Starting phenix.real_space_refine on Thu Sep 18 02:00:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c0h_45084/09_2025/9c0h_45084.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c0h_45084/09_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_45084/09_2025/9c0h_45084.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c0h_45084/09_2025/9c0h_45084.map" model { file = "/net/cci-nas-00/data/ceres_data/9c0h_45084/09_2025/9c0h_45084.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c0h_45084/09_2025/9c0h_45084.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.032 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'TPO:plan-1': 2, 'GLU:plan': 21, 'ASP:plan': 16, 'ASN:plan1': 9, 'PHE:plan': 2, 'GLN:plan1': 4, '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: {'TPO:plan-1': 2, 'GLU:plan': 21, 'ASP:plan': 16, 'ASN:plan1': 9, 'PHE:plan': 2, 'GLN:plan1': 4, '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: 3.30, per 1000 atoms: 0.25 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: 1.11 Conformation dependent library (CDL) restraints added in 661.3 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.46 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: 2.71 Time building geometry restraints manager: 1.56 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: 0.03 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: 2.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.130 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.440 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:9.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.020 ------------------------------------------------------------------------------- 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 : 8.97 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.001 ARG B1064 TYR 0.020 0.002 TYR A 915 PHE 0.015 0.002 PHE B 495 TRP 0.030 0.002 TRP A1028 HIS 0.006 0.001 HIS B 226 Details of bonding type rmsd covalent geometry : bond 0.00502 (13430) covalent geometry : angle 0.71737 (18266) SS BOND : bond 0.00393 ( 4) SS BOND : angle 0.79121 ( 8) hydrogen bonds : bond 0.13975 ( 805) hydrogen bonds : angle 5.53927 ( 2313) *********************** 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 : 0.494 Fit side-chains outliers start: 52 outliers final: 47 residues processed: 211 average time/residue: 0.3723 time to fit residues: 89.6156 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 : 0.478 ------------------------------------------------------------------------------- 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 98 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.5980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3526 r_free = 0.3526 target = 0.116206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.098892 restraints weight = 20238.771| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.63 r_work: 0.3172 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.0652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13434 Z= 0.146 Angle : 0.603 10.769 18274 Z= 0.308 Chirality : 0.042 0.135 2108 Planarity : 0.005 0.081 2268 Dihedral : 8.463 79.070 1972 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 4.93 % Allowed : 23.87 % Favored : 71.21 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.21), residues: 1724 helix: 1.38 (0.17), residues: 1008 sheet: 0.64 (0.42), residues: 138 loop : -1.38 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1080 TYR 0.016 0.001 TYR A 915 PHE 0.015 0.001 PHE B 907 TRP 0.025 0.001 TRP A1028 HIS 0.005 0.001 HIS B1204 Details of bonding type rmsd covalent geometry : bond 0.00325 (13430) covalent geometry : angle 0.60284 (18266) SS BOND : bond 0.00313 ( 4) SS BOND : angle 0.75295 ( 8) hydrogen bonds : bond 0.04886 ( 805) hydrogen bonds : angle 4.51879 ( 2313) *********************** 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 230 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 167 time to evaluate : 0.466 Fit side-chains REVERT: A 431 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7261 (tm-30) REVERT: B 891 ASP cc_start: 0.8509 (p0) cc_final: 0.8213 (p0) outliers start: 63 outliers final: 37 residues processed: 210 average time/residue: 0.3951 time to fit residues: 94.0918 Evaluate side-chains 192 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 155 time to evaluate : 0.517 ------------------------------------------------------------------------------- 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 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 710 TYR Chi-restraints excluded: chain A residue 713 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 900 VAL 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 347 VAL 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 612 LEU 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 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 36 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 166 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 156 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 148 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 chunk 144 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** ** B 905 ASN ** 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 = 0.3531 r_free = 0.3531 target = 0.116638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.099370 restraints weight = 20454.500| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.63 r_work: 0.3178 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.0810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13434 Z= 