Starting phenix.real_space_refine on Wed Sep 17 22:12:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9asn_43820/09_2025/9asn_43820.cif Found real_map, /net/cci-nas-00/data/ceres_data/9asn_43820/09_2025/9asn_43820.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9asn_43820/09_2025/9asn_43820.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9asn_43820/09_2025/9asn_43820.map" model { file = "/net/cci-nas-00/data/ceres_data/9asn_43820/09_2025/9asn_43820.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9asn_43820/09_2025/9asn_43820.cif" } 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-2.0-5805/lib/python3.9/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, 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: 3.11, per 1000 atoms: 0.27 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: 1.13 Conformation dependent library (CDL) restraints added in 611.7 milliseconds Enol-peptide restraints added in 2.6 microseconds 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: 1.66 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: 3.19 Time building geometry restraints manager: 1.49 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: 3.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 17.490 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12161 Z= 0.226 Angle : 0.607 10.696 16877 Z= 0.317 Chirality : 0.037 0.269 1917 Planarity : 0.003 0.033 1822 Dihedral : 17.264 156.283 5269 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.00 % Allowed : 9.37 % Favored : 90.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (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 covalent geometry : bond 0.00501 (12153) covalent geometry : angle 0.60627 (16873) hydrogen bonds : bond 0.18449 ( 548) hydrogen bonds : angle 6.10833 ( 1519) metal coordination : bond 0.00941 ( 8) metal coordination : angle 1.92398 ( 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 : 0.441 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.0946 time to fit residues: 7.4453 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 : 0.474 ------------------------------------------------------------------------------- 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: 10.0000 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... Flipped N/Q/H residues before XYZ refinement: B 678 GLN B 730 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.061007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.042060 restraints weight = 64069.147| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 3.57 r_work: 0.2901 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1073 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= 0.113 Angle : 0.508 9.044 16877 Z= 0.259 Chirality : 0.035 0.182 1917 Planarity : 0.003 0.031 1822 Dihedral : 18.283 158.806 2797 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.66 % Allowed : 8.33 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.25), residues: 1172 helix: 2.20 (0.22), residues: 582 sheet: 0.19 (0.44), residues: 140 loop : -0.44 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1308 TYR 0.019 0.001 TYR B 698 PHE 0.027 0.001 PHE A 970 TRP 0.007 0.001 TRP B 665 HIS 0.005 0.001 HIS B 730 Details of bonding type rmsd covalent geometry : bond 0.00224 (12153) covalent geometry : angle 0.50790 (16873) hydrogen bonds : bond 0.05019 ( 548) hydrogen bonds : angle 4.23911 ( 1519) metal coordination : bond 0.01014 ( 8) metal coordination : angle 1.61987 ( 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 54 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.454 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 52 average time/residue: 0.0906 time to fit residues: 7.9265 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 : 0.428 ------------------------------------------------------------------------------- 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: 2.9990 chunk 9 optimal weight: 20.0000 chunk 57 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 119 optimal weight: 8.9990 chunk 73 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 122 optimal weight: 20.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 495 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.059797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.040459 restraints weight = 64026.312| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 3.51 r_work: 0.2840 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 12161 Z= 0.243 Angle : 0.573 7.214 16877 Z= 0.291 Chirality : 0.038 0.207 1917 Planarity : 0.003 0.032 1822 Dihedral : 18.202 161.402 2797 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.66 % Allowed : 9.08 % Favored : 90.26 % 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 aren not related in a simple way. whole: 1.33 (0.25), residues: 1172 helix: 2.20 (0.22), residues: 583 sheet: -0.14 (0.43), residues: 136 loop : -0.53 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 801 TYR 0.021 0.002 TYR B 597 PHE 0.032 0.002 PHE A 970 TRP 0.009 0.001 TRP A1078 HIS 0.006 0.001 HIS B 730 Details of bonding type rmsd covalent geometry : bond 0.00549 (12153) covalent geometry : angle 0.57226 (16873) hydrogen bonds : bond 0.06452 ( 548) hydrogen bonds : angle 4.32983 ( 1519) metal coordination : bond 0.00683 ( 8) metal coordination : angle 2.19594 ( 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 