Starting phenix.real_space_refine on Fri Jul 3 02:55:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9asn_43820/07_2026/9asn_43820.cif Found real_map, /net/cci-nas-00/data/ceres_data/9asn_43820/07_2026/9asn_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 { model { file = "/net/cci-nas-00/data/ceres_data/9asn_43820/07_2026/9asn_43820.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9asn_43820/07_2026/9asn_43820.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9asn_43820/07_2026/9asn_43820.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9asn_43820/07_2026/9asn_43820.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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, 3 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2, 'water': 1} Link IDs: {None: 1} Chain breaks: 2 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: 2.60, per 1000 atoms: 0.22 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: 0.99 Conformation dependent library (CDL) restraints added in 487.6 milliseconds 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: 1.51 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: 2.59 Time building geometry restraints manager: 1.35 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=" N1 C E 17 " pdb=" C6 C E 17 " ideal model delta sigma weight residual 1.367 1.355 0.012 6.00e-03 2.78e+04 4.23e+00 bond pdb=" N1 C E 12 " pdb=" C6 C E 12 " ideal model delta sigma weight residual 1.367 1.356 0.011 6.00e-03 2.78e+04 3.24e+00 bond pdb=" N1 C E 10 " pdb=" C6 C E 10 " ideal model delta sigma weight residual 1.367 1.356 0.011 6.00e-03 2.78e+04 3.24e+00 bond pdb=" N1 C E 101 " pdb=" C6 C E 101 " ideal model delta sigma weight residual 1.367 1.356 0.011 6.00e-03 2.78e+04 3.20e+00 bond pdb=" N7 A E 13 " pdb=" C5 A E 13 " ideal model delta sigma weight residual 1.388 1.378 0.010 6.00e-03 2.78e+04 2.98e+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=" C1' U E 107 " pdb=" N1 U E 107 " pdb=" C2 U E 107 " ideal model delta sigma weight residual 117.70 122.63 -4.93 1.20e+00 6.94e-01 1.68e+01 angle pdb=" O4 U E 107 " pdb=" C4 U E 107 " pdb=" C5 U E 107 " ideal model delta sigma weight residual 125.90 123.59 2.31 6.00e-01 2.78e+00 1.48e+01 angle pdb=" C1' C E 99 " pdb=" N1 C E 99 " pdb=" C2 C E 99 " ideal model delta sigma weight residual 118.80 122.95 -4.15 1.10e+00 8.26e-01 1.42e+01 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=" C1' U E 77 " pdb=" N1 U E 77 " pdb=" C2 U E 77 " ideal model delta sigma weight residual 117.70 121.88 -4.18 1.20e+00 6.94e-01 1.21e+01 ... (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 3.250 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: 3.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.010 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 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= 0.279 Angle : 0.607 10.696 16877 Z= 0.391 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (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 ARG 0.007 0.000 ARG C 741 TYR 0.018 0.001 TYR B 597 PHE 0.034 0.001 PHE A 970 TRP 0.010 0.001 TRP A1078 HIS 0.012 0.001 HIS B 730 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.28 (12153) covalent geometry : angle 0.60629 / 0.39 (16873) hydrogen bonds : bond 0.18449 / 12.21 ( 548) hydrogen bonds : angle 6.10833 / 4.52 ( 1519) metal coordination : bond 0.00941 / 0.62 ( 8) metal coordination : angle 1.92398 / 1.12 ( 4) *********************** 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 : 0.422 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.0808 time to fit residues: 6.4215 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 : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 0.0000 chunk 33 optimal weight: 0.0040 chunk 123 optimal weight: 20.0000 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3664 r_free = 0.3664 target = 0.060757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.041636 restraints weight = 63379.389| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 3.53 r_work: 0.2889 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.0787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12161 Z= 0.125 Angle : 0.502 9.301 16877 Z= 0.273 Chirality : 0.036 0.191 1917 Planarity : 0.003 0.033 1822 Dihedral : 18.450 161.941 2797 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.47 % Allowed : 8.89 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.25), residues: 1172 helix: 2.15 (0.22), residues: 580 sheet: 0.08 (0.44), residues: 