Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 01:30:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asd_15614/04_2023/8asd_15614_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asd_15614/04_2023/8asd_15614.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asd_15614/04_2023/8asd_15614_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asd_15614/04_2023/8asd_15614_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asd_15614/04_2023/8asd_15614_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asd_15614/04_2023/8asd_15614.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asd_15614/04_2023/8asd_15614.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asd_15614/04_2023/8asd_15614_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asd_15614/04_2023/8asd_15614_updated.pdb" } resolution = 2.6 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= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 784 atoms to isotropic. 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 P 46 5.49 5 Mg 3 5.21 5 S 84 5.16 5 C 9631 2.51 5 N 2717 2.21 5 O 3050 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 81": "OD1" <-> "OD2" Residue "A TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 220": "OE1" <-> "OE2" Residue "A GLU 254": "OE1" <-> "OE2" Residue "A GLU 378": "OE1" <-> "OE2" Residue "A GLU 457": "OE1" <-> "OE2" Residue "A ASP 461": "OD1" <-> "OD2" Residue "A ASP 476": "OD1" <-> "OD2" Residue "A ASP 495": "OD1" <-> "OD2" Residue "A GLU 592": "OE1" <-> "OE2" Residue "A GLU 831": "OE1" <-> "OE2" Residue "A PHE 911": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1113": "OE1" <-> "OE2" Residue "A ASP 1141": "OD1" <-> "OD2" Residue "A GLU 1169": "OE1" <-> "OE2" Residue "A TYR 1177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1480": "OE1" <-> "OE2" Residue "A ASP 1501": "OD1" <-> "OD2" Residue "A GLU 1612": "OE1" <-> "OE2" Residue "A GLU 1748": "OE1" <-> "OE2" Residue "A GLU 1749": "OE1" <-> "OE2" Residue "A ASP 1760": "OD1" <-> "OD2" Residue "A GLU 1763": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 15531 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 14524 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1826, 14496 Classifications: {'peptide': 1826} Link IDs: {'PCIS': 2, 'PTRANS': 67, 'TRANS': 1756} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 1826, 14496 Classifications: {'peptide': 1826} Link IDs: {'PCIS': 2, 'PTRANS': 67, 'TRANS': 1756} Chain breaks: 3 bond proxies already assigned to first conformer: 14761 Chain: "T" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 366 Classifications: {'RNA': 17} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 3, 'rna3p_pur': 9, 'rna3p_pyr': 4} Link IDs: {'rna2p': 3, 'rna3p': 13} Chain breaks: 1 Chain: "G" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 190 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 5} Link IDs: {'rna3p': 8} Chain: "E" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 151 Classifications: {'RNA': 7} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "P" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 236 Classifications: {'RNA': 11} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna3p_pur': 5, 'rna3p_pyr': 3} Link IDs: {'rna2p': 3, 'rna3p': 7} Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 40 Unusual residues: {' MG': 3, '2KH': 1} Classifications: {'undetermined': 4, 'water': 8} Link IDs: {None: 11} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AHIS A1452 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A1452 " occ=0.50 Time building chain proxies: 14.88, per 1000 atoms: 0.96 Number of scatterers: 15531 At special positions: 0 Unit cell: (98.6, 124.1, 126.65, 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) S 84 16.00 P 46 15.00 Mg 3 11.99 O 3050 8.00 N 2717 7.00 C 9631 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: 7.52 Conformation dependent library (CDL) restraints added in 4.2 seconds 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3420 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 77 helices and 14 sheets defined 46.5% alpha, 9.6% beta 8 base pairs and 25 stacking pairs defined. Time for finding SS restraints: 7.51 Creating SS restraints... Processing helix chain 'A' and resid 3 through 8 Processing helix chain 'A' and resid 75 through 83 removed outlier: 3.930A pdb=" N ILE A 78 " --> pdb=" O ALA A 75 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N ASN A 79 " --> pdb=" O TYR A 76 