Starting phenix.real_space_refine on Wed May 14 11:29:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9asn_43820/05_2025/9asn_43820.cif Found real_map, /net/cci-nas-00/data/ceres_data/9asn_43820/05_2025/9asn_43820.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9asn_43820/05_2025/9asn_43820.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9asn_43820/05_2025/9asn_43820.map" model { file = "/net/cci-nas-00/data/ceres_data/9asn_43820/05_2025/9asn_43820.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9asn_43820/05_2025/9asn_43820.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.023 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: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 2 6.06 5 P 96 5.49 5 S 61 5.16 5 C 7047 2.51 5 N 2048 2.21 5 O 2441 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 11697 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1955 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 235} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 203 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 1, 'TRANS': 22} Chain: "A" Number of atoms: 7482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 915, 7482 Classifications: {'peptide': 915} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 52, 'TRANS': 862} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 2051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 2051 Inner-chain residues flagged as termini: ['pdbres=" G E 62 "'] Classifications: {'RNA': 97} Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 3, 'rna3p_pur': 43, 'rna3p_pyr': 49} Link IDs: {'rna2p': 4, 'rna3p': 92} Chain breaks: 1 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' CA': 2, ' ZN': 2} Classifications: {'undetermined': 4, 'water': 1} Link IDs: {None: 4} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3113 SG CYS A 561 46.200 22.519 47.519 1.00172.12 S ATOM 4071 SG CYS A 676 48.469 25.642 47.779 1.00178.36 S ATOM 2921 SG CYS A 536 62.125 44.877 61.619 1.00181.72 S ATOM 2936 SG CYS A 538 62.058 46.288 65.185 1.00190.39 S Time building chain proxies: 7.70, per 1000 atoms: 0.66 Number of scatterers: 11697 At special positions: 0 Unit cell: (86.9, 106.7, 195.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 Ca 2 19.99 S 61 16.00 P 96 15.00 O 2441 8.00 N 2048 7.00 C 7047 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.93 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1401 " pdb="ZN ZN A1401 " - pdb=" NE2 HIS A 609 " pdb="ZN ZN A1401 " - pdb=" NE2 HIS A 680 " pdb="ZN ZN A1401 " - pdb=" SG CYS A 561 " pdb="ZN ZN A1401 " - pdb=" SG CYS A 676 " pdb=" ZN A1402 " pdb="ZN ZN A1402 " - pdb=" NE2 HIS A1026 " pdb="ZN ZN A1402 " - pdb=" NE2 HIS A 549 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 536 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 538 " Number of angles added : 4 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2252 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 9 sheets defined 56.3% alpha, 12.5% beta 32 base pairs and 53 stacking pairs defined. Time for finding SS restraints: 3.95 Creating SS restraints... Processing helix chain 'B' and resid 511 through 524 Processing helix chain 'B' and resid 560 through 577 Processing helix chain 'B' and resid 591 through 601 removed outlier: 3.520A pdb=" N TYR B 597 " --> pdb=" O GLU B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 614 removed outlier: 4.455A pdb=" N GLU B 610 " --> pdb=" O SER B 606 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS B 614 " --> pdb=" O GLU B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 631 Processing helix chain 'B' and resid 668 through 685 removed outlier: 3.917A pdb=" N GLN B 674 " --> pdb=" O ARG B 670 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN B 678 " --> pdb=" O GLN B 674 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LYS B 679 " --> pdb=" O LEU B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 708 removed outlier: 3.762A pdb=" N LEU B 694 " --> pdb=" O ASN B 690 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN B 708 " --> pdb=" O LYS B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 711 No H-bonds generated for 'chain 'B' and resid 709 through 711' Processing helix chain 'B' and resid 712 through 721 removed outlier: 3.815A pdb=" N LEU B 718 " --> pdb=" O SER B 714 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLN B 719 " --> pdb=" O VAL B 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 728 through 749 Processing helix chain 'C' and resid 728 through 749 removed outlier: 3.656A pdb=" N LEU C 732 " --> pdb=" O ASN C 728 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS C 734 " --> pdb=" O HIS C 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 463 removed outlier: 4.225A pdb=" N ASP A 446 " --> pdb=" O ARG A 442 