Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 01:52:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y9y_33696/04_2023/7y9y_33696.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y9y_33696/04_2023/7y9y_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y9y_33696/04_2023/7y9y_33696.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y9y_33696/04_2023/7y9y_33696.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y9y_33696/04_2023/7y9y_33696.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y9y_33696/04_2023/7y9y_33696.pdb" } 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 ------------------------------------------------------------------------------- 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 Residue "A GLU 32": "OE1" <-> "OE2" Residue "A GLU 93": "OE1" <-> "OE2" Residue "A ASP 111": "OD1" <-> "OD2" Residue "A GLU 201": "OE1" <-> "OE2" Residue "A GLU 267": "OE1" <-> "OE2" Residue "A GLU 280": "OE1" <-> "OE2" Residue "A ASP 338": "OD1" <-> "OD2" Residue "A PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 423": "OE1" <-> "OE2" Residue "A GLU 491": "OE1" <-> "OE2" Residue "A GLU 513": "OE1" <-> "OE2" Residue "A ASP 539": "OD1" <-> "OD2" Residue "A GLU 573": "OE1" <-> "OE2" Residue "A GLU 578": "OE1" <-> "OE2" Residue "A ASP 599": "OD1" <-> "OD2" Residue "A GLU 604": "OE1" <-> "OE2" Residue "A GLU 616": "OE1" <-> "OE2" Residue "A ASP 622": "OD1" <-> "OD2" Residue "A ASP 642": "OD1" <-> "OD2" Residue "A TYR 661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 730": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 735": "OE1" <-> "OE2" Residue "A TYR 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 853": "OE1" <-> "OE2" Residue "A GLU 878": "OE1" <-> "OE2" Residue "A GLU 888": "OE1" <-> "OE2" Residue "A TYR 930": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 937": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 959": "OE1" <-> "OE2" Residue "A PHE 1073": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1081": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1132": "OE1" <-> "OE2" Residue "A GLU 1142": "OE1" <-> "OE2" Residue "A ASP 1160": "OD1" <-> "OD2" Residue "A GLU 1202": "OE1" <-> "OE2" Residue "A TYR 1209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1229": "OE1" <-> "OE2" Residue "A GLU 1232": "OE1" <-> "OE2" Residue "A ASP 1298": "OD1" <-> "OD2" Residue "A ASP 1315": "OD1" <-> "OD2" Residue "A PHE 1381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1446": "OE1" <-> "OE2" Residue "A GLU 1465": "OE1" <-> "OE2" Residue "A ASP 1499": "OD1" <-> "OD2" Residue "A ASP 1508": "OD1" <-> "OD2" Residue "A GLU 1518": "OE1" <-> "OE2" Residue "A GLU 1537": "OE1" <-> "OE2" Residue "A ASP 1539": "OD1" <-> "OD2" Residue "A ASP 1581": "OD1" <-> "OD2" Residue "B GLU 34": "OE1" <-> "OE2" Residue "B PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/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: {'RNA': 38} Modifications used: {'5*END': 1, 'rna2p_pur': 12, 'rna2p_pyr': 9, 'rna3p_pur': 5, 'rna3p_pyr': 12} Link IDs: {'rna2p': 21, 'rna3p': 16} Chain: "D" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 492 Classifications: {'RNA': 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: 7.63, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 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: 6.00 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 4.97 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: 8.19 Time building geometry restraints manager: 6.40 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: 91.92 - 100.53: 9 100.53 - 109.14: 1681 109.14 - 117.74: 9112 117.74 - 126.35: 8230 126.35 - 134.96: 409 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 - 22.71: 7695 22.71 - 45.42: 625 45.42 - 68.12: 141 68.12 - 90.83: 18 90.83 - 113.54: 2 Dihedral angle restraints: 8481 sinusoidal: 4027 harmonic: 4454 Sorted by residual: dihedral pdb=" CA ASN A1207 " pdb=" C ASN A1207 " pdb=" N TYR A1208 " pdb=" CA TYR A1208 " ideal model delta harmonic sigma weight residual -180.00 -157.10 -22.90 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA ASP A1203 " pdb=" C ASP A1203 " pdb=" N ASP A1204 " pdb=" CA ASP A1204 " ideal model delta harmonic sigma weight residual 180.00 159.46 20.54 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA ASN A 640 " pdb=" C ASN A 640 " pdb=" N GLY A 641 " pdb=" CA GLY A 641 " ideal model delta harmonic sigma weight residual -180.00 -160.40 -19.60 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 8478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1709 0.051 - 0.102: 318 0.102 - 0.153: 60 0.153 - 0.203: 0 0.203 - 0.254: 2 Chirality restraints: 2089 Sorted by residual: chirality pdb=" C1' G R 19 " pdb=" O4' G R 19 " pdb=" C2' G R 19 " pdb=" N9 G R 19 " both_signs ideal model delta sigma weight residual False 2.44 2.18 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" C1' U R 1 " pdb=" O4' U R 1 " pdb=" C2' U R 1 " pdb=" N1 U R 1 " both_signs ideal