Starting phenix.real_space_refine on Wed Jul 30 16:18:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k2w_61999/07_2025/9k2w_61999.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k2w_61999/07_2025/9k2w_61999.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k2w_61999/07_2025/9k2w_61999.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k2w_61999/07_2025/9k2w_61999.map" model { file = "/net/cci-nas-00/data/ceres_data/9k2w_61999/07_2025/9k2w_61999.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k2w_61999/07_2025/9k2w_61999.cif" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 81 5.16 5 C 7885 2.51 5 N 2151 2.21 5 O 2319 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12438 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4311 Classifications: {'peptide': 524} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 496} Chain: "B" Number of atoms: 8125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8125 Classifications: {'peptide': 1035} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 21} Link IDs: {'CIS': 4, 'PTRANS': 66, 'TRANS': 964} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 6, 'ARG:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 85 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6515 SG CYS B 820 37.303 32.655 34.153 1.00131.48 S ATOM 7103 SG CYS B 893 40.493 30.762 35.132 1.00157.83 S ATOM 7122 SG CYS B 896 37.038 29.570 36.307 1.00146.21 S ATOM 11435 SG CYS B1476 32.264 102.957 33.164 1.00172.24 S ATOM 11447 SG CYS B1478 30.941 99.333 33.096 1.00165.22 S ATOM 11492 SG CYS B1485 34.398 100.121 31.619 1.00164.54 S Time building chain proxies: 9.08, per 1000 atoms: 0.73 Number of scatterers: 12438 At special positions: 0 Unit cell: (88.3712, 146.365, 135.318, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 81 16.00 O 2319 8.00 N 2151 7.00 C 7885 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.10 Conformation dependent library (CDL) restraints added in 2.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1701 " pdb="ZN ZN B1701 " - pdb=" NE2 HIS B 793 " pdb="ZN ZN B1701 " - pdb=" SG CYS B 820 " pdb="ZN ZN B1701 " - pdb=" SG CYS B 896 " pdb="ZN ZN B1701 " - pdb=" SG CYS B 893 " pdb=" ZN B1702 " pdb="ZN ZN B1702 " - pdb=" NE2 HIS B1502 " pdb="ZN ZN B1702 " - pdb=" SG CYS B1478 " pdb="ZN ZN B1702 " - pdb=" SG CYS B1485 " pdb="ZN ZN B1702 " - pdb=" SG CYS B1476 " Number of angles added : 6 3086 Ramachandran restraints generated. 1543 Oldfield, 0 Emsley, 1543 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2938 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 15 sheets defined 32.6% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.17 Creating SS restraints... Processing helix chain 'A' and resid 560 through 562 No H-bonds generated for 'chain 'A' and resid 560 through 562' Processing helix chain 'A' and resid 571 through 575 Processing helix chain 'A' and resid 601 through 614 Processing helix chain 'A' and resid 647 through 652 Processing helix chain 'A' and resid 666 through 671 Processing helix chain 'A' and resid 712 through 724 removed outlier: 3.575A pdb=" N LEU A 716 " --> pdb=" O LYS A 712 " (cutoff:3.500A) Proline residue: A 718 - end of helix Processing helix chain 'A' and resid 752 through 757 Processing helix chain 'A' and resid 772 through 778 Processing helix chain 'A' and resid 782 through 792 Processing helix chain 'A' and resid 818 through 831 Processing helix chain 'A' and resid 833 through 835 No H-bonds generated for 'chain 'A' and resid 833 through 835' Processing helix chain 'A' and resid 860 through 866 removed outlier: 3.585A pdb=" N LEU A 864 " --> pdb=" O THR A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 890 Processing helix chain 'A' and resid 917 through 929 Processing helix chain 'A' and resid 958 through 962 removed outlier: 3.515A pdb=" N LEU A 962 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 981 removed outlier: 4.733A pdb=" N ASP A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1029 removed outlier: 3.557A pdb=" N VAL A1020 " --> pdb=" O HIS A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1038 Processing helix chain 'A' and resid 1052 through 1056 removed outlier: 3.896A pdb=" N TYR A1056 " --> pdb=" O GLU A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1059 through 1063 Processing helix chain 'B' and resid 495 through 519 Processing helix chain 'B' and resid 523 through 534 Processing helix chain 'B' and resid 546 through 568 removed outlier: 5.827A pdb=" N GLN B 555 " --> pdb=" O LEU B 551 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N PHE B 556 " --> pdb=" O ARG B 552 " (cutoff:3.500A) WARNING: missing atoms! removed outlier: 4.039A pdb=" N GLY B 568 " --> pdb=" O TYR B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 577 Processing helix chain 'B' and resid 578 through 588 Processing helix chain 'B' and resid 621 through 632 Processing helix chain 'B' and resid 633 through 637 removed outlier: 4.067A pdb=" N ILE B 636 " --> pdb=" O ALA B 633 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU B 637 " --> pdb=" O GLU B 634 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 633 through 637' Processing helix chain 'B' and resid 656 through 661 Processing helix chain 'B' and resid 686 through 690 removed outlier: 3.966A pdb=" N ARG B 690 " --> pdb=" O GLN B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 704 Processing helix chain 'B' and resid 801 through 803 No H-bonds generated for 'chain 'B' and resid 801 through 803' Processing helix chain 'B' and resid 805 through 809 Processing helix chain 'B' and resid 826 through 828 No H-bonds generated for 'chain 'B' and resid 826 through 828' Processing helix chain 'B' and resid 842 through 846 Processing helix chain 'B' and resid 893 through 907 Processing helix chain 'B' and resid 971 through 975 Processing helix chain 'B' and resid 1030 through 1035 removed outlier: 3.682A pdb=" N TYR B1035 " --> pdb=" O PRO B1032 " (cutoff:3.500A) Processing helix chain 'B' and resid 1054 through 1056 No H-bonds generated for 'chain 'B' and resid 1054 through 1056' Processing helix chain 'B' and resid 1071 through 1079 removed outlier: 4.137A pdb=" N GLY B1079 " --> pdb=" O TYR B1075 " (cutoff:3.500A) Processing helix chain 'B' and resid 1100 through 1104 Processing helix chain 'B' and resid 1149 through 1159 Processing helix chain 'B' and resid 1170 through 1181 Processing helix chain 'B' and resid 1190 through 1201 Processing helix chain 'B' and resid 1236 through 1245 removed outlier: 3.777A pdb=" N ASN B1245 " --> pdb=" O SER B1241 " (cutoff:3.500A) Processing helix chain 'B' and resid 1246 through 1259 removed outlier: 3.812A pdb=" N SER B1250 " --> pdb=" O SER B1246 " (cutoff:3.500A) Processing helix chain 'B' and resid 1270 through 1272 No H-bonds generated for 'chain 'B' and resid 1270 through 1272' Processing helix chain 'B' and resid 1277 through 1290 Processing helix chain 'B' and resid 1302 through 1305 removed outlier: 4.104A pdb=" N GLY B1305 " --> pdb=" O GLY B1302 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1302 through 1305' Processing helix chain 'B' and resid 1335 through 1339 Processing helix chain 'B' and resid 1367 through 1372 removed outlier: 3.821A pdb=" N SER B1372 " --> pdb=" O ARG B1368 " (cutoff:3.500A) Processing helix chain 'B' and resid 1394 through 1402 Processing helix chain 'B' and resid 1418 through 1427 Processing helix chain 'B' and resid 1435 through 1439 Processing helix chain 'B' and resid 1476 through 1480 Processing helix chain 'B' and resid 1498 through 1503 Processing helix chain 'B' and resid 1507 through 1511 Processing helix chain 'B' and resid 1549 through 1558 Processing