0.135 Angle : 0.583 11.009 18274 Z= 0.296 Chirality : 0.041 0.136 2108 Planarity : 0.005 0.081 2268 Dihedral : 7.577 75.620 1932 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 4.54 % Allowed : 23.87 % Favored : 71.60 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.21), residues: 1724 helix: 1.46 (0.17), residues: 1010 sheet: 0.56 (0.42), residues: 138 loop : -1.33 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 546 TYR 0.015 0.001 TYR A 915 PHE 0.015 0.001 PHE A 495 TRP 0.021 0.001 TRP A1028 HIS 0.004 0.001 HIS B1204 Details of bonding type rmsd covalent geometry : bond 0.00300 (13430) covalent geometry : angle 0.58246 (18266) SS BOND : bond 0.00405 ( 4) SS BOND : angle 0.85607 ( 8) hydrogen bonds : bond 0.04605 ( 805) hydrogen bonds : angle 4.35756 ( 2313) *********************** 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 222 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 164 time to evaluate : 0.485 Fit side-chains REVERT: A 431 GLU cc_start: 0.7716 (tm-30) cc_final: 0.7259 (tm-30) REVERT: A 468 TYR cc_start: 0.7709 (m-80) cc_final: 0.7419 (m-80) REVERT: B 468 TYR cc_start: 0.7800 (m-80) cc_final: 0.7491 (m-80) outliers start: 58 outliers final: 38 residues processed: 207 average time/residue: 0.3758 time to fit residues: 88.9725 Evaluate side-chains 195 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 157 time to evaluate : 0.466 ------------------------------------------------------------------------------- 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 493 ILE 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 710 TYR Chi-restraints excluded: chain A residue 713 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 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 296 MET Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 450 VAL 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 688 LEU 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 1023 THR Chi-restraints excluded: chain B residue 1036 THR Chi-restraints excluded: chain B residue 1076 LEU Chi-restraints excluded: chain B residue 1102 ILE 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 43 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 135 optimal weight: 4.9990 chunk 32 optimal weight: 0.0980 chunk 142 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 169 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 905 ASN B1203 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.117414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.100286 restraints weight = 20426.239| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.62 r_work: 0.3192 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13434 Z= 0.125 Angle : 0.577 11.096 18274 Z= 0.292 Chirality : 0.041 0.134 2108 Planarity : 0.004 0.081 2268 Dihedral : 7.274 71.592 1928 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 4.62 % Allowed : 24.49 % Favored : 70.89 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.21), residues: 1724 helix: 1.59 (0.17), residues: 998 sheet: 0.60 (0.43), residues: 138 loop : -1.26 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1080 TYR 0.014 0.001 TYR A 353 PHE 0.014 0.001 PHE A 495 TRP 0.017 0.001 TRP A1028 HIS 0.004 0.001 HIS B1204 Details of bonding type rmsd covalent geometry : bond 0.00272 (13430) covalent geometry : angle 0.57675 (18266) SS BOND : bond 0.00356 ( 4) SS BOND : angle 1.42859 ( 8) hydrogen bonds : bond 0.04383 ( 805) hydrogen bonds : angle 4.25911 ( 2313) *********************** 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 234 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 175 time to evaluate : 0.373 Fit side-chains REVERT: A 431 GLU cc_start: 0.7690 (tm-30) cc_final: 0.7261 (tm-30) REVERT: A 468 TYR cc_start: 0.7685 (m-80) cc_final: 0.7428 (m-80) REVERT: A 850 LYS cc_start: 0.9103 (OUTLIER) cc_final: 0.8794 (mptp) REVERT: B 468 TYR cc_start: 0.7724 (m-80) cc_final: 0.7398 (m-80) outliers start: 59 outliers final: 40 residues processed: 212 average time/residue: 0.3737 time to fit residues: 90.3780 Evaluate side-chains 205 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 164 time to evaluate : 0.413 ------------------------------------------------------------------------------- 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 417 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 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 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 1045 THR 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 347 VAL Chi-restraints excluded: chain B residue 385 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 1102 ILE 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 24 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 74 optimal weight: 0.4980 chunk 31 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3519 r_free = 0.3519 target = 0.115798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.098510 restraints weight = 20485.532| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.63 r_work: 0.3164 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13434 Z= 0.152 Angle : 0.602 11.047 18274 Z= 0.305 Chirality : 0.042 0.139 2108 Planarity : 0.005 0.081 2268 Dihedral : 7.216 67.447 1928 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 4.54 % Allowed : 24.88 % Favored : 70.58 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.21), residues: 1724 helix: 1.53 (0.17), residues: 1000 sheet: 0.56 (0.43), residues: 138 loop : -1.30 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1080 TYR 0.015 0.001 TYR A 353 PHE 0.016 0.001 PHE A 495 