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LYS A 447 " --> pdb=" O ASP A 443 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N SER A 454 " --> pdb=" O GLU A 450 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ARG A 455 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLN A 456 " --> pdb=" O LEU A 452 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLU A 457 " --> pdb=" O GLY A 453 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA A 462 " --> pdb=" O LYS A 458 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ARG A 463 " --> pdb=" O ALA A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 512 Processing helix chain 'A' and resid 541 through 545 removed outlier: 3.628A pdb=" N THR A 545 " --> pdb=" O ALA A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 571 removed outlier: 3.959A pdb=" N LEU A 571 " --> pdb=" O ALA A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 655 Processing helix chain 'A' and resid 698 through 709 removed outlier: 3.501A pdb=" N ILE A 702 " --> pdb=" O SER A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 724 Processing helix chain 'A' and resid 726 through 736 removed outlier: 3.736A pdb=" N GLU A 736 " --> pdb=" O LYS A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 786 removed outlier: 3.531A pdb=" N GLY A 786 " --> pdb=" O SER A 783 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 783 through 786' Processing helix chain 'A' and resid 787 through 807 removed outlier: 3.619A pdb=" N ASN A 806 " --> pdb=" O HIS A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 830 removed outlier: 4.209A pdb=" N LYS A 815 " --> pdb=" O LYS A 811 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLN A 816 " --> pdb=" O GLN A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 861 Processing helix chain 'A' and resid 862 through 884 removed outlier: 3.667A pdb=" N LEU A 866 " --> pdb=" O MET A 862 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N MET A 877 " --> pdb=" O HIS A 873 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N HIS A 878 " --> pdb=" O GLN A 874 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LEU A 879 " --> pdb=" O CYS A 875 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY A 884 " --> pdb=" O ASP A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 897 removed outlier: 3.701A pdb=" N MET A 897 " --> pdb=" O LEU A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 921 removed outlier: 3.522A pdb=" N ALA A 913 " --> pdb=" O ASN A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 938 removed outlier: 4.520A pdb=" N HIS A 934 " --> pdb=" O ARG A 930 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N HIS A 936 " --> pdb=" O VAL A 932 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG A 938 " --> pdb=" O HIS A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 950 removed outlier: 3.656A pdb=" N SER A 950 " --> pdb=" O ILE A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 988 removed outlier: 3.667A pdb=" N PHE A 970 " --> pdb=" O GLU A 966 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 971 " --> pdb=" O ARG A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 1005 Processing helix chain 'A' and resid 1005 through 1017 removed outlier: 3.858A pdb=" N LYS A1015 " --> pdb=" O MET A1011 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1022 removed outlier: 3.978A pdb=" N PHE A1021 " --> pdb=" O GLU A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1031 removed outlier: 4.000A pdb=" N LEU A1030 " --> pdb=" O GLY A1027 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N CYS A1031 " --> pdb=" O PRO A1028 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1027 through 1031' Processing helix chain 'A' and resid 1032 through 1055 removed outlier: 3.580A pdb=" N LEU A1036 " --> pdb=" O ARG A1032 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR A1052 " --> pdb=" O ILE A1048 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1069 removed outlier: 4.143A pdb=" N ALA A1060 " --> pdb=" O SER A1056 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE A1069 " --> pdb=" O GLY A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1071 through 1079 Processing helix chain 'A' and resid 1084 through 1090 removed outlier: 4.099A pdb=" N GLU A1090 " --> pdb=" O LEU A1086 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1098 Processing helix chain 'A' and resid 1101 through 1115 removed outlier: 3.715A pdb=" N GLN A1105 " --> pdb=" O SER A1101 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU A1109 " --> pdb=" O GLN A1105 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE A1110 " --> pdb=" O LYS A1106 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1129 removed outlier: 4.001A pdb=" N LEU A1124 " --> pdb=" O HIS A1120 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1166 