model delta sigma weight residual False 2.47 2.26 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA ILE A1372 " pdb=" N ILE A1372 " pdb=" C ILE A1372 " pdb=" CB ILE A1372 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.16e-01 ... (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 2.440 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 2.440 nonbonded pdb=" OG1 THR A1072 " pdb=" OD1 ASN A1084 " model vdw 2.138 2.440 nonbonded pdb=" O2' C R 27 " pdb=" O GLU A1392 " model vdw 2.225 2.440 ... (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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.470 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: 14.450 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 48.000 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 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 14216 Z= 0.203 Angle : 0.604 14.176 19441 Z= 0.337 Chirality : 0.041 0.254 2089 Planarity : 0.005 0.053 2307 Dihedral : 16.355 113.537 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 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (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 *********************** 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 fitting. rotamer outliers: 22 poor density : 151 time to evaluate : 1.600 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 12 residues processed: 170 average time/residue: 1.5439 time to fit residues: 283.7297 Evaluate side-chains 156 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 144 time to evaluate : 1.585 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 12 residues processed: 0 time to fit residues: 2.2007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 0.0870 chunk 120 optimal weight: 0.0470 chunk 66 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 64 optimal weight: 0.3980 chunk 124 optimal weight: 0.0870 chunk 48 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 overall best weight: 0.3034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS A 45 ASN A 118 ASN A 170 GLN A 208 ASN A 331 GLN A 344 ASN A 427 GLN A 531 GLN A 712 GLN 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 ** B 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 GLN B 19 ASN B 25 ASN B 55 ASN B 59 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.0805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 14216 Z= 0.137 Angle : 0.494 7.194 19441 Z= 0.266 Chirality : 0.039 0.263 2089 Planarity : 0.004 0.038 2307 Dihedral : 10.237 113.976 2413 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer Outliers : 3.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.21), residues: 1521 helix: 1.26 (0.27), residues: 403 sheet: 0.58 (0.28), residues: 312 loop : -0.17 (0.22), residues: 806 *********************** 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 204 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 161 time to evaluate : 1.752 Fit side-chains revert: symmetry clash outliers start: 43 outliers final: 15 residues processed: 193 average time/residue: 1.4452 time to fit residues: 302.5618 Evaluate side-chains 164 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 149 time to evaluate : 1.453 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 12 residues processed: 4 average time/residue: 0.4061 time to fit residues: 4.0638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 144 optimal weight: 0.4980 chunk 156 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 143 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 691 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 887 HIS A1168 ASN A1571 ASN ** B 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN B 36 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 14216 Z= 0.355 Angle : 0.630 7.376 19441 Z= 0.333 Chirality : 0.046 0.277 2089 Planarity : 0.006 0.052 2307 Dihedral : 10.435 113.120 2413 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer Outliers : 4.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.21), residues: 1521 helix: 1.01 (0.26), residues: 403 sheet: 0.36 (0.28), residues: 302 loop : -0.40 (0.21), residues: 816 *********************** 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 221 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 156 time to evaluate : 1.704 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 31 residues processed: 206 average time/residue: 1.4605 time to fit residues: 327.2211 Evaluate side-chains 181 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 150 time to evaluate : 1.604 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 26 residues processed: 6 average time/residue: 0.5138 time to fit residues: 5.9926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 0.5980 chunk 108 optimal weight: 2.9990 chunk 75 optimal weight: 0.0870 chunk 16 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 145 optimal weight: 0.5980 chunk 153 optimal weight: 5.9990 chunk 137 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 691 HIS ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 940 HIS A1168 ASN ** B 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.047 14216 Z= 0.163 Angle : 0.502 6.279 19441 Z= 0.268 Chirality : 0.040 0.262 2089 Planarity : 0.004 0.042 2307 Dihedral : 10.318 114.944 2413 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer Outliers : 4.