TRP 0.021 0.001 TRP A1028 HIS 0.005 0.001 HIS B1204 Details of bonding type rmsd covalent geometry : bond 0.00345 (13430) covalent geometry : angle 0.60172 (18266) SS BOND : bond 0.00430 ( 4) SS BOND : angle 0.98986 ( 8) hydrogen bonds : bond 0.04701 ( 805) hydrogen bonds : angle 4.29477 ( 2313) *********************** 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 227 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 169 time to evaluate : 0.554 Fit side-chains REVERT: A 431 GLU cc_start: 0.7701 (tm-30) cc_final: 0.7290 (tm-30) REVERT: A 468 TYR cc_start: 0.7783 (m-80) cc_final: 0.7473 (m-80) REVERT: A 850 LYS cc_start: 0.9105 (OUTLIER) cc_final: 0.8802 (mptp) outliers start: 58 outliers final: 44 residues processed: 211 average time/residue: 0.3825 time to fit residues: 92.3293 Evaluate side-chains 204 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 159 time to evaluate : 0.523 ------------------------------------------------------------------------------- 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 417 VAL Chi-restraints excluded: chain A residue 425 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 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 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 1045 THR 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 347 VAL Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 450 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 612 LEU Chi-restraints excluded: chain B residue 673 VAL 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 155 optimal weight: 9.9990 chunk 46 optimal weight: 0.0000 chunk 149 optimal weight: 0.6980 chunk 138 optimal weight: 0.3980 chunk 10 optimal weight: 0.0980 chunk 166 optimal weight: 0.6980 chunk 117 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 overall best weight: 0.3784 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.119325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.102235 restraints weight = 20206.102| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.63 r_work: 0.3220 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13434 Z= 0.111 Angle : 0.561 11.327 18274 Z= 0.281 Chirality : 0.041 0.139 2108 Planarity : 0.004 0.081 2268 Dihedral : 6.636 57.982 1928 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.68 % Allowed : 25.43 % Favored : 70.89 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.21), residues: 1724 helix: 1.73 (0.17), residues: 996 sheet: 0.59 (0.43), residues: 138 loop : -1.20 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1080 TYR 0.014 0.001 TYR A 903 PHE 0.011 0.001 PHE A 495 TRP 0.015 0.001 TRP B 732 HIS 0.002 0.001 HIS A 695 Details of bonding type rmsd covalent geometry : bond 0.00237 (13430) covalent geometry : angle 0.56117 (18266) SS BOND : bond 0.00352 ( 4) SS BOND : angle 0.92366 ( 8) hydrogen bonds : bond 0.04035 ( 805) hydrogen bonds : angle 4.12938 ( 2313) *********************** 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: 47 poor density : 171 time to evaluate : 0.488 Fit side-chains REVERT: A 431 GLU cc_start: 0.7708 (tm-30) cc_final: 0.7311 (tm-30) REVERT: A 468 TYR cc_start: 0.7687 (m-80) cc_final: 0.7386 (m-80) REVERT: A 850 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8810 (mptp) REVERT: B 468 TYR cc_start: 0.7751 (m-80) cc_final: 0.7425 (m-80) REVERT: B 1168 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.7805 (tpp) outliers start: 47 outliers final: 35 residues processed: 204 average time/residue: 0.3744 time to fit residues: 87.0364 Evaluate side-chains 202 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 165 time to evaluate : 0.432 ------------------------------------------------------------------------------- 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 417 VAL Chi-restraints excluded: chain A residue 425 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 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 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 296 MET 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 385 VAL 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 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 1036 THR Chi-restraints excluded: chain B residue 1168 MET 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 154 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 148 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 94 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 136 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 118 optimal weight: 8.9990 chunk 101 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3545 r_free = 0.3545 target = 0.117795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.100610 restraints weight = 20389.342| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.63 r_work: 0.3196 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1217 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= 0.130 Angle : 0.581 11.142 18274 Z= 0.291 Chirality : 0.042 0.141 2108 Planarity : 0.004 0.081 2268 Dihedral : 6.484 58.258 1927 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.91 % Allowed : 25.51 % Favored : 70.58 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.21), residues: 1724 helix: 1.77 (0.17), residues: 996 sheet: 0.59 (0.43), residues: 138 loop : -1.16 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1080 TYR 0.014 0.001 TYR A 353 PHE 0.014 0.001 PHE A 495 TRP 0.017 0.001 TRP B 732 HIS 0.004 0.001 HIS B1204 Details of bonding type rmsd covalent geometry : bond 0.00288 (13430) covalent geometry : angle 0.58138 (18266) SS BOND : bond 0.00333 ( 