removed outlier: 3.648A pdb=" N GLU A1147 " --> pdb=" O ASN A1143 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER A1152 " --> pdb=" O PHE A1148 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE A1166 " --> pdb=" O LEU A1162 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1183 Processing helix chain 'A' and resid 1183 through 1195 removed outlier: 3.519A pdb=" N GLN A1187 " --> pdb=" O ASN A1183 " (cutoff:3.500A) Processing helix chain 'A' and resid 1196 through 1200 Processing helix chain 'A' and resid 1203 through 1207 Processing helix chain 'A' and resid 1213 through 1232 Processing helix chain 'A' and resid 1233 through 1245 removed outlier: 4.320A pdb=" N VAL A1237 " --> pdb=" O ASP A1233 " (cutoff:3.500A) Processing helix chain 'A' and resid 1248 through 1256 removed outlier: 3.684A pdb=" N PHE A1252 " --> pdb=" O ARG A1248 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU A1254 " --> pdb=" O LYS A1250 " (cutoff:3.500A) Processing helix chain 'A' and resid 1260 through 1271 Processing helix chain 'A' and resid 1316 through 1332 Processing helix chain 'A' and resid 1334 through 1348 removed outlier: 3.740A pdb=" N ALA A1338 " --> pdb=" O PHE A1334 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS A1347 " --> pdb=" O PHE A1343 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR A1348 " --> pdb=" O ILE A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1350 through 1357 Processing sheet with id=AA1, first strand: chain 'B' and resid 495 through 496 Processing sheet with id=AA2, first strand: chain 'B' and resid 529 through 534 removed outlier: 3.774A pdb=" N VAL B 529 " --> pdb=" O THR B 547 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLY B 554 " --> pdb=" O VAL B 546 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ILE B 548 " --> pdb=" O THR B 552 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N THR B 552 " --> pdb=" O ILE B 548 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 651 through 657 removed outlier: 3.599A pdb=" N SER B 651 " --> pdb=" O CYS B 666 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 413 through 415 removed outlier: 4.685A pdb=" N GLY A 603 " --> pdb=" O ARG A 684 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL A 686 " --> pdb=" O PHE A 601 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N PHE A 601 " --> pdb=" O VAL A 686 " (cutoff:3.500A) removed outlier: 9.160A pdb=" N PHE A 688 " --> pdb=" O TYR A 599 " (cutoff:3.500A) removed outlier: 9.541A pdb=" N TYR A 599 " --> pdb=" O PHE A 688 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 413 through 415 removed outlier: 4.685A pdb=" N GLY A 603 " --> pdb=" O ARG A 684 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL A 686 " --> pdb=" O PHE A 601 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N PHE A 601 " --> pdb=" O VAL A 686 " (cutoff:3.500A) removed outlier: 9.160A pdb=" N PHE A 688 " --> pdb=" O TYR A 599 " (cutoff:3.500A) removed outlier: 9.541A pdb=" N TYR A 599 " --> pdb=" O PHE A 688 " (cutoff:3.500A) removed outlier: 12.189A pdb=" N GLU A 602 " --> pdb=" O VAL A 578 " (cutoff:3.500A) removed outlier: 9.206A pdb=" N VAL A 578 " --> pdb=" O GLU A 602 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N PHE A 604 " --> pdb=" O ILE A 576 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE A 576 " --> pdb=" O PHE A 604 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N CYS A 618 " --> pdb=" O ILE A 629 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 422 through 423 Processing sheet with id=AA7, first strand: chain 'A' and resid 751 through 753 removed outlier: 4.801A pdb=" N ILE A 741 " --> pdb=" O THR A 850 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR A 850 " --> pdb=" O ILE A 741 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 755 through 758 removed outlier: 5.094A pdb=" N LEU A 757 " --> pdb=" O ILE A 771 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ILE A 771 " --> pdb=" O LEU A 757 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1283 through 1290 removed outlier: 3.618A pdb=" N ALA A1301 " --> pdb=" O LYS A1285 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N THR A1299 " --> pdb=" O LEU A1287 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N THR A1289 " --> pdb=" O THR A1297 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N THR A1297 " --> pdb=" O THR A1289 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N TYR A1298 " --> pdb=" O LYS A1313 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LYS A1313 " --> pdb=" O TYR A1298 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL A1300 " --> pdb=" O CYS A1311 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N CYS A1311 " --> pdb=" O VAL A1300 " (cutoff:3.500A) 478 hydrogen bonds defined for protein. 