54 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.445 Fit side-chains REVERT: A 861 MET cc_start: 0.9221 (mmm) cc_final: 0.8968 (mmm) REVERT: A 937 MET cc_start: 0.9046 (mmp) cc_final: 0.8436 (ptt) outliers start: 7 outliers final: 6 residues processed: 51 average time/residue: 0.0921 time to fit residues: 7.9441 Evaluate side-chains 53 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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 452 LEU Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 1121 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 114 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 119 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 = 0.3663 r_free = 0.3663 target = 0.060766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.041777 restraints weight = 63430.742| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 3.49 r_work: 0.2889 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12161 Z= 0.109 Angle : 0.473 8.111 16877 Z= 0.241 Chirality : 0.035 0.242 1917 Planarity : 0.003 0.030 1822 Dihedral : 18.053 162.200 2797 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.38 % Allowed : 9.74 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.25), residues: 1172 helix: 2.39 (0.22), residues: 583 sheet: -0.05 (0.44), residues: 136 loop : -0.48 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1178 TYR 0.018 0.001 TYR B 597 PHE 0.021 0.001 PHE A 970 TRP 0.005 0.001 TRP B 691 HIS 0.003 0.001 HIS A 630 Details of bonding type rmsd covalent geometry : bond 0.00233 (12153) covalent geometry : angle 0.47231 (16873) hydrogen bonds : bond 0.04444 ( 548) hydrogen bonds : angle 3.86901 ( 1519) metal coordination : bond 0.00791 ( 8) metal coordination : angle 1.51559 ( 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 51 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.439 Fit side-chains REVERT: A 861 MET cc_start: 0.9193 (mmm) cc_final: 0.8902 (mmm) outliers start: 4 outliers final: 3 residues processed: 50 average time/residue: 0.0925 time to fit residues: 7.7520 Evaluate side-chains 49 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.436 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 28 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 chunk 112 optimal weight: 7.9990 chunk 124 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 121 optimal weight: 40.0000 chunk 86 optimal weight: 0.8980 chunk 71 optimal weight: 0.0370 chunk 12 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 overall best weight: 2.5864 ------------------------------------------------------------------------------- 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 = 0.3640 r_free = 0.3640 target = 0.059958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.040677 restraints weight = 64244.198| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 3.52 r_work: 0.2848 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 12161 Z= 0.202 Angle : 0.536 8.926 16877 Z= 0.270 Chirality : 0.037 0.230 1917 Planarity : 0.003 0.031 1822 Dihedral : 18.064 164.865 2797 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.14 % Allowed : 10.31 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.45 (0.26), residues: 1172 helix: 2.36 (0.22), residues: 584 sheet: -0.19 (0.44), residues: 136 loop : -0.54 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1000 TYR 0.019 0.001 TYR B 597 PHE 0.026 0.001 PHE A 970 TRP 0.009 0.001 TRP A1078 HIS 0.005 0.001 HIS B 730 Details of bonding type rmsd covalent geometry : bond 0.00454 (12153) covalent geometry : angle 0.53552 (16873) hydrogen bonds : bond 0.05691 ( 548) hydrogen bonds : angle 4.03394 ( 1519) metal coordination : bond 0.00569 ( 8) metal coordination : angle 1.90085 ( 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 59 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.434 Fit side-chains REVERT: A 861 MET cc_start: 0.9233 (mmm) cc_final: 0.8933 (mmm) REVERT: A 937 MET cc_start: 0.9052 (OUTLIER) cc_final: 0.8187 (ptm) outliers start: 12 outliers final: 7 residues processed: 57 average time/residue: 0.0867 time to fit residues: 8.2919 Evaluate side-chains 55 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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 647 LEU Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 937 MET Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1281 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 90 optimal weight: 0.8980 chunk 95 optimal weight: 7.9990 chunk 26 optimal weight: 0.0070 chunk 44 optimal weight: 0.8980 chunk 33 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 overall best weight: 1.