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.21), residues: 1521 helix: 1.30 (0.26), residues: 404 sheet: 0.40 (0.29), residues: 306 loop : -0.36 (0.21), residues: 811 *********************** 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 214 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 152 time to evaluate : 1.624 Fit side-chains outliers start: 62 outliers final: 29 residues processed: 202 average time/residue: 1.3697 time to fit residues: 301.5836 Evaluate side-chains 175 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 146 time to evaluate : 1.568 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 28 residues processed: 1 average time/residue: 0.1224 time to fit residues: 2.3313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 87 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 114 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 chunk 106 optimal weight: 0.0970 chunk 0 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 137 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 691 HIS A 712 GLN A1168 ASN ** B 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 14216 Z= 0.207 Angle : 0.520 6.348 19441 Z= 0.276 Chirality : 0.041 0.262 2089 Planarity : 0.004 0.043 2307 Dihedral : 10.266 114.979 2413 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer Outliers : 4.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.21), residues: 1521 helix: 1.33 (0.26), residues: 404 sheet: 0.40 (0.28), residues: 316 loop : -0.37 (0.21), residues: 801 *********************** 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 205 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 145 time to evaluate : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 34 residues processed: 197 average time/residue: 1.4452 time to fit residues: 310.2778 Evaluate side-chains 177 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 143 time to evaluate : 1.633 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 30 residues processed: 4 average time/residue: 1.0607 time to fit residues: 6.9189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 153 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 71 optimal weight: 0.2980 chunk 12 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 80 optimal weight: 0.0870 chunk 148 optimal weight: 0.3980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1168 ASN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.049 14216 Z= 0.146 Angle : 0.481 6.211 19441 Z= 0.256 Chirality : 0.039 0.264 2089 Planarity : 0.004 0.041 2307 Dihedral : 10.205 115.809 2413 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer Outliers : 3.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.21), residues: 1521 helix: 1.58 (0.27), residues: 404 sheet: 0.52 (0.29), residues: 306 loop : -0.30 (0.21), residues: 811 *********************** 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 208 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 155 time to evaluate : 1.482 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 30 residues processed: 201 average time/residue: 1.4251 time to fit residues: 313.1795 Evaluate side-chains 176 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 146 time to evaluate : 1.642 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 28 residues processed: 2 average time/residue: 0.1366 time to fit residues: 2.8073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 17 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1001 HIS A1168 ASN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 14216 Z= 0.308 Angle : 0.588 6.324 19441 Z= 0.310 Chirality : 0.044 0.269 2089 Planarity : 0.005 0.044 2307 Dihedral : 10.304 114.548 2413 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer Outliers : 4.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.21), residues: 1521 helix: 1.31 (0.26), residues: 404 sheet: 0.43 (0.28), residues: 307 loop : -0.43 (0.21), residues: 810 *********************** 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 210 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 152 time to evaluate : 1.465 Fit side-chains revert: symmetry clash outliers start: 58 outliers final: 32 residues processed: 201 average time/residue: 1.4625 time to fit residues: 320.1872 Evaluate side-chains 182 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 150 time to evaluate : 1.532 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 30 residues processed: 3 average time/residue: 1.0979 time to fit residues: 5.8324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 91 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 104 optimal weight: 7.9990 chunk 75 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 chunk 139 optimal weight: 0.9990 chunk 146 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1001 HIS A1168 ASN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 14216 Z= 0.200 Angle : 0.530 6.231 19441 Z= 0.281 Chirality : 0.041 0.264 2089 Planarity : 0.004 0.043 2307 Dihedral : 10.282 115.063 2413 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer Outliers : 3.