134 loop : -0.44 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 575 TYR 0.019 0.001 TYR B 597 PHE 0.027 0.001 PHE A 970 TRP 0.006 0.001 TRP A1258 HIS 0.009 0.001 HIS B 730 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.13 (12153) covalent geometry : angle 0.50169 / 0.27 (16873) hydrogen bonds : bond 0.06343 / 4.22 ( 548) hydrogen bonds : angle 4.53599 / 3.33 ( 1519) metal coordination : bond 0.00726 / 0.30 ( 8) metal coordination : angle 1.27736 / 0.74 ( 4) *********************** 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 52 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.427 Fit side-chains revert: symmetry clash REVERT: A 861 MET cc_start: 0.9174 (mmm) cc_final: 0.8915 (mmm) outliers start: 5 outliers final: 1 residues processed: 52 average time/residue: 0.0825 time to fit residues: 7.2252 Evaluate side-chains 47 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 78 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 57 optimal weight: 9.9990 chunk 61 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 112 optimal weight: 5.9990 chunk 119 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 91 optimal weight: 0.0870 chunk 122 optimal weight: 50.0000 overall best weight: 2.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.060342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.041108 restraints weight = 64087.993| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 3.52 r_work: 0.2867 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.0897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12161 Z= 0.167 Angle : 0.488 6.864 16877 Z= 0.264 Chirality : 0.036 0.206 1917 Planarity : 0.003 0.031 1822 Dihedral : 18.336 164.497 2797 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.47 % Allowed : 9.08 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.25), residues: 1172 helix: 2.26 (0.22), residues: 579 sheet: -0.09 (0.44), residues: 134 loop : -0.50 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 746 TYR 0.020 0.001 TYR B 597 PHE 0.027 0.001 PHE A 970 TRP 0.007 0.001 TRP A1078 HIS 0.005 0.001 HIS B 730 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.17 (12153) covalent geometry : angle 0.48736 / 0.26 (16873) hydrogen bonds : bond 0.06166 / 4.15 ( 548) hydrogen bonds : angle 4.34944 / 3.16 ( 1519) metal coordination : bond 0.00575 / 0.34 ( 8) metal coordination : angle 1.86736 / 1.06 ( 4) *********************** 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 to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.440 Fit side-chains revert: symmetry clash REVERT: A 861 MET cc_start: 0.9222 (mmm) cc_final: 0.8941 (mmm) outliers start: 5 outliers final: 3 residues processed: 50 average time/residue: 0.0841 time to fit residues: 7.0809 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 : 0.418 ------------------------------------------------------------------------------- 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 114 optimal weight: 0.0370 chunk 103 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 119 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 102 optimal weight: 4.9990 overall best weight: 1.3262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 495 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.060684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.041520 restraints weight = 64727.429| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 3.59 r_work: 0.2881 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12161 Z= 0.119 Angle : 0.451 7.956 16877 Z= 0.245 Chirality : 0.036 0.236 1917 Planarity : 0.003 0.031 1822 Dihedral : 18.267 166.641 2797 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.66 % Allowed : 9.37 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.25), residues: 1172 helix: 2.37 (0.22), residues: 582 sheet: -0.05 (0.44), residues: 134 loop : -0.47 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 801 TYR 0.023 0.001 TYR B 597 PHE 0.024 0.001 PHE A 970 TRP 0.006 0.001 TRP A 725 HIS 0.003 0.001 HIS A 630 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (12153) covalent geometry : angle 0.45078 / 0.24 (16873) hydrogen bonds : bond 0.05146 / 3.50 ( 548) hydrogen bonds : angle 4.02381 / 2.92 ( 1519) metal coordination : bond 0.00641 / 0.25 ( 8) metal coordination : angle 1.49313 / 0.86 ( 4) *********************** 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 54 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: A 861 MET cc_start: 0.9237 (mmm) cc_final: 0.8932 (mmm) outliers start: 7 outliers final: 2 residues processed: 52 average time/residue: 0.0676 time to fit residues: 5.9318 Evaluate side-chains 49 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 1164 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 28 optimal weight: 8.9990 chunk 57 optimal weight: 7.9990 chunk 112 optimal weight: 0.0970 chunk 124 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 121 optimal weight: 50.0000 chunk 86 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 overall best weight: 1.