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.060097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.040905 restraints weight = 63621.459| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 3.49 r_work: 0.2857 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12161 Z= 0.152 Angle : 0.496 9.394 16877 Z= 0.251 Chirality : 0.036 0.222 1917 Planarity : 0.003 0.030 1822 Dihedral : 18.036 165.661 2797 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.85 % Allowed : 10.97 % 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 aren not related in a simple way. whole: 1.52 (0.26), residues: 1172 helix: 2.46 (0.22), residues: 582 sheet: -0.16 (0.45), residues: 133 loop : -0.54 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 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 0.004 0.001 HIS B 730 Details of bonding type rmsd covalent geometry : bond 0.00338 (12153) covalent geometry : angle 0.49533 (16873) hydrogen bonds : bond 0.04985 ( 548) hydrogen bonds : angle 3.88444 ( 1519) metal coordination : bond 0.00610 ( 8) metal coordination : angle 1.69920 ( 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 57 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.475 Fit side-chains REVERT: B 636 ASP cc_start: 0.7371 (t70) cc_final: 0.7152 (t70) REVERT: A 861 MET cc_start: 0.9224 (mmm) cc_final: 0.8878 (mmm) REVERT: A 937 MET cc_start: 0.9041 (mmp) cc_final: 0.8140 (ptm) outliers start: 9 outliers final: 8 residues processed: 56 average time/residue: 0.0877 time to fit residues: 8.3122 Evaluate side-chains 55 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 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 452 LEU Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 1121 VAL Chi-restraints excluded: chain A residue 1225 ILE Chi-restraints excluded: chain A residue 1281 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 78 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 102 optimal weight: 9.9990 chunk 115 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 40 optimal weight: 7.9990 chunk 67 optimal weight: 0.9990 chunk 74 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 816 GLN A 983 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.059069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.039753 restraints weight = 63804.856| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 3.50 r_work: 0.2813 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 12161 Z= 0.315 Angle : 0.626 10.215 16877 Z= 0.315 Chirality : 0.040 0.202 1917 Planarity : 0.004 0.032 1822 Dihedral : 18.146 167.294 2797 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.95 % Allowed : 11.45 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.26), residues: 1172 helix: 2.20 (0.22), residues: 582 sheet: -0.42 (0.44), residues: 134 loop : -0.67 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1000 TYR 0.019 0.002 TYR B 698 PHE 0.026 0.002 PHE A 970 TRP 0.012 0.001 TRP A1078 HIS 0.006 0.001 HIS B 730 Details of bonding type rmsd covalent geometry : bond 0.00708 (12153) covalent geometry : angle 0.62483 (16873) hydrogen bonds : bond 0.06719 ( 548) hydrogen bonds : angle 4.29090 ( 1519) metal coordination : bond 0.01046 ( 8) metal coordination : angle 2.30956 ( 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 58 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.455 Fit side-chains REVERT: B 605 ASP cc_start: 0.8540 (t0) cc_final: 0.8199 (t0) REVERT: A 635 MET cc_start: 0.8985 (tpp) cc_final: 0.8694 (tpt) REVERT: A 725 TRP cc_start: 0.8942 (OUTLIER) cc_final: 0.8079 (m-90) REVERT: A 861 MET cc_start: 0.9306 (mmm) cc_final: 0.9087 (mmm) REVERT: A 937 MET cc_start: 0.9158 (mmp) cc_final: 0.8248 (ptm) outliers start: 10 outliers final: 8 residues processed: 57 average time/residue: 0.1007 time to fit residues: 9.3225 Evaluate side-chains 57 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.462 ------------------------------------------------------------------------------- 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 725 TRP Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 1121 VAL 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 30 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 65 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 = 0.3641 r_free = 0.3641 target = 0.059962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.040833 restraints weight = 63696.440| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 3.45 r_work: 0.2853 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12161 Z= 0.144 Angle : 0.508 11.108 16877 Z= 0.255 Chirality : 0.036 0.187 1917 Planarity : 0.003 0.035 1822 Dihedral : 18.077 166.765 2797 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.85 % Allowed : 11.64 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.26), residues: 1172 helix: 2.41 (0.22), residues: 582 sheet: -0.38 (0.44), residues: 135 loop : -0.61 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 440 TYR 0.018 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 630 Details of bonding type rmsd covalent geometry : bond 0.00319 (12153) covalent geometry : angle 0.50757 (16873) hydrogen bonds : bond 0.04982 ( 548) hydrogen bonds : angle 3.89168 ( 1519) metal coordination : bond 0.00666 ( 8) metal coordination : angle 1.72837 ( 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 57 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.538 Fit side-chains REVERT: B 605 ASP cc_start: 0.8501 (t0) cc_final: 0.8158 (t0) REVERT: A 635 MET cc_start: 0.9008 (tpp) cc_final: 0.8749 (tpt) REVERT: A 725 TRP cc_start: 0.8970 (OUTLIER) cc_final: 0.8106 (m-90) outliers start: 9 outliers final: 7 residues processed: 55 average time/residue: 0.0928 time to fit residues: 8.5225 Evaluate side-chains 55 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain A residue 725 TRP Chi-restraints excluded: chain A residue 875 CYS Chi-restraints excluded: chain A residue 1121 VAL 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 56 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 105 optimal weight: 0.4980 chunk 45 