1, ' CL': 1, ' NA': 1, '82U': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 28 Unusual residues: {' K': 1, ' CL': 1, ' NA': 1, '82U': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 8.21, per 1000 atoms: 0.63 Number of scatterers: 13126 At special positions: 0 Unit cell: (124.02, 85.86, 146.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) K 2 19.00 Cl 2 17.00 S 78 16.00 P 4 15.00 Na 2 11.00 O 2256 8.00 N 2210 7.00 C 8572 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 563 " - pdb=" SG CYS A 568 " distance=2.03 Simple disulfide: pdb=" SG CYS A 577 " - pdb=" SG CYS A 582 " distance=2.04 Simple disulfide: pdb=" SG CYS B 563 " - pdb=" SG CYS B 568 " distance=2.03 Simple disulfide: pdb=" SG CYS B 577 " - pdb=" SG CYS B 582 " distance=2.04 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: 3.60 Conformation dependent library (CDL) restraints added in 1.7 seconds 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3168 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 3 sheets defined 64.2% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 207 through 211 Processing helix chain 'A' and resid 223 through 228 removed outlier: 3.615A pdb=" N ARG A 228 " --> pdb=" O ASP A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 248 Processing helix chain 'A' and resid 286 through 291 Processing helix chain 'A' and resid 291 through 300 Processing helix chain 'A' and resid 302 through 306 removed outlier: 3.761A pdb=" N PHE A 305 " --> pdb=" O VAL A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 315 Processing helix chain 'A' and resid 316 through 343 Processing helix chain 'A' and resid 351 through 361 Processing helix chain 'A' and resid 361 through 398 removed outlier: 3.685A pdb=" N ALA A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N HIS A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 427 removed outlier: 3.821A pdb=" N ARG A 410 " --> pdb=" O ILE A 406 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE A 415 " --> pdb=" O ILE A 411 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLY A 427 " --> pdb=" O ILE A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 454 removed outlier: 3.576A pdb=" N PHE A 454 " --> pdb=" O VAL A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 477 removed outlier: 3.613A pdb=" N PHE A 477 " --> pdb=" O PHE A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 495 Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 507 through 511 Processing helix chain 'A' and resid 517 through 542 Processing helix chain 'A' and resid 591 through 597 removed outlier: 3.526A pdb=" N SER A 597 " --> pdb=" O MET A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 632 removed outlier: 3.705A pdb=" N ILE A 603 " --> pdb=" O PHE A 599 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER A 614 " --> pdb=" O ALA A 610 " (cutoff:3.500A) Proline residue: A 623 - end of helix removed outlier: 3.700A pdb=" N ASP A 632 " --> pdb=" O ALA A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 643 removed outlier: 3.734A pdb=" N GLN A 639 " --> pdb=" O PRO A 636 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N MET A 640 " --> pdb=" O ALA A 637 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LYS A 643 " --> pdb=" O MET A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 669 removed outlier: 3.728A pdb=" N ILE A 668 " --> pdb=" O GLY A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 699 Processing helix chain 'A' and resid 712 through 730 Processing helix chain 'A' and resid 731 through 753 Processing helix chain 'A' and resid 760 through 778 removed outlier: 3.519A pdb=" N ALA A 764 " --> pdb=" O SER A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 787 Processing helix chain 'A' and resid 801 through 811 removed outlier: 3.678A pdb=" N PHE A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 849 removed outlier: 3.611A pdb=" N LYS A 833 " --> pdb=" O ARG A 829 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA A 840 " --> pdb=" O SER A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 874 Processing helix chain 'A' and resid 896 through 913 removed outlier: 3.640A pdb=" N VAL A 900 " --> pdb=" O ASP A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1046 Proline residue: A1040 - end of helix removed outlier: 3.604A pdb=" N LYS A1046 " --> pdb=" O LEU A1042 " (cutoff:3.500A) Processing helix chain 'A' and resid 1064 through 1079 Processing helix chain 'A' and resid 1097 through 1109 Processing helix chain 'A' and resid 1110 through 1112 No H-bonds generated for 'chain 'A' and resid 1110 through 1112' Processing helix chain 'A' and resid 1114 through 1119 removed outlier: 6.347A pdb=" N GLU A1119 " --> pdb=" O ASP A1116 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1129 removed outlier: 4.061A pdb=" N ASP A1124 " --> pdb=" O GLN A1120 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS A1127 " --> pdb=" O ALA A1123 " (cutoff:3.500A) Processing helix chain 'A' and resid 1135 through 1142 Processing helix chain 'A' and resid 1142 through 1160 Processing helix chain 'A' and resid 1179 through 1192 Processing helix chain 'B' and resid 207 through 211 removed outlier: 3.567A pdb=" N LEU B 210 " --> pdb=" O THR B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 227 Processing helix chain 'B' and resid 242 through 248 Processing helix chain 'B' and resid 286 through 291 Processing helix chain 'B' and resid 291 through 300 Processing helix chain 'B' and resid 307 through 315 Processing helix chain 'B' and resid 316 through 343 removed outlier: 3.544A pdb=" N ALA B 327 " --> pdb=" O VAL B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 