Starting phenix.real_space_refine on Fri Feb 16 19:43:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asd_15614/02_2024/8asd_15614_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asd_15614/02_2024/8asd_15614.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asd_15614/02_2024/8asd_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_15614/02_2024/8asd_15614_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asd_15614/02_2024/8asd_15614_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asd_15614/02_2024/8asd_15614.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asd_15614/02_2024/8asd_15614.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asd_15614/02_2024/8asd_15614_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asd_15614/02_2024/8asd_15614_updated.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 16.82, per 1000 atoms: 1.08 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: 6.52 Conformation dependent library (CDL) restraints added in 5.2 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: 11.68 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: 9.53 Time building geometry restraints manager: 6.91 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: 9161 26.36 - 52.73: 388 52.73 - 79.09: 102 79.09 - 105.46: 5 105.46 - 131.82: 1 Dihedral angle restraints: 9657 sinusoidal: 4356 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 9654 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: 2.030 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: 0.000 Extract box with map and model: 8.120 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 65.280 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.800 ------------------------------------------------------------------------------- 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 : 15.149 131.824 6237 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 % Allowed : 0.31 % Favored : 99.63 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 520 HIS 0.006 0.001 HIS A 949 PHE 0.020 0.002 PHE A1283 TYR 0.019 0.002 TYR A 193 ARG 0.008 0.001 ARG A 481 *********************** 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 : 1.687 Fit side-chains revert: symmetry clash REVERT: A 389 ASP cc_start: 0.7176 (m-30) cc_final: 0.6872 (m-30) REVERT: A 1347 LYS cc_start: 0.7542 (ttpt) cc_final: 0.7338 (ttpp) REVERT: A 1463 MET cc_start: 0.7860 (mtp) cc_final: 0.7636 (mtp) REVERT: A 1535 LYS cc_start: 0.8053 (tmtt) cc_final: 0.7663 (tppp) REVERT: A 1672 MET cc_start: 0.2190 (tmm) cc_final: 0.1837 (ttp) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 1.7296 time to fit residues: 409.3243 Evaluate side-chains 170 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 1.685 ------------------------------------------------------------------------------- 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: 7.9990 overall best weight: 4.5994 ------------------------------------------------------------------------------- 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 990 ASN A1095 GLN A1204 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.0933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 15910 Z= 0.368 Angle : 0.670 7.519 21694 Z= 0.348 Chirality : 0.046 0.188 2439 Planarity : 0.005 0.100 2606 Dihedral : 12.503 137.001 2660 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.56 % Allowed : 7.47 % Favored : 90.97 % 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: -0.23 (0.19), residues: 1824 helix: 0.71 (0.17), residues: 873 sheet: -0.42 (0.37), residues: 185 loop : -1.02 (0.21), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 989 HIS 0.008 0.002 HIS A 949 PHE 0.021 0.003 PHE A 166 TYR 0.017 0.002 TYR A 193 ARG 0.006 0.001 ARG A1766 *********************** 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 195 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 171 time to evaluate : 1.726 Fit side-chains REVERT: A 26 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.6535 (tm-30) REVERT: A 173 SER cc_start: 0.8340 (p) cc_final: 0.8051 (p) REVERT: A 213 GLU cc_start: 0.5933 (pt0) cc_final: 0.5722 (pt0) REVERT: A 252 MET cc_start: 0.8381 (ttm) cc_final: 0.8117 (ttm) REVERT: A 303 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7134 (tm-30) REVERT: A 389 ASP cc_start: 0.7224 (m-30) cc_final: 0.6891 (m-30) REVERT: A 912 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.8063 (ttmm) REVERT: A 1006 MET cc_start: 0.8745 (mmm) cc_final: 0.8481 (mmm) REVERT: A 1364 GLN cc_start: 0.8413 (mt0) cc_final: 0.8145 (mt0) REVERT: A 1463 MET cc_start: 0.7912 (mtp) cc_final: 0.7690 (mtp) REVERT: A 1535 LYS cc_start: 0.8016 (tmtt) cc_final: 0.7630 (tppp) REVERT: A 1672 MET cc_start: 0.2171 (tmm) cc_final: 0.1937 (tmm) REVERT: A 1768 LEU cc_start: 0.6670 (tp) cc_final: 0.6280 (tp) outliers start: 24 outliers final: 11 residues processed: 183 average time/residue: 1.6581 time to fit residues: 330.1791 Evaluate side-chains 174 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 160 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 780 ASP Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 912 LYS Chi-restraints excluded: chain A residue 1045 SER Chi-restraints excluded: chain A residue 1157 LYS Chi-restraints excluded: chain A residue 1564 HIS Chi-restraints excluded: chain A residue 1565 VAL Chi-restraints excluded: chain A residue 1597 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 139 optimal weight: 9.9990 chunk 113 optimal weight: 10.0000 chunk 46 optimal weight: 0.8980 chunk 167 optimal weight: 9.9990 chunk 180 optimal weight: 20.0000 chunk 149 optimal weight: 8.9990 chunk 165 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 134 optimal weight: 6.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- 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: 0.8238 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 15910 Z= 0.301 Angle : 0.608 7.113 21694 Z= 0.317 Chirality : 0.043 0.181 2439 Planarity : 0.005 0.069 2606 Dihedral : 12.433 135.631 2660 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.87 % Allowed : 9.03 % Favored : 89.10 % 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: -0.13 (0.19), residues: 1824 helix: 0.84 (0.17), residues: 871 sheet: -0.39 (0.37), residues: 183 loop : -1.03 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 989 HIS 0.005 0.001 HIS A 949 PHE 0.017 0.002 PHE A 166 TYR 0.016 0.002 TYR A 193 ARG 0.006 0.001 ARG A1766 *********************** 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 200 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 171 time to evaluate : 1.693 Fit side-chains revert: symmetry clash REVERT: A 213 GLU cc_start: 0.5995 (pt0) cc_final: 0.5789 (pt0) REVERT: A 303 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7094 (tm-30) REVERT: A 389 ASP cc_start: 0.7280 (m-30) cc_final: 0.6903 (m-30) REVERT: A 654 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7340 (tt0) REVERT: A 1006 MET cc_start: 0.8754 (mmm) cc_final: 0.8472 (mmm) REVERT: A 1248 MET cc_start: 0.8276 (mmt) cc_final: 0.7968 (mmt) REVERT: A 1364 GLN cc_start: 0.8388 (mt0) cc_final: 0.8160 (mt0) REVERT: A 1463 MET cc_start: 0.7925 (mtp) cc_final: 0.7723 (mtp) REVERT: A 1612 GLU cc_start: 0.6610 (OUTLIER) cc_final: 0.5360 (mp0) REVERT: A 1672 MET cc_start: 0.2367 (tmm) cc_final: 0.2110 (tmm) REVERT: A 1768 LEU cc_start: 0.6651 (tp) cc_final: 0.6194 (tp) outliers start: 29 outliers final: 12 residues processed: 188 average time/residue: 1.6131 time to fit residues: 330.2620 Evaluate side-chains 176 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 161 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 780 ASP Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 1045 SER Chi-restraints excluded: chain A residue 1157 LYS Chi-restraints