Starting phenix.real_space_refine on Sat Oct 12 07:10:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9asn_43820/10_2024/9asn_43820.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9asn_43820/10_2024/9asn_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9asn_43820/10_2024/9asn_43820.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9asn_43820/10_2024/9asn_43820.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9asn_43820/10_2024/9asn_43820.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9asn_43820/10_2024/9asn_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-5477/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: 7.60, per 1000 atoms: 0.65 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: 3.11 Conformation dependent library (CDL) restraints added in 1.4 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: 4.31 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: 5.21 Time building geometry restraints manager: 3.46 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: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 35.450 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.730 ------------------------------------------------------------------------------- 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 12153 Z= 0.330 Angle : 0.606 10.696 16873 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 1.290 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.2003 time to fit residues: 15.7134 Evaluate side-chains 46 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 1.228 ------------------------------------------------------------------------------- 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: 0.1980 chunk 60 optimal weight: 0.7980 chunk 73 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12153 Z= 0.146 Angle : 0.510 9.704 16873 Z= 0.260 Chirality : 0.036 0.179 1917 Planarity : 0.003 0.032 1822 Dihedral : 18.295 158.759 2797 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.76 % Allowed : 8.23 % Favored : 91.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.42 (0.25), residues: 1172 helix: 2.19 (0.22), residues: 582 sheet: 0.17 (0.44), residues: 140 loop : -0.45 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 665 HIS 0.005 0.001 HIS B 730 PHE 0.027 0.001 PHE A 970 TYR 0.019 0.001 TYR B 698 ARG 0.003 0.000 ARG A1308 *********************** 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 fitting. rotamer outliers: 8 poor density : 47 time to evaluate : 1.299 Fit side-chains revert: symmetry clash REVERT: A 908 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.8368 (ptp) outliers start: 8 outliers final: 1 residues processed: 52 average time/residue: 0.2047 time to fit residues: 17.6518 Evaluate side-chains 48 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 46 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 908 MET 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 63 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 77 optimal weight: 8.9990 chunk 31 optimal weight: 7.9990 chunk 114 optimal weight: 5.9990 chunk 123 optimal weight: 10.0000 chunk 102 optimal weight: 0.0770 chunk 113 optimal weight: 5.9990 chunk 39 optimal weight: 0.0980 chunk 91 optimal weight: 0.5980 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12153 Z= 0.145 Angle : 0.466 6.608 16873 Z= 0.237 Chirality : 0.035 0.226 1917 Planarity : 0.003 0.030 1822 Dihedral : 18.098 160.732 2797 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.47 % Allowed : 8.61 % Favored : 90.92 % 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: 1.59 (0.25), residues: 1172 helix: 2.39 (0.22), residues: 583 sheet: 0.01 (0.46), residues: 130 loop : -0.37 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 725 HIS 0.004 0.001 HIS B 730 PHE 0.023 0.001 PHE A 970 TYR 0.020 0.001 TYR B 597 ARG 0.001 0.000 ARG A 801 *********************** 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 52 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 47 time to evaluate : 1.313 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 50 average time/residue: 0.2012 time to fit residues: 16.7912 Evaluate side-chains 51 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 47 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain B residue 553 TYR 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 113 optimal weight: 6.9990 chunk 86 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 12 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 chunk 76 optimal weight: 0.9990 chunk 115 optimal weight: 5.9990 chunk 121 optimal weight: 50.0000 chunk 60 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 12153 Z= 0.309 Angle : 0.539 8.071 16873 Z= 0.273 Chirality : 0.037 0.225 1917 Planarity : 0.003 0.031 1822 Dihedral : 18.098 163.672 2797 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.76 % Allowed : 9.37 % Favored : 89.88 % 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: 1.49 (0.26), residues: 1172 helix: 2.35 (0.22), residues: 585 sheet: -0.07 (0.43), residues: 136 loop : -0.50 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1078 HIS 0.005 0.001 HIS B 730 PHE 0.030 0.001 PHE A 970 TYR 0.019 0.001 TYR B 597 ARG 0.003 0.000 ARG A 801 *********************** 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 55 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 47 time to evaluate : 1.356 Fit side-chains REVERT: A 937 MET cc_start: 0.8256 (mmp) cc_final: 0.8000 (ptm) outliers start: 8 outliers final: 5 residues processed: 53 average time/residue: 0.1973 time to fit residues: 17.5203 Evaluate side-chains 