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.060211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.040951 restraints weight = 63782.441| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 3.56 r_work: 0.2859 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12161 Z= 0.153 Angle : 0.477 8.358 16877 Z= 0.254 Chirality : 0.036 0.237 1917 Planarity : 0.003 0.031 1822 Dihedral : 18.185 169.151 2797 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.47 % Allowed : 10.03 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.26), residues: 1172 helix: 2.44 (0.22), residues: 583 sheet: -0.11 (0.44), residues: 136 loop : -0.47 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 801 TYR 0.020 0.001 TYR B 597 PHE 0.025 0.001 PHE A 970 TRP 0.006 0.001 TRP A1078 HIS 0.004 0.001 HIS B 730 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (12153) covalent geometry : angle 0.47617 / 0.25 (16873) hydrogen bonds : bond 0.05512 / 3.75 ( 548) hydrogen bonds : angle 4.00864 / 2.90 ( 1519) metal coordination : bond 0.00544 / 0.30 ( 8) metal coordination : angle 1.77349 / 1.01 ( 4) *********************** 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 52 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.428 Fit side-chains REVERT: A 861 MET cc_start: 0.9248 (mmm) cc_final: 0.8934 (mmm) outliers start: 5 outliers final: 3 residues processed: 51 average time/residue: 0.0686 time to fit residues: 5.9738 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 : 0.318 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 90 optimal weight: 0.0050 chunk 95 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 118 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 overall best weight: 2.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.059848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.040520 restraints weight = 64754.455| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 3.56 r_work: 0.2840 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 12161 Z= 0.202 Angle : 0.510 7.254 16877 Z= 0.269 Chirality : 0.037 0.232 1917 Planarity : 0.003 0.032 1822 Dihedral : 18.192 169.907 2797 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.47 % Allowed : 11.35 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.26), residues: 1172 helix: 2.39 (0.22), residues: 585 sheet: -0.14 (0.44), residues: 135 loop : -0.53 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 801 TYR 0.021 0.001 TYR B 597 PHE 0.027 0.001 PHE A 970 TRP 0.008 0.001 TRP A1078 HIS 0.004 0.001 HIS B 730 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.20 (12153) covalent geometry : angle 0.50916 / 0.27 (16873) hydrogen bonds : bond 0.05903 / 4.02 ( 548) hydrogen bonds : angle 4.07977 / 2.95 ( 1519) metal coordination : bond 0.00700 / 0.45 ( 8) metal coordination : angle 1.99528 / 1.15 ( 4) *********************** 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 52 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.289 Fit side-chains REVERT: A 635 MET cc_start: 0.9117 (tpp) cc_final: 0.8882 (tpt) REVERT: A 861 MET cc_start: 0.9255 (mmm) cc_final: 0.8995 (mmm) REVERT: A 937 MET cc_start: 0.9033 (mmp) cc_final: 0.8232 (ptm) outliers start: 5 outliers final: 3 residues processed: 50 average time/residue: 0.0697 time to fit residues: 5.9474 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 : 0.267 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 78 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 11 optimal weight: 0.0570 chunk 102 optimal weight: 7.9990 chunk 115 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 67 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.060708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.041695 restraints weight = 63320.007| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 3.49 r_work: 0.2885 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12161 Z= 0.099 Angle : 0.448 9.369 16877 Z= 0.240 Chirality : 0.035 0.211 1917 Planarity : 0.003 0.030 1822 Dihedral : 18.155 170.018 2797 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.57 % Allowed : 11.35 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.26), residues: 1172 helix: 2.52 (0.22), residues: 583 sheet: -0.07 (0.44), residues: 136 loop : -0.50 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 522 TYR 0.019 0.001 TYR B 597 PHE 0.021 0.001 PHE A 970 TRP 0.006 0.001 TRP A 725 HIS 0.003 0.001 HIS A 869 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.10 (12153) covalent geometry : angle 0.44739 / 0.24 (16873) hydrogen bonds : bond 0.04640 / 3.17 ( 548) hydrogen bonds : angle 3.81154 / 2.75 ( 1519) metal coordination : bond 0.00810 / 0.35 ( 8) metal coordination : angle 1.34860 / 0.78 ( 4) *********************** 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: 6 poor density : 48 time to evaluate : 0.328 Fit side-chains REVERT: B 636 ASP cc_start: 0.7503 (t70) cc_final: 0.7284 (t70) REVERT: A 635 MET cc_start: 0.9100 (tpp) cc_final: 0.8872 (tpt) REVERT: A 861 MET cc_start: 0.9195 (mmm) cc_final: 0.8902 (mmm) outliers start: 6 outliers final: 4 residues processed: 52 average time/residue: 0.0679 time to fit residues: 5.9990 Evaluate side-chains 51 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.312 ------------------------------------------------------------------------------- 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 875 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 9 optimal weight: 20.0000 chunk 45 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 816 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.059534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.040260 restraints weight = 64165.533| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 3.51 r_work: 0.2828 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12161 Z= 0.245 Angle : 0.556 9.000 16877 Z= 0.289 Chirality : 0.038 0.210 1917 Planarity : 0.003 0.031 1822 Dihedral : 18.131 171.603 2797 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.85 % Allowed : 11.26 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.26), residues: 1172 helix: 2.38 (0.22), residues: 583 sheet: -0.27 (0.44), residues: 136 loop : -0.62 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1248 TYR 0.020 0.002 TYR B 597 PHE 0.025 0.002 PHE A 970 TRP 0.010 0.001 TRP A1078 HIS 0.005 0.001 HIS B 730 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.24 (12153) covalent geometry : angle 0.55529 / 0.29 (16873) hydrogen bonds : bond 0.06221 / 4.24 ( 548) hydrogen bonds : angle 4.11093 / 2.97 ( 1519) metal coordination : bond 0.01033 / 0.69 ( 8) metal coordination : angle 2.30432 / 1.32 ( 4) *********************** 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 55 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.429 Fit side-chains REVERT: A 635 MET cc_start: 0.9125 (tpp) cc_final: 0.8889 (tpt) REVERT: A 861 MET cc_start: 0.9288 (mmm) cc_final: 0.8982 (mmm) REVERT: A 937 MET cc_start: 0.9087 (mmp) cc_final: 0.8285 (ptm) outliers start: 9 outliers final: 4 residues processed: 54 average time/residue: 0.0783 time to fit residues: 7.1005 Evaluate side-chains 49 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.432 ------------------------------------------------------------------------------- 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 875 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 56 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 105 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 80 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.060267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.041210 restraints weight = 64255.786| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 3.53 r_work: 0.2863 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1606 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= 0.123 Angle : 0.476 11.565 16877 Z= 0.251 Chirality : 0.035 0.191 1917 Planarity : 0.003 0.031 1822 Dihedral : 18.158 170.764 2797 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.38 % Allowed : 11.64 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.26), residues: 1172 helix: 2.48 (0.22), residues: 582 sheet: -0.23 (0.44), residues: 136 loop : -0.57 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 440 TYR 0.019 0.001 TYR B 597 PHE 0.022 0.001 PHE A 970 TRP 0.006 0.001 TRP A 725 HIS 0.003 0.001 HIS B 730 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (12153) covalent geometry : angle 0.47571 / 0.25 (16873) hydrogen