Starting phenix.real_space_refine on Sat Sep 12 05:57:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7y9y_33696/09_2026/7y9y_33696.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y9y_33696/09_2026/7y9y_33696.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7y9y_33696/09_2026/7y9y_33696.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y9y_33696/09_2026/7y9y_33696.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7y9y_33696/09_2026/7y9y_33696.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7y9y_33696/09_2026/7y9y_33696.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7y9y_33696/09_2026/7y9y_33696.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y9y_33696/09_2026/7y9y_33696.map" } resolution = 2.77 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= -0.001 sd= 0.108 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 60 5.49 5 S 59 5.16 5 C 8482 2.51 5 N 2448 2.21 5 O 2728 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13781 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 801 Classifications: {'RNAv2': 38} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 9, 'rna3p_pur': 5, 'rna3p_pyr': 12} Link IDs: {'rna2p': 21, 'rna3p': 16} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 492 Classifications: {'RNAv2': 23} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 11, 'rna3p_pyr': 8} Link IDs: {'rna2p': 4, 'rna3p': 18} Chain: "A" Number of atoms: 11976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1482, 11976 Classifications: {'peptide': 1482} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 80, 'TRANS': 1401} Chain breaks: 10 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 508 Classifications: {'peptide': 63} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 60} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 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 1997 SG CYS A 86 43.488 71.566 13.212 1.00 73.56 S ATOM 2243 SG CYS A 115 43.027 74.576 11.089 1.00 85.34 S ATOM 2305 SG CYS A 123 40.244 73.448 13.682 1.00 72.06 S ATOM 2329 SG CYS A 126 43.502 74.935 14.847 1.00 67.16 S ATOM 4469 SG CYS A 463 49.806 50.388 38.636 1.00 47.08 S ATOM 4531 SG CYS A 472 50.505 51.218 34.935 1.00 41.02 S ATOM 4545 SG CYS A 474 47.858 48.711 35.793 1.00 29.05 S ATOM 4567 SG CYS A 477 47.269 52.321 36.707 1.00 25.85 S ATOM 6279 SG CYS A 706 59.042 37.439 62.684 1.00 55.19 S ATOM 6294 SG CYS A 708 57.042 35.701 63.568 1.00 47.73 S ATOM 6316 SG CYS A 711 55.965 38.883 62.624 1.00 46.20 S ATOM 8177 SG CYS A 965 54.392 40.463 100.894 1.00 10.52 S ATOM 10920 SG CYS A1312 57.406 40.558 98.511 1.00 11.55 S ATOM 11159 SG CYS A1342 55.686 37.298 99.338 1.00 14.75 S ATOM 11177 SG CYS A1345 54.000 39.651 97.060 1.00 10.74 S Time building chain proxies: 3.19, per 1000 atoms: 0.23 Number of scatterers: 13781 At special positions: 0 Unit cell: (91.3, 104.58, 181.77, 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 59 16.00 P 60 15.00 O 2728 8.00 N 2448 7.00 C 8482 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: 1.15 Conformation dependent library (CDL) restraints added in 633.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1701 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 86 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 126 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 115 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 123 " pdb=" ZN A1702 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 477 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 474 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 463 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 472 " pdb=" ZN A1703 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 708 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 706 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 711 " pdb=" ZN A1704 " pdb="ZN ZN A1704 " - pdb=" SG CYS A1342 " pdb="ZN ZN A1704 " - pdb=" SG CYS A1312 " pdb="ZN ZN A1704 " - pdb=" SG CYS A1345 " pdb="ZN ZN A1704 " - pdb=" SG CYS A 965 " Number of angles added : 18 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2876 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 23 sheets defined 30.7% alpha, 27.6% beta 18 base pairs and 25 stacking pairs defined. Time for finding SS restraints: 2.03 Creating SS restraints... Processing helix chain 'A' and resid 30 through 36 Processing helix chain 'A' and resid 57 through 76 removed outlier: 3.723A pdb=" N LEU A 61 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 98 removed outlier: 3.777A pdb=" N ARG A 97 " --> pdb=" O ASP A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 130 Processing helix chain 'A' and resid 163 through 166 Processing helix chain 'A' and resid 211 through 225 Processing helix chain 'A' and resid 261 through 276 Processing helix chain 'A' and resid 278 through 280 No H-bonds generated for 'chain 'A' and resid 278 through 280' Processing helix chain 'A' and resid 281 through 292 Processing helix chain 'A' and resid 293 through 295 No H-bonds generated for 'chain 'A' and resid 293 through 295' Processing helix chain 'A' and resid 296 through 300 Processing helix chain 'A' and resid 328 through 339 Processing helix chain 'A' and resid 340 through 343 Processing helix chain 'A' and resid 344 through 365 Processing helix chain 'A' and resid 443 through 460 Processing helix chain 'A' and resid 474 through 481 Processing helix chain 'A' and resid 542 through 554 Processing helix chain 'A' and resid 562 through 566 Processing helix chain 'A' and resid 584 through 594 Processing helix chain 'A' and resid 595 through 598 Processing helix chain 'A' and resid 599 through 608 Processing helix chain 'A' and resid 643 through 648 removed outlier: 3.719A pdb=" N VAL A 648 " --> pdb=" O ILE A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 688 Processing helix chain 'A' and resid 708 through 715 Processing helix chain 'A' and resid 780 through 784 Processing helix chain 'A' and resid 785 through 801 Processing helix chain 'A' and resid 809 through 813 Processing helix chain 'A' and resid 946 through 962 removed outlier: 3.557A pdb=" N LEU A 950 " --> pdb=" O PRO A 946 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL A 957 " --> pdb=" O MET A 953 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR A 960 " --> pdb=" O SER A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1024 removed outlier: 3.510A pdb=" N ILE A1023 " --> pdb=" O LYS A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1031 Processing helix chain 'A' and resid 1204 through 1206 No H-bonds generated for 'chain 'A' and resid 1204 through 1206' Processing helix chain 'A' and resid 1231 through 1247 Processing helix chain 'A' and resid 1254 through 1258 Processing helix chain 'A' and resid 1259 through 1264 Processing helix chain 'A' and resid 1300 through 1305 removed outlier: 3.922A pdb=" N MET A1305 " --> pdb=" O GLY A1302 " (cutoff:3.500A) Processing helix chain 'A' and resid 1328 through 1335 removed outlier: 3.654A pdb=" N LYS A1331 " --> pdb=" O TYR A1328 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1348 Processing helix chain 