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N PHE A 82 " --> pdb=" O ASN A 79 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR A 83 " --> pdb=" O HIS A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 97 No H-bonds generated for 'chain 'A' and resid 95 through 97' Processing helix chain 'A' and resid 105 through 108 removed outlier: 4.359A pdb=" N GLY A 108 " --> pdb=" O GLY A 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 105 through 108' Processing helix chain 'A' and resid 135 through 159 removed outlier: 3.725A pdb=" N TYR A 149 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ASP A 151 " --> pdb=" O GLU A 147 " (cutoff:3.500A) Proline residue: A 152 - end of helix removed outlier: 3.901A pdb=" N ILE A 159 " --> pdb=" O ARG A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 208 Processing helix chain 'A' and resid 218 through 233 Processing helix chain 'A' and resid 238 through 244 Processing helix chain 'A' and resid 251 through 258 Processing helix chain 'A' and resid 263 through 284 Processing helix chain 'A' and resid 293 through 317 Processing helix chain 'A' and resid 353 through 356 No H-bonds generated for 'chain 'A' and resid 353 through 356' Processing helix chain 'A' and resid 359 through 374 removed outlier: 3.570A pdb=" N LEU A 374 " --> pdb=" O LEU A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 391 Processing helix chain 'A' and resid 404 through 407 Processing helix chain 'A' and resid 417 through 426 removed outlier: 3.743A pdb=" N GLN A 426 " --> pdb=" O GLU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 447 removed outlier: 3.839A pdb=" N HIS A 447 " --> pdb=" O GLU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 464 Processing helix chain 'A' and resid 478 through 494 removed outlier: 4.600A pdb=" N MET A 493 " --> pdb=" O LYS A 489 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N GLN A 494 " --> pdb=" O ALA A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 510 Processing helix chain 'A' and resid 513 through 532 removed outlier: 3.653A pdb=" N TRP A 520 " --> pdb=" O GLN A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 574 No H-bonds generated for 'chain 'A' and resid 572 through 574' Processing helix chain 'A' and resid 603 through 610 removed outlier: 4.225A pdb=" N THR A 607 " --> pdb=" O THR A 603 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ASN A 608 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU A 609 " --> pdb=" O LYS A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 626 Processing helix chain 'A' and resid 639 through 654 Processing helix chain 'A' and resid 657 through 674 removed outlier: 3.551A pdb=" N ILE A 663 " --> pdb=" O THR A 659 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR A 666 " --> pdb=" O ILE A 662 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ARG A 667 " --> pdb=" O ILE A 663 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N TYR A 668 " --> pdb=" O THR A 664 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLU A 672 " --> pdb=" O TYR A 668 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N GLY A 673 " --> pdb=" O THR A 669 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N PHE A 674 " --> pdb=" O GLN A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 688 removed outlier: 4.209A pdb=" N GLY A 688 " --> pdb=" O LYS A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 715 Processing helix chain 'A' and resid 743 through 755 removed outlier: 4.133A pdb=" N TYR A 751 " --> pdb=" O VAL A 747 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE A 752 " --> pdb=" O ASN A 748 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N GLY A 753 " --> pdb=" O SER A 749 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N TYR A 754 " --> pdb=" O TRP A 750 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N TYR A 755 " --> pdb=" O TYR A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 780 removed outlier: 3.770A pdb=" N GLU A 776 " --> pdb=" O LYS A 772 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N MET A 777 " --> pdb=" O LYS A 773 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU A 778 " --> pdb=" O ILE A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 821 Processing helix chain 'A' and resid 825 through 839 Processing helix chain 'A' and resid 843 through 845 No H-bonds generated for 'chain 'A' and resid 843 through 845' Processing helix chain 'A' and resid 856 through 858 No H-bonds generated for 'chain 'A' and