4) SS BOND : angle 0.79696 ( 8) hydrogen bonds : bond 0.04295 ( 805) hydrogen bonds : angle 4.11857 ( 2313) *********************** 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 220 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 170 time to evaluate : 0.342 Fit side-chains REVERT: A 431 GLU cc_start: 0.7718 (tm-30) cc_final: 0.7332 (tm-30) REVERT: A 468 TYR cc_start: 0.7757 (m-80) cc_final: 0.7471 (m-80) REVERT: A 850 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8816 (mptp) outliers start: 50 outliers final: 37 residues processed: 208 average time/residue: 0.3619 time to fit residues: 85.9842 Evaluate side-chains 200 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 162 time to evaluate : 0.398 ------------------------------------------------------------------------------- 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 417 VAL Chi-restraints excluded: chain A residue 425 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 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 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 296 MET Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 385 VAL 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 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 1023 THR Chi-restraints excluded: chain B residue 1036 THR 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 36 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 157 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 145 optimal weight: 5.9990 chunk 121 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3531 r_free = 0.3531 target = 0.116746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.099475 restraints weight = 20299.430| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.63 r_work: 0.3176 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 13434 Z= 0.145 Angle : 0.603 11.194 18274 Z= 0.303 Chirality : 0.042 0.145 2108 Planarity : 0.005 0.081 2268 Dihedral : 6.445 54.866 1927 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.83 % Allowed : 25.82 % Favored : 70.34 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.21), residues: 1724 helix: 1.70 (0.16), residues: 1008 sheet: 0.57 (0.43), residues: 138 loop : -1.12 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1080 TYR 0.015 0.001 TYR A 353 PHE 0.015 0.001 PHE A 495 TRP 0.021 0.002 TRP A 732 HIS 0.004 0.001 HIS B1204 Details of bonding type rmsd covalent geometry : bond 0.00328 (13430) covalent geometry : angle 0.60311 (18266) SS BOND : bond 0.00360 ( 4) SS BOND : angle 0.80232 ( 8) hydrogen bonds : bond 0.04545 ( 805) hydrogen bonds : angle 4.18217 ( 2313) *********************** 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 214 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 165 time to evaluate : 0.398 Fit side-chains REVERT: A 431 GLU cc_start: 0.7725 (tm-30) cc_final: 0.7341 (tm-30) REVERT: A 468 TYR cc_start: 0.7809 (m-80) cc_final: 0.7526 (m-80) REVERT: A 850 LYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8822 (mptp) REVERT: B 468 TYR cc_start: 0.7840 (m-80) cc_final: 0.7532 (m-80) REVERT: B 1168 MET cc_start: 0.8881 (OUTLIER) cc_final: 0.7707 (tpp) outliers start: 49 outliers final: 41 residues processed: 202 average time/residue: 0.3785 time to fit residues: 87.0701 Evaluate side-chains 202 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 159 time to evaluate : 0.607 ------------------------------------------------------------------------------- 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 417 VAL Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 543 CYS 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 784 VAL Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 850 LYS Chi-restraints excluded: chain A residue 865 GLU Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1045 THR 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 319 LEU Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 385 VAL 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 612 LEU 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 1023 THR Chi-restraints excluded: chain B residue 1036 THR Chi-restraints excluded: chain B residue 1168 MET 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 17 optimal weight: 0.6980 chunk 163 optimal weight: 0.4980 chunk 77 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 158 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 170 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3521 r_free = 0.3521 target = 0.116057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.098748 restraints weight = 20713.545| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.64 r_work: 0.3168 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13434 Z= 0.151 Angle : 0.615 11.271 18274 Z= 0.309 Chirality : 0.043 0.153 2108 Planarity : 0.005 0.081 2268 Dihedral : 6.473 56.536 1927 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 4.15 % Allowed : 25.82 % Favored : 70.03 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.21), residues: 1724 helix: 1.65 (0.16), residues: 1010 sheet: 0.51 (0.43), residues: 138 loop : -1.14 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1080 TYR 0.015 0.001 TYR A 353 PHE 0.016 0.001 PHE A 495 TRP 0.025 0.002 TRP B 732 HIS 0.005 0.001 HIS B1204 Details of bonding type rmsd covalent geometry : bond 0.00342 (13430) covalent geometry : angle 0.61454 (18266) SS BOND : bond 0.00382 ( 4) SS BOND : angle 0.75394 ( 8) hydrogen bonds : bond 0.04617 ( 805) hydrogen bonds : angle 4.21086 ( 2313) *********************** 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 