361 Processing helix chain 'B' and resid 361 through 398 removed outlier: 3.600A pdb=" N ALA B 381 " --> pdb=" O ALA B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 427 removed outlier: 3.765A pdb=" N GLY B 427 " --> pdb=" O ILE B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 454 removed outlier: 3.504A pdb=" N PHE B 454 " --> pdb=" O VAL B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 477 Processing helix chain 'B' and resid 486 through 499 Proline residue: B 496 - end of helix removed outlier: 3.628A pdb=" N THR B 499 " --> pdb=" O PHE B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 511 removed outlier: 4.950A pdb=" N GLY B 509 " --> pdb=" O ASN B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 542 removed outlier: 4.257A pdb=" N LYS B 520 " --> pdb=" O SER B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 571 removed outlier: 4.172A pdb=" N LEU B 570 " --> pdb=" O ALA B 566 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN B 571 " --> pdb=" O ALA B 567 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 566 through 571' Processing helix chain 'B' and resid 591 through 597 removed outlier: 3.589A pdb=" N SER B 597 " --> pdb=" O MET B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 632 removed outlier: 3.600A pdb=" N ILE B 603 " --> pdb=" O PHE B 599 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER B 614 " --> pdb=" O ALA B 610 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA B 615 " --> pdb=" O THR B 611 " (cutoff:3.500A) Proline residue: B 623 - end of helix removed outlier: 3.708A pdb=" N ASP B 632 " --> pdb=" O ALA B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 643 removed outlier: 5.020A pdb=" N MET B 640 " --> pdb=" O ALA B 637 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS B 643 " --> pdb=" O MET B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 669 removed outlier: 3.760A pdb=" N ILE B 668 " --> pdb=" O GLY B 664 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA B 669 " --> pdb=" O PHE B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 699 Processing helix chain 'B' and resid 712 through 730 Processing helix chain 'B' and resid 731 through 753 Processing helix chain 'B' and resid 760 through 778 removed outlier: 3.505A pdb=" N ALA B 764 " --> pdb=" O SER B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 787 Processing helix chain 'B' and resid 801 through 811 removed outlier: 3.620A pdb=" N PHE B 811 " --> pdb=" O LEU B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 849 removed outlier: 3.577A pdb=" N LYS B 833 " --> pdb=" O ARG B 829 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA B 840 " --> pdb=" O SER B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 874 Processing helix chain 'B' and resid 891 through 895 removed outlier: 3.912A pdb=" N ALA B 895 " --> pdb=" O TRP B 892 " (cutoff:3.500A) Processing helix chain 'B' and resid 896 through 913 removed outlier: 3.619A pdb=" N VAL B 900 " --> pdb=" O ASP B 896 " (cutoff:3.500A) Processing helix chain 'B' and resid 1034 through 1045 Proline residue: B1040 - end of helix Processing helix chain 'B' and resid 1064 through 1079 Processing helix chain 'B' and resid 1097 through 1109 Processing helix chain 'B' and resid 1110 through 1112 No H-bonds generated for 'chain 'B' and resid 1110 through 1112' Processing helix chain 'B' and resid 1114 through 1118 Processing helix chain 'B' and resid 1119 through 1120 No H-bonds generated for 'chain 'B' and resid 1119 through 1120' Processing helix chain 'B' and resid 1121 through 1129 removed outlier: 3.620A pdb=" N LYS B1125 " --> pdb=" O ASP B1121 " (cutoff:3.500A) Processing helix chain 'B' and resid 1135 through 1142 Processing helix chain 'B' and resid 1142 through 1160 Processing helix chain 'B' and resid 1179 through 1192 Processing sheet with id=AA1, first strand: chain 'A' and resid 854 through 859 removed outlier: 6.686A pdb=" N CYS A 791 " --> pdb=" O ILE A 819 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N GLY A 821 " --> pdb=" O CYS A 791 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL A 793 " --> pdb=" O GLY A 821 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N VAL A 823 " --> pdb=" O VAL A 793 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU A 792 " --> pdb=" O VAL A 885 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N GLY A 887 " --> pdb=" O LEU A 792 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE A1165 " --> pdb=" O THR A1023 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ILE A1024 " --> pdb=" O ARG A1055 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N PHE A1057 " --> pdb=" O ILE A1024 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL A1026 " --> pdb=" O PHE A1057 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N GLY A1059 " --> pdb=" O VAL A1026 " (cutoff:3.500A) removed outlier: 8.837A pdb=" N MET A1087 " --> pdb=" O ILE A1054 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL A1056 " --> pdb=" O MET A1087 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N LEU A1089 " --> pdb=" O VAL A1056 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE A1058 " --> pdb=" O LEU A1089 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 547 through 548 removed outlier: 3.592A pdb=" N TYR B 584 " --> pdb=" O ALA B 548 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 854 through 859 removed outlier: 6.654A pdb=" N CYS B 791 " --> pdb=" O ILE B 819 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N GLY B 821 " --> pdb=" O CYS B 791 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL B 793 " --> pdb=" O GLY B 821 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N VAL B 823 " --> pdb=" O VAL B 793 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU B 792 " --> pdb=" O VAL B 885 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N GLY B 887 " --> pdb=" O LEU B 792 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE B1166 " --> pdb=" O LEU B1198 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N VAL B1200 " --> pdb=" O ILE B1166 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N MET B1168 " --> pdb=" O VAL B1200 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE B1165 " --> pdb=" O THR B1023 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ILE B1024 " --> pdb=" O ARG B1055 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N PHE B1057 " --> pdb=" O ILE B1024 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL B1026 " --> pdb=" O PHE B1057 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N GLY B1059 " --> pdb=" O VAL B1026 " (cutoff:3.500A) removed outlier: 8.834A pdb=" N MET B1087 " --> pdb=" O ILE B1054 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL B1056 " --> pdb=" O MET B1087 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N LEU B1089 " --> pdb=" O VAL B1056 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE B1058 " --> pdb=" O LEU B1089 " (cutoff:3.500A) 805 hydrogen bonds defined for protein. 2313 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: 4.55 Time building geometry restraints manager: 4.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4097 1.34 - 1.46: 3104 1.46 - 1.58: 6085 1.58 - 1.70: 12 1.70 - 1.81: 132 Bond restraints: 13430 Sorted by residual: bond pdb=" OG1 TPO A 212 " pdb=" P TPO A 212 " ideal model delta sigma weight residual 1.717 1.606 0.111 2.00e-02 2.50e+03 3.06e+01 bond pdb=" OG1 TPO B 217 " pdb=" P TPO B 217 " ideal model delta sigma weight residual 1.717 1.606 0.111 2.00e-02 2.50e+03 3.05e+01 bond pdb=" OG1 TPO B 212 " pdb=" P TPO B 212 " ideal model delta sigma weight residual 1.717 1.607 0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" OG1 TPO A 217 " pdb=" P TPO A 217 " ideal model delta sigma weight residual 1.717 1.608 0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" O3P TPO A 212 " pdb=" P TPO A 212 " ideal model delta sigma weight residual 1.528 1.608 -0.080 2.00e-02 2.50e+03 1.62e+01 ... (remaining 13425 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 18003 2.43 - 4.85: 210 4.85 - 7.28: 33 7.28 - 9.71: 12 9.71 - 12.14: 8 Bond angle restraints: 18266 Sorted by residual: angle pdb=" CB TPO B 212 " pdb=" OG1 TPO B 212 " pdb=" P TPO B 212 " ideal model delta sigma weight residual 119.31 107.17 12.14 3.00e+00 1.11e-01 1.64e+01 angle pdb=" CB TPO B 217 " pdb=" OG1 TPO B 217 " pdb=" P TPO B 217 " ideal model delta sigma weight residual 119.31 107.27 12.04 3.00e+00 1.11e-01 1.61e+01 angle pdb=" CB TPO A 217 " pdb=" OG1 TPO A 217 " pdb=" P TPO A 217 " ideal model delta sigma weight residual 119.31 107.36 11.95 3.00e+00 1.11e-01 1.59e+01 angle pdb=" CB TPO A 212 " pdb=" OG1 TPO A 212 " pdb=" P TPO A 212 " ideal model delta sigma weight residual 119.31 107.42 11.89 3.00e+00 1.11e-01 1.57e+01 angle pdb=" N 82U B1304 " pdb=" CA 82U B1304 " pdb=" CB 82U B1304 " ideal model delta sigma weight residual 122.43 110.61 11.82 3.00e+00 1.11e-01 1.55e+01 ... (remaining 18261 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 6670 17.83 - 35.65: 862 35.65 - 53.48: 193 53.48 - 71.30: 33 71.30 - 89.13: 18 Dihedral angle restraints: 7776 sinusoidal: 2802 harmonic: 4974 Sorted by residual: dihedral pdb=" CB CYS B 577 " pdb=" SG CYS B 577 " pdb=" SG CYS B 582 " pdb=" CB CYS B 582 " ideal model delta sinusoidal sigma weight residual -86.00 -0.21 -85.79 1 1.00e+01 1.00e-02 8.90e+01 dihedral pdb=" CB CYS A 577 " pdb=" SG CYS A 577 " pdb=" SG CYS A 582 " pdb=" CB CYS A 582 " ideal model delta sinusoidal sigma weight residual 93.00 27.18 65.82 1 1.00e+01 1.00e-02 5.67e+01 dihedral pdb=" C 82U A1304 " pdb=" N 82U A1304 " pdb=" CA 82U A1304 " pdb=" CB 82U A1304 " ideal model delta harmonic sigma weight residual -122.60 -138.52 15.92 0 2.50e+00 1.60e-01 4.05e+01 ... (remaining 7773 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1121 0.028 - 0.056: 611 0.056 - 0.084: 247 0.084 - 0.112: 103 0.112 - 0.140: 26 Chirality restraints: 2108 Sorted by residual: chirality pdb=" CB THR A 416 " pdb=" CA THR A 416 " pdb=" OG1 THR A 416 " pdb=" CG2 THR A 416 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CB THR B 416 " pdb=" CA THR B 416 " pdb=" OG1 THR B 416 " pdb=" CG2 THR B 416 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA MET B 897 " pdb=" N MET B 897 " pdb=" C MET B 897 " pdb=" CB MET B 897 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.76e-01 ... (remaining 2105 not shown) Planarity restraints: 2268 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N 82U A1304 " -0.072 2.00e-02 2.50e+03 8.12e-02 1.65e+02 pdb=" CA 82U A1304 " 0.223 2.00e-02 2.50e+03 pdb=" C 82U A1304 " -0.077 2.00e-02 2.50e+03 pdb=" O 82U A1304 " -0.002 2.00e-02 2.50e+03 pdb=" CB 82U A1304 " -0.071 2.00e-02 2.50e+03 pdb=" CG 82U A1304 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 82U A1304 " 0.004 2.00e-02 2.50e+03 pdb=" C1 82U A1304 " -0.001 2.00e-02 2.50e+03 pdb=" C17 82U A1304 " -0.001 2.00e-02 2.50e+03 pdb=" S1 82U A1304 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N 82U B1304 " 0.071 2.00e-02 2.50e+03 8.08e-02 1.63e+02 pdb=" CA 82U B1304 " -0.221 2.00e-02 2.50e+03 pdb=" C 82U B1304 " 0.079 2.00e-02 2.50e+03 pdb=" O 82U B1304 " 0.002 2.00e-02 2.50e+03 pdb=" CB 82U B1304 " 0.070 2.00e-02 2.50e+03 pdb=" CG 82U B1304 