Starting phenix.real_space_refine on Sun Oct 25 20:47:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9z07_73698/10_2026/9z07_73698_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9z07_73698/10_2026/9z07_73698.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9z07_73698/10_2026/9z07_73698_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9z07_73698/10_2026/9z07_73698_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9z07_73698/10_2026/9z07_73698.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9z07_73698/10_2026/9z07_73698.map" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.025 sd= 0.725 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: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 298 5.49 5 S 53 5.16 5 C 10368 2.51 5 N 3293 2.21 5 O 3901 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17917 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 854, 5705 Classifications: {'peptide': 854} Incomplete info: {'truncation_to_alanine': 275} Link IDs: {'CIS': 2, 'PTRANS': 53, 'TRANS': 798} Chain breaks: 6 Unresolved non-hydrogen bonds: 1104 Unresolved non-hydrogen angles: 1369 Unresolved non-hydrogen dihedrals: 925 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'ASP:plan': 36, 'TYR:plan': 11, 'GLU:plan': 36, 'ASN:plan1': 17, 'GLN:plan1': 15, 'PHE:plan': 5, 'HIS:plan': 11, 'TRP:plan': 3, 'ARG:plan': 36} Unresolved non-hydrogen planarities: 732 Chain: "N" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 849 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 105} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "O" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "P" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 808 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 95} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Q" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 647 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "X" Number of atoms: 3073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 3073 Classifications: {'DNA': 149} Link IDs: {'rna3p': 148} Chain: "Y" Number of atoms: 3036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 3036 Classifications: {'DNA': 149} Link IDs: {'rna3p': 148} Chain: "n" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 836 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 104} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "o" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 766 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 95} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "p" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 820 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "q" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 102 SG CYS A 653 86.316 65.961 44.061 1.00157.26 S ATOM 119 SG CYS A 656 88.562 68.417 44.333 1.00145.97 S ATOM 141 SG CYS A 659 88.506 67.332 47.035 1.00137.45 S ATOM 382 SG CYS A 691 85.299 68.668 45.949 1.00151.90 S ATOM 181 SG CYS A 664 97.998 76.069 53.890 1.00128.45 S ATOM 200 SG CYS A 667 95.289 76.987 55.366 1.00121.40 S ATOM 220 SG CYS A 670 97.384 73.701 56.323 1.00126.44 S ATOM 336 SG CYS A 686 94.941 74.159 53.061 1.00129.94 S ATOM 4841 SG CYS A1476 92.043 57.066 38.224 1.00 70.45 S ATOM 4852 SG CYS A1478 89.365 55.522 40.329 1.00 97.86 S ATOM 4889 SG CYS A1485 90.056 58.242 41.513 1.00115.97 S ATOM 937 SG CYS A 820 26.499 53.739 62.032 1.00148.75 S ATOM 1422 SG CYS A 893 24.253 57.154 62.784 1.00138.60 S ATOM 1441 SG CYS A 896 23.313 53.070 61.410 1.00138.83 S Time building chain proxies: 3.26, per 1000 atoms: 0.18 Number of scatterers: 17917 At special positions: 0 Unit cell: (118.77, 118.77, 163.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 53 16.00 P 298 15.00 O 3901 8.00 N 3293 7.00 C 10368 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.62 Conformation dependent library (CDL) restraints added in 642.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1701 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 691 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 656 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 653 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 659 " pdb=" ZN A1702 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 686 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 664 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 667 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 670 " pdb=" ZN A1703 " pdb="ZN ZN A1703 " - pdb=" NE2 HIS A1502 " pdb="ZN ZN A1703 " - pdb=" SG CYS A1485 " pdb="ZN ZN A1703 " - pdb=" SG CYS A1478 " pdb="ZN ZN A1703 " - pdb=" SG CYS A1476 " pdb=" ZN A1704 " pdb="ZN ZN A1704 " - pdb=" NE2 HIS A 793 " pdb="ZN ZN A1704 " - pdb=" SG CYS A 896 " pdb="ZN ZN A1704 " - pdb=" SG CYS A 820 " pdb="ZN ZN A1704 " - pdb=" SG CYS A 893 " Number of angles added : 18 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3040 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 17 sheets defined 47.7% alpha, 14.3% beta 138 base pairs and 266 stacking pairs defined. Time for finding SS restraints: 2.33 Creating SS restraints... Processing helix chain 'A' and resid 656 through 661 removed outlier: 3.555A pdb=" N GLN A 660 " --> pdb=" O CYS A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 673 removed outlier: 4.013A pdb=" N MET A 673 " --> pdb=" O ALA A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 677 Processing helix chain 'A' and resid 686 through 690 Processing helix chain 'A' and resid 805 through 809 removed outlier: 3.778A pdb=" N THR A 808 " --> pdb=" O LEU A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 828 No H-bonds generated for 'chain 'A' and resid 826 through 828' Processing helix chain 'A' and resid 893 through 906 removed outlier: 3.606A pdb=" N MET A 902 " --> pdb=" O ARG A 898 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG A 903 " --> pdb=" O LEU A 899 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU A 906 " --> pdb=" O MET A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 975 Processing helix chain 'A' and resid 1030 through 1035 Processing helix chain 'A' and resid 1054 through 1056 No H-bonds generated for 'chain 'A' and resid 1054 through 1056' Processing helix chain 'A' and resid 1071 through 1079 removed outlier: 3.528A pdb=" N MET A1077 " --> pdb=" O GLN A1073 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLY A1079 " --> pdb=" O TYR A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1100 through 1104 Processing helix chain 'A' and resid 1149 through 1158 removed outlier: 3.586A pdb=" N GLY A1154 " --> pdb=" O GLY A1150 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1181 removed outlier: 3.505A pdb=" N ASN A1180 " --> pdb=" O ALA A1176 " (cutoff:3.500A) Processing helix chain 'A' and resid 1190 through 1200 removed outlier: 3.588A pdb=" N LEU A1195 " --> pdb=" O CYS A1191 " (cutoff:3.500A) Processing helix chain 'A' and resid 1246 through 1259 Processing helix chain 'A' and resid 1270 through 1273 Processing helix chain 'A' and resid 1277 through 1291 Processing helix chain 'A' and resid 1302 through 1305 removed outlier: 3.986A pdb=" N GLY A1305 " --> pdb=" O GLY A1302 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1302 through 1305' Processing helix chain 