1377 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 79 hydrogen bonds 142 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 53 stacking parallelities Total time for adding SS restraints: 5.18 Time building geometry restraints manager: 3.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3312 1.33 - 1.46: 2706 1.46 - 1.58: 5848 1.58 - 1.70: 190 1.70 - 1.82: 97 Bond restraints: 12153 Sorted by residual: bond pdb=" C THR A 898 " pdb=" N HIS A 899 " ideal model delta sigma weight residual 1.330 1.312 0.018 1.47e-02 4.63e+03 1.48e+00 bond pdb=" C ASN A1080 " pdb=" N TYR A1081 " ideal model delta sigma weight residual 1.329 1.293 0.036 3.03e-02 1.09e+03 1.42e+00 bond pdb=" CB TRP A 794 " pdb=" CG TRP A 794 " ideal model delta sigma weight residual 1.498 1.462 0.036 3.10e-02 1.04e+03 1.33e+00 bond pdb=" CA ASP B 712 " pdb=" CB ASP B 712 " ideal model delta sigma weight residual 1.529 1.547 -0.018 1.63e-02 3.76e+03 1.19e+00 bond pdb=" CA GLN A 756 " pdb=" C GLN A 756 " ideal model delta sigma weight residual 1.532 1.522 0.010 9.60e-03 1.09e+04 1.12e+00 ... (remaining 12148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 16649 2.14 - 4.28: 199 4.28 - 6.42: 17 6.42 - 8.56: 5 8.56 - 10.70: 3 Bond angle restraints: 16873 Sorted by residual: angle pdb=" CB MET A 722 " pdb=" CG MET A 722 " pdb=" SD MET A 722 " ideal model delta sigma weight residual 112.70 123.40 -10.70 3.00e+00 1.11e-01 1.27e+01 angle pdb=" CB MET B 520 " pdb=" CG MET B 520 " pdb=" SD MET B 520 " ideal model delta sigma weight residual 112.70 122.63 -9.93 3.00e+00 1.11e-01 1.09e+01 angle pdb=" CB MET A1355 " pdb=" CG MET A1355 " pdb=" SD MET A1355 " ideal model delta sigma weight residual 112.70 122.37 -9.67 3.00e+00 1.11e-01 1.04e+01 angle pdb=" N GLU C 745 " pdb=" CA GLU C 745 " pdb=" CB GLU C 745 " ideal model delta sigma weight residual 110.28 114.92 -4.64 1.55e+00 4.16e-01 8.97e+00 angle pdb=" N GLY A1141 " pdb=" CA GLY A1141 " pdb=" C GLY A1141 " ideal model delta sigma weight residual 110.56 114.46 -3.90 1.36e+00 5.41e-01 8.21e+00 ... (remaining 16868 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.26: 7084 31.26 - 62.51: 359 62.51 - 93.77: 75 93.77 - 125.03: 2 125.03 - 156.28: 1 Dihedral angle restraints: 7521 sinusoidal: 4049 harmonic: 3472 Sorted by residual: dihedral pdb=" O4' U E 77 " pdb=" C1' U E 77 " pdb=" N1 U E 77 " pdb=" C2 U E 77 " ideal model delta sinusoidal sigma weight residual -128.00 28.28 -156.28 1 1.70e+01 3.46e-03 6.36e+01 dihedral pdb=" CA ILE B 548 " pdb=" C ILE B 548 " pdb=" N ASP B 549 " pdb=" CA ASP B 549 " ideal model delta harmonic sigma weight residual -180.00 -162.99 -17.01 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA TYR B 698 " pdb=" C TYR B 698 " pdb=" N GLY B 699 " pdb=" CA GLY B 699 " ideal model delta harmonic sigma weight residual 180.00 163.29 16.71 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 7518 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1661 0.054 - 0.108: 225 0.108 - 0.161: 30 0.161 - 0.215: 0 0.215 - 0.269: 1 Chirality restraints: 1917 Sorted by residual: chirality pdb=" CB THR B 552 " pdb=" CA THR B 552 " pdb=" OG1 THR B 552 " pdb=" CG2 THR B 552 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA LYS A 748 " pdb=" N LYS A 748 " pdb=" C LYS A 748 " pdb=" CB LYS A 748 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.47e-01 chirality pdb=" CA SER A 579 " pdb=" N SER A 579 " pdb=" C SER A 579 " pdb=" CB SER A 579 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.96e-01 ... (remaining 1914 not shown) Planarity restraints: 1822 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU C 745 " 0.013 2.00e-02 2.50e+03 2.72e-02 7.39e+00 pdb=" CD GLU C 745 " -0.047 2.00e-02 2.50e+03 pdb=" OE1 GLU C 745 " 0.017 2.00e-02 2.50e+03 pdb=" OE2 GLU C 745 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 970 " -0.017 2.00e-02 2.50e+03 1.46e-02 3.71e+00 pdb=" CG PHE A 970 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE A 970 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 970 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 970 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 970 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 970 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U E 107 " 0.018 2.00e-02 2.50e+03 9.93e-03 2.22e+00 pdb=" N1 U E 107 " -0.023 2.00e-02 2.50e+03 pdb=" C2 U E 107 " 0.002 2.00e-02 2.50e+03 pdb=" O2 U E 107 " -0.002 2.00e-02 2.50e+03 pdb=" N3 U E 107 " 0.001 2.00e-02 2.50e+03 pdb=" C4 U E 107 " 0.002 2.00e-02 2.50e+03 pdb=" O4 U E 107 " 0.005 2.00e-02 2.50e+03 pdb=" C5 U E 107 " 0.000 2.00e-02 2.50e+03 pdb=" C6 U E 107 " -0.003 2.00e-02 2.50e+03 ... (remaining 1819 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1207 2.74 - 3.28: 11013 3.28 - 3.82: 19149 3.82 - 4.36: 22161 4.36 - 4.90: 36258 Nonbonded interactions: 89788 Sorted by model distance: nonbonded pdb=" O2' U E 43 " pdb=" N1 A E 78 " model vdw 2.197 3.120 nonbonded pdb=" NH2 ARG A 801 " pdb=" OP2 C E 7 " model vdw 2.218 3.120 nonbonded pdb=" OE2 GLU A1147 " pdb="CA CA A1403 " model vdw 2.237 2.510 nonbonded pdb=" O VAL A 435 " pdb=" OG1 THR A 565 " model vdw 2.281 3.040 nonbonded pdb=" O CYS A 538 " pdb=" NH1 ARG A 543 " model vdw 2.293 3.120 ... (remaining 89783 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 35.050 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 39.