helix chain 'B' and resid 1568 through 1579 Processing helix chain 'B' and resid 1581 through 1603 removed outlier: 3.526A pdb=" N CYS B1595 " --> pdb=" O GLU B1591 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N SER B1603 " --> pdb=" O LYS B1599 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 592 through 597 removed outlier: 9.183A pdb=" N TRP A 658 " --> pdb=" O TYR A 564 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLN A 566 " --> pdb=" O TRP A 658 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N ILE A 660 " --> pdb=" O GLN A 566 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLN A 568 " --> pdb=" O ILE A 660 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N LEU A 662 " --> pdb=" O GLN A 568 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N VAL A 570 " --> pdb=" O LEU A 662 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N THR A 664 " --> pdb=" O VAL A 570 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N THR A 659 " --> pdb=" O MET A 625 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 698 through 708 removed outlier: 4.929A pdb=" N LEU A 689 " --> pdb=" O CYS A 702 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N HIS A 704 " --> pdb=" O LEU A 687 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU A 687 " --> pdb=" O HIS A 704 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N TYR A 706 " --> pdb=" O VAL A 685 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL A 685 " --> pdb=" O TYR A 706 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N ILE A 766 " --> pdb=" O MET A 686 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N PHE A 688 " --> pdb=" O ILE A 766 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N PHE A 768 " --> pdb=" O PHE A 688 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LYS A 690 " --> pdb=" O PHE A 768 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N LYS A 770 " --> pdb=" O LYS A 690 " (cutoff:3.500A) removed outlier: 8.728A pdb=" N TYR A 692 " --> pdb=" O LYS A 770 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ILE A 765 " --> pdb=" O GLU A 737 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LEU A 742 " --> pdb=" O VAL A 738 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 809 through 814 removed outlier: 8.197A pdb=" N LYS A 875 " --> pdb=" O SER A 842 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SER A 842 " --> pdb=" O LYS A 875 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N PHE A 839 " --> pdb=" O PRO A 852 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N LYS A 841 " --> pdb=" O GLY A 850 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 905 through 910 removed outlier: 7.750A pdb=" N LYS A 895 " --> pdb=" O PHE A 970 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N ILE A 972 " --> pdb=" O LYS A 895 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ILE A 897 " --> pdb=" O ILE A 972 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N GLU A 974 " --> pdb=" O ILE A 897 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N LEU A 899 " --> pdb=" O GLU A 974 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N LEU A 941 " --> pdb=" O VAL A 952 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N VAL A 952 " --> pdb=" O LEU A 941 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLU A 943 " --> pdb=" O ILE A 950 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1002 through 1011 removed outlier: 7.825A pdb=" N ILE A1005 " --> pdb=" O HIS A 994 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N HIS A 994 " --> pdb=" O ILE A1005 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N LEU A1077 " --> pdb=" O LEU A 989 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N THR A 991 " --> pdb=" O LEU A1077 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N LEU A1079 " --> pdb=" O THR A 991 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ALA A 993 " --> pdb=" O LEU A1079 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 732 through 734 removed outlier: 4.575A pdb=" N VAL B 750 " --> pdb=" O VAL B 734 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 739 through 740 removed outlier: 4.506A pdb=" N LEU B 782 " --> pdb=" O LYS B 748 " (cutoff:3.500A) removed outlier: 10.648A pdb=" N TYR B 775 " --> pdb=" O ALA B 799 " (cutoff:3.500A) removed outlier: 9.145A pdb=" N ALA B 799 " --> pdb=" O TYR B 775 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ALA B 777 " --> pdb=" O PHE B 797 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N PHE B 797 " --> pdb=" O ALA B 777 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N VAL B 779 " --> pdb=" O HIS B 795 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N HIS B 795 " --> pdb=" O VAL B 779 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA B 781 " --> pdb=" O HIS B 793 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N GLU B 819 " --> pdb=" O TRP B 796 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N CYS B 798 " --> pdb=" O VAL B 817 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N VAL B 817 " --> pdb=" O CYS B 798 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N LEU B 814 " --> pdb=" O LEU B 867 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N TYR B 869 " --> pdb=" O LEU B 814 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N LEU B 816 " --> pdb=" O TYR B 869 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ILE B 835 " --> pdb=" O TYR B 865 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N LEU B 867 " --> pdb=" O ILE B 835 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 830 through 832 removed outlier: 3.833A pdb=" N CYS B 762 " --> pdb=" O VAL B 832 " (cutoff:3.500A) removed outlier: 10.648A pdb=" N TYR B 775 " --> pdb=" O ALA B 799 " (cutoff:3.500A) removed outlier: 9.145A pdb=" N ALA B 799 " --> pdb=" O TYR B 775 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ALA B 777 " --> pdb=" O PHE B 797 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N PHE B 797 " --> pdb=" O ALA B 777 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N VAL B 779 " --> pdb=" O HIS B 795 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N HIS B 795 " --> pdb=" O VAL B 779 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA B 781 " --> pdb=" O HIS B 793 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N GLU B 819 " --> pdb=" O TRP B 796 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N CYS B 798 " --> pdb=" O VAL B 817 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N VAL B 817 " --> pdb=" O CYS B 798 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N LEU B 814 " --> pdb=" O LEU B 867 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N TYR B 869 " --> pdb=" O LEU B 814 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N LEU B 816 " --> pdb=" O TYR B 869 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 909 through 916 removed outlier: 7.773A pdb=" N ARG B 909 " --> pdb=" O LYS B 928 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N LYS B 928 " --> pdb=" O ARG B 909 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N LEU B 911 " --> pdb=" O ALA B 926 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ALA B 926 " --> pdb=" O LEU B 911 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N GLN B 913 " --> pdb=" O TYR B 924 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N TYR B 924 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE B 999 " --> pdb=" O TYR B 923 " (cutoff:3.500A) removed outlier: 9.605A pdb=" N SER B 925 " --> pdb=" O LYS B 997 " (cutoff:3.500A) removed outlier: 12.016A pdb=" N LYS B 997 " --> pdb=" O SER B 925 " (cutoff:3.500A) removed outlier: 15.503A pdb=" N THR B 927 " --> pdb=" O ARG B 995 " (cutoff:3.500A) removed outlier: 17.167A pdb=" N ARG B 995 " --> pdb=" O THR B 927 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 909 through 916 removed outlier: 7.773A pdb=" N ARG B 909 " --> pdb=" O LYS B 928 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N LYS B 928 " --> pdb=" O ARG B 909 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N LEU B 911 " --> pdb=" O ALA B 926 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ALA B 926 " --> pdb=" O LEU B 911 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N GLN B 913 " --> pdb=" O TYR B 924 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N TYR B 924 " --> pdb=" O GLN B 913 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 920 through 928 current: chain 'B' and resid 1041 through 1052 removed outlier: 8.844A pdb=" N PHE B1083 " --> pdb=" O ARG B1059 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N THR B1061 " --> pdb=" O PHE B1083 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N PHE B1085 " --> pdb=" O THR B1061 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLU B1063 " --> pdb=" O PHE B1085 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLY B1058 " --> pdb=" O TYR B 940 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 1088 through 1090 Processing sheet with id=AB3, first strand: chain 'B' and resid 1185 through 1187 removed outlier: 9.006A pdb=" N THR B1185 " --> pdb=" O ASP B1162 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU B1164 " --> pdb=" O THR B1185 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N PHE B1187 " --> pdb=" O LEU B1164 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ALA B1166 " --> pdb=" O PHE B1187 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU B1139 " --> pdb=" O ASP B1162 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU B1164 " --> pdb=" O LEU B1139 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N THR B1141 " --> pdb=" O LEU B1164 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ALA B1166 " --> pdb=" O THR B1141 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ASP B1143 " --> pdb=" O ALA B1166 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 1343 through 1345 Processing sheet with id=AB5, first strand: chain 'B' and resid 1385 through 1386 Processing sheet with id=AB6, first strand: chain 'B' and resid 1444 through 1445 removed outlier: 3.846A pdb=" N VAL B1444 " --> pdb=" O ALA B1452 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA B1452 " --> pdb=" O VAL B1444 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 428 hydrogen bonds defined for protein. 1113 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.02 Time building geometry restraints manager: 3.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4018 1.34 - 1.46: 2218 1.46 - 1.58: 6369 1.58 - 1.70: 0 1.70 - 1.82: 123 Bond restraints: 12728 Sorted by residual: bond pdb=" CA GLN A1013 " pdb=" C GLN A1013 " ideal model delta sigma weight residual 1.521 1.488 0.033 1.17e-02 7.31e+03 8.03e+00 bond pdb=" CG GLU A 737 " pdb=" CD GLU A 737 " ideal model delta sigma weight residual 1.516 1.466 0.050 2.50e-02 1.60e+03 4.06e+00 bond pdb=" CA GLN A 568 " pdb=" CB GLN A 568 " ideal model delta sigma weight residual 1.527 1.506 0.021 1.30e-02 5.92e+03 2.69e+00 bond pdb=" SD MET A1021 " pdb=" CE MET A1021 " ideal model delta sigma weight residual 1.791 1.751 0.040 2.50e-02 1.60e+03 2.59e+00 bond pdb=" CG LEU A 602 " pdb=" CD2 LEU A 602 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.08e+00 ... (remaining 12723 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.35: 17111 4.35 - 8.71: 90 8.71 - 13.06: 13 13.06 - 17.41: 0 17.41 - 21.77: 1 Bond angle restraints: 17215 Sorted by residual: angle pdb=" C GLU B 711 " pdb=" N MET B 712 " pdb=" CA MET B 712 " ideal model delta sigma weight residual 121.70 134.70 -13.00 1.80e+00 3.09e-01 5.22e+01 angle pdb=" CA LEU A 717 " pdb=" CB LEU A 717 " pdb=" CG LEU A 717 " ideal model delta sigma weight residual 116.30 138.07 -21.77 3.50e+00 8.16e-02 3.87e+01 angle pdb=" CA MET A 613 " pdb=" CB MET A 613 " pdb=" CG MET A 613 " ideal model delta sigma weight residual 114.10 126.19 -12.09 2.00e+00 2.50e-01 3.65e+01 angle pdb=" C VAL A 952 " pdb=" N HIS A 953 " pdb=" CA HIS A 953 " ideal model delta sigma weight residual 122.77 115.83 6.94 1.33e+00 5.65e-01 2.72e+01 angle pdb=" N ILE A1030 " pdb=" CA ILE A1030 " pdb=" C ILE A1030 " ideal model delta sigma weight residual 109.34 98.75 10.59 2.08e+00 2.31e-01 2.59e+01 ... (remaining 17210 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 6707 17.96 - 35.91: 766 35.91 - 53.86: 195 53.86 - 71.82: 45 71.82 - 89.77: 29 Dihedral angle restraints: 7742 sinusoidal: 3194 harmonic: 4548 Sorted by residual: dihedral pdb=" CA TYR B1405 " pdb=" C TYR B1405 " pdb=" N GLN B1406 " pdb=" CA GLN B1406 " ideal model delta harmonic sigma weight residual 180.00 150.86 29.14 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA GLN A1031 " pdb=" C GLN A1031 " pdb=" N GLU A1032 " pdb=" CA GLU A1032 " ideal model delta harmonic sigma weight residual -180.00 -157.37 -22.63 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" C ILE A1051 " pdb=" N ILE A1051 " pdb=" CA ILE A1051 " pdb=" CB ILE A1051 " ideal model delta harmonic sigma weight residual -122.00 -132.37 10.37 0 2.50e+00 1.60e-01 1.72e+01 ... (remaining 7739 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1608 0.073 - 0.145: 206 0.145 - 0.218: 22 0.218 - 0.291: 3 0.291 - 0.364: 1 Chirality restraints: 1840 Sorted by residual: chirality pdb=" CG LEU A 687 " pdb=" CB LEU A 687 " pdb=" CD1 LEU A 687 " pdb=" CD2 LEU A 687 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" CB THR B1188 " pdb=" CA THR B1188 " pdb=" OG1 THR B1188 " pdb=" CG2 THR B1188 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CA GLU A 737 " pdb=" N GLU A 737 " pdb=" C GLU A 737 " pdb=" CB GLU A 737 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 1837 not shown) Planarity restraints: 2262 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS A1012 " 0.038 2.00e-02 2.50e+03 7.69e-02 5.91e+01 pdb=" C HIS A1012 " -0.133 2.00e-02 2.50e+03 pdb=" O HIS A1012 " 0.050 2.00e-02 2.50e+03 pdb=" N GLN A1013 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 568 " 0.020 2.00e-02 2.50e+03 4.00e-02 1.60e+01 pdb=" C GLN A 568 " -0.069 2.00e-02 2.50e+03 pdb=" O GLN A 568 " 0.026 2.00e-02 2.50e+03 pdb=" N ILE A 569 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A1062 " 0.019 2.00e-02 2.50e+03 3.81e-02 1.45e+01 pdb=" C ASP A1062 " -0.066 2.00e-02 2.50e+03 pdb=" O ASP A1062 " 0.025 2.00e-02 2.50e+03 pdb=" N PHE A1063 " 0.022 2.00e-02 2.50e+03 ... (remaining 2259 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 226 2.67 - 3.23: 11866 3.23 - 3.78: 18885 3.78 - 4.34: 25207 4.34 - 4.90: 40675 Nonbonded interactions: 96859 Sorted by model distance: nonbonded pdb=" NE2 GLN A 626 " pdb=" O ALA A 627 " model vdw 2.112 3.120 nonbonded pdb=" O HIS A1016 " pdb=" N GLU A1019 " model vdw 2.125 3.120 nonbonded pdb=" O PRO B1260 " pdb=" OH TYR B1292 " model vdw 2.145 3.040 nonbonded pdb=" OD1 ASN A 986 " pdb=" N GLU A 987 " model vdw 2.156 3.120 nonbonded pdb=" O LEU A 597 " pdb=" OG SER A 600 " model vdw 2.163 3.040 ... (remaining 96854 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 group one per residue 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: 65.