'A' and resid 1395 through 1400 removed outlier: 3.898A pdb=" N SER A1399 " --> pdb=" O ARG A1395 " (cutoff:3.500A) Processing helix chain 'A' and resid 1420 through 1427 removed outlier: 3.729A pdb=" N ILE A1424 " --> pdb=" O ALA A1420 " (cutoff:3.500A) Processing helix chain 'A' and resid 1464 through 1477 Processing helix chain 'A' and resid 1488 through 1492 Processing helix chain 'A' and resid 1518 through 1534 removed outlier: 3.624A pdb=" N TRP A1522 " --> pdb=" O GLU A1518 " (cutoff:3.500A) Processing helix chain 'A' and resid 1538 through 1548 removed outlier: 4.043A pdb=" N GLU A1542 " --> pdb=" O LEU A1538 " (cutoff:3.500A) Processing helix chain 'A' and resid 1565 through 1569 Processing helix chain 'A' and resid 1575 through 1581 removed outlier: 3.850A pdb=" N ASP A1581 " --> pdb=" O GLU A1577 " (cutoff:3.500A) Processing helix chain 'A' and resid 1588 through 1594 Processing helix chain 'B' and resid 4 through 14 Processing helix chain 'B' and resid 19 through 39 Processing helix chain 'B' and resid 41 through 46 Processing helix chain 'B' and resid 52 through 65 Processing sheet with id=AA1, first strand: chain 'A' and resid 148 through 150 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 17 removed outlier: 3.684A pdb=" N ASP A 185 " --> pdb=" O ARG A 175 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 46 removed outlier: 8.230A pdb=" N LYS A 51 " --> pdb=" O ASN A 45 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 79 through 80 Processing sheet with id=AA5, first strand: chain 'A' and resid 106 through 107 removed outlier: 5.092A pdb=" N THR A 106 " --> pdb=" O VAL A 395 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 483 through 485 removed outlier: 4.924A pdb=" N GLU A 409 " --> pdb=" O ASN A 574 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N ASN A 574 " --> pdb=" O GLU A 409 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL A 411 " --> pdb=" O MET A 572 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N MET A 572 " --> pdb=" O VAL A 411 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A 557 " --> pdb=" O PHE A 570 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 483 through 485 removed outlier: 4.924A pdb=" N GLU A 409 " --> pdb=" O ASN A 574 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N ASN A 574 " --> pdb=" O GLU A 409 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL A 411 " --> pdb=" O MET A 572 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N MET A 572 " --> pdb=" O VAL A 411 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 441 through 442 Processing sheet with id=AA9, first strand: chain 'A' and resid 497 through 504 removed outlier: 10.754A pdb=" N GLU A 497 " --> pdb=" O ASN A 518 " (cutoff:3.500A) removed outlier: 9.424A pdb=" N ASN A 518 " --> pdb=" O GLU A 497 " (cutoff:3.500A) removed outlier: 11.023A pdb=" N ARG A 499 " --> pdb=" O LEU A 516 " (cutoff:3.500A) removed outlier: 9.658A pdb=" N LEU A 516 " --> pdb=" O ARG A 499 " (cutoff:3.500A) removed outlier: 9.512A pdb=" N ARG A 501 " --> pdb=" O GLY A 514 " (cutoff:3.500A) removed outlier: 9.363A pdb=" N GLY A 514 " --> pdb=" O ARG A 501 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ARG A 503 " --> pdb=" O ALA A 512 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 659 through 664 removed outlier: 7.198A pdb=" N CYS A 672 " --> pdb=" O PHE A 730 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N PHE A 730 " --> pdb=" O CYS A 672 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 659 through 664 removed outlier: 7.198A pdb=" N CYS A 672 " --> pdb=" O PHE A 730 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N PHE A 730 " --> pdb=" O CYS A 672 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 641 through 642 removed outlier: 3.765A pdb=" N VAL A 656 " --> pdb=" O ASP A 642 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 739 through 744 removed outlier: 11.314A pdb=" N PHE A 739 " --> pdb=" O LYS A 756 " (cutoff:3.500A) removed outlier: 10.223A pdb=" N LYS A 756 " --> pdb=" O PHE A 739 " (cutoff:3.500A) removed outlier: 10.631A pdb=" N HIS A 741 " --> pdb=" O LYS A 754 " (cutoff:3.500A) removed outlier: 9.494A pdb=" N LYS A 754 " --> pdb=" O HIS A 741 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ALA A 743 " --> pdb=" O ALA A 752 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1558 through 1559 removed outlier: 6.667A pdb=" N VAL A 861 " --> pdb=" O TRP A1600 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 865 through 868 Processing sheet with id=AB7, first strand: chain 'A' and resid 944 through 945 removed outlier: 6.713A pdb=" N SER A1453 " --> pdb=" O THR A 901 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR A 901 " --> pdb=" O SER A1453 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N SER A1455 " --> pdb=" O LEU A 899 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LEU A 899 " --> pdb=" O SER A1455 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N GLU A1457 " --> pdb=" O CYS A 897 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N CYS A 897 " --> pdb=" O GLU A1457 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ALA A1459 " --> pdb=" O ILE A 895 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE A 895 " --> pdb=" O ALA A1459 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N GLU A1461 " --> pdb=" O GLY A 893 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N GLY A 893 " --> pdb=" O GLU A1461 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N THR A 892 " --> pdb=" O ARG A1506 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LYS A 898 " --> pdb=" O VAL A1500 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N VAL A1500 " --> pdb=" O LYS A 898 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ILE A 900 " --> pdb=" O ILE A1498 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ILE A1498 " --> pdb=" O ILE A 900 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1357 through 1359 removed outlier: 6.713A pdb=" N SER A1453 " --> pdb=" O THR A 901 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR A 901 " --> pdb=" O SER A1453 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N SER A1455 " --> pdb=" O LEU A 899 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LEU A 899 " --> pdb=" O SER A1455 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N GLU A1457 " --> pdb=" O CYS A 897 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N CYS A 897 " --> pdb=" O GLU A1457 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ALA A1459 " --> pdb=" O ILE A 895 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE A 895 " --> pdb=" O ALA A1459 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N GLU A1461 " --> pdb=" O GLY A 893 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N GLY A 893 " --> pdb=" O GLU A1461 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N THR A 892 " --> pdb=" O ARG A1506 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LYS A 898 " --> pdb=" O VAL A1500 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N VAL A1500 " --> pdb=" O LYS A 898 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ILE