214 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 161 time to evaluate : 0.431 Fit side-chains REVERT: A 431 GLU cc_start: 0.7721 (tm-30) cc_final: 0.7346 (tm-30) REVERT: A 468 TYR cc_start: 0.7815 (m-80) cc_final: 0.7540 (m-80) REVERT: A 850 LYS cc_start: 0.9107 (OUTLIER) cc_final: 0.8823 (mptp) REVERT: B 1168 MET cc_start: 0.8884 (OUTLIER) cc_final: 0.7693 (tpp) outliers start: 53 outliers final: 44 residues processed: 204 average time/residue: 0.3585 time to fit residues: 83.1589 Evaluate side-chains 204 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 158 time to evaluate : 0.490 ------------------------------------------------------------------------------- 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 417 VAL Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 543 CYS 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 865 GLU Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1045 THR 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 319 LEU Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 480 ASP 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 612 LEU Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 710 TYR Chi-restraints excluded: chain B residue 728 PHE 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 1168 MET 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 6 optimal weight: 0.8980 chunk 167 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 147 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 128 optimal weight: 2.9990 chunk 75 optimal weight: 0.1980 chunk 17 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 172 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3533 r_free = 0.3533 target = 0.116971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.099950 restraints weight = 20341.059| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.58 r_work: 0.3187 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1237 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= 0.134 Angle : 0.610 11.340 18274 Z= 0.305 Chirality : 0.042 0.175 2108 Planarity : 0.005 0.081 2268 Dihedral : 6.378 54.555 1927 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.76 % Allowed : 26.21 % Favored : 70.03 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.21), residues: 1724 helix: 1.70 (0.16), residues: 1008 sheet: 0.50 (0.43), residues: 138 loop : -1.08 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1080 TYR 0.014 0.001 TYR A 353 PHE 0.015 0.001 PHE A 495 TRP 0.033 0.002 TRP B 732 HIS 0.004 0.001 HIS B1204 Details of bonding type rmsd covalent geometry : bond 0.00297 (13430) covalent geometry : angle 0.61026 (18266) SS BOND : bond 0.00386 ( 4) SS BOND : angle 0.74003 ( 8) hydrogen bonds : bond 0.04467 ( 805) hydrogen bonds : angle 4.18149 ( 2313) ********************** 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 211 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 163 time to evaluate : 0.357 Fit side-chains REVERT: A 431 GLU cc_start: 0.7705 (tm-30) cc_final: 0.7293 (tm-30) REVERT: A 468 TYR cc_start: 0.7793 (m-80) cc_final: 0.7521 (m-80) REVERT: A 850 LYS cc_start: 0.9104 (OUTLIER) cc_final: 0.8831 (mptp) REVERT: B 468 TYR cc_start: 0.7825 (m-80) cc_final: 0.7587 (m-80) REVERT: B 1168 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.7703 (tpp) outliers start: 48 outliers final: 42 residues processed: 198 average time/residue: 0.3688 time to fit residues: 83.3665 Evaluate side-chains 203 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 159 time to evaluate : 0.483 ------------------------------------------------------------------------------- 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 417 VAL Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 543 CYS 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 1045 THR 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 319 LEU Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 385 VAL 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 612 LEU 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 794 MET 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 1168 MET 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 86 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 143 optimal weight: 0.7980 chunk 128 optimal weight: 3.9990 chunk 17 optimal weight: 0.2980 chunk 75 optimal weight: 3.9990 chunk 155 optimal weight: 0.8980 chunk 164 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.117886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.101008 restraints weight = 20218.255| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.56 r_work: 0.3204 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13434 Z= 0.127 Angle : 0.600 11.319 18274 Z= 0.299 Chirality : 0.042 0.151 2108 Planarity : 0.005 0.081 2268 Dihedral : 6.218 54.828 1927 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.60 % Allowed : 26.37 % Favored : 70.03 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.21), residues: 1724 helix: 1.72 (0.16), residues: 1012 sheet: 0.50 (0.43), residues: 138 loop : -1.02 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1080 TYR 0.014 0.001 TYR A 353 PHE 0.014 0.001 PHE A 495 TRP 0.036 0.001 TRP B 732 HIS 0.003 0.001 HIS B1204 Details of bonding type rmsd covalent geometry : bond 0.00281 (13430) covalent geometry : angle 0.60020 (18266) SS BOND : bond 0.00325 ( 4) SS BOND : angle 0.95256 ( 8) hydrogen bonds : bond 0.04301 ( 805) hydrogen bonds : angle 4.13364 ( 2313) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4632.09 seconds wall clock time: 79 minutes 33.80 seconds (4773.80 seconds total)