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 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 0.038 12161 Z= 0.226 Angle : 0.607 10.696 16877 Z= 0.317 Chirality : 0.037 0.269 1917 Planarity : 0.003 0.033 1822 Dihedral : 17.264 156.283 5269 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.00 % Allowed : 9.37 % Favored : 90.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.25), residues: 1172 helix: 1.94 (0.22), residues: 572 sheet: 0.21 (0.45), residues: 132 loop : -0.55 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1078 HIS 0.012 0.001 HIS B 730 PHE 0.034 0.001 PHE A 970 TYR 0.018 0.001 TYR B 597 ARG 0.007 0.000 ARG C 741 Details of bonding type rmsd hydrogen bonds : bond 0.18449 ( 548) hydrogen bonds : angle 6.10833 ( 1519) metal coordination : bond 0.00941 ( 8) metal coordination : angle 1.92398 ( 4) covalent geometry : bond 0.00501 (12153) covalent geometry : angle 0.60627 (16873) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 1.202 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1996 time to fit residues: 15.7385 Evaluate side-chains 46 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 0.2980 chunk 95 optimal weight: 7.9990 chunk 52 optimal weight: 0.6980 chunk 32 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 73 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 678 GLN B 730 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.060320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.041207 restraints weight = 63245.354| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 3.51 r_work: 0.2870 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.0843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12161 Z= 0.145 Angle : 0.526 9.110 16877 Z= 0.269 Chirality : 0.036 0.187 1917 Planarity : 0.003 0.032 1822 Dihedral : 18.326 159.055 2797 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.76 % Allowed : 8.70 % Favored : 90.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.25), residues: 1172 helix: 2.18 (0.22), residues: 581 sheet: -0.02 (0.44), residues: 135 loop : -0.50 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 665 HIS 0.005 0.001 HIS B 730 PHE 0.028 0.001 PHE A 970 TYR 0.018 0.001 TYR B 597 ARG 0.003 0.000 ARG A1308 Details of bonding type rmsd hydrogen bonds : bond 0.05864 ( 548) hydrogen bonds : angle 4.43688 ( 1519) metal coordination : bond 0.00699 ( 8) metal coordination : angle 1.77379 ( 4) covalent geometry : bond 0.00307 (12153) covalent geometry : angle 0.52564 (16873) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 1.207 Fit side-chains REVERT: A 937 MET cc_start: 0.8940 (mmp) cc_final: 0.8391 (ptt) outliers start: 8 outliers final: 2 residues processed: 53 average time/residue: 0.1873 time to fit residues: 16.4648 Evaluate side-chains 48 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 1164 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 82 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 84 optimal weight: 0.7980 chunk 95 optimal weight: 7.9990 chunk 83 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.060147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.040887 restraints weight = 63789.513| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 3.49 r_work: 0.2858 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12161 Z= 0.184 Angle : 0.533 6.977 16877 Z= 0.272 Chirality : 0.037 0.235 1917 Planarity : 0.003 0.031 1822 Dihedral : 18.217 160.486 2797 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.57 % Allowed : 9.27 % Favored : 90.