51 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 1.199 ------------------------------------------------------------------------------- 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 1121 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 1 optimal weight: 7.9990 chunk 90 optimal weight: 0.0370 chunk 50 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 62 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 overall best weight: 1.6064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12153 Z= 0.187 Angle : 0.485 8.729 16873 Z= 0.245 Chirality : 0.035 0.234 1917 Planarity : 0.003 0.030 1822 Dihedral : 18.028 164.273 2797 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.66 % Allowed : 10.31 % Favored : 89.03 % 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: 1.56 (0.26), residues: 1172 helix: 2.44 (0.22), residues: 583 sheet: -0.17 (0.45), residues: 132 loop : -0.45 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 725 HIS 0.003 0.001 HIS B 730 PHE 0.021 0.001 PHE A 970 TYR 0.018 0.001 TYR B 597 ARG 0.002 0.000 ARG A1000 *********************** 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 55 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 48 time to evaluate : 1.332 Fit side-chains REVERT: B 636 ASP cc_start: 0.7130 (t70) cc_final: 0.6930 (t70) REVERT: A 908 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8374 (ptp) outliers start: 7 outliers final: 3 residues processed: 53 average time/residue: 0.2250 time to fit residues: 19.5951 Evaluate side-chains 52 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 1.306 ------------------------------------------------------------------------------- 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 908 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 6.9990 chunk 109 optimal weight: 0.4980 chunk 24 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 121 optimal weight: 50.0000 chunk 101 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 10 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 117 optimal weight: 8.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12153 Z= 0.344 Angle : 0.557 9.369 16873 Z= 0.281 Chirality : 0.038 0.208 1917 Planarity : 0.003 0.031 1822 Dihedral : 18.080 166.442 2797 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.95 % Allowed : 11.26 % 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: 1.42 (0.26), residues: 1172 helix: 2.36 (0.22), residues: 583 sheet: -0.28 (0.44), residues: 134 loop : -0.56 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1078 HIS 0.005 0.001 HIS B 730 PHE 0.024 0.001 PHE A 970 TYR 0.018 0.001 TYR B 698 ARG 0.003 0.000 ARG A1000 *********************** 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 58 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 48 time to evaluate : 1.278 Fit side-chains REVERT: B 636 ASP cc_start: 0.7053 (t70) cc_final: 0.6845 (t70) REVERT: A 908 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.8439 (ptp) REVERT: A 937 MET cc_start: 0.8364 (mmp) cc_final: 0.7819 (ptm) outliers start: 10 outliers final: 7 residues processed: 56 average time/residue: 0.1896 time to fit residues: 17.7834 Evaluate side-chains 55 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 47 time to evaluate : 1.369 ------------------------------------------------------------------------------- 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 647 LEU Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 908 MET 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 13 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 102 optimal weight: 20.0000 chunk 121 optimal weight: 40.0000 chunk 76 optimal weight: 0.0050 chunk 74 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12153 Z= 0.155 Angle : 0.480 9.966 16873 Z= 0.241 Chirality : 0.035 0.186 1917 Planarity : 0.003 0.034 1822 Dihedral : 17.995 166.386 2797 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.57 % Allowed : 11.54 % 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: 1.59 (0.26), residues: 1172 helix: 2.53 (0.22), residues: 582 sheet: -0.19 (0.45), residues: 134 loop : -0.50 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 725 HIS 0.003 0.001 HIS B 730 PHE 0.019 0.001 PHE A 970 TYR 0.017 0.001 TYR B 597 ARG 0.001 0.000 ARG A 440 *********************** 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 53 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 47 time to evaluate : 1.233 Fit side-chains REVERT: B 636 ASP cc_start: 0.7111 (t70) cc_final: 0.6891 (t70) REVERT: A 908 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.8439 (ptp) outliers start: 6 outliers final: 5 residues processed: 52 average time/residue: 0.1997 time to fit residues: 17.3196 Evaluate side-chains 53 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 47 time to evaluate : 1.389 ------------------------------------------------------------------------------- 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 908 MET Chi-restraints excluded: chain A residue 1225 ILE 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 72 optimal weight: 0.0270 chunk 36 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 95 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 overall best weight: 1.