excluded: chain A residue 1564 HIS Chi-restraints excluded: chain A residue 1565 VAL Chi-restraints excluded: chain A residue 1612 GLU 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: 0.7980 chunk 86 optimal weight: 0.0070 chunk 18 optimal weight: 6.9990 chunk 79 optimal weight: 0.2980 chunk 112 optimal weight: 0.4980 chunk 167 optimal weight: 7.9990 chunk 177 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 chunk 159 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 overall best weight: 0.7200 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15910 Z= 0.137 Angle : 0.462 6.422 21694 Z= 0.244 Chirality : 0.038 0.163 2439 Planarity : 0.003 0.034 2606 Dihedral : 12.135 131.515 2660 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.06 % Allowed : 10.71 % Favored : 88.23 % 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: 0.44 (0.19), residues: 1824 helix: 1.39 (0.18), residues: 873 sheet: -0.15 (0.37), residues: 193 loop : -0.87 (0.21), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 520 HIS 0.003 0.001 HIS A1057 PHE 0.016 0.001 PHE A 649 TYR 0.020 0.001 TYR A 193 ARG 0.008 0.000 ARG A1766 *********************** 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 191 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 175 time to evaluate : 1.536 Fit side-chains REVERT: A 68 ILE cc_start: 0.6694 (mt) cc_final: 0.6178 (tp) REVERT: A 389 ASP cc_start: 0.7195 (m-30) cc_final: 0.6834 (m-30) REVERT: A 776 GLU cc_start: 0.6885 (mp0) cc_final: 0.6665 (mm-30) REVERT: A 887 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.8052 (tpt) REVERT: A 1364 GLN cc_start: 0.8327 (mt0) cc_final: 0.8107 (mt0) REVERT: A 1463 MET cc_start: 0.7852 (mtp) cc_final: 0.7628 (mtp) REVERT: A 1512 LYS cc_start: 0.7893 (mttm) cc_final: 0.7611 (mtpp) REVERT: A 1535 LYS cc_start: 0.7982 (tmtt) cc_final: 0.7594 (tppp) REVERT: A 1612 GLU cc_start: 0.6479 (OUTLIER) cc_final: 0.5203 (mp0) REVERT: A 1768 LEU cc_start: 0.6645 (tp) cc_final: 0.6152 (tp) outliers start: 16 outliers final: 3 residues processed: 184 average time/residue: 1.6092 time to fit residues: 323.2622 Evaluate side-chains 167 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 162 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 780 ASP Chi-restraints excluded: chain A residue 887 MET Chi-restraints excluded: chain A residue 1045 SER Chi-restraints excluded: chain A residue 1564 HIS Chi-restraints excluded: chain A residue 1612 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 132 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 151 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 90 optimal weight: 0.0770 chunk 159 optimal weight: 10.0000 chunk 44 optimal weight: 0.0470 overall best weight: 1.8242 ------------------------------------------------------------------------------- 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 990 ASN A1224 GLN A1494 ASN A1566 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15910 Z= 0.188 Angle : 0.506 6.613 21694 Z= 0.263 Chirality : 0.039 0.167 2439 Planarity : 0.004 0.051 2606 Dihedral : 12.147 134.387 2660 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.31 % Allowed : 11.15 % Favored : 87.55 % 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: 0.51 (0.19), residues: 1824 helix: 1.48 (0.18), residues: 870 sheet: -0.15 (0.37), residues: 193 loop : -0.84 (0.21), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 520 HIS 0.004 0.001 HIS A1245 PHE 0.015 0.002 PHE A 911 TYR 0.017 0.001 TYR A 193 ARG 0.005 0.000 ARG A1766 *********************** 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 184 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 164 time to evaluate : 1.577 Fit side-chains revert: symmetry clash REVERT: A 26 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.6437 (tm-30) REVERT: A 68 ILE cc_start: 0.6818 (mt) cc_final: 0.6220 (tp) REVERT: A 213 GLU