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 82U B1304 " -0.004 2.00e-02 2.50e+03 pdb=" C1 82U B1304 " 0.001 2.00e-02 2.50e+03 pdb=" C17 82U B1304 " 0.000 2.00e-02 2.50e+03 pdb=" S1 82U B1304 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 513 " 0.011 2.00e-02 2.50e+03 2.18e-02 4.75e+00 pdb=" CG ASP B 513 " -0.038 2.00e-02 2.50e+03 pdb=" OD1 ASP B 513 " 0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP B 513 " 0.013 2.00e-02 2.50e+03 ... (remaining 2265 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.75: 2079 2.75 - 3.35: 15084 3.35 - 3.95: 25989 3.95 - 4.54: 36583 4.54 - 5.14: 52863 Nonbonded interactions: 132598 Sorted by model distance: nonbonded pdb=" O GLY B 887 " pdb=" OH TYR B 903 " model vdw 2.157 3.040 nonbonded pdb=" O ASN B1203 " pdb=" ND2 ASN B1203 " model vdw 2.170 3.120 nonbonded pdb=" O THR A 328 " pdb=" OG1 THR A 332 " model vdw 2.187 3.040 nonbonded pdb=" O PHE B 572 " pdb=" OG SER B 575 " model vdw 2.190 3.040 nonbonded pdb=" O GLY A 887 " pdb=" OH TYR A 903 " model vdw 2.193 3.040 ... (remaining 132593 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.340 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: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 31.960 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.060 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:11.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 13434 Z= 0.233 Angle : 0.717 12.136 18274 Z= 0.345 Chirality : 0.043 0.140 2108 Planarity : 0.005 0.081 2268 Dihedral : 16.943 89.129 4596 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 4.07 % Allowed : 27.46 % Favored : 68.47 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.20), residues: 1724 helix: 1.31 (0.17), residues: 972 sheet: 0.72 (0.42), residues: 142 loop : -1.44 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A1028 HIS 0.006 0.001 HIS B 226 PHE 0.015 0.002 PHE B 495 TYR 0.020 0.002 TYR A 915 ARG 0.005 0.001 ARG B1064 Details of bonding type rmsd hydrogen bonds : bond 0.13975 ( 805) hydrogen bonds : angle 5.53927 ( 2313) SS BOND : bond 0.00393 ( 4) SS BOND : angle 0.79121 ( 8) covalent geometry : bond 0.00502 (13430) covalent geometry : angle 0.71737 (18266) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 163 time to evaluate : 1.263 Fit side-chains outliers start: 52 outliers final: 47 residues processed: 211 average time/residue: 0.7436 time to fit residues: 180.0288 Evaluate side-chains 203 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 156 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain A residue 643 LYS Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 710 TYR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1162 THR Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 536 ILE Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 543 CYS Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 692 SER Chi-restraints excluded: chain B residue 710 TYR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain B residue 815 VAL Chi-restraints excluded: chain B residue 834 GLU Chi-restraints excluded: chain B residue 900 VAL Chi-restraints excluded: chain B residue 1036 THR Chi-restraints excluded: chain B residue 1045 THR Chi-restraints excluded: chain B residue 1207 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 70 optimal weight: 0.3980 chunk 136 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 158 optimal weight: 4.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1203 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.112446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.094961 restraints weight = 20174.802| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.62 r_work: 0.3110 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.0760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 13434 Z= 0.245 Angle : 0.691 10.629 18274 Z= 0.356 Chirality : 0.046 0.147 2108 Planarity : 0.005 0.081 2268 Dihedral : 8.884 79.036 1972 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 6.42 % Allowed : 21.91 % Favored : 71.67 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.20), residues: 1724 helix: 1.12 (0.16), residues: 1000 sheet: 0.47 (0.41), residues: 142 loop : -1.50 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A1028 HIS 0.010 0.002 HIS B1204 PHE 0.020 0.002 PHE A 495 TYR 0.023 0.002 TYR A 915 ARG 0.005 0.001 ARG B1080 Details of bonding type rmsd hydrogen bonds : bond 0.05784 ( 805) hydrogen bonds : angle 4.73254 ( 2313) SS BOND : bond 0.00405 ( 4) SS BOND : angle 0.86171 ( 8) covalent geometry : bond 0.00570 (13430) covalent geometry : angle 0.69044 (18266) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 162 time to evaluate : 1.461 Fit side-chains REVERT: A 468 TYR cc_start: 0.7739 (m-10) cc_final: 0.7518 (m-80) outliers start: 82 outliers final: 54 residues processed: 222 average time/residue: 0.7875 time to fit residues: 200.4350 Evaluate side-chains 209 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 155 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 GLU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 865 GLU Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 1045 THR Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 536 ILE Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 543 CYS Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 710 TYR Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 753 LYS Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 815 VAL Chi-restraints excluded: chain B residue 836 SER Chi-restraints excluded: chain B residue 900 VAL Chi-restraints excluded: chain B residue 1023 THR Chi-restraints