resid 856 through 858' Processing helix chain 'A' and resid 861 through 863 No H-bonds generated for 'chain 'A' and resid 861 through 863' Processing helix chain 'A' and resid 874 through 884 Processing helix chain 'A' and resid 889 through 903 removed outlier: 3.707A pdb=" N GLY A 894 " --> pdb=" O ILE A 890 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLN A 895 " --> pdb=" O ASP A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 946 removed outlier: 4.050A pdb=" N GLY A 935 " --> pdb=" O LEU A 931 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL A 936 " --> pdb=" O VAL A 932 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU A 946 " --> pdb=" O CYS A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 963 removed outlier: 4.058A pdb=" N SER A 960 " --> pdb=" O LEU A 957 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ILE A 961 " --> pdb=" O LYS A 958 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU A 963 " --> pdb=" O SER A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 973 Processing helix chain 'A' and resid 995 through 1005 removed outlier: 3.693A pdb=" N PHE A1005 " --> pdb=" O VAL A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1008 through 1022 removed outlier: 4.767A pdb=" N ARG A1012 " --> pdb=" O LYS A1009 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N TRP A1015 " --> pdb=" O ARG A1012 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA A1016 " --> pdb=" O PHE A1013 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A1017 " --> pdb=" O ILE A1014 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE A1018 " --> pdb=" O TRP A1015 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N MET A1020 " --> pdb=" O ALA A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1037 Processing helix chain 'A' and resid 1047 through 1057 Processing helix chain 'A' and resid 1084 through 1108 Processing helix chain 'A' and resid 1139 through 1154 removed outlier: 3.610A pdb=" N VAL A1143 " --> pdb=" O ASP A1139 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG A1144 " --> pdb=" O MET A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1156 through 1163 Proline residue: A1161 - end of helix Processing helix chain 'A' and resid 1195 through 1201 removed outlier: 4.006A pdb=" N ALA A1201 " --> pdb=" O ARG A1197 " (cutoff:3.500A) Processing helix chain 'A' and resid 1211 through 1227 removed outlier: 4.044A pdb=" N GLN A1215 " --> pdb=" O LEU A1211 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN A1224 " --> pdb=" O ASN A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1232 through 1249 Processing helix chain 'A' and resid 1258 through 1266 Processing helix chain 'A' and resid 1271 through 1273 No H-bonds generated for 'chain 'A' and resid 1271 through 1273' Processing helix chain 'A' and resid 1281 through 1283 No H-bonds generated for 'chain 'A' and resid 1281 through 1283' Processing helix chain 'A' and resid 1289 through 1299 Processing helix chain 'A' and resid 1302 through 1314 Processing helix chain 'A' and resid 1331 through 1335 Processing helix chain 'A' and resid 1345 through 1353 Processing helix chain 'A' and resid 1361 through 1367 Processing helix chain 'A' and resid 1369 through 1372 Processing helix chain 'A' and resid 1379 through 1390 Processing helix chain 'A' and resid 1393 through 1400 Processing helix chain 'A' and resid 1405 through 1413 removed outlier: 4.234A pdb=" N GLY A1412 " --> pdb=" O VAL A1408 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N VAL A1413 " --> pdb=" O VAL A1409 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1428 No H-bonds generated for 'chain 'A' and resid 1425 through 1428' Processing helix chain 'A' and resid 1438 through 1447 Processing helix chain 'A' and resid 1449 through 1451 No H-bonds generated for 'chain 'A' and resid 1449 through 1451' Processing helix chain 'A' and resid 1458 through 1464 Processing helix chain 'A' and resid 1468 through 1478 Processing helix chain 'A' and resid 1513 through 1522 Processing helix chain 'A' and resid 1531 through 1544 Processing helix chain 'A' and resid 1552 through 1558 Processing helix chain 'A' and resid 1564 through 1573 removed outlier: 3.877A pdb=" N HIS A1573 " --> pdb=" O ASN A1569 " (cutoff:3.500A) Processing helix chain 'A' and resid 1596 through 1603 Processing helix chain 'A' and resid 1626 through 1637 removed outlier: 3.540A pdb=" N MET A1635 " --> pdb=" O HIS A1631 " (cutoff:3.500A) Processing helix chain 'A' and resid 