bonds : bond 0.05060 / 3.46 ( 548) hydrogen bonds : angle 3.87484 / 2.80 ( 1519) metal coordination : bond 0.00608 / 0.26 ( 8) metal coordination : angle 1.40878 / 0.82 ( 4) *********************** 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 50 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.355 Fit side-chains REVERT: B 636 ASP cc_start: 0.7396 (t70) cc_final: 0.7179 (t70) REVERT: A 635 MET cc_start: 0.9078 (tpp) cc_final: 0.8863 (tpt) REVERT: A 861 MET cc_start: 0.9230 (mmm) cc_final: 0.8969 (mmm) outliers start: 4 outliers final: 4 residues processed: 49 average time/residue: 0.0779 time to fit residues: 6.4444 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 : 0.374 ------------------------------------------------------------------------------- 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 875 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 10 optimal weight: 20.0000 chunk 23 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 73 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 31 optimal weight: 0.4980 chunk 89 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 124 optimal weight: 10.0000 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.060449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.041292 restraints weight = 64849.363| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 3.54 r_work: 0.2870 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1736 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= 0.126 Angle : 0.475 12.244 16877 Z= 0.245 Chirality : 0.035 0.141 1917 Planarity : 0.003 0.030 1822 Dihedral : 18.081 172.164 2797 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.47 % Allowed : 11.54 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.26), residues: 1172 helix: 2.53 (0.22), residues: 582 sheet: -0.17 (0.44), residues: 133 loop : -0.55 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 746 TYR 0.017 0.001 TYR B 597 PHE 0.021 0.001 PHE A 970 TRP 0.005 0.001 TRP A1258 HIS 0.003 0.001 HIS A 869 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (12153) covalent geometry : angle 0.47396 / 0.25 (16873) hydrogen bonds : bond 0.04819 / 3.30 ( 548) hydrogen bonds : angle 3.76255 / 2.72 ( 1519) metal coordination : bond 0.00595 / 0.30 ( 8) metal coordination : angle 1.65431 / 0.95 ( 4) ********************** 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 49 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.334 Fit side-chains REVERT: B 636 ASP cc_start: 0.7396 (t70) cc_final: 0.7169 (t70) REVERT: A 635 MET cc_start: 0.9122 (tpp) cc_final: 0.8901 (tpt) REVERT: A 861 MET cc_start: 0.9225 (mmm) cc_final: 0.8920 (mmm) REVERT: A 937 MET cc_start: 0.9006 (mmp) cc_final: 0.8135 (ptm) outliers start: 5 outliers final: 5 residues processed: 49 average time/residue: 0.0764 time to fit residues: 6.2799 Evaluate side-chains 49 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.423 ------------------------------------------------------------------------------- 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 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 16 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 chunk 110 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 78 optimal weight: 0.5980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.060484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.041322 restraints weight = 64908.087| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 3.55 r_work: 0.2871 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12161 Z= 0.120 Angle : 0.474 11.812 16877 Z= 0.244 Chirality : 0.035 0.143 1917 Planarity : 0.003 0.031 1822 Dihedral : 18.088 172.371 2797 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.38 % Allowed : 11.92 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.26), residues: 1172 helix: 2.54 (0.22), residues: 582 sheet: -0.23 (0.44), residues: 134 loop : -0.52 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 440 TYR 0.017 0.001 TYR B 597 PHE 0.021 0.001 PHE A 970 TRP 0.006 0.001 TRP A 725 HIS 0.003 0.001 HIS B 730 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (12153) covalent geometry : angle 0.47378 / 0.24 (16873) hydrogen bonds : bond 0.04727 / 3.25 ( 548) hydrogen bonds : angle 3.72386 / 2.69 ( 1519) metal coordination : bond 0.00606 / 0.27 ( 8) metal coordination : angle 1.57122 / 0.90 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2968.66 seconds wall clock time: 51 minutes 27.07 seconds (3087.07 seconds total)