excluded: chain B residue 1036 THR Chi-restraints excluded: chain B residue 1045 THR Chi-restraints excluded: chain B residue 1076 LEU Chi-restraints excluded: chain B residue 1207 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 19 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 22 optimal weight: 0.0980 chunk 124 optimal weight: 0.6980 chunk 152 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1203 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.116877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.099818 restraints weight = 20410.458| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.61 r_work: 0.3184 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.0881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 13434 Z= 0.127 Angle : 0.581 11.211 18274 Z= 0.295 Chirality : 0.041 0.148 2108 Planarity : 0.005 0.081 2268 Dihedral : 7.797 74.343 1940 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 4.07 % Allowed : 24.57 % Favored : 71.36 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.21), residues: 1724 helix: 1.43 (0.17), residues: 1008 sheet: 0.54 (0.42), residues: 138 loop : -1.37 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1028 HIS 0.003 0.001 HIS B 859 PHE 0.013 0.001 PHE A 495 TYR 0.014 0.001 TYR A 903 ARG 0.003 0.000 ARG B1080 Details of bonding type rmsd hydrogen bonds : bond 0.04530 ( 805) hydrogen bonds : angle 4.35161 ( 2313) SS BOND : bond 0.00451 ( 4) SS BOND : angle 1.35421 ( 8) covalent geometry : bond 0.00278 (13430) covalent geometry : angle 0.58051 (18266) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 166 time to evaluate : 1.545 Fit side-chains REVERT: A 431 GLU cc_start: 0.7693 (tm-30) cc_final: 0.7252 (tm-30) REVERT: B 468 TYR cc_start: 0.7738 (m-80) cc_final: 0.7428 (m-80) outliers start: 52 outliers final: 32 residues processed: 203 average time/residue: 0.7856 time to fit residues: 182.5664 Evaluate side-chains 187 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 155 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 710 TYR Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 536 ILE Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 543 CYS Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 710 TYR Chi-restraints excluded: chain B residue 751 TYR Chi-restraints excluded: chain B residue 753 LYS Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 815 VAL Chi-restraints excluded: chain B residue 900 VAL Chi-restraints excluded: chain B residue 1036 THR Chi-restraints excluded: chain B residue 1207 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 18 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 67 optimal weight: 0.0980 chunk 38 optimal weight: 0.9990 chunk 127 optimal weight: 0.0040 chunk 51 optimal weight: 0.5980 chunk 78 optimal weight: 9.9990 chunk 59 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 167 optimal weight: 0.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.117677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.100668 restraints weight = 20224.218| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.61 r_work: 0.3197 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13434 Z= 0.120 Angle : 0.570 11.185 18274 Z= 0.288 Chirality : 0.041 0.135 2108 Planarity : 0.004 0.081 2268 Dihedral : 7.195 68.190 1930 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.99 % Allowed : 25.04 % Favored : 70.97 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.21), residues: 1724 helix: 1.61 (0.17), residues: 996 sheet: 0.54 (0.42), residues: 138 loop : -1.28 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1028 HIS 0.003 0.001 HIS B1204 PHE 0.013 0.001 PHE A 495 TYR 0.014 0.001 TYR A 353 ARG 0.003 0.000 ARG B1080 Details of bonding type rmsd hydrogen bonds : bond 0.04290 ( 805) hydrogen bonds : angle 4.21402 ( 2313) SS BOND : bond 0.00395 ( 4) SS BOND : angle 1.01856 ( 8) covalent geometry : bond 0.00261 (13430) covalent geometry : angle 0.56945 (18266) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 176 time to evaluate : 1.567 Fit side-chains REVERT: A 431 GLU cc_start: 0.7661 (tm-30) cc_final: 0.7241 (tm-30) REVERT: A 468 TYR cc_start: 0.7681 (m-80) cc_final: 0.7394 (m-80) REVERT: A 584 TYR cc_start: 0.5977 (OUTLIER) cc_final: 0.5548 (p90) REVERT: A 850 LYS cc_start: 0.9098 (OUTLIER) cc_final: 0.8813 (mptp) REVERT: B 468 TYR cc_start: 0.7746 (m-80) cc_final: 0.7403 (m-80) outliers start: 51 outliers final: 34 residues processed: 209 average time/residue: 0.8260 time to fit residues: 196.4229 Evaluate side-chains 195 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 159 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 584 TYR Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 710 TYR Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 751 TYR Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 850 LYS Chi-restraints excluded: chain A residue 879 MET Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 536 ILE Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 543 CYS Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 710 TYR Chi-restraints excluded: chain B residue 751 TYR Chi-restraints excluded: chain B residue 753 LYS Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 815 VAL Chi-restraints excluded: chain B residue 900 VAL Chi-restraints excluded: chain B residue 1036 THR Chi-restraints excluded: chain B residue 1207 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 125 optimal weight: 0.5980 chunk 128 optimal weight: 0.5980 chunk 6 optimal weight: 0.0770 chunk 77 optimal weight: 3.9990 chunk 65 optimal weight: 0.0270 chunk 168 