1643 through 1656 removed outlier: 3.616A pdb=" N GLU A1648 " --> pdb=" O GLU A1644 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N MET A1649 " --> pdb=" O TYR A1645 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE A1650 " --> pdb=" O LYS A1646 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE A1651 " --> pdb=" O LEU A1647 " (cutoff:3.500A) Processing helix chain 'A' and resid 1670 through 1680 Processing helix chain 'A' and resid 1688 through 1695 Processing helix chain 'A' and resid 1758 through 1772 removed outlier: 3.750A pdb=" N ASP A1771 " --> pdb=" O ARG A1767 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A1772 " --> pdb=" O LEU A1768 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 22 through 25 Processing sheet with id= B, first strand: chain 'A' and resid 38 through 40 removed outlier: 3.569A pdb=" N ILE A 49 " --> pdb=" O GLY A 66 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 410 through 412 Processing sheet with id= D, first strand: chain 'A' and resid 569 through 571 Processing sheet with id= E, first strand: chain 'A' and resid 719 through 722 Processing sheet with id= F, first strand: chain 'A' and resid 921 through 925 removed outlier: 3.920A pdb=" N LEU A 910 " --> pdb=" O MET A1027 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 978 through 984 Processing sheet with id= H, first strand: chain 'A' and resid 1178 through 1181 removed outlier: 3.689A pdb=" N PHE A1185 " --> pdb=" O VAL A1192 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 1338 through 1340 Processing sheet with id= J, first strand: chain 'A' and resid 1486 through 1488 Processing sheet with id= K, first strand: chain 'A' and resid 1496 through 1502 Processing sheet with id= L, first strand: chain 'A' and resid 1709 through 1711 Processing sheet with id= M, first strand: chain 'A' and resid 1700 through 1705 removed outlier: 6.234A pdb=" N VAL A1724 " --> pdb=" O SER A1704 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ASP A1739 " --> pdb=" O LEU A1747 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LEU A1747 " --> pdb=" O ASP A1739 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N LEU A1752 " --> pdb=" O PRO A1805 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ARG A1807 " --> pdb=" O LEU A1752 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL A1788 " --> pdb=" O VAL A1806 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 1825 through 1829 removed outlier: 3.519A pdb=" N LEU A1833 " --> pdb=" O TYR A1850 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N VAL A1837 " --> pdb=" O ASN A1846 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ASN A1846 " --> pdb=" O VAL A1837 " (cutoff:3.500A) 608 hydrogen bonds defined for protein. 1714 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 22 hydrogen bonds 44 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 25 stacking parallelities Total time for adding SS restraints: 7.90 Time building geometry restraints manager: 8.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 2445 1.30 - 1.43: 4367 1.43 - 1.56: 8871 1.56 - 1.68: 87 1.68 - 1.81: 140 Bond restraints: 15910 Sorted by residual: bond pdb=" C3' 2KH A2104 " pdb=" C4' 2KH A2104 " ideal model delta sigma weight residual 1.643 1.300 0.343 2.00e-02 2.50e+03 2.94e+02 bond pdb=" C4' 2KH A2104 " pdb=" O4' 2KH A2104 " ideal model delta sigma weight residual 1.310 1.613 -0.303 2.00e-02 2.50e+03 2.29e+02 bond pdb=" C1' 2KH A2104 " pdb=" O4' 2KH A2104 " ideal model delta sigma weight residual 1.561 1.307 0.254 2.00e-02 2.50e+03 1.62e+02 bond pdb=" C2' 2KH A2104 " pdb=" C3' 2KH A2104 " ideal model delta sigma weight residual 1.312 1.534 -0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" C1' 2KH A2104 " pdb=" N1 2KH A2104 " ideal model delta sigma weight residual 1.322 1.478 -0.156 2.00e-02 2.50e+03 6.08e+01 ... (remaining 15905 not shown) Histogram of bond angle deviations from ideal: 97.65 - 104.94: 424 104.94 - 112.23: 8051 112.23 - 119.52: 5532 119.52 - 126.81: 7354 126.81 - 134.10: 333 Bond angle restraints: 21694 Sorted by residual: angle pdb=" N ILE A 392 " pdb=" CA ILE A 392 " pdb=" C ILE A 392 " ideal model delta sigma weight residual 112.29 108.90 3.39 9.40e-01 1.13e+00 1.30e+01 angle pdb=" CB MET A 770 " pdb=" CG MET A 770 " pdb=" SD MET A 770 " ideal model delta sigma weight residual 112.70 103.80 8.90 3.00e+00 1.11e-01 8.79e+00 angle pdb=" C HIS A1188 " pdb=" CA HIS A1188 " pdb=" CB HIS A1188 " ideal model delta