'A' and resid 1335 through 1339 Processing helix chain 'A' and resid 1394 through 1402 Processing helix chain 'A' and resid 1418 through 1426 removed outlier: 3.645A pdb=" N ARG A1424 " --> pdb=" O LEU A1420 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET A1425 " --> pdb=" O VAL A1421 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG A1426 " --> pdb=" O ALA A1422 " (cutoff:3.500A) Processing helix chain 'A' and resid 1435 through 1439 Processing helix chain 'A' and resid 1476 through 1480 removed outlier: 3.617A pdb=" N VAL A1479 " --> pdb=" O CYS A1476 " (cutoff:3.500A) Processing helix chain 'A' and resid 1499 through 1504 Processing helix chain 'A' and resid 1505 through 1511 removed outlier: 4.332A pdb=" N ASN A1508 " --> pdb=" O ASN A1505 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N HIS A1509 " --> pdb=" O ARG A1506 " (cutoff:3.500A) Processing helix chain 'A' and resid 1549 through 1557 removed outlier: 3.755A pdb=" N SER A1556 " --> pdb=" O GLU A1552 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN A1557 " --> pdb=" O CYS A1553 " (cutoff:3.500A) Processing helix chain 'A' and resid 1568 through 1579 Processing helix chain 'A' and resid 1581 through 1600 removed outlier: 3.874A pdb=" N ALA A1587 " --> pdb=" O PRO A1583 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE A1588 " --> pdb=" O LEU A1584 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA A1600 " --> pdb=" O MET A1596 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 21 Processing helix chain 'N' and resid 26 through 37 Processing helix chain 'N' and resid 46 through 73 Processing helix chain 'N' and resid 79 through 90 Processing helix chain 'N' and resid 90 through 97 Processing helix chain 'N' and resid 112 through 116 Processing helix chain 'O' and resid 34 through 46 Processing helix chain 'O' and resid 52 through 80 Processing helix chain 'O' and resid 87 through 99 Processing helix chain 'O' and resid 100 through 121 removed outlier: 3.666A pdb=" N ALA O 104 " --> pdb=" O PRO O 100 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS O 105 " --> pdb=" O GLY O 101 " (cutoff:3.500A) Processing helix chain 'P' and resid 44 through 57 Processing helix chain 'P' and resid 63 through 76 Processing helix chain 'P' and resid 85 through 114 Processing helix chain 'P' and resid 120 through 131 Processing helix chain 'Q' and resid 25 through 29 Processing helix chain 'Q' and resid 30 through 42 Processing helix chain 'Q' and resid 49 through 76 removed outlier: 3.955A pdb=" N GLU Q 53 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 82 through 94 Processing helix chain 'n' and resid 16 through 21 Processing helix chain 'n' and resid 26 through 37 Processing helix chain 'n' and resid 46 through 74 Processing helix chain 'n' and resid 79 through 90 removed outlier: 3.821A pdb=" N ASP n 90 " --> pdb=" O ALA n 86 " (cutoff:3.500A) Processing helix chain 'n' and resid 91 through 97 removed outlier: 3.690A pdb=" N LYS n 95 " --> pdb=" O GLU n 91 " (cutoff:3.500A) Processing helix chain 'o' and resid 34 through 46 removed outlier: 3.648A pdb=" N VAL o 38 " --> pdb=" O TYR o 34 " (cutoff:3.500A) Processing helix chain 'o' and resid 52 through 81 Processing helix chain 'o' and resid 87 through 99 Processing helix chain 'o' and resid 100 through 122 removed outlier: 3.669A pdb=" N ALA o 104 " --> pdb=" O PRO o 100 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS o 105 " --> pdb=" O GLY o 101 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA o 121 " --> pdb=" O LYS o 117 " (cutoff:3.500A) Processing helix chain 'p' and resid 44 through 56 removed outlier: 3.790A pdb=" N LYS p 56 " --> pdb=" O ARG p 52 " (cutoff:3.500A) Processing helix chain 'p' and resid 63 through 79 removed outlier: 3.577A pdb=" N PHE p 67 " --> pdb=" O ARG p 63 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASP p 77 " --> pdb=" O GLU p 73 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N PHE p 78 " --> pdb=" O ILE p 74 " (cutoff:3.500A) Processing helix chain 'p' and resid 85 through 114 Processing helix chain 'p' and resid 120 through 131 removed outlier: 3.632A pdb=" N ILE p 124 " --> pdb=" O MET p 120 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG p 131 " --> pdb=" O ALA p 127 " (cutoff:3.500A) Processing helix chain 'q' and resid 30 through 42 Processing helix chain 'q' and resid 49 through 76 removed outlier: 3.932A pdb=" N GLU q 53 " --> pdb=" O LEU q 49 " (cutoff:3.500A) Processing helix chain 'q' and resid 82 through 93 removed outlier: 3.550A pdb=" N VAL q 86 " --> pdb=" O THR q 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 750 through 752 Processing sheet with id=AA2, first strand: chain 'A' and resid 830 through 831 removed outlier: 3.685A pdb=" N SER A 830 " --> pdb=" O SER A 764 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LEU A 776 " --> pdb=" O PHE A 797 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N HIS A 793 " --> pdb=" O THR A 780 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N LEU A 782 " --> pdb=" O MET A 791 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N MET A 791 " --> pdb=" O LEU A 782 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N GLN A 790 " --> pdb=" O MET A 823 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N MET A 823 " --> pdb=" O GLN A 790 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N PHE A 792 " --> pdb=" O GLU A 821 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N GLU A 821 " --> pdb=" O PHE A 792 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ALA A 794 " --> pdb=" O GLU A 819 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N GLU A 819 " --> pdb=" O ALA A 794 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N TRP A 796 " --> pdb=" O VAL A 817 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N VAL A 817 " --> pdb=" O TRP A 796 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLN A 866 " --> pdb=" O LEU A 814 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N LEU A 816 " --> pdb=" O GLN A 866 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N TRP A 868 " --> pdb=" O LEU A 816 " (cutoff:3.500A) removed outlier: 8.851A pdb=" N ASP A 818 " --> pdb=" O TRP A 868 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 830 through 831 removed outlier: 3.685A pdb=" N SER A 830 " --> pdb=" O SER A 764 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LEU A 776 " --> pdb=" O PHE A 797 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N HIS A 793 " --> pdb=" O THR A 780 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N LEU A 782 " --> pdb=" O MET A 791 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N MET A 791 " --> pdb=" O LEU A 782 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N GLN A 790 " --> pdb=" O MET A 823 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N MET A 823 " --> pdb=" O GLN A 790 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N PHE A 792 " --> pdb=" O GLU A 821 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N GLU A 821 " --> pdb=" O PHE A 792 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ALA A 794 " --> pdb=" O GLU A 819 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N GLU A 819 " --> pdb=" O ALA A 794 