cc_start: 0.5931 (pt0) cc_final: 0.5717 (pt0) REVERT: A 389 ASP cc_start: 0.7186 (m-30) cc_final: 0.6822 (m-30) REVERT: A 887 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.8029 (tpt) REVERT: A 912 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.8051 (ttmm) REVERT: A 1006 MET cc_start: 0.8734 (mmm) cc_final: 0.8483 (mmm) REVERT: A 1463 MET cc_start: 0.7857 (mtp) cc_final: 0.7642 (mtp) REVERT: A 1512 LYS cc_start: 0.7877 (mttm) cc_final: 0.7588 (mtpp) REVERT: A 1535 LYS cc_start: 0.8022 (tmtt) cc_final: 0.7612 (tppp) REVERT: A 1612 GLU cc_start: 0.6548 (OUTLIER) cc_final: 0.5354 (mp0) REVERT: A 1672 MET cc_start: 0.2117 (tmm) cc_final: 0.1717 (ttp) REVERT: A 1768 LEU cc_start: 0.6642 (tp) cc_final: 0.6166 (tp) outliers start: 20 outliers final: 7 residues processed: 176 average time/residue: 1.5546 time to fit residues: 298.7247 Evaluate side-chains 174 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 163 time to evaluate : 1.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 780 ASP Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 887 MET Chi-restraints excluded: chain A residue 912 LYS Chi-restraints excluded: chain A residue 1045 SER Chi-restraints excluded: chain A residue 1564 HIS Chi-restraints excluded: chain A residue 1565 VAL Chi-restraints excluded: chain A residue 1597 ILE Chi-restraints excluded: chain A residue 1612 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 10.0000 chunk 160 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 43 optimal weight: 0.0050 chunk 178 optimal weight: 3.9990 chunk 147 optimal weight: 0.0870 chunk 82 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 58 optimal weight: 8.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.6178 ------------------------------------------------------------------------------- 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 819 GLN ** A 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1494 ASN A1566 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15910 Z= 0.173 Angle : 0.486 6.820 21694 Z= 0.253 Chirality : 0.039 0.164 2439 Planarity : 0.004 0.042 2606 Dihedral : 12.118 134.025 2660 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.25 % Allowed : 11.77 % Favored : 86.99 % 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: 0.59 (0.20), residues: 1824 helix: 1.55 (0.18), residues: 871 sheet: -0.12 (0.37), residues: 193 loop : -0.81 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 520 HIS 0.003 0.001 HIS A1245 PHE 0.015 0.001 PHE A 911 TYR 0.017 0.001 TYR A 193 ARG 0.005 0.000 ARG A1766 *********************** 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 184 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 165 time to evaluate : 1.622 Fit side-chains REVERT: A 68 ILE cc_start: 0.6812 (mt) cc_final: 0.6192 (tp) REVERT: A 97 GLU cc_start: 0.6799 (pm20) cc_final: 0.6582 (pt0) REVERT: A 213 GLU cc_start: 0.6002 (pt0) cc_final: 0.5790 (pt0) REVERT: A 389 ASP cc_start: 0.7179 (m-30) cc_final: 0.6811 (m-30) REVERT: A 912 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7998 (ttmm) REVERT: A 1006 MET cc_start: 0.8706 (mmm) cc_final: 0.8461 (mmm) REVERT: A 1135 ARG cc_start: 0.6851 (OUTLIER) cc_final: 0.6648 (ttt180) REVERT: A 1364 GLN cc_start: 0.8420 (mt0) cc_final: 0.8192 (mt0) REVERT: A 1463 MET cc_start: 0.7859 (mtp) cc_final: 0.7643 (mtp) REVERT: A 1512 LYS cc_start: 0.7880 (mttm) cc_final: 0.7583 (mtpp) REVERT: A 1535 LYS cc_start: 0.7993 (tmtt) cc_final: 0.7591 (tppp) REVERT: A 1612 GLU cc_start: 0.6553 (OUTLIER) cc_final: 0.5335 (mp0) REVERT: A 1768 LEU cc_start: 0.6656 (tp) cc_final: 0.6156 (tp) outliers start: 19 outliers final: 6 residues processed: 179 average time/residue: 1.6838 time to fit residues: 327.5920 Evaluate side-chains 170 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 161 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 912 LYS Chi-restraints