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.030 Check model and map are aligned: 0.130 Set scattering table: 0.200 Process input model: 42.860 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 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 : 0.003 0.063 12736 Z= 0.168 Angle : 0.894 21.768 17221 Z= 0.491 Chirality : 0.050 0.364 1840 Planarity : 0.005 0.077 2262 Dihedral : 17.200 89.775 4804 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.22 % Allowed : 24.05 % Favored : 75.72 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.21), residues: 1543 helix: 0.06 (0.27), residues: 395 sheet: -0.25 (0.29), residues: 293 loop : 0.07 (0.22), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1076 HIS 0.017 0.002 HIS A1012 PHE 0.047 0.002 PHE A 605 TYR 0.029 0.002 TYR A 857 ARG 0.006 0.000 ARG A 854 Details of bonding type rmsd hydrogen bonds : bond 0.14914 ( 418) hydrogen bonds : angle 7.00009 ( 1113) metal coordination : bond 0.00548 ( 8) metal coordination : angle 1.36034 ( 6) covalent geometry : bond 0.00338 (12728) covalent geometry : angle 0.89419 (17215) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3086 Ramachandran restraints generated. 1543 Oldfield, 0 Emsley, 1543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3086 Ramachandran restraints generated. 1543 Oldfield, 0 Emsley, 1543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 129 time to evaluate : 1.692 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL B 561 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 625 MET cc_start: 0.5071 (tpp) cc_final: 0.4130 (tmm) REVERT: A 857 TYR cc_start: 0.7909 (t80) cc_final: 0.7468 (t80) REVERT: B 557 VAL cc_start: 0.8669 (p) cc_final: 0.8329 (p) REVERT: B 712 MET cc_start: 0.5689 (mmm) cc_final: 0.4849 (mmt) REVERT: B 997 LYS cc_start: 0.8878 (mtpp) cc_final: 0.8489 (ttmm) outliers start: 3 outliers final: 2 residues processed: 131 average time/residue: 0.3560 time to fit residues: 67.9930 Evaluate side-chains 121 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 119 time to evaluate : 2.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 561 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 5.9990 chunk 117 optimal weight: 0.0770 chunk 65 optimal weight: 9.9990 chunk 40 optimal weight: 0.5980 chunk 79 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 121 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 73 optimal weight: 30.0000 chunk 90 optimal weight: 8.9990 chunk 140 optimal weight: 9.9990 overall best weight: 1.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 HIS A 815 ASN A 818 ASN A 821 GLN A 855 HIS A1059 ASN ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 GLN B 790 GLN B 888 ASN B1026 ASN B1427 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.169814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.114221 restraints weight = 21290.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.110636 restraints weight = 11667.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.112039 restraints weight = 12248.732| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.0967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12736 Z= 0.181 Angle : 0.625 13.591 17221 Z= 0.321 Chirality : 0.044 0.166 1840 Planarity : 0.005 0.063 2262 Dihedral : 4.473 31.419 1706 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.38 % Allowed : 22.35 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.22), residues: 1543 helix: 0.58 (0.26), residues: 401 sheet: -0.03 (0.29), residues: 312 loop : 0.21 (0.23), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1076 HIS 0.006 0.001 HIS B 719 PHE 0.018 0.002 PHE A 867 TYR 0.011 0.001 TYR B 969 ARG 0.006 0.000 ARG A 891 Details of bonding type rmsd hydrogen bonds : bond 0.04531 ( 418) hydrogen bonds : angle 5.29260 ( 1113) metal coordination : bond 0.00954 ( 8) metal coordination : angle 2.01879 ( 6) covalent geometry : bond 0.00421 (12728) covalent geometry : angle 0.62425 (17215) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3086 Ramachandran restraints generated. 1543 Oldfield, 0 Emsley, 1543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3086 Ramachandran restraints generated. 1543 Oldfield, 0 Emsley, 1543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 120 time to evaluate : 2.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "VAL B 561 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 720 MET cc_start: 0.8027 (mmp) cc_final: 0.7760 (ptt) REVERT: A 857 TYR cc_start: 0.8108 (t80) cc_final: 0.7842 (t80) REVERT: A 883 MET cc_start: 0.7897 (pmm) cc_final: 0.7527 (pmm) REVERT: B 712 MET cc_start: 0.6272 (mmm) cc_final: 0.5450 (mmt) REVERT: B 976 TYR cc_start: 0.7137 (OUTLIER) cc_final: 0.6630 (t80) REVERT: B 997 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8222 (ttmm) REVERT: B 1425 MET cc_start: 0.8826 (ptt) cc_final: 0.8493 (ptt) REVERT: B 1563 TYR cc_start: 0.8744 (t80) cc_final: 0.8351 (t80) REVERT: B 1602 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6341 (tm-30) outliers start: 32 outliers final: 14 residues processed: 143 average time/residue: 0.3143 time to fit residues: 68.3748 Evaluate side-chains 130 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 2.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 591 TYR Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 976 TYR Chi-restraints excluded: chain B residue 997 LYS Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1136 LEU Chi-restraints excluded: chain B residue 1194 LEU Chi-restraints excluded: chain B residue 1219 MET Chi-restraints excluded: chain B residue 1272 VAL Chi-restraints excluded: chain B residue 1344 VAL Chi-restraints excluded: chain B residue 1428 ILE Chi-restraints excluded: chain B residue 1539 VAL Chi-restraints excluded: chain B residue 1550 VAL Chi-restraints excluded: chain B residue 1602 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 126 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 150 optimal weight: 0.5980 chunk 148 optimal weight: 0.0570 chunk 108 optimal weight: 0.0050 chunk 16 optimal weight: 30.0000 chunk 139 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 chunk 45 optimal weight: 50.0000 chunk 119 optimal weight: 4.9990 chunk 2 optimal weight: 0.0980 overall best weight: 0.2912 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 566 GLN ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.173704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.110498 restraints weight = 21399.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.110291 restraints weight = 12163.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.111216 restraints weight = 8525.122| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12736 Z= 0.096 Angle : 0.551 11.569 17221 Z= 0.277 Chirality : 0.042 0.159 1840 Planarity : 0.004 0.062 2262 Dihedral : 4.033 28.618 1704 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.78 % Allowed : 23.31 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.22), residues: 1543 helix: 0.94 (0.27), residues: 397 sheet: 0.15 (0.29), residues: 316 loop : 0.34 (0.23), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 783 HIS 0.006 0.001 HIS B 719 PHE 0.013 0.001 PHE B1251 TYR 0.013 0.001 TYR B 827 ARG 0.003 0.000 ARG A 854 Details of bonding type rmsd hydrogen bonds : bond 0.03539 ( 418) hydrogen bonds : angle 4.78708 ( 1113) metal coordination : bond 0.00473 ( 8) metal coordination : angle 1.59297 ( 6) covalent geometry : bond 0.00208 (12728) covalent geometry : angle 0.54982 (17215) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3086 Ramachandran restraints generated. 1543 Oldfield, 0 Emsley, 1543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3086 Ramachandran restraints generated. 