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.25), residues: 1172 helix: 2.25 (0.22), residues: 579 sheet: -0.18 (0.44), residues: 135 loop : -0.51 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1078 HIS 0.005 0.001 HIS B 730 PHE 0.028 0.001 PHE A 970 TYR 0.021 0.001 TYR B 597 ARG 0.002 0.000 ARG A 801 Details of bonding type rmsd hydrogen bonds : bond 0.05865 ( 548) hydrogen bonds : angle 4.26694 ( 1519) metal coordination : bond 0.00582 ( 8) metal coordination : angle 1.95850 ( 4) covalent geometry : bond 0.00406 (12153) covalent geometry : angle 0.53237 (16873) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 1.224 Fit side-chains revert: symmetry clash REVERT: A 861 MET cc_start: 0.9216 (mmm) cc_final: 0.8970 (mmm) outliers start: 6 outliers final: 3 residues processed: 51 average time/residue: 0.1910 time to fit residues: 16.3108 Evaluate side-chains 50 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain A residue 875 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 78 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 76 optimal weight: 0.5980 chunk 17 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 chunk 109 optimal weight: 0.0370 chunk 37 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 overall best weight: 2.3264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.060091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.041007 restraints weight = 64002.638| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 3.43 r_work: 0.2859 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12161 Z= 0.181 Angle : 0.523 8.707 16877 Z= 0.266 Chirality : 0.037 0.230 1917 Planarity : 0.003 0.032 1822 Dihedral : 18.134 162.411 2797 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.57 % Allowed : 10.03 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.26), residues: 1172 helix: 2.28 (0.22), residues: 582 sheet: -0.18 (0.44), residues: 136 loop : -0.53 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1078 HIS 0.004 0.001 HIS A1120 PHE 0.026 0.001 PHE A 970 TYR 0.020 0.001 TYR B 597 ARG 0.002 0.000 ARG A1000 Details of bonding type rmsd hydrogen bonds : bond 0.05525 ( 548) hydrogen bonds : angle 4.11080 ( 1519) metal coordination : bond 0.00588 ( 8) metal coordination : angle 1.92643 ( 4) covalent geometry : bond 0.00404 (12153) covalent geometry : angle 0.52176 (16873) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 1.189 Fit side-chains REVERT: A 861 MET cc_start: 0.9246 (mmm) cc_final: 0.8917 (mmm) REVERT: A 937 MET cc_start: 0.8944 (mmp) cc_final: 0.8333 (ptm) outliers start: 6 outliers final: 4 residues processed: 52 average time/residue: 0.1943 time to fit residues: 16.9202 Evaluate side-chains 50 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 1121 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 21 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 28 optimal weight: 0.3980 chunk 98 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 58 optimal weight: 0.0970 chunk 27 optimal weight: 0.0980 chunk 71 optimal weight: 2.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.060602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.041584 restraints weight = 62995.047| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 3.52 r_work: 0.2881 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 12161 Z= 0.117 Angle : 0.473 8.429 16877 Z= 0.241 Chirality : 0.035 0.241 1917 Planarity : 0.003 0.034 1822 Dihedral : 18.017 164.037 2797 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.76 % Allowed : 10.60 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.26), residues: 1172 helix: 2.43 (0.22), residues: 582 sheet: -0.11 (0.44), residues: 136 loop : -0.49 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 691 HIS 0.003 0.001 HIS B 730 PHE 0.020 0.001 PHE A 970 TYR 0.018 0.001 TYR B 597 ARG 0.001 0.000 ARG C 746 Details of bonding type rmsd hydrogen bonds : bond 0.04525 ( 548) hydrogen bonds : angle 3.82199 ( 1519) metal coordination : bond 0.00784 ( 8) metal coordination : angle 1.68465 ( 4) covalent geometry : bond 0.00254 (12153) covalent geometry : angle 0.47278 (16873) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 1.217 Fit side-chains REVERT: B 636 ASP cc_start: 0.7400 (t70) cc_final: 0.7196 (t70) REVERT: A 861 MET cc_start: 0.9189 (mmm) cc_final: 0.8916 (mmm) outliers start: 8 outliers final: 4 residues processed: 55 average time/residue: 0.1882 time to fit residues: 17.4062 Evaluate side-chains 52 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 1225 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 3 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 86 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 102 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.060515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.041335 restraints weight = 63720.170| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 3.55 r_work: 0.2875 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12161 Z= 0.120 Angle : 0.474 9.376 16877 Z= 0.239 Chirality : 0.035 0.223 1917 Planarity : 0.003 0.030 1822 Dihedral : 17.983 166.679 2797 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.57 % Allowed : 10.88 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.26), residues: 1172 helix: 2.54 (0.22), residues: 582 sheet: -0.08 (0.45), residues: 133 loop : -0.46 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1078 HIS 0.004 0.001 HIS B 730 PHE 0.020 0.001 PHE A 970 TYR 0.017 0.001 TYR B 597 ARG 0.002 0.000 ARG A1145 