sigma weight residual 110.42 116.07 -5.65 1.99e+00 2.53e-01 8.07e+00 angle pdb=" C GLU A1492 " pdb=" N ARG A1493 " pdb=" CA ARG A1493 " ideal model delta sigma weight residual 121.54 126.84 -5.30 1.91e+00 2.74e-01 7.69e+00 angle pdb=" N SER A 57 " pdb=" CA SER A 57 " pdb=" C SER A 57 " ideal model delta sigma weight residual 114.09 109.91 4.18 1.55e+00 4.16e-01 7.28e+00 ... (remaining 21689 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.36: 9104 26.36 - 52.73: 351 52.73 - 79.09: 50 79.09 - 105.46: 5 105.46 - 131.82: 1 Dihedral angle restraints: 9511 sinusoidal: 4210 harmonic: 5301 Sorted by residual: dihedral pdb=" O1A 2KH A2104 " pdb=" N3A 2KH A2104 " pdb=" PA 2KH A2104 " pdb=" PB 2KH A2104 " ideal model delta sinusoidal sigma weight residual -34.41 -166.23 131.82 1 3.00e+01 1.11e-03 1.78e+01 dihedral pdb=" CA GLY A1077 " pdb=" C GLY A1077 " pdb=" N MET A1078 " pdb=" CA MET A1078 " ideal model delta harmonic sigma weight residual 180.00 159.03 20.97 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA LEU A1153 " pdb=" C LEU A1153 " pdb=" N HIS A1154 " pdb=" CA HIS A1154 " ideal model delta harmonic sigma weight residual 180.00 159.63 20.37 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 9508 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1798 0.044 - 0.088: 492 0.088 - 0.132: 133 0.132 - 0.176: 12 0.176 - 0.221: 4 Chirality restraints: 2439 Sorted by residual: chirality pdb=" CB ILE A 212 " pdb=" CA ILE A 212 " pdb=" CG1 ILE A 212 " pdb=" CG2 ILE A 212 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" C1' 2KH A2104 " pdb=" C2' 2KH A2104 " pdb=" N1 2KH A2104 " pdb=" O4' 2KH A2104 " both_signs ideal model delta sigma weight residual False 2.54 2.33 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ILE A 564 " pdb=" N ILE A 564 " pdb=" C ILE A 564 " pdb=" CB ILE A 564 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.72e-01 ... (remaining 2436 not shown) Planarity restraints: 2606 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP A 549 " 0.037 5.00e-02 4.00e+02 5.73e-02 5.26e+00 pdb=" N PRO A 550 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 550 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 550 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A1505 " 0.029 5.00e-02 4.00e+02 4.32e-02 2.99e+00 pdb=" N PRO A1506 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A1506 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A1506 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 590 " 0.009 2.00e-02 2.50e+03 1.71e-02 2.93e+00 pdb=" C ALA A 590 " -0.030 2.00e-02 2.50e+03 pdb=" O ALA A 590 " 0.011 2.00e-02 2.50e+03 pdb=" N GLY A 591 " 0.010 2.00e-02 2.50e+03 ... (remaining 2603 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 146 2.60 - 3.18: 12622 3.18 - 3.75: 25098 3.75 - 4.33: 35963 4.33 - 4.90: 57161 Nonbonded interactions: 130990 Sorted by model distance: nonbonded pdb=" OP1 A E 5 " pdb="MG MG A2103 " model vdw 2.030 2.170 nonbonded pdb=" OE2 GLU A 126 " pdb="MG MG A2103 " model vdw 2.105 2.170 nonbonded pdb=" OH TYR A 286 " pdb=" OE1 GLU A 303 " model vdw 2.140 2.440 nonbonded pdb="MG MG A2102 " pdb=" O3G 2KH A2104 " model vdw 2.142 2.170 nonbonded pdb=" OD1 ASP A1127 " pdb="MG MG A2101 " model vdw 2.147 2.170 ... (remaining 130985 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=0.31 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: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 8.410 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 58.450 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.100 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:12.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 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 : 0.006 0.343 15910 Z= 0.363 Angle : 0.647 8.897 21694 Z= 0.351 Chirality : 0.043 0.221 2439 Planarity : 0.005 0.058 2606 Dihedral : 13.761 131.824 6091 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: -0.27 (0.19), residues: 1824 helix: 0.66 (0.17), residues: 864 sheet: -0.27 (0.38), residues: 183 loop : -1.06 (0.20), residues: 777 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 2.018 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 1.7439 time to fit residues: 413.5314 Evaluate side-chains 170 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 2.044 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.0010 chunk 139 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 94 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 144 optimal weight: 6.9990 chunk 55 optimal weight: 8.9990 chunk 87 optimal weight: 5.9990 chunk 107 optimal weight: 8.9990 chunk 167 optimal weight: 0.9980 overall best weight: 3.