1543 Oldfield, 0 Emsley, 1543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 737 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.6541 (pm20) REVERT: A 857 TYR cc_start: 0.8010 (t80) cc_final: 0.7722 (t80) REVERT: A 883 MET cc_start: 0.7861 (pmm) cc_final: 0.7362 (pmm) REVERT: B 507 TYR cc_start: 0.8792 (t80) cc_final: 0.8515 (t80) REVERT: B 514 GLU cc_start: 0.8291 (mp0) cc_final: 0.7817 (mt-10) REVERT: B 997 LYS cc_start: 0.8531 (mtpp) cc_final: 0.8319 (ttmm) REVERT: B 1232 MET cc_start: 0.7816 (mtp) cc_final: 0.7602 (ttp) REVERT: B 1236 ASN cc_start: 0.8667 (t0) cc_final: 0.8377 (t0) REVERT: B 1445 ARG cc_start: 0.8033 (tpp80) cc_final: 0.7525 (tpp80) REVERT: B 1563 TYR cc_start: 0.8701 (t80) cc_final: 0.8482 (t80) outliers start: 24 outliers final: 11 residues processed: 145 average time/residue: 0.2340 time to fit residues: 50.3572 Evaluate side-chains 127 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 591 TYR Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 737 GLU Chi-restraints excluded: chain A residue 821 GLN Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 1136 LEU Chi-restraints excluded: chain B residue 1185 THR Chi-restraints excluded: chain B residue 1194 LEU Chi-restraints excluded: chain B residue 1235 PHE Chi-restraints excluded: chain B residue 1344 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 53 optimal weight: 9.9990 chunk 43 optimal weight: 0.9980 chunk 110 optimal weight: 5.9990 chunk 94 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 chunk 115 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 20 optimal weight: 10.0000 chunk 120 optimal weight: 0.5980 chunk 106 optimal weight: 0.9980 overall best weight: 1.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 566 GLN A 654 ASN A 683 HIS ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1308 GLN B1573 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.170666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.105319 restraints weight = 21324.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.106147 restraints weight = 12445.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.107908 restraints weight = 8003.426| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12736 Z= 0.166 Angle : 0.570 11.168 17221 Z= 0.286 Chirality : 0.043 0.183 1840 Planarity : 0.004 0.060 2262 Dihedral : 4.028 28.705 1703 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.60 % Allowed : 23.01 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.22), residues: 1543 helix: 1.04 (0.27), residues: 397 sheet: 0.13 (0.29), residues: 317 loop : 0.35 (0.23), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 783 HIS 0.005 0.001 HIS B 719 PHE 0.018 0.001 PHE B 515 TYR 0.010 0.001 TYR B1084 ARG 0.004 0.000 ARG A 634 Details of bonding type rmsd hydrogen bonds : bond 0.03692 ( 418) hydrogen bonds : angle 4.76434 ( 1113) metal coordination : bond 0.00832 ( 8) metal coordination : angle 1.65502 ( 6) covalent geometry : bond 0.00391 (12728) covalent geometry : angle 0.56917 (17215) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3086 Ramachandran restraints generated. 1543 Oldfield, 0 Emsley, 1543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3086 Ramachandran restraints generated. 1543 Oldfield, 0 Emsley, 1543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 120 time to evaluate : 1.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 672 SER cc_start: 0.6333 (OUTLIER) cc_final: 0.5732 (t) REVERT: A 691 MET cc_start: 0.7937 (tpt) cc_final: 0.7538 (tpt) REVERT: A 737 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.6532 (pm20) REVERT: A 821 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.7518 (mp10) REVERT: A 857 TYR cc_start: 0.8274 (t80) cc_final: 0.7956 (t80) REVERT: A 883 MET cc_start: 0.7931 (pmm) cc_final: 0.7386 (pmm) REVERT: A 894 PHE cc_start: 0.6826 (OUTLIER) cc_final: 0.5823 (t80) REVERT: B 507 TYR cc_start: 0.8880 (t80) cc_final: 0.8491 (t80) REVERT: B 976 TYR cc_start: 0.7024 (OUTLIER) cc_final: 0.6569 (t80) REVERT: B 997 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8414 (ttmm) REVERT: B 1236 ASN cc_start: 0.8639 (t0) cc_final: 0.8356 (t0) REVERT: B 1445 ARG cc_start: 0.8091 (tpp80) cc_final: 0.7696 (tpp80) REVERT: B 1563 TYR cc_start: 0.8781 (t80) cc_final: 0.8519 (t80) outliers start: 35 outliers final: 18 residues processed: 146 average time/residue: 0.2432 time to fit residues: 53.6505 Evaluate side-chains 137 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 591 TYR Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 737 GLU Chi-restraints excluded: chain A residue 821 GLN Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 976 TYR Chi-restraints excluded: chain B residue 997 LYS Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1136 LEU Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain B residue 1185 THR Chi-restraints excluded: chain B residue 1194 LEU Chi-restraints excluded: chain B residue 1219 MET Chi-restraints excluded: chain B residue 1235 PHE Chi-restraints excluded: chain B residue 1272 VAL Chi-restraints excluded: chain B residue 1344 VAL Chi-restraints excluded: chain B residue 1539 VAL Chi-restraints excluded: chain B residue 1550 VAL Chi-restraints excluded: chain B residue 1573 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 75 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 100 optimal weight: 0.5980 chunk 142 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 69 optimal weight: 0.0570 chunk 93 optimal weight: 0.8980 chunk 13 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 chunk 15 optimal weight: 20.0000 overall best weight: 1.3102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.171168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.105974 restraints weight = 21191.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.106769 restraints weight = 11896.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.107794 restraints weight = 7939.197| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 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 : 0.003 0.036 12736 Z= 0.132 Angle : 0.555 10.626 17221 Z= 0.277 Chirality : 0.042 0.194 1840 Planarity : 0.004 0.058 2262 Dihedral : 3.983 29.118 1703 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.45 % Allowed : 23.31 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.22), residues: 1543 helix: 1.01 (0.27), residues: 403 sheet: 0.15 (0.29), residues: 314 loop : 0.34 (0.23), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 783 HIS 0.007 0.001 HIS B1573 PHE 0.013 0.001 PHE B1274 TYR 0.011 0.001 TYR B 775 ARG 0.006 0.000 ARG B1238 Details of bonding type rmsd hydrogen bonds : bond 0.03539 ( 418) hydrogen bonds : angle 4.68439 ( 1113) metal coordination : bond 0.00660 ( 8) metal coordination : angle 1.51554 ( 6) covalent geometry : bond 0.00308 (12728) covalent geometry : angle 0.55464 (17215) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3086 Ramachandran restraints generated. 1543 Oldfield, 0 Emsley, 1543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3086 Ramachandran restraints generated. 