optimal weight: 7.9990 chunk 124 optimal weight: 10.0000 chunk 96 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 = 0.3651 r_free = 0.3651 target = 0.060347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.041195 restraints weight = 64584.524| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 3.56 r_work: 0.2866 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12161 Z= 0.131 Angle : 0.503 11.248 16877 Z= 0.247 Chirality : 0.035 0.140 1917 Planarity : 0.003 0.034 1822 Dihedral : 17.998 168.222 2797 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.85 % Allowed : 12.20 % Favored : 86.94 % 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 aren not related in a simple way. whole: 1.55 (0.26), residues: 1172 helix: 2.53 (0.22), residues: 582 sheet: -0.29 (0.45), residues: 134 loop : -0.55 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 938 TYR 0.017 0.001 TYR B 597 PHE 0.019 0.001 PHE A 970 TRP 0.005 0.001 TRP A 725 HIS 0.003 0.001 HIS A 630 Details of bonding type rmsd covalent geometry : bond 0.00291 (12153) covalent geometry : angle 0.50251 (16873) hydrogen bonds : bond 0.04569 ( 548) hydrogen bonds : angle 3.72662 ( 1519) metal coordination : bond 0.00628 ( 8) metal coordination : angle 1.71310 ( 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 55 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.442 Fit side-chains REVERT: A 635 MET cc_start: 0.8991 (tpp) cc_final: 0.8737 (tpt) REVERT: A 725 TRP cc_start: 0.9033 (OUTLIER) cc_final: 0.8197 (m-90) REVERT: A 937 MET cc_start: 0.9016 (mmp) cc_final: 0.8123 (ptm) outliers start: 9 outliers final: 8 residues processed: 55 average time/residue: 0.0884 time to fit residues: 8.1745 Evaluate side-chains 54 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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 1121 VAL 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 10 optimal weight: 8.9990 chunk 23 optimal weight: 0.7980 chunk 115 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 73 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 chunk 31 optimal weight: 8.9990 chunk 89 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 124 optimal weight: 10.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.3654 r_free = 0.3654 target = 0.060395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.041348 restraints weight = 63860.251| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 3.53 r_work: 0.2872 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12161 Z= 0.119 Angle : 0.492 12.275 16877 Z= 0.243 Chirality : 0.035 0.138 1917 Planarity : 0.003 0.033 1822 Dihedral : 17.991 168.495 2797 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.66 % Allowed : 12.68 % Favored : 86.66 % 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 aren not related in a simple way. whole: 1.53 (0.26), residues: 1172 helix: 2.51 (0.22), residues: 582 sheet: -0.33 (0.44), residues: 135 loop : -0.53 (0.30), residues: 455 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 0.020 0.001 PHE A 970 TRP 0.005 0.001 TRP B 691 HIS 0.003 0.001 HIS A 630 Details of bonding type rmsd covalent geometry : bond 0.00264 (12153) covalent geometry : angle 0.49147 (16873) hydrogen bonds : bond 0.04439 ( 548) hydrogen bonds : angle 3.69011 ( 1519) metal coordination : bond 0.00611 ( 8) metal coordination : angle 1.60619 ( 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 52 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.467 Fit side-chains REVERT: A 725 TRP cc_start: 0.9032 (OUTLIER) cc_final: 0.8227 (m-90) REVERT: A 861 MET cc_start: 0.9174 (mmm) cc_final: 0.8878 (mmm) REVERT: A 937 MET cc_start: 0.9025 (mmp) cc_final: 0.8081 (ptm) outliers start: 7 outliers final: 6 residues processed: 52 average time/residue: 0.0907 time to fit residues: 7.9466 Evaluate side-chains 51 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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 1121 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 16 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 chunk 110 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 = 0.3636 r_free = 0.3636 target = 0.059850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.040724 restraints weight = 64837.587| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 3.53 r_work: 0.2845 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12161 Z= 0.182 Angle : 0.534 12.019 16877 Z= 0.263 Chirality : 0.036 0.145 1917 Planarity : 0.003 0.033 1822 Dihedral : 18.019 169.193 2797 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.95 % Allowed : 12.58 % Favored : 86.47 % 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 aren not related in a simple way. whole: 1.45 (0.26), residues: 1172 helix: 2.44 (0.22), residues: 582 sheet: -0.39 (0.44), residues: 134 loop : -0.57 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1000 TYR 0.017 0.001 TYR B 597 PHE 0.021 0.001 PHE A 970 TRP 0.008 0.001 TRP A1078 HIS 0.003 0.001 HIS A 869 Details of bonding type rmsd covalent geometry : bond 0.00409 (12153) covalent geometry : angle 0.53363 (16873) hydrogen bonds : bond 0.05275 ( 548) hydrogen bonds : angle 3.84713 ( 1519) metal coordination : bond 0.00550 ( 8) metal coordination : angle 1.77687 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3639.99 seconds wall clock time: 63 minutes 3.12 seconds (3783.12 seconds total)