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 500 HIS A 742 ASN A 819 GLN A 827 GLN A 990 ASN A1095 GLN A1204 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.0851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 15910 Z= 0.291 Angle : 0.607 7.131 21694 Z= 0.316 Chirality : 0.043 0.182 2439 Planarity : 0.005 0.080 2606 Dihedral : 7.605 135.469 2514 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer Outliers : 1.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: -0.07 (0.19), residues: 1824 helix: 0.85 (0.17), residues: 875 sheet: -0.31 (0.37), residues: 183 loop : -0.97 (0.21), residues: 766 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 179 time to evaluate : 1.798 Fit side-chains outliers start: 23 outliers final: 11 residues processed: 189 average time/residue: 1.6093 time to fit residues: 331.8804 Evaluate side-chains 178 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 167 time to evaluate : 1.775 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 5 residues processed: 6 average time/residue: 0.1698 time to fit residues: 4.3167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 9.9990 chunk 51 optimal weight: 8.9990 chunk 139 optimal weight: 4.9990 chunk 113 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 167 optimal weight: 10.0000 chunk 180 optimal weight: 20.0000 chunk 149 optimal weight: 7.9990 chunk 165 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 134 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 500 HIS A 742 ASN A 819 GLN ** A 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1224 GLN A1364 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.068 15910 Z= 0.438 Angle : 0.724 8.190 21694 Z= 0.375 Chirality : 0.048 0.190 2439 Planarity : 0.006 0.097 2606 Dihedral : 7.879 140.227 2514 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.68 % Favored : 95.27 % Rotamer Outliers : 2.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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 (0.19), residues: 1824 helix: 0.61 (0.17), residues: 873 sheet: -0.53 (0.37), residues: 185 loop : -1.05 (0.21), residues: 766 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 165 time to evaluate : 1.803 Fit side-chains revert: symmetry clash outliers start: 36 outliers final: 14 residues processed: 184 average time/residue: 1.6399 time to fit residues: 329.9381 Evaluate side-chains 175 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 161 time to evaluate : 1.845 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 8 residues processed: 6 average time/residue: 0.8173 time to fit residues: 8.2722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 8.9990 chunk 125 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 79 optimal weight: 0.0070 chunk 112 optimal weight: 4.9990 chunk 167 optimal weight: 5.9990 chunk 177 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 chunk 159 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 overall best weight: 2.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 500 HIS A 742 ASN A 819 GLN ** A 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 15910 Z= 0.214 Angle : 0.541 6.467 21694 Z= 0.283 Chirality : 0.040 0.173 2439 Planarity : 0.004 0.052 2606 Dihedral : 7.527 134.774 2514 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer Outliers : 1.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.07 (0.19), residues: 1824 helix: 1.02 (0.17), residues: 873 sheet: -0.35 (0.37), residues: 183 loop : -0.95 (0.21), residues: 768 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 172 time to evaluate : 1.825 Fit side-chains outliers start: 23 outliers final: 12 residues processed: 185 average time/residue: 1.6290 time to fit residues: 329.7828 Evaluate side-chains 173 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 161 time to evaluate : 1.635 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 9 residues processed: 3 average time/residue: 0.1398 time to fit residues: 3.1390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 chunk 132 optimal weight: 9.9990 chunk 73 optimal weight: 10.0000 chunk 151 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 159 optimal weight: 2.9990 chunk 44 optimal weight: 0.0370 overall best weight: 2.