Details of bonding type rmsd hydrogen bonds : bond 0.04546 ( 548) hydrogen bonds : angle 3.72411 ( 1519) metal coordination : bond 0.00645 ( 8) metal coordination : angle 1.55802 ( 4) covalent geometry : bond 0.00264 (12153) covalent geometry : angle 0.47357 (16873) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 1.217 Fit side-chains REVERT: A 861 MET cc_start: 0.9213 (mmm) cc_final: 0.8882 (mmm) outliers start: 6 outliers final: 6 residues processed: 53 average time/residue: 0.2005 time to fit residues: 17.5940 Evaluate side-chains 52 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 1225 ILE Chi-restraints excluded: chain A residue 1281 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 7 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 14 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 chunk 13 optimal weight: 9.9990 chunk 118 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.059723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.040469 restraints weight = 64616.137| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 3.54 r_work: 0.2839 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12161 Z= 0.199 Angle : 0.532 9.564 16877 Z= 0.267 Chirality : 0.036 0.208 1917 Planarity : 0.003 0.033 1822 Dihedral : 18.031 167.834 2797 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.66 % Allowed : 11.54 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.26), residues: 1172 helix: 2.47 (0.22), residues: 584 sheet: -0.27 (0.44), residues: 134 loop : -0.52 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1078 HIS 0.004 0.001 HIS B 730 PHE 0.023 0.001 PHE A 970 TYR 0.017 0.001 TYR B 597 ARG 0.003 0.000 ARG A1000 Details of bonding type rmsd hydrogen bonds : bond 0.05525 ( 548) hydrogen bonds : angle 3.92473 ( 1519) metal coordination : bond 0.00625 ( 8) metal coordination : angle 1.87570 ( 4) covalent geometry : bond 0.00447 (12153) covalent geometry : angle 0.53116 (16873) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 1.152 Fit side-chains REVERT: A 861 MET cc_start: 0.9218 (mmm) cc_final: 0.8923 (mmm) REVERT: A 937 MET cc_start: 0.9054 (mmp) cc_final: 0.8212 (ptm) outliers start: 7 outliers final: 6 residues processed: 54 average time/residue: 0.1793 time to fit residues: 16.2711 Evaluate side-chains 52 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 1281 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 119 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 110 optimal weight: 0.0010 chunk 125 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 chunk 122 optimal weight: 20.0000 chunk 88 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 overall best weight: 1.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.060147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.041044 restraints weight = 64019.368| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 3.51 r_work: 0.2861 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12161 Z= 0.144 Angle : 0.497 10.937 16877 Z= 0.248 Chirality : 0.035 0.161 1917 Planarity : 0.003 0.034 1822 Dihedral : 18.001 167.692 2797 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.76 % Allowed : 11.35 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.26), residues: 1172 helix: 2.55 (0.22), residues: 582 sheet: -0.22 (0.45), residues: 134 loop : -0.56 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1078 HIS 0.003 0.001 HIS A 630 PHE 0.020 0.001 PHE A 970 TYR 0.016 0.001 TYR B 597 ARG 0.002 0.000 ARG A 801 Details of bonding type rmsd hydrogen bonds : bond 0.04802 ( 548) hydrogen bonds : angle 3.77335 ( 1519) metal coordination : bond 0.00629 ( 8) metal coordination : angle 1.72887 ( 4) covalent geometry : bond 0.00320 (12153) covalent geometry : angle 0.49614 (16873) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 1.188 Fit side-chains REVERT: A 725 TRP cc_start: 0.9016 (OUTLIER) cc_final: 0.8189 (m-90) REVERT: A 861 MET cc_start: 0.9238 (mmm) cc_final: 0.8964 (mmm) REVERT: A 937 MET cc_start: 0.9019 (mmp) cc_final: 0.8105 (ptm) outliers start: 8 outliers final: 7 residues processed: 54 average time/residue: 0.1846 time to fit residues: 16.5817 Evaluate side-chains 53 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 725 TRP Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 1281 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 115 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 20 optimal weight: 40.0000 chunk 105 optimal weight: 4.9990 chunk 54 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 36 optimal weight: 0.4980 chunk 64 optimal weight: 5.9990 chunk 41 optimal weight: 0.0570 chunk 75 optimal weight: 5.9990 overall best weight: 2.5104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 983 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.059693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.040391 