A 900 " --> pdb=" O ILE A1498 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ILE A1498 " --> pdb=" O ILE A 900 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 908 through 909 removed outlier: 4.124A pdb=" N ALA A 935 " --> pdb=" O ASP A 909 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LYS A 932 " --> pdb=" O THR A1444 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N GLU A1446 " --> pdb=" O LYS A 932 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N TYR A 934 " --> pdb=" O GLU A1446 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 976 through 978 Processing sheet with id=AC2, first strand: chain 'A' and resid 1035 through 1036 removed outlier: 9.009A pdb=" N GLU A1145 " --> pdb=" O ASP A1221 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASP A1221 " --> pdb=" O GLU A1145 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR A1217 " --> pdb=" O HIS A1149 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU A1222 " --> pdb=" O PHE A1005 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N PHE A1005 " --> pdb=" O LEU A1222 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N GLU A1224 " --> pdb=" O GLN A1003 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLN A1003 " --> pdb=" O GLU A1224 " (cutoff:3.500A) removed outlier: 10.001A pdb=" N GLU A1226 " --> pdb=" O HIS A1001 " (cutoff:3.500A) removed outlier: 9.226A pdb=" N HIS A1001 " --> pdb=" O GLU A1226 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG A 994 " --> pdb=" O GLN A1003 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TYR A1276 " --> pdb=" O ILE A1287 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ILE A1287 " --> pdb=" O TYR A1276 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LYS A1278 " --> pdb=" O GLU A1285 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1038 through 1047 removed outlier: 4.560A pdb=" N VAL A1039 " --> pdb=" O LYS A1128 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LYS A1128 " --> pdb=" O VAL A1039 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG A1041 " --> pdb=" O TYR A1126 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS A1067 " --> pdb=" O VAL A1121 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N TYR A1082 " --> pdb=" O ILE A1074 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLN A1076 " --> pdb=" O SER A1080 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N SER A1080 " --> pdb=" O GLN A1076 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1187 through 1190 removed outlier: 7.209A pdb=" N GLU A1196 " --> pdb=" O LYS A1189 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 1349 through 1350 483 hydrogen bonds defined for protein. 1299 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 43 hydrogen bonds 82 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 25 stacking parallelities Total time for adding SS restraints: 4.11 Time building geometry restraints manager: 1.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4169 1.34 - 1.46: 2700 1.46 - 1.58: 7143 1.58 - 1.69: 119 1.69 - 1.81: 85 Bond restraints: 14216 Sorted by residual: bond pdb=" CG PRO A 87 " pdb=" CD PRO A 87 " ideal model delta sigma weight residual 1.503 1.447 0.056 3.40e-02 8.65e+02 2.71e+00 bond pdb=" C ILE A1519 " pdb=" N PRO A1520 " ideal model delta sigma weight residual 1.335 1.357 -0.022 1.38e-02 5.25e+03 2.49e+00 bond pdb=" C LYS A 158 " pdb=" O LYS A 158 " ideal model delta sigma weight residual 1.235 1.228 0.007 4.70e-03 4.53e+04 2.20e+00 bond pdb=" CB ASP A 311 " pdb=" CG ASP A 311 " ideal model delta sigma weight residual 1.516 1.547 -0.031 2.50e-02 1.60e+03 1.58e+00 bond pdb=" CA GLU A1196 " pdb=" CB GLU A1196 " ideal model delta sigma weight residual 1.522 1.530 -0.008 7.00e-03 2.04e+04 1.32e+00 ... (remaining 14211 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 19184 2.84 - 5.67: 247 5.67 - 8.51: 6 8.51 - 11.34: 3 11.34 - 14.18: 1 Bond angle restraints: 19441 Sorted by residual: angle pdb=" N PRO A 87 " pdb=" CD PRO A 87 " pdb=" CG PRO A 87 " ideal model delta sigma weight residual 103.20 94.19 9.01 1.50e+00 4.44e-01 3.61e+01 angle pdb=" CA PRO A 87 " pdb=" CB PRO A 87 " pdb=" CG PRO A 87 " ideal model delta sigma weight residual 104.50 93.58 10.92 1.90e+00 2.77e-01 3.30e+01 angle pdb=" CA PRO A 87 " pdb=" N PRO A 87 " pdb=" CD PRO A 87 " ideal model delta sigma weight residual 112.00 105.14 6.86 1.40e+00 5.10e-01 2.40e+01 angle pdb=" CB PRO A 87 " pdb=" CG PRO A 87 " pdb=" CD PRO A 87 " ideal model delta sigma weight residual 106.10 91.92 14.18 3.20e+00 9.77e-02 1.96e+01 angle pdb=" N PRO A 87 " pdb=" CA PRO A 87 " pdb=" CB PRO A 87 " ideal model delta sigma weight residual 103.52 99.64 3.88 9.50e-01 1.11e+00 1.67e+01 ... (remaining 19436 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.56: 7106 16.56 - 33.12: 875 33.12 - 49.68: 277 49.68 - 66.25: 179 66.25 - 82.81: 44 Dihedral angle restraints: 8481 sinusoidal: 4027 harmonic: 4454 Sorted by residual: dihedral pdb=" C4' A R 29 " pdb=" C3' A R 29 " pdb=" C2' A R 29 " pdb=" C1' A R 29 " ideal model delta sinusoidal sigma weight residual 36.34 -38.85 75.19 1 3.10e+00 1.04e-01 7.44e+02 dihedral pdb=" C4' G R 28 " pdb=" C3' G R 28 " pdb=" C2' G R 28 " pdb=" C1' G R 28 " ideal model delta sinusoidal sigma weight residual 36.35 -38.25 74.59 1 3.10e+00 1.04e-01 7.34e+02 dihedral pdb=" C4' A R 13 " pdb=" C3' A R 13 " pdb=" C2' A R 13 " pdb=" C1' A R 13 " ideal model delta sinusoidal sigma weight residual 36.34 -37.85 74.20 1 3.10e+00 1.04e-01 7.27e+02 ... (remaining 8478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1773 0.065 - 0.130: 197 0.130 - 0.195: 12 0.195 - 0.260: 72 0.260 - 0.326: 35 Chirality restraints: 2089 Sorted by residual: chirality pdb=" C3' A R 13 " pdb=" C4' A R 13 " pdb=" O3' A R 13 " pdb=" C2' A R 13 " both_signs ideal model delta sigma weight residual False -2.50 -2.82 0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" C3' G R 19 " pdb=" C4' G R 19 " pdb=" O3' G R 19 " pdb=" C2' G R 19 " both_signs ideal model delta sigma weight residual False -2.50 -2.82 0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" C3' G R 28 " pdb=" C4' G R 28 " pdb=" O3' G R 28 " pdb=" C2' G R 28 " both_signs ideal model delta sigma weight residual False -2.50 -2.81 0.31 2.00e-01 2.50e+01 2.43e+00 ... (remaining 2086 not shown) Planarity restraints: 2307 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G R 19 " 0.039 2.00e-02 2.50e+03 1.76e-02 9.25e+00 pdb=" N9 G R 19 " -0.045 2.00e-02 2.50e+03 pdb=" C8 G R 19 " -0.002 2.00e-02 2.50e+03 pdb=" N7 G R 19 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G R 19 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G R 19 " 0.004 2.00e-02 2.50e+03 pdb=" O6 G R 19 " 0.009 2.00e-02 2.50e+03 pdb=" N1 G R 19 " 0.003 2.00e-02 2.50e+03 pdb=" C2 G R 19 " -0.002 2.00e-02 2.50e+03 pdb=" N2 G R 19 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G R 19 " -0.005 2.00e-02 2.50e+03 pdb=" C4 G R 19 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U R 1 " -0.033 2.00e-02 2.50e+03 1.71e-02 6.57e+00 pdb=" N1 U R 1 " 0.037 2.00e-02 2.50e+03 pdb=" C2 U R 1 " 0.001 