1543 Oldfield, 0 Emsley, 1543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 121 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 672 SER cc_start: 0.6689 (OUTLIER) cc_final: 0.6364 (t) REVERT: A 737 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.6527 (pm20) REVERT: A 821 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.7747 (mp10) REVERT: A 857 TYR cc_start: 0.8298 (t80) cc_final: 0.8050 (t80) REVERT: A 894 PHE cc_start: 0.6821 (OUTLIER) cc_final: 0.5831 (t80) REVERT: B 507 TYR cc_start: 0.8857 (t80) cc_final: 0.8416 (t80) REVERT: B 976 TYR cc_start: 0.7035 (OUTLIER) cc_final: 0.6655 (t80) REVERT: B 997 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8386 (ttmm) REVERT: B 1425 MET cc_start: 0.8747 (ptt) cc_final: 0.8544 (ptt) REVERT: B 1563 TYR cc_start: 0.8735 (t80) cc_final: 0.8496 (t80) outliers start: 33 outliers final: 18 residues processed: 145 average time/residue: 0.2993 time to fit residues: 64.9409 Evaluate side-chains 137 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 591 TYR Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 737 GLU Chi-restraints excluded: chain A residue 821 GLN Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 762 CYS Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 976 TYR Chi-restraints excluded: chain B residue 997 LYS Chi-restraints excluded: chain B residue 1136 LEU Chi-restraints excluded: chain B residue 1185 THR Chi-restraints excluded: chain B residue 1194 LEU Chi-restraints excluded: chain B residue 1219 MET Chi-restraints excluded: chain B residue 1235 PHE Chi-restraints excluded: chain B residue 1272 VAL Chi-restraints excluded: chain B residue 1277 SER Chi-restraints excluded: chain B residue 1344 VAL Chi-restraints excluded: chain B residue 1428 ILE Chi-restraints excluded: chain B residue 1580 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 86 optimal weight: 0.9980 chunk 10 optimal weight: 8.9990 chunk 152 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 106 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 60 optimal weight: 8.9990 chunk 74 optimal weight: 0.7980 chunk 128 optimal weight: 0.9980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 792 HIS ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1573 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.170195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.104527 restraints weight = 21480.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.105842 restraints weight = 11859.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.106453 restraints weight = 7762.083| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12736 Z= 0.160 Angle : 0.567 10.586 17221 Z= 0.286 Chirality : 0.043 0.220 1840 Planarity : 0.004 0.056 2262 Dihedral : 4.013 29.174 1703 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.41 % Allowed : 22.57 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.22), residues: 1543 helix: 0.92 (0.27), residues: 409 sheet: 0.11 (0.29), residues: 314 loop : 0.31 (0.23), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 783 HIS 0.006 0.001 HIS B 719 PHE 0.018 0.001 PHE B 515 TYR 0.013 0.001 TYR A 584 ARG 0.004 0.000 ARG B1238 Details of bonding type rmsd hydrogen bonds : bond 0.03634 ( 418) hydrogen bonds : angle 4.65868 ( 1113) metal coordination : bond 0.00661 ( 8) metal coordination : angle 1.53564 ( 6) covalent geometry : bond 0.00376 (12728) covalent geometry : angle 0.56651 (17215) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3086 Ramachandran restraints generated. 1543 Oldfield, 0 Emsley, 1543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3086 Ramachandran restraints generated. 1543 Oldfield, 0 Emsley, 1543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 124 time to evaluate : 1.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 672 SER cc_start: 0.6687 (OUTLIER) cc_final: 0.6346 (t) REVERT: A 691 MET cc_start: 0.7977 (tpt) cc_final: 0.7503 (tpt) REVERT: A 737 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.6553 (pm20) REVERT: A 821 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.7606 (mp10) REVERT: A 857 TYR cc_start: 0.8402 (t80) cc_final: 0.8188 (t80) REVERT: A 894 PHE cc_start: 0.6839 (OUTLIER) cc_final: 0.5852 (t80) REVERT: A 1013 GLN cc_start: 0.6540 (OUTLIER) cc_final: 0.6267 (tp40) REVERT: B 507 TYR cc_start: 0.8816 (t80) cc_final: 0.8375 (t80) REVERT: B 976 TYR cc_start: 0.7069 (OUTLIER) cc_final: 0.6664 (t80) REVERT: B 997 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8377 (ttmm) REVERT: B 1425 MET cc_start: 0.8862 (ptt) cc_final: 0.8582 (ptt) REVERT: B 1445 ARG cc_start: 0.8143 (tpp80) cc_final: 0.7849 (tpp80) outliers start: 46 outliers final: 27 residues processed: 157 average time/residue: 0.2403 time to fit residues: 56.4276 Evaluate side-chains 151 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 117 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 591 TYR Chi-restraints excluded: chain A residue 633 LYS Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 737 GLU Chi-restraints excluded: chain A residue 821 GLN Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 1013 GLN Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 541 ASN Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 762 CYS Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 976 TYR Chi-restraints excluded: chain B residue 997 LYS Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1136 LEU Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain B residue 1185 THR Chi-restraints excluded: chain B residue 1191 CYS Chi-restraints excluded: chain B residue 1194 LEU Chi-restraints excluded: chain B residue 1219 MET Chi-restraints excluded: chain B residue 1235 PHE Chi-restraints excluded: chain B residue 1272 VAL Chi-restraints excluded: chain B residue 1277 SER Chi-restraints excluded: chain B residue 1344 VAL Chi-restraints excluded: chain B residue 1428 ILE Chi-restraints excluded: chain B residue 1539 VAL Chi-restraints excluded: chain B residue 1550 VAL Chi-restraints excluded: chain B residue 1580 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 72 optimal weight: 7.9990 chunk 44 optimal weight: 40.0000 chunk 25 optimal weight: 9.9990 chunk 145 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 130 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 5 optimal weight: 20.0000 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 578 HIS ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1573 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.165474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.099242 restraints weight = 21379.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.099620 restraints weight = 12514.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.101451 restraints weight = 8214.396| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 12736 Z= 0.302 Angle : 0.678 12.715 17221 Z= 0.347 Chirality : 0.046 0.226 1840 Planarity : 0.005 0.059 2262 Dihedral : 4.494 32.767 1703 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.01 % Allowed : 22.27 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.22), residues: 1543 helix: 0.61 (0.26), residues: 410 sheet: -0.09 (0.30), residues: 305 loop : 0.15 (0.23), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 868 HIS 0.007 0.001 HIS B1332 PHE 0.026 0.002 PHE B1021 TYR 0.020 0.002 TYR A 584 ARG 0.004 0.001 ARG A 634 Details of bonding type rmsd hydrogen bonds : bond 0.04509 ( 418) hydrogen bonds : angle 5.02439 ( 1113) metal coordination : bond 0.01313 ( 8) metal coordination : angle 1.91487 ( 6) covalent geometry : bond 0.00704 (12728) covalent geometry : angle 0.67701 (17215) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3086 Ramachandran restraints generated. 1543 Oldfield, 0 Emsley, 1543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3086 Ramachandran restraints generated. 1543 Oldfield, 0 Emsley, 1543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 117 time to evaluate : 1.