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N TRP A 796 " --> pdb=" O VAL A 817 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N VAL A 817 " --> pdb=" O TRP A 796 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLN A 866 " --> pdb=" O LEU A 814 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N LEU A 816 " --> pdb=" O GLN A 866 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N TRP A 868 " --> pdb=" O LEU A 816 " (cutoff:3.500A) removed outlier: 8.851A pdb=" N ASP A 818 " --> pdb=" O TRP A 868 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 909 through 912 removed outlier: 6.696A pdb=" N SER A 925 " --> pdb=" O LEU A 911 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 915 through 916 removed outlier: 3.919A pdb=" N VAL A 921 " --> pdb=" O CYS A1001 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS A1001 " --> pdb=" O VAL A 921 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLY A1058 " --> pdb=" O TYR A 940 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N PHE A1083 " --> pdb=" O ARG A1059 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N THR A1061 " --> pdb=" O PHE A1083 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N PHE A1085 " --> pdb=" O THR A1061 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLU A1063 " --> pdb=" O PHE A1085 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N GLU A1087 " --> pdb=" O GLU A1063 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 915 through 916 removed outlier: 3.919A pdb=" N VAL A 921 " --> pdb=" O CYS A1001 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS A1001 " --> pdb=" O VAL A 921 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLY A 994 " --> pdb=" O PHE A1021 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N PHE A1021 " --> pdb=" O GLY A 994 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE A 996 " --> pdb=" O ASN A1019 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ASN A1019 " --> pdb=" O ILE A 996 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU A 998 " --> pdb=" O ARG A1017 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE A1016 " --> pdb=" O ALA A1049 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ALA A1049 " --> pdb=" O ILE A1016 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N VAL A1018 " --> pdb=" O GLU A1047 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N GLU A1047 " --> pdb=" O VAL A1018 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LYS A1020 " --> pdb=" O SER A1045 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU A1042 " --> pdb=" O PHE A1085 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N GLU A1087 " --> pdb=" O LEU A1042 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N ASP A1046 " --> pdb=" O TYR A1089 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1185 through 1187 removed outlier: 8.553A pdb=" N THR A1185 " --> pdb=" O ASP A1162 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU A1164 " --> pdb=" O THR A1185 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N PHE A1187 " --> pdb=" O LEU A1164 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ALA A1166 " --> pdb=" O PHE A1187 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ASP A1143 " --> pdb=" O LEU A1164 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ALA A1166 " --> pdb=" O ASP A1143 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET A1219 " --> pdb=" O ARG A1140 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N CYS A1221 " --> pdb=" O LEU A1142 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU A1220 " --> pdb=" O LEU A1264 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N GLU A1266 " --> pdb=" O LEU A1220 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1343 through 1345 Processing sheet with id=AA9, first strand: chain 'A' and resid 1444 through 1445 removed outlier: 3.616A pdb=" N VAL A1444 " --> pdb=" O ALA A1452 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 42 through 43 removed outlier: 7.529A pdb=" N ARG N 42 " --> pdb=" O ILE O 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'N' and resid 77 through 78 Processing sheet with id=AB3, first strand: chain 'N' and resid 100 through 102 Processing sheet with id=AB4, first strand: chain 'P' and resid 83 through 84 removed outlier: 7.501A pdb=" N ARG P 83 " --> pdb=" O VAL Q 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'Q' and resid 96 through 98 removed outlier: 6.674A pdb=" N THR Q 96 " --> pdb=" O THR n 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'n' and resid 42 through 43 removed outlier: 7.174A pdb=" N ARG n 42 " --> pdb=" O ILE o 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'n' and resid 77 through 78 Processing sheet with id=AB8, first strand: chain 'p' and resid 83 through 84 removed outlier: 6.867A pdb=" N ARG p 83 " --> pdb=" O VAL q 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 600 hydrogen bonds defined for protein. 1683 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 354 hydrogen bonds 708 hydrogen bond angles 0 basepair planarities 138 basepair parallelities 266 stacking parallelities Total time for adding SS restraints: 5.04 Time building geometry restraints manager: 2.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3519 1.33 - 1.45: 5713 1.45 - 1.57: 8966 1.57 - 1.69: 590 1.69 - 1.82: 77 Bond restraints: 18865 Sorted by residual: bond pdb=" O3' DC X 134 " pdb=" P DC X 135 " ideal model delta sigma weight residual 1.607 1.716 -0.109 1.20e-02 6.94e+03 8.29e+01 bond pdb=" O3' DT X 143 " pdb=" P DC X 144 " ideal model delta sigma weight residual 1.607 1.704 -0.097 1.20e-02 6.94e+03 6.57e+01 bond pdb=" O3' DC X 2 " pdb=" P DA X 3 " ideal model delta sigma weight residual 1.607 1.703 -0.096 1.20e-02 6.94e+03 6.46e+01 bond pdb=" O3' DA Y 8 " pdb=" P DT Y 9 " ideal model delta sigma weight residual 1.607 1.520 0.087 1.20e-02 6.94e+03 5.26e+01 bond pdb=" C1' DC X 2 " pdb=" N1 DC X 2 " ideal model delta sigma weight residual 1.468 1.568 -0.100 1.40e-02 5.10e+03 5.11e+01 ... (remaining 18860 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.94: 26786 4.94 - 9.89: 98 9.89 - 14.83: 8 14.83 - 19.77: 0 19.77 - 24.72: 2 Bond angle restraints: 26894 Sorted by residual: angle pdb=" C TYR q 88 " pdb=" CA TYR q 88 " pdb=" CB TYR q 88 " ideal model delta sigma weight residual 110.85 87.48 23.37 1.70e+00 3.46e-01 1.89e+02 angle pdb=" O3' DA Y 8 " pdb=" P DT Y 9 " pdb=" O5' DT Y 9 " ideal model delta sigma weight residual 104.00 79.28 24.72 1.90e+00 2.77e-01 1.69e+02 angle pdb=" C3' DA Y 8 " pdb=" O3' DA Y 8 " pdb=" P DT Y 9 " ideal model delta sigma weight residual 119.70 134.10 -14.40 1.20e+00 6.94e-01 1.44e+02 angle pdb=" C3' DC X 127 " pdb=" O3' DC X 127 " pdb=" P DT X 128 " ideal model delta sigma weight residual 119.70 133.09 -13.39 1.20e+00 6.94e-01 1.24e+02 angle pdb=" C3' DC Y 12 " pdb=" O3' DC Y 12 " pdb=" P DG Y 13 " ideal model delta sigma weight residual 119.70 128.77 -9.07 1.20e+00 6.94e-01 5.72e+01 ... (remaining 26889 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.25: 8822 33.25 - 66.49: 1655 66.49 - 99.74: 28 99.74 - 132.98: 0 132.98 - 166.23: 2 Dihedral angle restraints: 10507 sinusoidal: 5801 harmonic: 4706 Sorted by residual: dihedral pdb=" C TYR q 88 " pdb=" N TYR q 88 " pdb=" CA TYR