2.00e-02 2.50e+03 pdb=" O2 U R 1 " 0.004 2.00e-02 2.50e+03 pdb=" N3 U R 1 " -0.004 2.00e-02 2.50e+03 pdb=" C4 U R 1 " -0.004 2.00e-02 2.50e+03 pdb=" O4 U R 1 " -0.008 2.00e-02 2.50e+03 pdb=" C5 U R 1 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U R 1 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U R 17 " -0.032 2.00e-02 2.50e+03 1.62e-02 5.93e+00 pdb=" N1 U R 17 " 0.035 2.00e-02 2.50e+03 pdb=" C2 U R 17 " 0.003 2.00e-02 2.50e+03 pdb=" O2 U R 17 " 0.002 2.00e-02 2.50e+03 pdb=" N3 U R 17 " 0.000 2.00e-02 2.50e+03 pdb=" C4 U R 17 " -0.004 2.00e-02 2.50e+03 pdb=" O4 U R 17 " -0.010 2.00e-02 2.50e+03 pdb=" C5 U R 17 " -0.000 2.00e-02 2.50e+03 pdb=" C6 U R 17 " 0.007 2.00e-02 2.50e+03 ... (remaining 2304 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 157 2.63 - 3.20: 11610 3.20 - 3.77: 21816 3.77 - 4.33: 32200 4.33 - 4.90: 51256 Nonbonded interactions: 117039 Sorted by model distance: nonbonded pdb=" OG SER A1047 " pdb=" OD2 ASP A1104 " model vdw 2.064 3.040 nonbonded pdb=" N2 G R 19 " pdb=" O2 C D 19 " model vdw 2.079 2.496 nonbonded pdb=" OH TYR A1014 " pdb=" OE2 GLU A1216 " model vdw 2.136 3.040 nonbonded pdb=" OG1 THR A1072 " pdb=" OD1 ASN A1084 " model vdw 2.138 3.040 nonbonded pdb=" O2' C R 27 " pdb=" O GLU A1392 " model vdw 2.225 3.040 ... (remaining 117034 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.100 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: 0.280 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 19.090 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14231 Z= 0.151 Angle : 0.724 14.176 19459 Z= 0.367 Chirality : 0.070 0.326 2089 Planarity : 0.005 0.053 2307 Dihedral : 18.462 82.808 5605 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.63 % Allowed : 23.29 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.21), residues: 1521 helix: 0.71 (0.27), residues: 393 sheet: 0.48 (0.28), residues: 305 loop : -0.37 (0.21), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 768 TYR 0.015 0.002 TYR A 930 PHE 0.016 0.002 PHE A 937 TRP 0.010 0.001 TRP A1549 HIS 0.007 0.001 HIS A 741 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (14216) covalent geometry : angle 0.71917 / 0.37 (19441) hydrogen bonds : bond 0.16145 / 8.23 ( 491) hydrogen bonds : angle 6.53795 / 2.63 ( 1381) metal coordination : bond 0.00508 / 0.28 ( 15) metal coordination : angle 2.97225 / 0.99 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: A 470 ARG cc_start: 0.7457 (mmm160) cc_final: 0.7097 (mmm-85) REVERT: A 1046 LEU cc_start: 0.4332 (OUTLIER) cc_final: 0.4044 (pt) outliers start: 22 outliers final: 12 residues processed: 170 average time/residue: 0.7115 time to fit residues: 130.7535 Evaluate side-chains 157 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 896 ARG Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1350 THR Chi-restraints excluded: chain A residue 1468 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.2980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 ASN A 118 ASN A 170 GLN ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 GLN A 344 ASN A 427 GLN A 531 GLN A 691 HIS A 963 ASN A1088 ASN A1089 ASN A1131 GLN A1136 ASN A1149 HIS A1168 ASN A1246 ASN A1337 HIS A1366 ASN A1382 HIS A1418 HIS A1429 HIS A1511 GLN A1571 ASN B 3 ASN B 9 GLN B 19 ASN B 25 ASN B 55 ASN B 59 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.178501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.143047 restraints weight = 14226.645| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.39 r_work: 0.3449 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14231 Z= 0.198 Angle : 1.045 18.482 19459 Z= 0.449 Chirality : 0.106 1.429 2089 Planarity : 0.005 0.041 2307 Dihedral : 13.877 149.393 2433 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.56 % Allowed : 18.92 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.21), residues: 1521 helix: 1.02 (0.26), residues: 405 sheet: 0.38 (0.28), residues: 312 loop : -0.28 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 768 TYR 0.015 0.002 TYR A1126 PHE 0.016 0.002 PHE A 416 TRP 0.011 0.001 TRP A 597 HIS 0.007 0.001 HIS A 741 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.20 (14216) covalent geometry : angle 1.04165 / 0.45 (19441) hydrogen bonds : bond 0.05098 / 2.79 ( 491) hydrogen bonds : angle 4.98687 / 2.00 ( 1381) metal coordination : bond 0.00543 / 0.29 ( 15) metal coordination : angle 2.97274 / 0.99 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 155 time to evaluate : 0.516 Fit side-chains revert: symmetry clash REVERT: A 290 ARG cc_start: 0.7604 (ttt90) cc_final: 0.6780 (tmm-80) REVERT: A 311 ASP cc_start: 0.7436 (t70) cc_final: 0.7033 (t0) REVERT: A 470 ARG cc_start: 0.7448 (mmm160) cc_final: 0.7026 (mmm-85) REVERT: A 735 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7735 (mm-30) REVERT: A 786 GLU cc_start: 0.6392 (tt0) cc_final: 0.6020 (tm-30) REVERT: A 942 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.6613 (tm-30) REVERT: A 1021 PHE cc_start: 0.5958 (OUTLIER) cc_final: 0.4380 (t80) REVERT: A 1157 GLU cc_start: 0.6604 (OUTLIER) cc_final: 0.4797 (mm-30) outliers start: 48 outliers final: 18 residues processed: 188 average time/residue: 0.6880 time to fit residues: 139.7078 Evaluate side-chains 172 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 611 ASN Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 881 CYS Chi-restraints excluded: chain A residue 933 SER Chi-restraints excluded: chain A residue 942 GLN Chi-restraints excluded: chain A residue 1021 PHE Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1116 LYS Chi-restraints excluded: chain A residue 1157 GLU Chi-restraints excluded: chain A residue 1241 LEU Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1468 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 14 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 122 optimal weight: 0.4980 chunk 100 optimal weight: 0.9990 chunk 102 optimal weight: 10.0000 chunk 56 optimal weight: 0.9990 chunk 104 optimal weight: 9.9990 chunk 156 optimal weight: 1.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 GLN ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 691 HIS A 712 GLN A 940 HIS A1168 ASN B 25 ASN B 36 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.180043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.144052 restraints weight = 14403.175| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.40 r_work: 0.3453 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14231 Z= 0.164 Angle : 0.834 14.721 19459 Z= 0.371 Chirality : 0.079 0.858 2089 Planarity : 0.005 0.042 2307 Dihedral : 14.158 167.439 2422 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.12 % Allowed : 19.88 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.21), residues: 1521 helix: 1.18 (0.26), residues: 405 sheet: 0.37 (0.28), residues: 306 loop : -0.30 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 448 TYR 0.013 0.002 TYR A1576 PHE 0.015 0.002 PHE A 416 TRP 0.012 0.001 TRP A1141 HIS 0.005 0.001 HIS A 741 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (14216) covalent geometry : angle 0.83082 / 0.37 (19441) hydrogen bonds : bond 0.04521 / 2.69 ( 491) hydrogen bonds : angle 4.71487 / 1.88 ( 1381) metal coordination : bond 0.00477 / 0.25 ( 15) metal coordination : angle 2.60438 / 0.87 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 154 time to evaluate : 0.499 Fit side-chains revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7717 (tp) REVERT: A 99 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7018 (tt) REVERT: A 267 GLU cc_start: 0.6679 (mm-30) cc_final: 0.6375 (mt-10) REVERT: A 290 ARG cc_start: 0.7592 (ttt90) cc_final: 0.6760 (tmm-80) REVERT: A 311 ASP cc_start: 0.7390 (t70) cc_final: 0.6912 (t0) REVERT: A 498 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8428 (mm) REVERT: A 667 GLU cc_start: 0.6589 (mm-30) cc_final: 0.6351 (tm-30) REVERT: A 735 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7718 (mm-30) REVERT: A 786 GLU cc_start: 0.6452 (tt0) cc_final: 0.6080 (tm-30) REVERT: A 857 GLU cc_start: 0.7408 (mt-10) cc_final: 0.7071 (mt-10) REVERT: A 942 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.6537 (tm-30) REVERT: A 1021 PHE cc_start: 0.5944 (OUTLIER) cc_final: 0.4178 (t80) REVERT: A 1229 GLU cc_start: 0.5635 (tp30) cc_final: 0.5398 (tp30) REVERT: B 42 GLU cc_start: 0.7515 (tm-30) cc_final: 0.7265 (tm-30) outliers start: 42 outliers final: 19 residues processed: 187 average time/residue: 0.6823 time to fit residues: 137.6444 Evaluate side-chains 171 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 146 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 611 ASN Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 881 CYS Chi-restraints excluded: chain A residue 933 SER Chi-restraints excluded: chain A residue 942 GLN Chi-restraints excluded: chain A residue 1021 PHE Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1116 LYS Chi-restraints excluded: chain A residue 1241 LEU Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1468 LEU Chi-restraints excluded: chain A residue 1598 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 24 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 114 optimal weight: 0.6980 chunk 16 optimal weight: 0.0070 chunk 108 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 104 optimal weight: 20.0000 chunk 25 optimal weight: 0.6980 chunk 95 optimal weight: 0.8980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 691 HIS A 712 GLN A1168 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.182150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.147034 restraints weight = 14346.102| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.49 r_work: 0.3500 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14231 Z= 0.135 Angle : 0.768 12.230 19459 Z= 0.341 Chirality : 0.072 0.765 2089 Planarity : 0.004 0.043 2307 Dihedral : 14.161 179.432 2422 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.56 % Allowed : 19.96 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.21), residues: 1521 helix: 1.30 (0.26), residues: 410 sheet: 0.45 (0.29), residues: 292 loop : -0.25 (0.21), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 768 TYR 0.013 0.001 TYR A1126 PHE 0.015 0.001 PHE A1073 TRP 0.008 0.001 TRP A1549 HIS 0.004 0.001 HIS A 741 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (14216) covalent geometry : angle 0.76512 / 0.34 (19441) hydrogen bonds : bond 0.04132 / 2.48 ( 491) hydrogen bonds : angle 4.48113 / 1.78 ( 1381) metal coordination : bond 0.00380 / 0.20 ( 15) metal coordination : angle 2.25329 / 0.75 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 161 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.6909 (tt) REVERT: A 290 ARG cc_start: 0.7568 (ttt90) cc_final: 0.6745 (tmm-80) REVERT: A 498 ILE cc_start: 0.8780 (OUTLIER) cc_final: 0.8431 (mm) REVERT: A 667 GLU cc_start: 0.6544 (mm-30) cc_final: 0.6327 (tm-30) REVERT: A 735 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7644 (mm-30) REVERT: A 857 GLU cc_start: 0.7409 (mt-10) cc_final: 0.7023 (mt-10) REVERT: A 872 LYS cc_start: 0.8003 (mmtm) cc_final: 0.7755 (mptt) REVERT: A 942 GLN cc_start: 0.7916 (OUTLIER) cc_final: 0.6427 (tm-30) REVERT: A 991 LEU cc_start: 0.7493 (OUTLIER) cc_final: 0.7170 (mt) REVERT: A 1021 PHE cc_start: 0.5902 (OUTLIER) cc_final: 0.4141 (t80) REVERT: A 1157 GLU cc_start: 0.6404 (OUTLIER) cc_final: 0.4955 (mm-30) REVERT: A 1209 TYR cc_start: 0.7708 (m-80) cc_final: 0.7427 (m-80) REVERT: A 1229 GLU cc_start: 0.5648 (tp30) cc_final: 0.5375 (tp30) REVERT: A 1232 GLU cc_start: 0.7227 (tp30) cc_final: 0.6422 (mp0) REVERT: A 1282 LYS cc_start: 0.6259 (tptp) cc_final: 0.5787 (mtmm) REVERT: A 1504 ARG cc_start: 0.6288 (mtp85) cc_final: 0.6037 (mtm180) outliers start: 48 outliers final: 17 residues processed: 200 average time/residue: 0.6923 time to fit residues: 149.8006 Evaluate side-chains 170 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 942 GLN Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 1021 PHE Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1116 LYS Chi-restraints excluded: chain A residue 1157 GLU Chi-restraints excluded: chain A residue 1241 LEU Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1439 SER Chi-restraints excluded: chain A residue 1468 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 15 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 113 optimal weight: 0.5980 chunk 69 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 80 optimal weight: 0.0270 chunk 31 optimal weight: 0.7980 chunk 125 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 712 GLN A1168 ASN B 3 ASN ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.182481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.147655 restraints weight = 14389.912| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 1.39 r_work: 0.3504 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14231 Z= 0.132 Angle : 0.747 11.978 19459 Z= 0.334 Chirality : 0.069 0.741 2089 Planarity : 0.004 0.046 2307 Dihedral : 14.088 178.579 2421 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.78 % Allowed : 20.10 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.21), residues: 1521 helix: 1.43 (0.26), residues: 410 sheet: 0.46 (0.29), residues: 296 loop : -0.24 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 768 TYR 0.012 0.001 TYR A1208 PHE 0.014 0.001 PHE A1073 TRP 0.009 0.001 TRP A1141 HIS 0.004 0.001 HIS A 741 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (14216) covalent geometry : angle 0.74513 / 0.33 (19441) hydrogen bonds : bond 0.04098 / 2.49 ( 491) hydrogen bonds : angle 4.39373 / 1.75 ( 1381) metal coordination : bond 0.00366 / 0.20 ( 15) metal coordination : angle 2.04213 / 0.68 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 156 time to evaluate : 0.487 Fit side-chains REVERT: A 99 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.6962 (tt) REVERT: A 290 ARG cc_start: 0.7548 (OUTLIER) cc_final: 0.6722 (tmm-80) REVERT: A 498 ILE cc_start: 0.8792 (OUTLIER) cc_final: 0.8433 (mm) REVERT: A 667 GLU cc_start: 0.6545 (mm-30) cc_final: 0.6334 (tm-30) REVERT: A 735 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7623 (mm-30) REVERT: A 759 ASP cc_start: 0.8037 (p0) cc_final: 0.7828 (p0) REVERT: A 872 LYS cc_start: 0.7993 (mmtm) cc_final: 0.7736 (mptt) REVERT: A 942 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.6413 (tm-30) REVERT: A 991 LEU cc_start: 0.7520 (OUTLIER) cc_final: 0.7196 (mt) REVERT: A 1021 PHE cc_start: 0.5868 (OUTLIER) cc_final: 0.4166 (t80) REVERT: A 1116 LYS cc_start: 0.6974 (OUTLIER) cc_final: 0.6716 (mppt) REVERT: A 1157 GLU cc_start: 0.6440 (OUTLIER) cc_final: 0.4902 (mm-30) REVERT: A 1209 TYR cc_start: 0.7690 (m-80) cc_final: 0.7454 (m-80) REVERT: A 1229 GLU cc_start: 0.5637 (tp30) cc_final: 0.5385 (tp30) REVERT: A 1232 GLU cc_start: 0.7242 (tp30) cc_final: 0.6451 (mp0) outliers start: 51 outliers final: 19 residues processed: 196 average time/residue: 0.6295 time to fit residues: 134.2311 Evaluate side-chains 174 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 290 ARG Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 933 SER Chi-restraints excluded: chain A residue 942 GLN Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 1021 PHE Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1116 LYS Chi-restraints excluded: chain A residue 1157 GLU Chi-restraints excluded: chain A residue 1241 LEU Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1439 SER Chi-restraints excluded: chain A residue 1468 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 87 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 138 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 712 GLN A1168 ASN ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.181460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.146326 restraints weight = 14289.888| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 1.45 r_work: 0.3475 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14231 Z= 0.143 Angle : 0.764 11.480 19459 Z= 0.342 Chirality : 0.070 0.756 2089 Planarity : 0.004 0.041 2307 Dihedral : 14.047 176.752 2420 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.93 % Allowed : 19.96 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.21), residues: 1521 helix: 1.46 (0.26), residues: 410 sheet: 0.30 (0.28), residues: 301 loop : -0.27 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 768 TYR 0.020 0.002 TYR A1208 PHE 0.014 0.001 PHE A 416 TRP 0.009 0.001 TRP A1141 HIS 0.005 0.001 HIS A 691 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (14216) covalent geometry : angle 0.76207 / 0.34 (19441) hydrogen bonds : bond 0.04170 / 2.49 ( 491) hydrogen bonds : angle 4.39149 / 1.75 ( 1381) metal coordination : bond 0.00408 / 0.22 ( 15) metal coordination : angle 2.05561 / 0.69 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 151 time to evaluate : 0.524 Fit side-chains REVERT: A 99 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.6985 (tt) REVERT: A 290 ARG cc_start: 0.7616 (ttt90) cc_final: 0.6791 (tmm-80) REVERT: A 498 ILE cc_start: 0.8834 (OUTLIER) cc_final: 0.8447 (mm) REVERT: A 667 GLU cc_start: 0.6572 (mm-30) cc_final: 0.6335 (tm-30) REVERT: A 735 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7641 (mm-30) REVERT: A 786 GLU cc_start: 0.6469 (tt0) cc_final: 0.6032 (tm-30) REVERT: A 872 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7759 (mptt) REVERT: A 895 ILE cc_start: 0.6886 (mt) cc_final: 0.6564 (mt) REVERT: A 942 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.6467 (tm-30) REVERT: A 991 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7248 (mt) REVERT: A 1021 PHE cc_start: 0.5900 (OUTLIER) cc_final: 0.4102 (t80) REVERT: A 1116 LYS cc_start: 0.7028 (OUTLIER) cc_final: 0.6734 (mppt) REVERT: A 1132 GLU cc_start: 0.6358 (OUTLIER) cc_final: 0.6031 (mm-30) REVERT: A 1157 GLU cc_start: 0.6511 (OUTLIER) cc_final: 0.4958 (mm-30) REVERT: A 1209 TYR cc_start: 0.7727 (m-80) cc_final: 0.7506 (m-80) REVERT: A 1232 GLU cc_start: 0.7268 (tp30) cc_final: 0.6494 (mp0) REVERT: A 1487 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7732 (ptp) outliers start: 53 outliers final: 24 residues processed: 194 average time/residue: 0.6575 time to fit residues: 138.3111 Evaluate side-chains 177 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 142 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 872 LYS Chi-restraints excluded: chain A residue 881 CYS Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 933 SER Chi-restraints excluded: chain A residue 942 GLN Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 1021 PHE Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1116 LYS Chi-restraints excluded: chain A residue 1132 GLU Chi-restraints excluded: chain A residue 1157 GLU Chi-restraints excluded: chain A residue 1241 LEU Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1367 ASP Chi-restraints excluded: chain A residue 1439 SER Chi-restraints excluded: chain A residue 1468 LEU Chi-restraints excluded: chain A residue 1487 MET Chi-restraints excluded: chain A residue 1503 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 14 optimal weight: 6.9990 chunk 154 optimal weight: 5.9990 chunk 128 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 141 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 123 optimal weight: 0.0570 chunk 97 optimal weight: 0.5980 overall best weight: 0.9102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 712 GLN A1168 ASN ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.180598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.145893 restraints weight = 14385.900| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.73 r_work: 0.3477 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14231 Z= 0.154 Angle : 0.777 11.763 19459 Z= 0.348 Chirality : 0.072 0.786 2089 Planarity : 0.004 0.041 2307 Dihedral : 14.069 174.852 2420 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.56 % Allowed : 20.47 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.21), residues: 1521 helix: 1.46 (0.26), residues: 410 sheet: 0.34 (0.28), residues: 311 loop : -0.30 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 768 TYR 0.018 0.002 TYR A1283 PHE 0.015 0.002 PHE A 416 TRP 0.012 0.001 TRP A1141 HIS 0.005 0.001 HIS A 691 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (14216) covalent geometry : angle 0.77430 / 0.35 (19441) hydrogen bonds : bond 0.04235 / 2.51 ( 491) hydrogen bonds : angle 4.40132 / 1.74 ( 1381) metal coordination : bond 0.00428 / 0.23 ( 15) metal coordination : angle 2.13298 / 0.71 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 147 time to evaluate : 0.529 Fit side-chains REVERT: A 29 ASN cc_start: 0.7742 (m110) cc_final: 0.7411 (m-40) REVERT: A 99 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.6932 (tt) REVERT: A 290 ARG cc_start: 0.7553 (OUTLIER) cc_final: 0.6687 (tmm-80) REVERT: A 498 ILE cc_start: 0.8812 (OUTLIER) cc_final: 0.8452 (mm) REVERT: A 667 GLU cc_start: 0.6543 (mm-30) cc_final: 0.6277 (tm-30) REVERT: A 735 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7624 (mm-30) REVERT: A 786 GLU cc_start: 0.6415 (tt0) cc_final: 0.5961 (tm-30) REVERT: A 942 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.6423 (tm-30) REVERT: A 991 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.7162 (mt) REVERT: A 1021 PHE cc_start: 0.5877 (OUTLIER) cc_final: 0.3998 (t80) REVERT: A 1116 LYS cc_start: 0.6993 (OUTLIER) cc_final: 0.6659 (mppt) REVERT: A 1132 GLU cc_start: 0.6391 (OUTLIER) cc_final: 0.6032 (mm-30) REVERT: A 1157 GLU cc_start: 0.6487 (OUTLIER) cc_final: 0.4942 (mm-30) REVERT: A 1229 GLU cc_start: 0.5618 (tp30) cc_final: 0.5394 (tp30) REVERT: A 1232 GLU cc_start: 0.7175 (tp30) cc_final: 0.6390 (mp0) outliers start: 48 outliers final: 23 residues processed: 185 average time/residue: 0.6846 time to fit residues: 137.0259 Evaluate side-chains 175 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 142 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 290 ARG Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 881 CYS Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 933 SER Chi-restraints excluded: chain A residue 942 GLN Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 1021 PHE Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1116 LYS Chi-restraints excluded: chain A residue 1132 GLU Chi-restraints excluded: chain A residue 1157 GLU Chi-restraints excluded: chain A residue 1241 LEU Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1367 ASP Chi-restraints excluded: chain A residue 1439 SER Chi-restraints excluded: chain A residue 1468 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 48 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 153 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 712 GLN A 887 HIS A1168 ASN ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.177985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.141670 restraints weight = 14284.381| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.39 r_work: 0.3441 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14231 Z= 0.195 Angle : 0.842 13.095 19459 Z= 0.376 Chirality : 0.078 0.863 2089 Planarity : 0.005 0.041 2307 Dihedral : 14.139 169.227 2420 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.64 % Allowed : 20.55 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.21), residues: 1521 helix: 1.40 (0.26), residues: 405 sheet: 0.35 (0.28), residues: 306 loop : -0.38 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 768 TYR 0.019 0.002 TYR A1283 PHE 0.017 0.002 PHE A 776 TRP 0.015 0.001 TRP A1141 HIS 0.006 0.001 HIS A 741 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.20 (14216) covalent geometry : angle 0.83884 / 0.38 (19441) hydrogen bonds : bond 0.04529 / 2.62 ( 491) hydrogen bonds : angle 4.53545 / 1.80 ( 1381) metal coordination : bond 0.00548 / 0.29 ( 15) metal coordination : angle 2.51575 / 0.84 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 144 time to evaluate : 0.452 Fit side-chains REVERT: A 29 ASN cc_start: 0.7853 (m110) cc_final: 0.7506 (m-40) REVERT: A 60 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7784 (tp) REVERT: A 99 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7034 (tt) REVERT: A 173 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8552 (mt) REVERT: A 290 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.6789 (tmm-80) REVERT: A 498 ILE cc_start: 0.8886 (OUTLIER) cc_final: 0.8523 (mm) REVERT: A 621 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.8107 (mtt-85) REVERT: A 667 GLU cc_start: 0.6597 (mm-30) cc_final: 0.6351 (tm-30) REVERT: A 735 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7681 (mm-30) REVERT: A 759 ASP cc_start: 0.8234 (p0) cc_final: 0.7885 (p0) REVERT: A 786 GLU cc_start: 0.6360 (tt0) cc_final: 0.5908 (tm-30) REVERT: A 942 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.6623 (tm-30) REVERT: A 1021 PHE cc_start: 0.5973 (OUTLIER) cc_final: 0.4007 (t80) REVERT: A 1116 LYS cc_start: 0.6981 (OUTLIER) cc_final: 0.6650 (mppt) REVERT: A 1132 GLU cc_start: 0.6548 (OUTLIER) cc_final: 0.6244 (mm-30) REVERT: A 1157 GLU cc_start: 0.6612 (OUTLIER) cc_final: 0.4991 (mm-30) REVERT: A 1229 GLU cc_start: 0.5674 (tp30) cc_final: 0.5424 (tp30) REVERT: A 1232 GLU cc_start: 0.7192 (tp30) cc_final: 0.6431 (mp0) REVERT: A 1563 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.7600 (mmp) outliers start: 49 outliers final: 27 residues processed: 182 average time/residue: 0.6250 time to fit residues: 123.4854 Evaluate side-chains 182 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 142 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 290 ARG Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 611 ASN Chi-restraints excluded: chain A residue 621 ARG Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 881 CYS Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 933 SER Chi-restraints excluded: chain A residue 942 GLN Chi-restraints excluded: chain A residue 1021 PHE Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1116 LYS Chi-restraints excluded: chain A residue 1132 GLU Chi-restraints excluded: chain A residue 1157 GLU Chi-restraints excluded: chain A residue 1241 LEU Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1367 ASP Chi-restraints excluded: chain A residue 1389 SER Chi-restraints excluded: chain A residue 1439 SER Chi-restraints excluded: chain A residue 1468 LEU Chi-restraints excluded: chain A residue 1503 VAL Chi-restraints excluded: chain A residue 1563 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 102 optimal weight: 20.0000 chunk 134 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 50 optimal weight: 0.3980 chunk 5 optimal weight: 0.9980 chunk 150 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 136 optimal weight: 0.0570 chunk 70 optimal weight: 5.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 712 GLN A1168 ASN ** A1483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.181688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.147358 restraints weight = 14386.525| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 1.52 r_work: 0.3477 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14231 Z= 0.135 Angle : 0.753 11.044 19459 Z= 0.338 Chirality : 0.068 0.740 2089 Planarity : 0.004 0.040 2307 Dihedral : 14.159 176.975 2420 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.74 % Allowed : 21.51 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.21), residues: 1521 helix: 1.52 (0.26), residues: 411 sheet: 0.30 (0.28), residues: 305 loop : -0.31 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 768 TYR 0.019 0.001 TYR A1283 PHE 0.014 0.001 PHE A1073 TRP 0.009 0.001 TRP A1600 HIS 0.004 0.001 HIS A 691 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (14216) covalent geometry : angle 0.75116 / 0.34 (19441) hydrogen bonds : bond 0.04118 / 2.49 ( 491) hydrogen bonds : angle 4.34934 / 1.71 ( 1381) metal coordination : bond 0.00359 / 0.19 ( 15) metal coordination : angle 2.04314 / 0.68 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 150 time to evaluate : 0.497 Fit side-chains REVERT: A 29 ASN cc_start: 0.7797 (m110) cc_final: 0.7450 (m-40) REVERT: A 290 ARG cc_start: 0.7589 (OUTLIER) cc_final: 0.6744 (tmm-80) REVERT: A 498 ILE cc_start: 0.8811 (OUTLIER) cc_final: 0.8434 (mm) REVERT: A 667 GLU cc_start: 0.6591 (mm-30) cc_final: 0.6314 (tm-30) REVERT: A 735 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7717 (mm-30) REVERT: A 759 ASP cc_start: 0.8160 (p0) cc_final: 0.7659 (p0) REVERT: A 786 GLU cc_start: 0.6450 (tt0) cc_final: 0.6014 (tm-30) REVERT: A 895 ILE cc_start: 0.6760 (mt) cc_final: 0.6421 (mt) REVERT: A 942 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.6475 (tm-30) REVERT: A 1021 PHE cc_start: 0.5892 (OUTLIER) cc_final: 0.3988 (t80) REVERT: A 1035 VAL cc_start: 0.5709 (OUTLIER) cc_final: 0.5432 (m) REVERT: A 1116 LYS cc_start: 0.6960 (OUTLIER) cc_final: 0.6639 (mppt) REVERT: A 1132 GLU cc_start: 0.6564 (OUTLIER) cc_final: 0.6214 (mm-30) REVERT: A 1143 CYS cc_start: 0.6738 (m) cc_final: 0.5764 (t) REVERT: A 1157 GLU cc_start: 0.6486 (OUTLIER) cc_final: 0.4929 (mm-30) REVERT: A 1202 GLU cc_start: 0.7580 (tp30) cc_final: 0.7130 (tp30) REVERT: A 1229 GLU cc_start: 0.5627 (tp30) cc_final: 0.5325 (tp30) REVERT: A 1232 GLU cc_start: 0.7265 (tp30) cc_final: 0.6434 (mp0) REVERT: A 1406 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7833 (ptpt) outliers start: 37 outliers final: 21 residues processed: 180 average time/residue: 0.6700 time to fit residues: 130.9624 Evaluate side-chains 177 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 290 ARG Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 933 SER Chi-restraints excluded: chain A residue 942 GLN Chi-restraints excluded: chain A residue 1021 PHE Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1116 LYS Chi-restraints excluded: chain A residue 1132 GLU Chi-restraints excluded: chain A residue 1157 GLU Chi-restraints excluded: chain A residue 1241 LEU Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1389 SER Chi-restraints excluded: chain A residue 1406 LYS Chi-restraints excluded: chain A residue 1439 SER Chi-restraints excluded: chain A residue 1468 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 22 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 149 optimal weight: 0.4980 chunk 36 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 712 GLN A1001 HIS A1168 ASN ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.178568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.142502 restraints weight = 14394.330| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.38 r_work: 0.3440 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14231 Z= 0.182 Angle : 0.827 12.948 19459 Z= 0.371 Chirality : 0.075 0.842 2089 Planarity : 0.005 0.041 2307 Dihedral : 14.113 171.118 2420 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.74 % Allowed : 21.59 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.21), residues: 1521 helix: 1.47 (0.26), residues: 405 sheet: 0.27 (0.29), residues: 301 loop : -0.37 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 768 TYR 0.017 0.002 TYR A1283 PHE 0.017 0.002 PHE A 776 TRP 0.014 0.001 TRP A1141 HIS 0.006 0.001 HIS A 741 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 (14216) covalent geometry : angle 0.82406 / 0.37 (19441) hydrogen bonds : bond 0.04435 / 2.59 ( 491) hydrogen bonds : angle 4.48390 / 1.77 ( 1381) metal coordination : bond 0.00520 / 0.28 ( 15) metal coordination : angle 2.47438 / 0.82 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3042 Ramachandran restraints generated. 1521 Oldfield, 0 Emsley, 1521 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 141 time to evaluate : 0.449 Fit side-chains REVERT: A 29 ASN cc_start: 0.7873 (m110) cc_final: 0.7561 (m-40) REVERT: A 60 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7791 (tp) REVERT: A 290 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.6775 (tmm-80) REVERT: A 498 ILE cc_start: 0.8875 (OUTLIER) cc_final: 0.8520 (mm) REVERT: A 667 GLU cc_start: 0.6632 (mm-30) cc_final: 0.6363 (tm-30) REVERT: A 735 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7723 (mm-30) REVERT: A 786 GLU cc_start: 0.6333 (tt0) cc_final: 0.5895 (tm-30) REVERT: A 942 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.6570 (tm-30) REVERT: A 1021 PHE cc_start: 0.5940 (OUTLIER) cc_final: 0.3921 (t80) REVERT: A 1035 VAL cc_start: 0.5763 (OUTLIER) cc_final: 0.5491 (m) REVERT: A 1116 LYS cc_start: 0.7007 (OUTLIER) cc_final: 0.6635 (mppt) REVERT: A 1132 GLU cc_start: 0.6577 (OUTLIER) cc_final: 0.6121 (mm-30) REVERT: A 1157 GLU cc_start: 0.6592 (OUTLIER) cc_final: 0.5047 (mm-30) REVERT: A 1216 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.5443 (mm-30) REVERT: A 1229 GLU cc_start: 0.5584 (tp30) cc_final: 0.5361 (tp30) REVERT: A 1232 GLU cc_start: 0.7228 (tp30) cc_final: 0.6444 (mp0) REVERT: A 1406 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7815 (ptpt) outliers start: 37 outliers final: 23 residues processed: 170 average time/residue: 0.6353 time to fit residues: 117.4638 Evaluate side-chains 175 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 140 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 290 ARG Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 611 ASN Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 933 SER Chi-restraints excluded: chain A residue 942 GLN Chi-restraints excluded: chain A residue 1021 PHE Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1116 LYS Chi-restraints excluded: chain A residue 1132 GLU Chi-restraints excluded: chain A residue 1157 GLU Chi-restraints excluded: chain A residue 1216 GLU Chi-restraints excluded: chain A residue 1241 LEU Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1367 ASP Chi-restraints excluded: chain A residue 1389 SER Chi-restraints excluded: chain A residue 1406 LYS Chi-restraints excluded: chain A residue 1439 SER Chi-restraints excluded: chain A residue 1468 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 67 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 138 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 chunk 153 optimal weight: 4.9990 chunk 147 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 57 optimal weight: 0.0980 chunk 38 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 712 GLN A1001 HIS A1168 ASN ** A1483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.181582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.147382 restraints weight = 14390.240| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 1.40 r_work: 0.3496 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14231 Z= 0.135 Angle : 0.758 10.872 19459 Z= 0.340 Chirality : 0.068 0.735 2089 Planarity : 0.004 0.040 2307 Dihedral : 14.145 175.830 2420 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.74 % Allowed : 21.88 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.21), residues: 1521 helix: 1.83 (0.27), residues: 393 sheet: 0.24 (0.29), residues: 300 loop : -0.27 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 11 TYR 0.012 0.001 TYR A1208 PHE 0.014 0.001 PHE A1073 TRP 0.012 0.001 TRP A 42 HIS 0.005 0.001 HIS A1001 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (14216) covalent geometry : angle 0.75535 / 0.34 (19441) hydrogen bonds : bond 0.04122 / 2.48 ( 491) hydrogen bonds : angle 4.35025 / 1.71 ( 1381) metal coordination : bond 0.00387 / 0.21 ( 15) metal coordination : angle 2.19902 / 0.73 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4792.27 seconds wall clock time: 82 minutes 31.16 seconds (4951.16 seconds total)