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 119 optimal weight: 0.0270 chunk 167 optimal weight: 0.9980 overall best weight: 0.2654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B 905 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.120858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.103903 restraints weight = 20334.760| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.64 r_work: 0.3248 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 13434 Z= 0.107 Angle : 0.554 11.272 18274 Z= 0.276 Chirality : 0.040 0.137 2108 Planarity : 0.004 0.081 2268 Dihedral : 6.475 57.251 1927 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.76 % Allowed : 25.20 % Favored : 71.05 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.21), residues: 1724 helix: 1.77 (0.17), residues: 994 sheet: 0.52 (0.42), residues: 138 loop : -1.19 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 733 HIS 0.002 0.000 HIS B 859 PHE 0.011 0.001 PHE B 495 TYR 0.016 0.001 TYR A 903 ARG 0.003 0.000 ARG B 482 Details of bonding type rmsd hydrogen bonds : bond 0.03858 ( 805) hydrogen bonds : angle 4.09861 ( 2313) SS BOND : bond 0.00351 ( 4) SS BOND : angle 0.73446 ( 8) covalent geometry : bond 0.00227 (13430) covalent geometry : angle 0.55343 (18266) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 178 time to evaluate : 1.482 Fit side-chains REVERT: A 431 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7272 (tm-30) REVERT: A 468 TYR cc_start: 0.7594 (m-80) cc_final: 0.7359 (m-80) REVERT: A 584 TYR cc_start: 0.5811 (OUTLIER) cc_final: 0.5602 (p90) REVERT: A 850 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8822 (mptp) REVERT: B 468 TYR cc_start: 0.7645 (m-80) cc_final: 0.7285 (m-80) outliers start: 48 outliers final: 27 residues processed: 212 average time/residue: 0.8373 time to fit residues: 202.3019 Evaluate side-chains 192 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 543 CYS Chi-restraints excluded: chain A residue 584 TYR Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 710 TYR Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 751 TYR Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 850 LYS Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 543 CYS Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 710 TYR Chi-restraints excluded: chain B residue 753 LYS Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 815 VAL Chi-restraints excluded: chain B residue 900 VAL Chi-restraints excluded: chain B residue 1207 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 166 optimal weight: 5.9990 chunk 156 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 144 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 127 optimal weight: 0.2980 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.113008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.095637 restraints weight = 20365.694| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.58 r_work: 0.3121 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 13434 Z= 0.246 Angle : 0.678 10.870 18274 Z= 0.346 Chirality : 0.046 0.151 2108 Planarity : 0.005 0.081 2268 Dihedral : 7.081 58.082 1922 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 4.77 % Allowed : 24.41 % Favored : 70.81 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.20), residues: 1724 helix: 1.41 (0.16), residues: 1010 sheet: 0.43 (0.42), residues: 138 loop : -1.31 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A1028 HIS 0.008 0.001 HIS B1204 PHE 0.022 0.002 PHE A 495 TYR 0.019 0.002 TYR A 915 ARG 0.005 0.001 ARG B 482 Details of bonding type rmsd hydrogen bonds : bond 0.05480 ( 805) hydrogen bonds : angle 4.40442 ( 2313) SS BOND : bond 0.00479 ( 4) SS BOND : angle 0.80837 ( 8) covalent geometry : bond 0.00571 (13430) covalent geometry : angle 0.67783 (18266) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 157 time to evaluate : 1.503 Fit side-chains REVERT: A 468 TYR cc_start: 0.7881 (m-80) cc_final: 0.7554 (m-80) REVERT: A 584 TYR cc_start: 0.6221 (OUTLIER) cc_final: 0.5619 (p90) REVERT: A 850 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8768 (mptp) outliers start: 61 outliers final: 42 residues processed: 205 average time/residue: 0.7854 time to fit residues: 184.4098 Evaluate side-chains 190 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 146 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 477 PHE Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 543 CYS Chi-restraints excluded: chain A residue 584 TYR Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 710 TYR Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 850 LYS Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 1062 ILE Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 543 CYS Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 596 VAL Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 753 LYS Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 815 VAL Chi-restraints excluded: chain B residue 900 VAL Chi-restraints excluded: chain B residue 1023 THR Chi-restraints excluded: chain B residue 1036 THR Chi-restraints excluded: chain B residue 1076 LEU Chi-restraints excluded: chain B residue 1207 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 23 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 135 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 35 optimal weight: 0.2980 chunk 50 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.116137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.098885 restraints weight = 20065.539| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.59 r_work: 0.3173 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13434 