q 88 " pdb=" CB TYR q 88 " ideal model delta harmonic sigma weight residual -122.60 -98.51 -24.09 0 2.50e+00 1.60e-01 9.29e+01 dihedral pdb=" CD ARG O 83 " pdb=" NE ARG O 83 " pdb=" CZ ARG O 83 " pdb=" NH1 ARG O 83 " ideal model delta sinusoidal sigma weight residual 0.00 81.03 -81.03 1 1.00e+01 1.00e-02 8.10e+01 dihedral pdb=" CD ARG A1023 " pdb=" NE ARG A1023 " pdb=" CZ ARG A1023 " pdb=" NH1 ARG A1023 " ideal model delta sinusoidal sigma weight residual 0.00 -77.41 77.41 1 1.00e+01 1.00e-02 7.51e+01 ... (remaining 10504 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 3029 0.127 - 0.255: 50 0.255 - 0.382: 2 0.382 - 0.510: 2 0.510 - 0.637: 18 Chirality restraints: 3101 Sorted by residual: chirality pdb=" P DC X 142 " pdb=" OP1 DC X 142 " pdb=" OP2 DC X 142 " pdb=" O5' DC X 142 " both_signs ideal model delta sigma weight residual True 2.34 -2.97 -0.64 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" P DT Y 2 " pdb=" OP1 DT Y 2 " pdb=" OP2 DT Y 2 " pdb=" O5' DT Y 2 " both_signs ideal model delta sigma weight residual True 2.34 -2.91 -0.58 2.00e-01 2.50e+01 8.28e+00 chirality pdb=" P DT Y 15 " pdb=" OP1 DT Y 15 " pdb=" OP2 DT Y 15 " pdb=" O5' DT Y 15 " both_signs ideal model delta sigma weight residual True 2.34 -2.91 -0.57 2.00e-01 2.50e+01 8.18e+00 ... (remaining 3098 not shown) Planarity restraints: 2419 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG O 83 " -1.101 9.50e-02 1.11e+02 4.94e-01 1.47e+02 pdb=" NE ARG O 83 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG O 83 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG O 83 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG O 83 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1023 " 1.078 9.50e-02 1.11e+02 4.83e-01 1.41e+02 pdb=" NE ARG A1023 " -0.065 2.00e-02 2.50e+03 pdb=" CZ ARG A1023 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A1023 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG A1023 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG p 131 " 0.897 9.50e-02 1.11e+02 4.02e-01 9.80e+01 pdb=" NE ARG p 131 " -0.054 2.00e-02 2.50e+03 pdb=" CZ ARG p 131 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG p 131 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG p 131 " 0.024 2.00e-02 2.50e+03 ... (remaining 2416 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 686 2.69 - 3.25: 16312 3.25 - 3.80: 31923 3.80 - 4.35: 40643 4.35 - 4.90: 59765 Nonbonded interactions: 149329 Sorted by model distance: nonbonded pdb=" OG1 THR A1458 " pdb=" O VAL A1475 " model vdw 2.142 3.040 nonbonded pdb=" N LEU A 917 " pdb=" O ARG A 920 " model vdw 2.208 3.120 nonbonded pdb=" O ARG A 909 " pdb=" OG1 THR A 927 " model vdw 2.242 3.040 nonbonded pdb=" OD1 ASN A1192 " pdb=" OG SER A1250 " model vdw 2.244 3.040 nonbonded pdb=" O ALA A1166 " pdb=" N PHE A1187 " model vdw 2.258 3.120 ... (remaining 149324 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 Found NCS groups: ncs_group { reference = (chain 'N' and (resid 10 or (resid 11 through 12 and (name N or name CA or name \ C or name O or name CB )) or resid 13 through 119)) selection = chain 'n' } ncs_group { reference = (chain 'O' and (resid 28 through 29 or (resid 30 through 31 and (name N or name \ CA or name C or name O or name CB )) or resid 32 through 121)) selection = (chain 'o' and resid 28 through 121) } ncs_group { reference = (chain 'P' and resid 36 through 134) selection = (chain 'p' and ((resid 36 through 37 and (name N or name CA or name C or name O \ or name CB )) or resid 38 through 41 or (resid 42 and (name N or name CA or name \ C or name O or name CB )) or resid 43 through 78 or (resid 79 and (name N or na \ me CA or name C or name O or name CB )) or resid 80 through 134)) } ncs_group { reference = (chain 'Q' and resid 23 through 102) selection = (chain 'q' and ((resid 23 and (name N or name CA or name C or name O or name CB \ )) or resid 24 through 102)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 21.780 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 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 : 0.009 0.237 18881 Z= 0.606 Angle : 1.022 25.630 26912 Z= 0.680 Chirality : 0.067 0.637 3101 Planarity : 0.023 0.494 2419 Dihedral : 25.664 166.229 7467 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.25 % Favored : 96.68 % Rotamer: Outliers : 2.94 % Allowed : 17.06 % Favored : 80.00 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.21), residues: 1598 helix: 1.22 (0.20), residues: 680 sheet: -1.09 (0.47), residues: 126 loop : -0.01 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG Q 45 TYR 0.041 0.003 TYR A1457 PHE 0.035 0.003 PHE A1251 TRP 0.020 0.002 TRP A 783 HIS 0.017 0.002 HIS P 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00778 / 0.59 (18865) covalent geometry : angle 0.94913 / 0.68 (26894) hydrogen bonds : bond 0.18343 / 12.06 ( 932) hydrogen bonds : angle 6.43538 / 4.49 ( 2391) metal coordination : bond 0.11992 / 7.62 ( 16) metal coordination : angle 14.73498 / 9.43 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 194 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 79 LYS cc_start: 0.8623 (mttp) cc_final: 0.8420 (mmmm) REVERT: q 24 ASP cc_start: 0.7789 (t0) cc_final: 0.7488 (t0) outliers start: 32 outliers final: 15 residues processed: 213 average time/residue: 0.1582 time to fit residues: 47.8944 Evaluate side-chains 174 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 778 ARG Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 866 GLN Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain N residue 101 THR Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 83 ARG Chi-restraints excluded: chain P residue 81 ASP Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 86 VAL Chi-restraints excluded: chain n residue 101 THR Chi-restraints excluded: chain o residue 102 GLU Chi-restraints excluded: chain p residue 46 VAL Chi-restraints excluded: chain q residue 43 VAL Chi-restraints excluded: chain q residue 86 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.0570 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 50.0000 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 30.0000 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 20.0000 overall best weight: 0.9300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1308 GLN A1505 ASN A1573 HIS P 108 ASN p 125 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.163292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.132615 restraints weight = 62257.861| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 3.24 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 18881 Z= 0.154 Angle : 0.692 9.876 26912 Z= 0.380 Chirality : 0.047 0.374 3101 Planarity : 0.005 0.073 2419 Dihedral : 27.984 167.591 5044 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.75 % Allowed : 17.43 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.22), residues: 1598 helix: 1.47 (0.20), residues: 698 sheet: -0.65 (0.43), residues: 149 loop : 0.01 (0.24), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A1023 TYR 0.025 0.002 TYR O 37 PHE 0.018 0.002 PHE A1251 TRP 0.013 0.002 TRP A1044 HIS 0.005 0.001 HIS P 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.15 (18865) covalent geometry : angle 0.67924 / 0.38 (26894) hydrogen bonds : bond 0.05619 / 3.82 ( 932) hydrogen bonds : angle 4.45259 / 3.18 ( 2391) metal coordination : bond 0.02200 / 1.71 ( 16) metal coordination : angle 5.08677 / 3.30 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 167 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: P 59 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7738 (pm20) REVERT: Q 79 LYS cc_start: 0.8741 (mttp) cc_final: 0.8405 (mmmm) outliers start: 30 outliers final: 21 residues processed: 191 average time/residue: 0.1628 time to fit residues: 44.4284 Evaluate side-chains 179 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 797 PHE Chi-restraints excluded: chain A residue 866 GLN Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 1165 TRP Chi-restraints excluded: chain A residue 1306 VAL Chi-restraints excluded: chain A residue 1496 ILE Chi-restraints excluded: chain A residue 1510 TRP Chi-restraints excluded: chain N residue 101 THR Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain P residue 59 GLU Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 86 VAL Chi-restraints excluded: chain Q residue 93 GLN Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain n residue 64 GLU Chi-restraints excluded: chain n residue 101 THR Chi-restraints excluded: chain p residue 46 VAL Chi-restraints excluded: chain p residue 80 THR Chi-restraints excluded: chain q residue 43 VAL Chi-restraints excluded: chain q residue 86 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: [183, 141, 142, 134, 171, 55, 39, 102, 158, 168, 108] chunk 183 optimal weight: 0.7980 chunk 141 optimal weight: 10.0000 chunk 142 optimal weight: 9.9990 chunk 134 optimal weight: 10.0000 chunk 171 optimal weight: 0.8980 chunk 55 optimal weight: 7.9990 chunk 39 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 chunk 158 optimal weight: 4.9990 chunk 168 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1399 GLN A1573 HIS N 112 GLN ** O 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 44 GLN p 93 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.164031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.133442 restraints weight = 63552.682| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 3.17 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18881 Z= 0.156 Angle : 0.629 8.429 26912 Z= 0.351 Chirality : 0.044 0.363 3101 Planarity : 0.004 0.051 2419 Dihedral : 27.916 167.432 5029 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.84 % Allowed : 18.17 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.22), residues: 1598 helix: 1.73 (0.20), residues: 699 sheet: -0.97 (0.43), residues: 144 loop : 0.02 (0.24), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 778 TYR 0.022 0.002 TYR O 37 PHE 0.017 0.002 PHE A 648 TRP 0.009 0.001 TRP A1165 HIS 0.004 0.001 HIS p 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.16 (18865) covalent geometry : angle 0.62055 / 0.35 (26894) hydrogen bonds : bond 0.05012 / 3.40 ( 932) hydrogen bonds : angle 4.04552 / 2.91 ( 2391) metal coordination : bond 0.00618 / 0.41 ( 16) metal coordination : angle 4.12213 / 2.62 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 165 time to evaluate : 0.387 Fit side-chains REVERT: A 663 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8126 (mp0) REVERT: A 1371 MET cc_start: 0.3131 (tpt) cc_final: 0.2431 (mmt) REVERT: A 1533 MET cc_start: 0.4260 (mmt) cc_final: 0.3613 (mmm) REVERT: O 39 TYR cc_start: 0.7354 (t80) cc_final: 0.7144 (t80) REVERT: Q 79 LYS cc_start: 0.8780 (mttp) cc_final: 0.8435 (mmmm) outliers start: 31 outliers final: 21 residues processed: 189 average time/residue: 0.1439 time to fit residues: 40.1615 Evaluate side-chains 178 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 157 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 797 PHE Chi-restraints excluded: chain A residue 1169 MET Chi-restraints excluded: chain A residue 1282 LEU Chi-restraints excluded: chain A residue 1306 VAL Chi-restraints excluded: chain A residue 1461 ASP Chi-restraints excluded: chain A residue 1496 ILE Chi-restraints excluded: chain N residue 101 THR Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 46 ILE Chi-restraints excluded: chain Q residue 86 VAL Chi-restraints excluded: chain Q residue 93 GLN Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 64 GLU Chi-restraints excluded: chain n residue 101 THR Chi-restraints excluded: chain p residue 46 VAL Chi-restraints excluded: chain q residue 43 VAL Chi-restraints excluded: chain q residue 86 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: [120, 143, 115, 146, 164, 8, 16, 37, 140, 136, 97] chunk 120 optimal weight: 0.6980 chunk 143 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 chunk 146 optimal weight: 9.9990 chunk 164 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 140 optimal weight: 10.0000 chunk 136 optimal weight: 40.0000 chunk 97 optimal weight: 0.8980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1573 HIS N 112 GLN O 81 ASN Q 27 GLN Q 75 HIS o 44 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.160326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.131939 restraints weight = 61905.890| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 3.62 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18881 Z= 0.188 Angle : 0.651 8.771 26912 Z= 0.358 Chirality : 0.046 0.411 3101 Planarity : 0.004 0.041 2419 Dihedral : 28.058 168.948 5024 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.94 % Allowed : 18.26 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.21), residues: 1598 helix: 1.78 (0.20), residues: 698 sheet: -0.78 (0.52), residues: 111 loop : -0.17 (0.23), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 83 TYR 0.020 0.002 TYR A1457 PHE 0.015 0.002 PHE q 100 TRP 0.008 0.001 TRP A1436 HIS 0.004 0.001 HIS p 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.19 (18865) covalent geometry : angle 0.64378 / 0.36 (26894) hydrogen bonds : bond 0.05226 / 3.57 ( 932) hydrogen bonds : angle 4.08622 / 2.95 ( 2391) metal coordination : bond 0.00743 / 0.57 ( 16) metal coordination : angle 3.71838 / 2.35 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 167 time to evaluate : 0.577 Fit side-chains revert: symmetry clash REVERT: A 660 GLN cc_start: 0.7433 (OUTLIER) cc_final: 0.6971 (pm20) REVERT: A 661 GLN cc_start: 0.8554 (tp40) cc_final: 0.8351 (tp40) REVERT: A 663 GLU cc_start: 0.8500 (mt-10) cc_final: 0.7957 (mp0) REVERT: A 1533 MET cc_start: 0.3946 (mmt) cc_final: 0.3328 (mmm) REVERT: Q 79 LYS cc_start: 0.8555 (mttp) cc_final: 0.8339 (mmmm) outliers start: 32 outliers final: 26 residues processed: 192 average time/residue: 0.1641 time to fit residues: 45.4325 Evaluate side-chains 188 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 161 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 660 GLN Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 797 PHE Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 1169 MET Chi-restraints excluded: chain A residue 1282 LEU Chi-restraints excluded: chain A residue 1306 VAL Chi-restraints excluded: chain A residue 1461 ASP Chi-restraints excluded: chain A residue 1496 ILE Chi-restraints excluded: chain N residue 101 THR Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain O residue 120 