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.21), residues: 1521 helix: 1.46 (0.26), residues: 405 sheet: 0.47 (0.29), residues: 306 loop : -0.38 (0.21), residues: 810 *********************** 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 191 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 148 time to evaluate : 1.570 Fit side-chains revert: symmetry clash outliers start: 43 outliers final: 30 residues processed: 184 average time/residue: 1.3996 time to fit residues: 281.1574 Evaluate side-chains 175 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 145 time to evaluate : 1.554 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 29 residues processed: 3 average time/residue: 0.4861 time to fit residues: 3.9674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 0.0270 chunk 142 optimal weight: 3.9990 chunk 146 optimal weight: 0.0030 chunk 85 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 112 optimal weight: 0.3980 chunk 43 optimal weight: 0.5980 chunk 129 optimal weight: 0.6980 chunk 135 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 overall best weight: 0.3248 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 611 ASN ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1001 HIS A1168 ASN B 25 ASN ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.051 14216 Z= 0.145 Angle : 0.493 6.609 19441 Z= 0.261 Chirality : 0.039 0.261 2089 Planarity : 0.004 0.043 2307 Dihedral : 10.194 116.135 2413 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer Outliers : 2.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.21), residues: 1521 helix: 1.78 (0.27), residues: 398 sheet: 0.44 (0.29), residues: 306 loop : -0.25 (0.21), residues: 817 *********************** 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 184 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 151 time to evaluate : 1.571 Fit side-chains revert: symmetry clash outliers start: 33 outliers final: 26 residues processed: 181 average time/residue: 1.4917 time to fit residues: 294.4033 Evaluate side-chains 174 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 148 time to evaluate : 1.579 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 26 residues processed: 0 time to fit residues: 2.2015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 158 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 611 ASN ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1001 HIS A1168 ASN ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.059 14216 Z= 0.408 Angle : 0.662 7.853 19441 Z= 0.346 Chirality : 0.047 0.286 2089 Planarity : 0.005 0.051 2307 Dihedral : 10.422 113.606 2413 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer Outliers : 2.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.21), residues: 1521 helix: 1.18 (0.26), residues: 403 sheet: 0.39 (0.29), residues: 301 loop : -0.53 (0.21), residues: 817 ********************** 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 187 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 150 time to evaluate : 1.517 Fit side-chains revert: symmetry clash outliers start: 37 outliers final: 29 residues processed: 183 average time/residue: 1.4956 time to fit residues: 298.8391 Evaluate side-chains 176 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 147 time to evaluate : 1.480 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 27 residues processed: 2 average time/residue: 1.7154 time to fit residues: 5.7426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 38 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 611 ASN ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1001 HIS A1168 ASN B 25 ASN B 36 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.173135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.136267 restraints weight = 14374.213| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.53 r_work: 0.3347 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 14216 Z= 0.217 Angle : 0.556 7.963 19441 Z= 0.294 Chirality : 0.042 0.266 2089 Planarity : 0.005 0.045 2307 Dihedral : 10.355 114.632 2413 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer Outliers : 2.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.21), residues: 1521 helix: 1.36 (0.26), residues: 405 sheet: 0.41 (0.29), residues: 300 loop : -0.44 (0.21), residues: 816 =============================================================================== Job complete usr+sys time: 5282.53 seconds wall clock time: 94 minutes 32.99 seconds (5672.99 seconds total)