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 500 HIS A 742 ASN A 819 GLN ** A 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1566 GLN A1569 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 15910 Z= 0.238 Angle : 0.557 6.626 21694 Z= 0.290 Chirality : 0.041 0.172 2439 Planarity : 0.004 0.059 2606 Dihedral : 7.488 135.534 2514 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer Outliers : 1.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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 (0.19), residues: 1824 helix: 1.12 (0.17), residues: 873 sheet: -0.34 (0.38), residues: 183 loop : -0.93 (0.21), residues: 768 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 159 time to evaluate : 1.931 Fit side-chains outliers start: 23 outliers final: 13 residues processed: 175 average time/residue: 1.6304 time to fit residues: 312.1876 Evaluate side-chains 175 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 162 time to evaluate : 1.841 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 10 residues processed: 3 average time/residue: 0.1929 time to fit residues: 3.6113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 1.9990 chunk 160 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 104 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 178 optimal weight: 0.9990 chunk 147 optimal weight: 7.9990 chunk 82 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 500 HIS A 742 ASN A 819 GLN ** A 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1569 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 15910 Z= 0.194 Angle : 0.518 6.763 21694 Z= 0.270 Chirality : 0.039 0.169 2439 Planarity : 0.004 0.049 2606 Dihedral : 7.372 134.409 2514 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer Outliers : 1.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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 (0.19), residues: 1824 helix: 1.27 (0.17), residues: 872 sheet: -0.26 (0.38), residues: 183 loop : -0.91 (0.21), residues: 769 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 165 time to evaluate : 1.799 Fit side-chains outliers start: 21 outliers final: 12 residues processed: 178 average time/residue: 1.5726 time to fit residues: 307.0371 Evaluate side-chains 175 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 163 time to evaluate : 1.676 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 10 residues processed: 2 average time/residue: 0.1510 time to fit residues: 3.0846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 149 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 177 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 108 optimal weight: 8.9990 chunk 81 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 500 HIS A 742 ASN A 819 GLN ** A 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1566 GLN A1569 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 15910 Z= 0.298 Angle : 0.605 7.071 21694 Z= 0.313 Chirality : 0.043 0.173 2439 Planarity : 0.005 0.069 2606 Dihedral : 7.584 137.286 2514 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer Outliers : 1.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.11 (0.19), residues: 1824 helix: 1.08 (0.17), residues: 871 sheet: -0.41 (0.37), residues: 185 loop : -0.93 (0.21), residues: 768 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 160 time to evaluate : 1.641 Fit side-chains outliers start: 22 outliers final: 13 residues processed: 175 average time/residue: 1.6609 time to fit residues: 317.3462 Evaluate side-chains 171 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 158 time to evaluate : 1.604 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 10 residues processed: 3 average time/residue: 0.1798 time to fit residues: 3.2158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 chunk 105 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 112 optimal weight: 7.9990 chunk 120 optimal weight: 9.9990 chunk 87 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 500 HIS A 742 ASN A 819 GLN ** A 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1566 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 15910 Z= 0.326 Angle : 0.627 7.283 21694 Z= 0.325 Chirality : 0.044 0.174 2439 Planarity : 0.005 0.072 2606 Dihedral : 7.666 138.029 2514 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer Outliers : 1.