SER Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 46 ILE Chi-restraints excluded: chain Q residue 50 ILE Chi-restraints excluded: chain Q residue 86 VAL Chi-restraints excluded: chain Q residue 93 GLN Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 101 THR Chi-restraints excluded: chain p residue 46 VAL Chi-restraints excluded: chain p residue 80 THR Chi-restraints excluded: chain q residue 43 VAL Chi-restraints excluded: chain q residue 86 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: [154, 71, 99, 98, 121, 165, 131, 148, 56, 142, 153] chunk 154 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 99 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 165 optimal weight: 0.6980 chunk 131 optimal weight: 8.9990 chunk 148 optimal weight: 9.9990 chunk 56 optimal weight: 30.0000 chunk 142 optimal weight: 10.0000 chunk 153 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1412 HIS N 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.161869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.131336 restraints weight = 62932.440| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 3.27 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18881 Z= 0.131 Angle : 0.597 8.012 26912 Z= 0.333 Chirality : 0.043 0.388 3101 Planarity : 0.004 0.041 2419 Dihedral : 27.974 168.762 5024 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.94 % Allowed : 18.72 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.22), residues: 1598 helix: 2.07 (0.20), residues: 688 sheet: -0.55 (0.47), residues: 132 loop : -0.08 (0.23), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG O 83 TYR 0.018 0.001 TYR O 37 PHE 0.013 0.001 PHE A1251 TRP 0.043 0.002 TRP A1498 HIS 0.006 0.001 HIS A1502 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.13 (18865) covalent geometry : angle 0.59002 / 0.33 (26894) hydrogen bonds : bond 0.04406 / 3.01 ( 932) hydrogen bonds : angle 3.87019 / 2.78 ( 2391) metal coordination : bond 0.00763 / 0.57 ( 16) metal coordination : angle 3.48820 / 2.19 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 166 time to evaluate : 0.526 Fit side-chains REVERT: A 660 GLN cc_start: 0.7325 (OUTLIER) cc_final: 0.6850 (pm20) REVERT: A 663 GLU cc_start: 0.8490 (mt-10) cc_final: 0.7946 (mp0) REVERT: A 1371 MET cc_start: 0.2465 (tpt) cc_final: 0.1919 (mmt) REVERT: A 1503 THR cc_start: 0.5060 (OUTLIER) cc_final: 0.4720 (p) REVERT: A 1533 MET cc_start: 0.4222 (mmt) cc_final: 0.3647 (mmm) REVERT: p 41 TYR cc_start: 0.7505 (OUTLIER) cc_final: 0.5883 (t80) outliers start: 32 outliers final: 22 residues processed: 192 average time/residue: 0.1556 time to fit residues: 43.2899 Evaluate side-chains 181 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 660 GLN Chi-restraints excluded: chain A residue 797 PHE Chi-restraints excluded: chain A residue 1282 LEU Chi-restraints excluded: chain A residue 1306 VAL Chi-restraints excluded: chain A residue 1475 VAL Chi-restraints excluded: chain A residue 1496 ILE Chi-restraints excluded: chain A residue 1503 THR Chi-restraints excluded: chain A residue 1526 THR Chi-restraints excluded: chain N residue 101 THR Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain O residue 120 SER Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 46 ILE Chi-restraints excluded: chain Q residue 50 ILE Chi-restraints excluded: chain Q residue 93 GLN Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 101 THR Chi-restraints excluded: chain p residue 41 TYR Chi-restraints excluded: chain p residue 46 VAL Chi-restraints excluded: chain p residue 80 THR Chi-restraints excluded: chain q residue 43 VAL Chi-restraints excluded: chain q residue 86 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: [86, 79, 37, 62, 128, 120, 164, 98, 142, 43, 107] chunk 86 optimal weight: 0.9980 chunk 79 optimal weight: 20.0000 chunk 37 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 128 optimal weight: 10.0000 chunk 120 optimal weight: 1.9990 chunk 164 optimal weight: 0.0470 chunk 98 optimal weight: 0.9990 chunk 142 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 overall best weight: 1.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 112 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.161286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.131551 restraints weight = 62230.220| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 3.07 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18881 Z= 0.144 Angle : 0.594 7.910 26912 Z= 0.332 Chirality : 0.043 0.389 3101 Planarity : 0.004 0.041 2419 Dihedral : 27.968 168.310 5023 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.12 % Allowed : 19.08 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.22), residues: 1598 helix: 2.17 (0.20), residues: 692 sheet: -0.21 (0.48), residues: 126 loop : -0.03 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG o 96 TYR 0.017 0.001 TYR O 37 PHE 0.012 0.001 PHE A1251 TRP 0.023 0.002 TRP A1498 HIS 0.004 0.001 HIS p 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.14 (18865) covalent geometry : angle 0.58701 / 0.33 (26894) hydrogen bonds : bond 0.04429 / 3.03 ( 932) hydrogen bonds : angle 3.82127 / 2.75 ( 2391) metal coordination : bond 0.00902 / 0.73 ( 16) metal coordination : angle 3.44571 / 2.14 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 156 time to evaluate : 0.490 Fit side-chains revert: symmetry clash REVERT: A 663 GLU cc_start: 0.8345 (mt-10) cc_final: 0.8080 (mp0) REVERT: A 1503 THR cc_start: 0.4831 (OUTLIER) cc_final: 0.4461 (p) REVERT: A 1533 MET cc_start: 0.4101 (mmt) cc_final: 0.3292 (mmp) REVERT: p 41 TYR cc_start: 0.7386 (OUTLIER) cc_final: 0.5702 (t80) outliers start: 34 outliers final: 22 residues processed: 184 average time/residue: 0.1554 time to fit residues: 41.4963 Evaluate side-chains 177 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 153 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 795 HIS Chi-restraints excluded: chain A residue 797 PHE Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 1282 LEU Chi-restraints excluded: chain A residue 1306 VAL Chi-restraints excluded: chain A residue 1503 THR Chi-restraints excluded: chain A residue 1526 THR Chi-restraints excluded: chain N residue 101 THR Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 80 THR Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 46 ILE Chi-restraints excluded: chain Q residue 93 GLN Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain n residue 27 VAL Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 92 GLU Chi-restraints excluded: chain n residue 101 THR Chi-restraints excluded: chain p residue 41 TYR Chi-restraints excluded: chain p residue 80 THR Chi-restraints excluded: chain q residue 43 VAL Chi-restraints excluded: chain q residue 86 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: [64, 59, 116, 174, 165, 68, 177, 118, 9, 185, 94] chunk 64 optimal weight: 20.0000 chunk 59 optimal weight: 30.0000 chunk 116 optimal weight: 1.9990 chunk 174 optimal weight: 0.4980 chunk 165 optimal weight: 2.9990 chunk 68 optimal weight: 20.0000 chunk 177 optimal weight: 1.9990 chunk 118 optimal weight: 0.0020 chunk 9 optimal weight: 4.9990 chunk 185 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 overall best weight: 1.