Z= 0.135 Angle : 0.593 11.324 18274 Z= 0.300 Chirality : 0.042 0.158 2108 Planarity : 0.005 0.081 2268 Dihedral : 6.581 59.817 1920 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.44 % Allowed : 25.90 % Favored : 70.66 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.21), residues: 1724 helix: 1.61 (0.17), residues: 1008 sheet: 0.42 (0.42), residues: 138 loop : -1.20 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1028 HIS 0.003 0.001 HIS B1204 PHE 0.015 0.001 PHE A 495 TYR 0.014 0.001 TYR A 353 ARG 0.004 0.000 ARG B1080 Details of bonding type rmsd hydrogen bonds : bond 0.04563 ( 805) hydrogen bonds : angle 4.21949 ( 2313) SS BOND : bond 0.00400 ( 4) SS BOND : angle 0.68938 ( 8) covalent geometry : bond 0.00296 (13430) covalent geometry : angle 0.59291 (18266) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 167 time to evaluate : 1.450 Fit side-chains REVERT: A 468 TYR cc_start: 0.7803 (m-80) cc_final: 0.7496 (m-80) REVERT: A 584 TYR cc_start: 0.6141 (OUTLIER) cc_final: 0.5572 (p90) REVERT: A 587 MET cc_start: 0.8152 (mpp) cc_final: 0.7944 (mpp) REVERT: A 850 LYS cc_start: 0.9118 (OUTLIER) cc_final: 0.8845 (mptp) REVERT: B 468 TYR cc_start: 0.7833 (m-80) cc_final: 0.7515 (m-80) outliers start: 44 outliers final: 30 residues processed: 202 average time/residue: 0.8001 time to fit residues: 184.9317 Evaluate side-chains 191 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 159 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 543 CYS Chi-restraints excluded: chain A residue 584 TYR Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 710 TYR Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 850 LYS Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 543 CYS Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 710 TYR Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 753 LYS Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 815 VAL Chi-restraints excluded: chain B residue 900 VAL Chi-restraints excluded: chain B residue 1207 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 63 optimal weight: 0.0470 chunk 54 optimal weight: 0.8980 chunk 148 optimal weight: 0.9990 chunk 129 optimal weight: 0.6980 chunk 103 optimal weight: 0.4980 chunk 146 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 142 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.117888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.100810 restraints weight = 20178.104| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.58 r_work: 0.3202 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13434 Z= 0.124 Angle : 0.591 11.703 18274 Z= 0.295 Chirality : 0.042 0.167 2108 Planarity : 0.004 0.081 2268 Dihedral : 6.103 58.796 1920 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.21 % Allowed : 26.37 % Favored : 70.42 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.21), residues: 1724 helix: 1.67 (0.17), residues: 1012 sheet: 0.40 (0.42), residues: 138 loop : -1.08 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 732 HIS 0.003 0.001 HIS B1204 PHE 0.013 0.001 PHE A 495 TYR 0.014 0.001 TYR A 353 ARG 0.003 0.000 ARG B1080 Details of bonding type rmsd hydrogen bonds : bond 0.04262 ( 805) hydrogen bonds : angle 4.16362 ( 2313) SS BOND : bond 0.00359 ( 4) SS BOND : angle 0.63261 ( 8) covalent geometry : bond 0.00270 (13430) covalent geometry : angle 0.59103 (18266) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 167 time to evaluate : 1.436 Fit side-chains REVERT: A 468 TYR cc_start: 0.7759 (m-80) cc_final: 0.7417 (m-80) REVERT: A 584 TYR cc_start: 0.6067 (OUTLIER) cc_final: 0.5626 (p90) REVERT: A 850 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8834 (mptp) REVERT: B 468 TYR cc_start: 0.7844 (m-80) cc_final: 0.7571 (m-80) outliers start: 41 outliers final: 31 residues processed: 199 average time/residue: 0.8072 time to fit residues: 183.4769 Evaluate side-chains 193 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 160 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 GLU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 543 CYS Chi-restraints excluded: chain A residue 584 TYR Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 710 TYR Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 850 LYS Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 543 CYS Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 710 TYR Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 753 LYS Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 815 VAL Chi-restraints excluded: chain B residue 900 VAL Chi-restraints excluded: chain B residue 1207 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 144 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.116186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.099036 restraints weight = 20118.596| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.57 r_work: 0.3171 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13434 Z= 0.151 Angle : 0.618 11.194 18274 Z= 0.311 Chirality : 0.043 0.153 2108 Planarity : 0.005 0.081 2268 Dihedral : 6.143 54.643 1920 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.21 % Allowed : 26.06 % Favored : 70.74 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.21), residues: 1724 helix: 1.59 (0.16), residues: 1014 sheet: 0.37 (0.42), residues: 138 loop : -1.13 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 732 HIS 0.004 0.001 HIS B1204 PHE 0.016 0.001 PHE A 495 TYR 0.015 0.001 TYR A 353 ARG 0.004 0.000 ARG B1080 Details of bonding type rmsd hydrogen bonds : bond 0.04603 ( 805) hydrogen bonds : angle 4.24288 ( 2313) SS BOND : bond 0.00385 ( 4) SS BOND : angle 0.70882 ( 8) covalent geometry : bond 0.00344 (13430) covalent geometry : angle 0.61812 (18266) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 162 time to evaluate : 1.357 Fit side-chains REVERT: A 303 MET cc_start: 0.8234 (ttp) cc_final: 0.8033 (ttp) REVERT: A 431 GLU cc_start: 0.7684 (tm-30) cc_final: 0.7305 (tm-30) REVERT: A 468 TYR cc_start: 0.7804 (m-80) cc_final: 0.7516 (m-80) REVERT: A 584 TYR cc_start: 0.6146 (OUTLIER) cc_final: 0.5537 (p90) REVERT: A 850 LYS cc_start: 0.9069 (OUTLIER) cc_final: 0.8798 (mptp) outliers start: 41 outliers final: 33 residues processed: 193 average time/residue: 0.8285 time to fit residues: 181.4017 Evaluate side-chains 189 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 154 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 GLU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 543 CYS Chi-restraints excluded: chain A residue 584 TYR Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 710 TYR Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 850 LYS Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 710 TYR Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 753 LYS Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 815 VAL Chi-restraints excluded: chain B residue 900 VAL Chi-restraints excluded: chain B residue 1036 THR Chi-restraints excluded: chain B residue 1207 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 106 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 chunk 173 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 113 optimal weight: 5.9990 chunk 114 optimal weight: 0.0870 chunk 105 optimal weight: 1.9990 chunk 138 optimal weight: 0.6980 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 905 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.116324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.099110 restraints weight = 20077.214| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.57 r_work: 0.3175 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13434 Z= 0.146 Angle : 0.623 11.247 18274 Z= 0.312 Chirality : 0.043 0.185 2108 Planarity : 0.005 0.081 2268 Dihedral : 6.133 56.160 1919 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 3.05 % Allowed : 26.45 % Favored : 70.50 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.21), residues: 1724 helix: 1.61 (0.16), residues: 1012 sheet: 0.36 (0.42), residues: 138 loop : -1.09 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 732 HIS 0.004 0.001 HIS B1204 PHE 0.016 0.001 PHE A 495 TYR 0.015 0.001 TYR A 353 ARG 0.004 0.000 ARG B1080 Details of bonding type rmsd hydrogen bonds : bond 0.04563 ( 805) hydrogen bonds : angle 4.23269 ( 2313) SS BOND : bond 0.00401 ( 4) SS BOND : angle 1.54847 ( 8) covalent geometry : bond 0.00331 (13430) covalent geometry : angle 0.62212 (18266) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3448 Ramachandran restraints generated. 1724 Oldfield, 0 Emsley, 1724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 160 time to evaluate : 1.406 Fit side-chains REVERT: A 431 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7315 (tm-30) REVERT: A 468 TYR cc_start: 0.7845 (m-80) cc_final: 0.7560 (m-80) REVERT: A 584 TYR cc_start: 0.6143 (OUTLIER) cc_final: 0.5659 (p90) REVERT: A 850 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8823 (mptp) REVERT: B 468 TYR cc_start: 0.7910 (m-80) cc_final: 0.7647 (m-80) outliers start: 39 outliers final: 35 residues processed: 191 average time/residue: 0.8876 time to fit residues: 192.2922 Evaluate side-chains 193 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 156 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 GLU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 543 CYS Chi-restraints excluded: chain A residue 584 TYR Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 710 TYR Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 850 LYS Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 710 TYR Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 753 LYS Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 815 VAL Chi-restraints excluded: chain B residue 900 VAL Chi-restraints excluded: chain B residue 1036 THR Chi-restraints excluded: chain B residue 1207 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 64 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 147 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 143 optimal weight: 0.0040 chunk 123 optimal weight: 1.9990 chunk 108 optimal weight: 0.0000 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.117963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.100870 restraints weight = 20150.001| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.58 r_work: 0.3204 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13434 Z= 0.123 Angle : 0.601 11.318 18274 Z= 0.300 Chirality : 0.042 0.154 2108 Planarity : 0.005 0.081 2268 Dihedral : 5.943 55.392 1919 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.74 % Allowed : 26.76 % Favored : 70.50 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.21), residues: 1724 helix: 1.71 (0.16), residues: 1012 sheet: 0.38 (0.42), residues: 138 loop : -1.06 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 732 HIS 0.003 0.001 HIS B1204 PHE 0.013 0.001 PHE A 495 TYR 0.014 0.001 TYR A 353 ARG 0.003 0.000 ARG B1080 Details of bonding type rmsd hydrogen bonds : bond 0.04243 ( 805) hydrogen bonds : angle 4.16487 ( 2313) SS BOND : bond 0.00384 ( 4) SS BOND : angle 1.35582 ( 8) covalent geometry : bond 0.00270 (13430) covalent geometry : angle 0.60085 (18266) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8830.03 seconds wall clock time: 152 minutes 43.18 seconds (9163.18 seconds total)