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: -0.01 (0.19), residues: 1824 helix: 0.95 (0.17), residues: 871 sheet: -0.44 (0.38), residues: 175 loop : -0.96 (0.21), residues: 778 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 160 time to evaluate : 1.804 Fit side-chains outliers start: 18 outliers final: 13 residues processed: 175 average time/residue: 1.6545 time to fit residues: 316.6119 Evaluate side-chains 170 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 157 time to evaluate : 1.749 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 11 residues processed: 2 average time/residue: 0.1878 time to fit residues: 3.3048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 7.9990 chunk 155 optimal weight: 0.0970 chunk 165 optimal weight: 0.8980 chunk 99 optimal weight: 10.0000 chunk 71 optimal weight: 0.7980 chunk 129 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 149 optimal weight: 7.9990 chunk 156 optimal weight: 0.9980 chunk 164 optimal weight: 0.4980 chunk 108 optimal weight: 1.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 500 HIS A 742 ASN A 819 GLN ** A 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1467 GLN A1566 GLN A1569 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 15910 Z= 0.138 Angle : 0.466 7.293 21694 Z= 0.245 Chirality : 0.038 0.164 2439 Planarity : 0.003 0.035 2606 Dihedral : 7.241 131.764 2514 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.54 (0.20), residues: 1824 helix: 1.55 (0.18), residues: 868 sheet: -0.28 (0.37), residues: 193 loop : -0.85 (0.21), residues: 763 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 176 time to evaluate : 1.930 Fit side-chains outliers start: 11 outliers final: 9 residues processed: 186 average time/residue: 1.6405 time to fit residues: 333.7381 Evaluate side-chains 172 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 163 time to evaluate : 1.730 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 9 residues processed: 0 time to fit residues: 2.4486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 121 optimal weight: 1.9990 chunk 183 optimal weight: 10.0000 chunk 168 optimal weight: 5.9990 chunk 145 optimal weight: 20.0000 chunk 15 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 500 HIS A 742 ASN A 819 GLN ** A 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1566 GLN A1569 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 15910 Z= 0.275 Angle : 0.594 7.868 21694 Z= 0.305 Chirality : 0.042 0.171 2439 Planarity : 0.004 0.066 2606 Dihedral : 7.458 137.168 2514 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer Outliers : 0.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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 (0.19), residues: 1824 helix: 1.28 (0.17), residues: 873 sheet: -0.37 (0.36), residues: 195 loop : -0.84 (0.22), residues: 756 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 166 time to evaluate : 1.819 Fit side-chains outliers start: 13 outliers final: 10 residues processed: 177 average time/residue: 1.6317 time to fit residues: 317.2276 Evaluate side-chains 174 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 164 time to evaluate : 1.638 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 9 residues processed: 1 average time/residue: 0.2266 time to fit residues: 2.9043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 134 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 40 optimal weight: 0.0980 chunk 146 optimal weight: 0.5980 chunk 61 optimal weight: 7.9990 chunk 150 optimal weight: 0.7980 chunk 18 optimal weight: 20.0000 chunk 26 optimal weight: 10.0000 chunk 128 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 500 HIS A 742 ASN A 819 GLN ** A 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1403 HIS A1566 GLN A1569 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.144715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.114541 restraints weight = 45807.619| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 3.15 r_work: 0.2947 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2942 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2942 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 15910 Z= 0.135 Angle : 0.467 8.332 21694 Z= 0.243 Chirality : 0.037 0.164 2439 Planarity : 0.003 0.040 2606 Dihedral : 7.155 131.542 2514 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.69 (0.20), residues: 1824 helix: 1.66 (0.18), residues: 867 sheet: -0.13 (0.36), residues: 203 loop : -0.78 (0.21), residues: 754 =============================================================================== Job complete usr+sys time: 5834.98 seconds wall clock time: 104 minutes 53.31 seconds (6293.31 seconds total)