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 672 SER cc_start: 0.6943 (OUTLIER) cc_final: 0.6615 (t) REVERT: A 737 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.6535 (pm20) REVERT: A 821 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8344 (mp10) REVERT: A 883 MET cc_start: 0.7977 (pmm) cc_final: 0.7294 (pmm) REVERT: A 894 PHE cc_start: 0.6895 (OUTLIER) cc_final: 0.5762 (t80) REVERT: A 1013 GLN cc_start: 0.6363 (OUTLIER) cc_final: 0.6085 (tp40) REVERT: B 503 GLN cc_start: 0.9111 (mm-40) cc_final: 0.8768 (mm-40) REVERT: B 507 TYR cc_start: 0.8869 (t80) cc_final: 0.8494 (t80) REVERT: B 712 MET cc_start: 0.5901 (mmm) cc_final: 0.5000 (mmt) REVERT: B 821 GLU cc_start: 0.7713 (tp30) cc_final: 0.7415 (tm-30) REVERT: B 918 ASP cc_start: 0.8493 (OUTLIER) cc_final: 0.8283 (p0) REVERT: B 976 TYR cc_start: 0.7128 (OUTLIER) cc_final: 0.6722 (t80) REVERT: B 997 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8482 (ttmm) outliers start: 54 outliers final: 31 residues processed: 160 average time/residue: 0.2561 time to fit residues: 61.3590 Evaluate side-chains 149 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 110 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 591 TYR Chi-restraints excluded: chain A residue 633 LYS Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 737 GLU Chi-restraints excluded: chain A residue 821 GLN Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 1013 GLN Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 541 ASN Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 762 CYS Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 918 ASP Chi-restraints excluded: chain B residue 976 TYR Chi-restraints excluded: chain B residue 997 LYS Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1038 ASP Chi-restraints excluded: chain B residue 1136 LEU Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain B residue 1185 THR Chi-restraints excluded: chain B residue 1191 CYS Chi-restraints excluded: chain B residue 1194 LEU Chi-restraints excluded: chain B residue 1219 MET Chi-restraints excluded: chain B residue 1235 PHE Chi-restraints excluded: chain B residue 1272 VAL Chi-restraints excluded: chain B residue 1277 SER Chi-restraints excluded: chain B residue 1344 VAL Chi-restraints excluded: chain B residue 1366 THR Chi-restraints excluded: chain B residue 1428 ILE Chi-restraints excluded: chain B residue 1517 LEU Chi-restraints excluded: chain B residue 1539 VAL Chi-restraints excluded: chain B residue 1550 VAL Chi-restraints excluded: chain B residue 1580 VAL Chi-restraints excluded: chain B residue 1594 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 78 optimal weight: 4.9990 chunk 124 optimal weight: 0.6980 chunk 134 optimal weight: 0.7980 chunk 101 optimal weight: 0.6980 chunk 42 optimal weight: 20.0000 chunk 61 optimal weight: 0.7980 chunk 150 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 578 HIS ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1397 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.170158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.105150 restraints weight = 21404.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.105833 restraints weight = 12596.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.107749 restraints weight = 8208.411| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12736 Z= 0.113 Angle : 0.595 11.158 17221 Z= 0.297 Chirality : 0.043 0.211 1840 Planarity : 0.004 0.053 2262 Dihedral : 4.150 30.857 1703 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.52 % Allowed : 24.13 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.22), residues: 1543 helix: 0.83 (0.27), residues: 409 sheet: 0.04 (0.30), residues: 314 loop : 0.37 (0.23), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 783 HIS 0.004 0.001 HIS B1028 PHE 0.021 0.001 PHE B 515 TYR 0.010 0.001 TYR B 827 ARG 0.004 0.000 ARG B1426 Details of bonding type rmsd hydrogen bonds : bond 0.03525 ( 418) hydrogen bonds : angle 4.70105 ( 1113) metal coordination : bond 0.00434 ( 8) metal coordination : angle 1.49986 ( 6) covalent geometry : bond 0.00257 (12728) covalent geometry : angle 0.59467 (17215) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3086 Ramachandran restraints generated. 1543 Oldfield, 0 Emsley, 1543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3086 Ramachandran restraints generated. 1543 Oldfield, 0 Emsley, 1543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 123 time to evaluate : 1.818 Fit side-chains revert: symmetry clash REVERT: A 737 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6439 (pm20) REVERT: A 821 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.7561 (mp10) REVERT: A 883 MET cc_start: 0.8004 (pmm) cc_final: 0.7286 (pmm) REVERT: A 894 PHE cc_start: 0.6851 (OUTLIER) cc_final: 0.5698 (t80) REVERT: A 1013 GLN cc_start: 0.6205 (OUTLIER) cc_final: 0.5967 (tp40) REVERT: B 507 TYR cc_start: 0.8873 (t80) cc_final: 0.8467 (t80) REVERT: B 657 GLU cc_start: 0.7909 (tt0) cc_final: 0.6701 (tp30) REVERT: B 712 MET cc_start: 0.5972 (mmm) cc_final: 0.5227 (mmt) REVERT: B 821 GLU cc_start: 0.7611 (tp30) cc_final: 0.7329 (tm-30) REVERT: B 892 PHE cc_start: 0.7771 (t80) cc_final: 0.7413 (t80) REVERT: B 976 TYR cc_start: 0.7114 (OUTLIER) cc_final: 0.6728 (t80) REVERT: B 1232 MET cc_start: 0.7262 (ttp) cc_final: 0.6834 (ttp) outliers start: 34 outliers final: 23 residues processed: 149 average time/residue: 0.3488 time to fit residues: 79.2503 Evaluate side-chains 141 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 591 TYR Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 737 GLU Chi-restraints excluded: chain A residue 821 GLN Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 1013 GLN Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 541 ASN Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 762 CYS Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 976 TYR Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1136 LEU Chi-restraints excluded: chain B residue 1194 LEU Chi-restraints excluded: chain B residue 1219 MET Chi-restraints excluded: chain B residue 1235 PHE Chi-restraints excluded: chain B residue 1272 VAL Chi-restraints excluded: chain B residue 1277 SER Chi-restraints excluded: chain B residue 1309 THR Chi-restraints excluded: chain B residue 1344 VAL Chi-restraints excluded: chain B residue 1580 VAL Chi-restraints excluded: chain B residue 1594 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 26 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 94 optimal weight: 0.0050 chunk 70 optimal weight: 0.0000 chunk 62 optimal weight: 20.0000 chunk 98 optimal weight: 7.9990 chunk 93 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 overall best weight: 0.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 578 HIS ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1332 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.170624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.105261 restraints weight = 21295.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.106565 restraints weight = 12229.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.108173 restraints weight = 7976.890| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12736 Z= 0.113 Angle : 0.574 10.681 17221 Z= 0.286 Chirality : 0.042 0.224 1840 Planarity : 0.004 0.052 2262 Dihedral : 4.002 29.365 1703 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.08 % Allowed : 24.72 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.22), residues: 1543 helix: 0.94 (0.27), residues: 410 sheet: 0.06 (0.30), residues: 315 loop : 0.43 (0.23), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 783 HIS 0.003 0.001 HIS B 795 PHE 0.016 0.001 PHE B1251 TYR 0.010 0.001 TYR A 584 ARG 0.003 0.000 ARG B1238 Details of bonding type rmsd hydrogen bonds : bond 0.03381 ( 418) hydrogen bonds : angle 4.58619 ( 1113) metal coordination : bond 0.00486 ( 8) metal coordination : angle 1.46602 ( 6) covalent geometry : bond 0.00262 (12728) covalent geometry : angle 0.57376 (17215) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3086 Ramachandran restraints generated. 1543 Oldfield, 0 Emsley, 1543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3086 Ramachandran restraints generated. 