restraints weight = 63883.964| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 3.51 r_work: 0.2838 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12161 Z= 0.190 Angle : 0.536 11.766 16877 Z= 0.266 Chirality : 0.036 0.148 1917 Planarity : 0.003 0.031 1822 Dihedral : 18.036 168.618 2797 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.76 % Allowed : 11.64 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.26), residues: 1172 helix: 2.47 (0.22), residues: 582 sheet: -0.33 (0.44), residues: 134 loop : -0.61 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1078 HIS 0.004 0.001 HIS B 730 PHE 0.021 0.001 PHE A 970 TYR 0.017 0.001 TYR B 698 ARG 0.002 0.000 ARG A 801 Details of bonding type rmsd hydrogen bonds : bond 0.05486 ( 548) hydrogen bonds : angle 3.90589 ( 1519) metal coordination : bond 0.00562 ( 8) metal coordination : angle 1.86213 ( 4) covalent geometry : bond 0.00426 (12153) covalent geometry : angle 0.53559 (16873) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 1.260 Fit side-chains REVERT: A 725 TRP cc_start: 0.9025 (OUTLIER) cc_final: 0.8164 (m-90) REVERT: A 861 MET cc_start: 0.9253 (mmm) cc_final: 0.8957 (mmm) REVERT: A 937 MET cc_start: 0.9046 (mmp) cc_final: 0.8166 (ptm) outliers start: 8 outliers final: 7 residues processed: 53 average time/residue: 0.1941 time to fit residues: 17.3758 Evaluate side-chains 53 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 725 TRP Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 1281 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 4 optimal weight: 0.1980 chunk 14 optimal weight: 8.9990 chunk 48 optimal weight: 0.0980 chunk 15 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.060634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.041636 restraints weight = 64177.574| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 3.48 r_work: 0.2883 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12161 Z= 0.104 Angle : 0.483 11.972 16877 Z= 0.239 Chirality : 0.034 0.138 1917 Planarity : 0.003 0.034 1822 Dihedral : 17.971 168.282 2797 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.76 % Allowed : 11.73 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.26), residues: 1172 helix: 2.59 (0.22), residues: 582 sheet: -0.20 (0.45), residues: 133 loop : -0.53 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 691 HIS 0.003 0.001 HIS A 630 PHE 0.019 0.001 PHE A 970 TYR 0.017 0.001 TYR B 597 ARG 0.001 0.000 ARG B 522 Details of bonding type rmsd hydrogen bonds : bond 0.04199 ( 548) hydrogen bonds : angle 3.63928 ( 1519) metal coordination : bond 0.00636 ( 8) metal coordination : angle 1.65753 ( 4) covalent geometry : bond 0.00225 (12153) covalent geometry : angle 0.48209 (16873) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 1.356 Fit side-chains REVERT: A 725 TRP cc_start: 0.9042 (OUTLIER) cc_final: 0.8233 (m-90) REVERT: A 861 MET cc_start: 0.9213 (mmm) cc_final: 0.8879 (mmm) REVERT: A 937 MET cc_start: 0.8978 (mmp) cc_final: 0.8020 (ptm) outliers start: 8 outliers final: 7 residues processed: 53 average time/residue: 0.2243 time to fit residues: 20.2142 Evaluate side-chains 52 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain A residue 725 TRP Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 1225 ILE Chi-restraints excluded: chain A residue 1281 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 115 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 78 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 31 optimal weight: 8.9990 chunk 82 optimal weight: 0.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.060505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.041544 restraints weight = 63257.443| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 3.51 r_work: 0.2877 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12161 Z= 0.115 Angle : 0.485 11.777 16877 Z= 0.239 Chirality : 0.034 0.139 1917 Planarity : 0.003 0.036 1822 Dihedral : 17.964 169.435 2797 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.66 % Allowed : 12.11 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.26), residues: 1172 helix: 2.57 (0.22), residues: 582 sheet: -0.21 (0.45), residues: 134 loop : -0.54 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1078 HIS 0.003 0.001 HIS A 630 PHE 0.019 0.001 PHE A 970 TYR 0.017 0.001 TYR B 597 ARG 0.002 0.000 ARG C 746 Details of bonding type rmsd hydrogen bonds : bond 0.04371 ( 548) hydrogen bonds : angle 3.63057 ( 1519) metal coordination : bond 0.00629 ( 8) metal coordination : angle 1.66085 ( 4) covalent geometry : bond 0.00253 (12153) covalent geometry : angle 0.48390 (16873) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6572.66 seconds wall clock time: 114 minutes 10.24 seconds (6850.24 seconds total)