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6794 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12153 Z= 0.215 Angle : 0.502 10.937 16873 Z= 0.249 Chirality : 0.035 0.143 1917 Planarity : 0.003 0.032 1822 Dihedral : 17.994 167.853 2797 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % 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: 1.61 (0.26), residues: 1172 helix: 2.55 (0.22), residues: 582 sheet: -0.18 (0.45), residues: 133 loop : -0.50 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1078 HIS 0.004 0.001 HIS A 869 PHE 0.021 0.001 PHE A 970 TYR 0.017 0.001 TYR B 597 ARG 0.002 0.000 ARG A1000 *********************** 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 fitting. rotamer outliers: 8 poor density : 46 time to evaluate : 1.428 Fit side-chains REVERT: B 636 ASP cc_start: 0.7099 (t70) cc_final: 0.6880 (t70) REVERT: A 635 MET cc_start: 0.8659 (tpp) cc_final: 0.8307 (tpt) REVERT: A 937 MET cc_start: 0.8324 (mmp) cc_final: 0.7838 (ptm) outliers start: 8 outliers final: 7 residues processed: 53 average time/residue: 0.1933 time to fit residues: 17.3274 Evaluate side-chains 52 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 45 time to evaluate : 1.426 ------------------------------------------------------------------------------- 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 875 CYS Chi-restraints excluded: chain A residue 1225 ILE 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 113 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 49 optimal weight: 0.3980 chunk 88 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 102 optimal weight: 6.9990 chunk 107 optimal weight: 0.4980 chunk 112 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 chunk 119 optimal weight: 8.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6759 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12153 Z= 0.138 Angle : 0.473 11.478 16873 Z= 0.234 Chirality : 0.034 0.136 1917 Planarity : 0.003 0.037 1822 Dihedral : 17.947 168.280 2797 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.85 % Allowed : 11.35 % 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: 1.69 (0.26), residues: 1172 helix: 2.60 (0.22), residues: 584 sheet: -0.15 (0.46), residues: 133 loop : -0.46 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 691 HIS 0.003 0.001 HIS A 630 PHE 0.018 0.001 PHE A 970 TYR 0.017 0.001 TYR B 597 ARG 0.001 0.000 ARG A 440 *********************** 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 54 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 45 time to evaluate : 1.262 Fit side-chains REVERT: B 636 ASP cc_start: 0.7109 (t70) cc_final: 0.6882 (t70) REVERT: A 635 MET cc_start: 0.8679 (tpp) cc_final: 0.8470 (tpt) REVERT: A 725 TRP cc_start: 0.8922 (OUTLIER) cc_final: 0.8171 (m-90) REVERT: A 937 MET cc_start: 0.8278 (mmp) cc_final: 0.7684 (ptm) outliers start: 9 outliers final: 7 residues processed: 54 average time/residue: 0.1957 time to fit residues: 17.8699 Evaluate side-chains 52 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 44 time to evaluate : 1.320 ------------------------------------------------------------------------------- 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 73 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 99 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 77 optimal weight: 0.0170 chunk 61 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 overall best weight: 2.1824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12153 Z= 0.246 Angle : 0.520 12.023 16873 Z= 0.256 Chirality : 0.035 0.143 1917 Planarity : 0.003 0.036 1822 Dihedral : 17.985 169.553 2797 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.44 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: 1.63 (0.26), residues: 1172 helix: 2.57 (0.22), residues: 583 sheet: -0.21 (0.45), residues: 132 loop : -0.49 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1078 HIS 0.004 0.001 HIS A 869 PHE 0.021 0.001 PHE A 970 TYR 0.017 0.001 TYR B 597 ARG 0.002 0.000 ARG C 746 ********************** 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 52 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 45 time to evaluate : 1.208 Fit side-chains REVERT: B 636 ASP cc_start: 0.7166 (t70) cc_final: 0.6942 (t70) REVERT: A 725 TRP cc_start: 0.8916 (OUTLIER) cc_final: 0.8133 (m-90) REVERT: A 937 MET cc_start: 0.8238 (mmp) cc_final: 0.7712 (ptm) outliers start: 7 outliers final: 6 residues processed: 52 average time/residue: 0.2069 time to fit residues: 17.8214 Evaluate side-chains 51 residues out of total 1062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 44 time to evaluate : 1.341 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 27 optimal weight: 0.0470 chunk 100 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 102 optimal weight: 0.0170 chunk 12 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 overall best weight: 2.0122 ------------------------------------------------------------------------------- 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 = 0.3647 r_free = 0.3647 target = 0.060185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.041069 restraints weight = 63768.404| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 3.51 r_work: 0.2860 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12153 Z= 0.230 Angle : 0.514 12.355 16873 Z= 0.253 Chirality : 0.035 0.143 1917 Planarity : 0.003 0.032 1822 Dihedral : 17.996 169.247 2797 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.66 % Allowed : 11.45 % 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: 1.54 (0.26), residues: 1172 helix: 2.51 (0.22), residues: 582 sheet: -0.30 (0.44), residues: 135 loop : -0.53 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 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 A 440 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2211.14 seconds wall clock time: 41 minutes 34.49 seconds (2494.49 seconds total)