1543 Oldfield, 0 Emsley, 1543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 1.381 Fit side-chains revert: symmetry clash REVERT: A 691 MET cc_start: 0.8000 (tpt) cc_final: 0.7550 (tpt) REVERT: A 737 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.6469 (pm20) REVERT: A 821 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.7568 (mp10) REVERT: A 883 MET cc_start: 0.8004 (pmm) cc_final: 0.7273 (pmm) REVERT: A 894 PHE cc_start: 0.6853 (OUTLIER) cc_final: 0.5708 (t80) REVERT: B 507 TYR cc_start: 0.8873 (t80) cc_final: 0.8467 (t80) REVERT: B 657 GLU cc_start: 0.7902 (tt0) cc_final: 0.6708 (tp30) REVERT: B 712 MET cc_start: 0.6009 (mmm) cc_final: 0.5233 (mmt) REVERT: B 821 GLU cc_start: 0.7527 (tp30) cc_final: 0.7234 (tm-30) REVERT: B 976 TYR cc_start: 0.7086 (OUTLIER) cc_final: 0.6706 (t80) REVERT: B 1232 MET cc_start: 0.7092 (ttp) cc_final: 0.6624 (ttp) REVERT: B 1425 MET cc_start: 0.8965 (ttp) cc_final: 0.8511 (ttp) outliers start: 28 outliers final: 22 residues processed: 136 average time/residue: 0.3776 time to fit residues: 79.7938 Evaluate side-chains 136 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 2.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 591 TYR Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 737 GLU Chi-restraints excluded: chain A residue 821 GLN Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 541 ASN Chi-restraints excluded: chain B residue 762 CYS Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 976 TYR Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1136 LEU Chi-restraints excluded: chain B residue 1194 LEU Chi-restraints excluded: chain B residue 1219 MET Chi-restraints excluded: chain B residue 1235 PHE Chi-restraints excluded: chain B residue 1272 VAL Chi-restraints excluded: chain B residue 1277 SER Chi-restraints excluded: chain B residue 1309 THR Chi-restraints excluded: chain B residue 1344 VAL Chi-restraints excluded: chain B residue 1580 VAL Chi-restraints excluded: chain B residue 1594 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 128 optimal weight: 2.9990 chunk 152 optimal weight: 5.9990 chunk 118 optimal weight: 0.3980 chunk 141 optimal weight: 10.0000 chunk 123 optimal weight: 0.8980 chunk 4 optimal weight: 8.9990 chunk 89 optimal weight: 4.9990 chunk 143 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 67 optimal weight: 20.0000 chunk 135 optimal weight: 1.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1573 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.167875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.102992 restraints weight = 21333.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.103440 restraints weight = 12285.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.104075 restraints weight = 8589.426| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 12736 Z= 0.198 Angle : 0.625 12.284 17221 Z= 0.313 Chirality : 0.044 0.260 1840 Planarity : 0.004 0.054 2262 Dihedral : 4.170 30.091 1703 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.30 % Allowed : 24.87 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.22), residues: 1543 helix: 0.90 (0.27), residues: 410 sheet: 0.07 (0.31), residues: 304 loop : 0.36 (0.23), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 868 HIS 0.004 0.001 HIS B1502 PHE 0.041 0.002 PHE B 576 TYR 0.032 0.002 TYR B 775 ARG 0.004 0.000 ARG A1074 Details of bonding type rmsd hydrogen bonds : bond 0.03826 ( 418) hydrogen bonds : angle 4.71473 ( 1113) metal coordination : bond 0.00932 ( 8) metal coordination : angle 1.65860 ( 6) covalent geometry : bond 0.00466 (12728) covalent geometry : angle 0.62447 (17215) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3086 Ramachandran restraints generated. 1543 Oldfield, 0 Emsley, 1543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3086 Ramachandran restraints generated. 1543 Oldfield, 0 Emsley, 1543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 114 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 625 MET cc_start: 0.5199 (tpp) cc_final: 0.3833 (tmm) REVERT: A 737 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.6505 (pm20) REVERT: A 821 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.7602 (mp10) REVERT: A 883 MET cc_start: 0.8012 (pmm) cc_final: 0.7267 (pmm) REVERT: A 894 PHE cc_start: 0.6907 (OUTLIER) cc_final: 0.5780 (t80) REVERT: B 503 GLN cc_start: 0.9103 (mm-40) cc_final: 0.8744 (mm-40) REVERT: B 507 TYR cc_start: 0.8877 (t80) cc_final: 0.8515 (t80) REVERT: B 657 GLU cc_start: 0.7781 (tt0) cc_final: 0.6622 (tp30) REVERT: B 712 MET cc_start: 0.5993 (mmm) cc_final: 0.5253 (mmt) REVERT: B 791 MET cc_start: 0.8305 (mmm) cc_final: 0.7935 (mmm) REVERT: B 976 TYR cc_start: 0.7111 (OUTLIER) cc_final: 0.6746 (t80) REVERT: B 1232 MET cc_start: 0.7392 (ttp) cc_final: 0.6933 (ttp) REVERT: B 1425 MET cc_start: 0.9051 (ttp) cc_final: 0.8690 (ttp) REVERT: B 1445 ARG cc_start: 0.7970 (tpp80) cc_final: 0.7366 (tpp80) outliers start: 31 outliers final: 25 residues processed: 138 average time/residue: 0.2366 time to fit residues: 48.7184 Evaluate side-chains 137 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 591 TYR Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 737 GLU Chi-restraints excluded: chain A residue 821 GLN Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 541 ASN Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 762 CYS Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 976 TYR Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1136 LEU Chi-restraints excluded: chain B residue 1185 THR Chi-restraints excluded: chain B residue 1194 LEU Chi-restraints excluded: chain B residue 1219 MET Chi-restraints excluded: chain B residue 1235 PHE Chi-restraints excluded: chain B residue 1272 VAL Chi-restraints excluded: chain B residue 1277 SER Chi-restraints excluded: chain B residue 1309 THR Chi-restraints excluded: chain B residue 1344 VAL Chi-restraints excluded: chain B residue 1539 VAL Chi-restraints excluded: chain B residue 1594 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 88 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 150 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 115 optimal weight: 6.9990 chunk 153 optimal weight: 0.9980 chunk 154 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 chunk 44 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1573 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.170420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.103684 restraints weight = 21321.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.107498 restraints weight = 11203.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.107375 restraints weight = 7147.337| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12736 Z= 0.116 Angle : 0.583 11.435 17221 Z= 0.289 Chirality : 0.042 0.193 1840 Planarity : 0.004 0.052 2262 Dihedral : 3.996 29.469 1703 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.15 % Allowed : 24.94 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.22), residues: 1543 helix: 0.98 (0.27), residues: 410 sheet: 0.01 (0.30), residues: 315 loop : 0.47 (0.23), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 783 HIS 0.003 0.001 HIS B 795 PHE 0.037 0.001 PHE B 576 TYR 0.026 0.001 TYR B 775 ARG 0.003 0.000 ARG B1410 Details of bonding type rmsd hydrogen bonds : bond 0.03342 ( 418) hydrogen bonds : angle 4.52863 ( 1113) metal coordination : bond 0.00551 ( 8) metal coordination : angle 1.63128 ( 6) covalent geometry : bond 0.00273 (12728) covalent geometry : angle 0.58263 (17215) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4709.27 seconds wall clock time: 88 minutes 36.26 seconds (5316.26 seconds total)