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 112 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.160443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.129593 restraints weight = 62507.961| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 3.20 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18881 Z= 0.154 Angle : 0.601 8.227 26912 Z= 0.334 Chirality : 0.043 0.385 3101 Planarity : 0.004 0.041 2419 Dihedral : 28.017 168.749 5022 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.66 % Allowed : 19.63 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.22), residues: 1598 helix: 2.15 (0.20), residues: 700 sheet: -0.28 (0.48), residues: 126 loop : -0.10 (0.23), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG o 96 TYR 0.017 0.002 TYR O 37 PHE 0.012 0.001 PHE A1251 TRP 0.022 0.002 TRP A1498 HIS 0.004 0.001 HIS p 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.15 (18865) covalent geometry : angle 0.59449 / 0.33 (26894) hydrogen bonds : bond 0.04518 / 3.09 ( 932) hydrogen bonds : angle 3.83750 / 2.78 ( 2391) metal coordination : bond 0.00720 / 0.52 ( 16) metal coordination : angle 3.52576 / 2.50 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 0.470 Fit side-chains revert: symmetry clash REVERT: A 663 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8096 (mp0) REVERT: A 1503 THR cc_start: 0.5055 (OUTLIER) cc_final: 0.4647 (p) REVERT: A 1533 MET cc_start: 0.4175 (mmt) cc_final: 0.3590 (mmp) REVERT: p 41 TYR cc_start: 0.7543 (OUTLIER) cc_final: 0.6092 (t80) outliers start: 29 outliers final: 25 residues processed: 186 average time/residue: 0.1620 time to fit residues: 43.5002 Evaluate side-chains 183 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 795 HIS Chi-restraints excluded: chain A residue 797 PHE Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 1165 TRP Chi-restraints excluded: chain A residue 1254 TYR Chi-restraints excluded: chain A residue 1282 LEU Chi-restraints excluded: chain A residue 1306 VAL Chi-restraints excluded: chain A residue 1475 VAL Chi-restraints excluded: chain A residue 1503 THR Chi-restraints excluded: chain A residue 1526 THR Chi-restraints excluded: chain N residue 101 THR Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 80 THR Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 46 ILE Chi-restraints excluded: chain Q residue 50 ILE Chi-restraints excluded: chain Q residue 93 GLN Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain n residue 27 VAL Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 101 THR Chi-restraints excluded: chain p residue 41 TYR Chi-restraints excluded: chain p residue 80 THR Chi-restraints excluded: chain q residue 43 VAL Chi-restraints excluded: chain q residue 86 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: [140, 171, 128, 32, 3, 61, 55, 10, 100, 185, 14] chunk 140 optimal weight: 10.0000 chunk 171 optimal weight: 0.9990 chunk 128 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 61 optimal weight: 8.9990 chunk 55 optimal weight: 50.0000 chunk 10 optimal weight: 0.0010 chunk 100 optimal weight: 5.9990 chunk 185 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 overall best weight: 2.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 112 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.157528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.127437 restraints weight = 62053.268| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 3.24 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18881 Z= 0.203 Angle : 0.656 10.018 26912 Z= 0.358 Chirality : 0.045 0.395 3101 Planarity : 0.005 0.047 2419 Dihedral : 28.176 170.295 5022 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.84 % Allowed : 19.36 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.22), residues: 1598 helix: 1.99 (0.20), residues: 699 sheet: -0.52 (0.50), residues: 121 loop : -0.29 (0.23), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 83 TYR 0.015 0.002 TYR O 37 PHE 0.011 0.002 PHE A1396 TRP 0.031 0.002 TRP A1498 HIS 0.004 0.001 HIS P 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.20 (18865) covalent geometry : angle 0.65065 / 0.36 (26894) hydrogen bonds : bond 0.05395 / 3.70 ( 932) hydrogen bonds : angle 4.14925 / 3.01 ( 2391) metal coordination : bond 0.01325 / 1.08 ( 16) metal coordination : angle 3.38864 / 2.19 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 163 time to evaluate : 0.566 Fit side-chains REVERT: A 663 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8021 (mp0) REVERT: A 1503 THR cc_start: 0.5146 (OUTLIER) cc_final: 0.4744 (p) REVERT: A 1533 MET cc_start: 0.3855 (mmt) cc_final: 0.3400 (mmm) REVERT: N 35 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7755 (ttm170) REVERT: P 39 HIS cc_start: 0.6885 (t-90) cc_final: 0.6644 (t-90) REVERT: p 41 TYR cc_start: 0.7638 (OUTLIER) cc_final: 0.6234 (t80) outliers start: 31 outliers final: 26 residues processed: 185 average time/residue: 0.1521 time to fit residues: 40.7830 Evaluate side-chains 187 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 158 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 795 HIS Chi-restraints excluded: chain A residue 797 PHE Chi-restraints excluded: chain A residue 810 ASP Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 1165 TRP Chi-restraints excluded: chain A residue 1282 LEU Chi-restraints excluded: chain A residue 1306 VAL Chi-restraints excluded: chain A residue 1475 VAL Chi-restraints excluded: chain A residue 1503 THR Chi-restraints excluded: chain A residue 1526 THR Chi-restraints excluded: chain N residue 35 ARG Chi-restraints excluded: chain N residue 74 LYS Chi-restraints excluded: chain N residue 101 THR Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 80 THR Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 46 ILE Chi-restraints excluded: chain Q residue 50 ILE Chi-restraints excluded: chain Q residue 93 GLN Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain n residue 27 VAL Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 101 THR Chi-restraints excluded: chain p residue 41 TYR Chi-restraints excluded: chain p residue 80 THR Chi-restraints excluded: chain q residue 43 VAL Chi-restraints excluded: chain q residue 86 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: [124, 116, 108, 8, 87, 9, 32, 73, 57, 72, 33] chunk 124 optimal weight: 50.0000 chunk 116 optimal weight: 0.6980 chunk 108 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 32 optimal weight: 7.9990 chunk 73 optimal weight: 7.9990 chunk 57 optimal weight: 0.0050 chunk 72 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 112 GLN O 106 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.160216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.130005 restraints weight = 62831.912| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 3.12 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 18881 Z= 0.126 Angle : 0.596 9.926 26912 Z= 0.332 Chirality : 0.042 0.377 3101 Planarity : 0.004 0.042 2419 Dihedral : 28.052 169.668 5022 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.57 % Allowed : 19.54 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.22), residues: 1598 helix: 2.15 (0.20), residues: 703 sheet: -0.40 (0.49), residues: 126 loop : -0.13 (0.23), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG O 83 TYR 0.017 0.001 TYR O 37 PHE 0.012 0.001 PHE A1251 TRP 0.019 0.002 TRP A1498 HIS 0.005 0.001 HIS O 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.13 (18865) covalent geometry : angle 0.59201 / 0.33 (26894) hydrogen bonds : bond 0.04269 / 2.92 ( 932) hydrogen bonds : angle 3.83812 / 2.78 ( 2391) metal coordination : bond 0.00457 / 0.35 ( 16) metal coordination : angle 2.82583 / 1.85 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 161 time to evaluate : 0.534 Fit side-chains REVERT: A 663 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8131 (mp0) REVERT: A 1371 MET cc_start: 0.3487 (mmt) cc_final: 0.3221 (mmt) REVERT: A 1503 THR cc_start: 0.5193 (OUTLIER) cc_final: 0.4792 (p) REVERT: A 1533 MET cc_start: 0.4122 (mmt) cc_final: 0.3545 (mmm) REVERT: P 39 HIS cc_start: 0.6919 (t-90) cc_final: 0.6615 (t-90) REVERT: o 76 ARG cc_start: 0.8490 (ttp-110) cc_final: 0.8287 (ttm110) REVERT: p 41 TYR cc_start: 0.7547 (OUTLIER) cc_final: 0.5912 (t80) outliers start: 28 outliers final: 25 residues processed: 181 average time/residue: 0.1523 time to fit residues: 39.6973 Evaluate side-chains 184 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 795 HIS Chi-restraints excluded: chain A residue 797 PHE Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 1165 TRP Chi-restraints excluded: chain A residue 1282 LEU Chi-restraints excluded: chain A residue 1306 VAL Chi-restraints excluded: chain A residue 1475 VAL Chi-restraints excluded: chain A residue 1503 THR Chi-restraints excluded: chain A residue 1526 THR Chi-restraints excluded: chain N residue 101 THR Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain O residue 120 SER Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 80 THR Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 46 ILE Chi-restraints excluded: chain Q residue 50 ILE Chi-restraints excluded: chain Q residue 93 GLN Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 92 GLU Chi-restraints excluded: chain n residue 101 THR Chi-restraints excluded: chain p residue 41 TYR Chi-restraints excluded: chain p residue 80 THR Chi-restraints excluded: chain q residue 43 VAL Chi-restraints excluded: chain q residue 86 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: [145, 187, 124, 69, 157, 33, 20, 101, 147, 172, 48] chunk 145 optimal weight: 10.0000 chunk 187 optimal weight: 3.9990 chunk 124 optimal weight: 50.0000 chunk 69 optimal weight: 6.9990 chunk 157 optimal weight: 2.9990 chunk 33 optimal weight: 20.0000 chunk 20 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 chunk 147 optimal weight: 10.0000 chunk 172 optimal weight: 0.9980 chunk 48 optimal weight: 50.0000 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 112 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.157130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.127740 restraints weight = 61527.264| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 3.34 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 18881 Z= 0.218 Angle : 0.657 11.802 26912 Z= 0.359 Chirality : 0.046 0.399 3101 Planarity : 0.005 0.045 2419 Dihedral : 28.177 170.632 5022 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.48 % Allowed : 19.54 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.22), residues: 1598 helix: 1.90 (0.20), residues: 715 sheet: -0.47 (0.54), residues: 109 loop : -0.35 (0.23), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG o 96 TYR 0.018 0.002 TYR O 37 PHE 0.011 0.002 PHE o 62 TRP 0.022 0.002 TRP A1498 HIS 0.009 0.001 HIS O 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.22 (18865) covalent geometry : angle 0.65282 / 0.36 (26894) hydrogen bonds : bond 0.05444 / 3.75 ( 932) hydrogen bonds : angle 4.11458 / 2.99 ( 2391) metal coordination : bond 0.01120 / 0.89 ( 16) metal coordination : angle 3.05408 / 1.99 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 0.597 Fit side-chains REVERT: A 663 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8241 (mp0) REVERT: A 1371 MET cc_start: 0.3449 (mmt) cc_final: 0.1652 (ttp) REVERT: A 1503 THR cc_start: 0.5433 (OUTLIER) cc_final: 0.4993 (p) REVERT: A 1533 MET cc_start: 0.3678 (mmt) cc_final: 0.3270 (mmm) REVERT: N 104 GLN cc_start: 0.8620 (mt0) cc_final: 0.8397 (mt0) REVERT: P 39 HIS cc_start: 0.6926 (t-90) cc_final: 0.6603 (t-90) REVERT: p 41 TYR cc_start: 0.7667 (OUTLIER) cc_final: 0.6297 (t80) outliers start: 27 outliers final: 23 residues processed: 179 average time/residue: 0.1567 time to fit residues: 40.6426 Evaluate side-chains 179 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 795 HIS Chi-restraints excluded: chain A residue 797 PHE Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 1282 LEU Chi-restraints excluded: chain A residue 1306 VAL Chi-restraints excluded: chain A residue 1475 VAL Chi-restraints excluded: chain A residue 1503 THR Chi-restraints excluded: chain A residue 1526 THR Chi-restraints excluded: chain N residue 101 THR Chi-restraints excluded: chain N residue 108 LEU Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain O residue 120 SER Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 80 THR Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 46 ILE Chi-restraints excluded: chain Q residue 93 GLN Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain n residue 27 VAL Chi-restraints excluded: chain n residue 51 LEU Chi-restraints excluded: chain n residue 101 THR Chi-restraints excluded: chain p residue 41 TYR Chi-restraints excluded: chain p residue 80 THR Chi-restraints excluded: chain q residue 43 VAL Chi-restraints excluded: chain q residue 86 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: [124, 64, 186, 160, 123, 86, 87, 132, 184, 62, 20] chunk 124 optimal weight: 50.0000 chunk 64 optimal weight: 3.9990 chunk 186 optimal weight: 0.9980 chunk 160 optimal weight: 2.9990 chunk 123 optimal weight: 50.0000 chunk 86 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 132 optimal weight: 10.0000 chunk 184 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 112 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.157745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.129734 restraints weight = 62430.294| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 3.53 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18881 Z= 0.171 Angle : 0.630 11.379 26912 Z= 0.346 Chirality : 0.044 0.390 3101 Planarity : 0.004 0.044 2419 Dihedral : 28.180 170.907 5022 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.57 % Allowed : 19.17 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.22), residues: 1598 helix: 1.95 (0.20), residues: 715 sheet: -0.50 (0.54), residues: 109 loop : -0.35 (0.23), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG o 96 TYR 0.016 0.002 TYR O 37 PHE 0.011 0.001 PHE A1251 TRP 0.025 0.002 TRP A1498 HIS 0.004 0.001 HIS p 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.17 (18865) covalent geometry : angle 0.62591 / 0.35 (26894) hydrogen bonds : bond 0.04862 / 3.33 ( 932) hydrogen bonds : angle 4.05377 / 2.95 ( 2391) metal coordination : bond 0.00814 / 0.64 ( 16) metal coordination : angle 2.96918 / 1.94 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3374.34 seconds wall clock time: 58 minutes 32.18 seconds (3512.18 seconds total)