excluded: chain A residue 936 VAL Chi-restraints excluded: chain A residue 1045 SER Chi-restraints excluded: chain A residue 1135 ARG Chi-restraints excluded: chain A residue 1564 HIS Chi-restraints excluded: chain A residue 1565 VAL Chi-restraints excluded: chain A residue 1597 ILE Chi-restraints excluded: chain A residue 1612 GLU 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: 2.9990 chunk 101 optimal weight: 7.9990 chunk 130 optimal weight: 0.4980 chunk 100 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 177 optimal weight: 9.9990 chunk 110 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 overall best weight: 2.4986 ------------------------------------------------------------------------------- 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** A1494 ASN A1566 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15910 Z= 0.228 Angle : 0.537 7.109 21694 Z= 0.279 Chirality : 0.040 0.169 2439 Planarity : 0.004 0.058 2606 Dihedral : 12.204 134.942 2660 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.37 % Allowed : 11.89 % Favored : 86.74 % 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: 0.48 (0.19), residues: 1824 helix: 1.43 (0.18), residues: 871 sheet: -0.22 (0.37), residues: 193 loop : -0.82 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 520 HIS 0.005 0.001 HIS A1245 PHE 0.016 0.002 PHE A 911 TYR 0.016 0.002 TYR A 193 ARG 0.007 0.000 ARG A1766 *********************** 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 181 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 160 time to evaluate : 1.679 Fit side-chains revert: symmetry clash REVERT: A 97 GLU cc_start: 0.6845 (pm20) cc_final: 0.6567 (pt0) REVERT: A 213 GLU cc_start: 0.5999 (pt0) cc_final: 0.5762 (pt0) REVERT: A 389 ASP cc_start: 0.7225 (m-30) cc_final: 0.6847 (m-30) REVERT: A 654 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7130 (tt0) REVERT: A 759 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.6937 (mp0) REVERT: A 912 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.8089 (ttmm) REVERT: A 1463 MET cc_start: 0.7853 (mtp) cc_final: 0.7653 (mtp) REVERT: A 1512 LYS cc_start: 0.7895 (mttm) cc_final: 0.7606 (mtpp) REVERT: A 1535 LYS cc_start: 0.7985 (tmtt) cc_final: 0.7730 (tptm) REVERT: A 1612 GLU cc_start: 0.6548 (OUTLIER) cc_final: 0.5404 (mp0) REVERT: A 1768 LEU cc_start: 0.6629 (tp) cc_final: 0.6151 (tp) outliers start: 21 outliers final: 10 residues processed: 175 average time/residue: 1.6355 time to fit residues: 311.8820 Evaluate side-chains 172 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 158 time to evaluate : 1.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 759 GLU Chi-restraints excluded: chain A residue 816 GLU Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 912 LYS Chi-restraints excluded: chain A residue 936 VAL Chi-restraints excluded: chain A residue 1045 SER Chi-restraints excluded: chain A residue 1564 HIS Chi-restraints excluded: chain A residue 1565 VAL Chi-restraints excluded: chain A residue 1597 ILE Chi-restraints excluded: chain A residue 1612 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 7.9990 chunk 70 optimal weight: 9.9990 chunk 105 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 112 optimal weight: 0.9980 chunk 120 optimal weight: 10.0000 chunk 87 optimal weight: 0.0770 chunk 16 optimal weight: 0.9990 chunk 139 optimal weight: 3.9990 chunk 161 optimal weight: 5.9990 overall best weight: 2.2144 ------------------------------------------------------------------------------- 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** ** A1403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1494 ASN A1566 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15910 Z= 0.210 Angle : 0.521 7.214 21694 Z= 0.272 Chirality : 0.040 0.167 2439 Planarity : 0.004 0.053 2606 Dihedral : 12.200 134.241 2660 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.31 % Allowed : 12.14 % Favored : 86.55 % 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: 0.48 (0.19), residues: 1824 helix: 1.44 (0.18), residues: 870 sheet: -0.22 (0.37), residues: 193 loop : -0.83 (0.21), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 520 HIS 0.004 0.001 HIS A1245 PHE 0.015 0.002 PHE A 911 TYR 0.016 0.001 TYR A 193 ARG 0.008 0.000 ARG A1766 *********************** 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 185 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 165 time to evaluate : 1.523 Fit side-chains revert: symmetry clash REVERT: A 97 GLU cc_start: 0.6844 (pm20) cc_final: 0.6558 (pt0) REVERT: A 213 GLU cc_start: 0.6000 (pt0) cc_final: 0.5761 (pt0) REVERT: A 389 ASP cc_start: 0.7225 (m-30) cc_final: 0.6852 (m-30) REVERT: A 654 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7083 (tt0) REVERT: A 912 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.8078 (ttmm) REVERT: A 1494 ASN cc_start: 0.6600 (OUTLIER) cc_final: 0.6347 (t0) REVERT: A 1512 LYS cc_start: 0.7908 (mttm) cc_final: 0.7611 (mtpp) REVERT: A 1535 LYS cc_start: 0.7981 (tmtt) cc_final: 0.7730 (tptm) REVERT: A 1612 GLU cc_start: 0.6559 (OUTLIER) cc_final: 0.5329 (mp0) REVERT: A 1768 LEU cc_start: 0.6645 (tp) cc_final: 0.6171 (tp) outliers start: 20 outliers final: 11 residues processed: 177 average time/residue: 1.6407 time to fit residues: 316.3811 Evaluate side-chains 173 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 158 time to evaluate : 1.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 912 LYS Chi-restraints excluded: chain A residue 936 VAL Chi-restraints excluded: chain A residue 1045 SER Chi-restraints excluded: chain A residue 1494 ASN Chi-restraints excluded: chain A residue 1564 HIS Chi-restraints excluded: chain A residue 1565 VAL Chi-restraints excluded: chain A residue 1597 ILE Chi-restraints excluded: chain A residue 1612 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 5.9990 chunk 155 optimal weight: 10.0000 chunk 165 optimal weight: 8.9990 chunk 99 optimal weight: 6.9990 chunk 71 optimal weight: 0.9980 chunk 129 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 chunk 156 optimal weight: 8.9990 chunk 164 optimal weight: 0.6980 chunk 108 optimal weight: 6.9990 overall best weight: 2.5184 ------------------------------------------------------------------------------- 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** ** A1403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1494 ASN A1566 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 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 : 0.004 0.035 15910 Z= 0.230 Angle : 0.540 7.406 21694 Z= 0.281 Chirality : 0.040 0.168 2439 Planarity : 0.004 0.057 2606 Dihedral : 12.221 134.522 2660 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.25 % Allowed : 12.33 % Favored : 86.43 % 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: 0.43 (0.19), residues: 1824 helix: 1.39 (0.17), residues: 871 sheet: -0.26 (0.37), residues: 193 loop : -0.83 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 520 HIS 0.004 0.001 HIS A1245 PHE 0.015 0.002 PHE A 911 TYR 0.016 0.002 TYR A 193 ARG 0.008 0.000 ARG A1766 *********************** 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 178 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 159 time to evaluate : 1.617 Fit side-chains revert: symmetry clash REVERT: A 26 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.6584 (tm-30) REVERT: A 97 GLU cc_start: 0.6792 (pm20) cc_final: 0.6485 (pt0) REVERT: A 160 MET cc_start: 0.7261 (mtp) cc_final: 0.6973 (mtp) REVERT: A 213 GLU cc_start: 0.6005 (pt0) cc_final: 0.5737 (pt0) REVERT: A 389 ASP cc_start: 0.7235 (m-30) cc_final: 0.6858 (m-30) REVERT: A 654 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7063 (tt0) REVERT: A 776 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6893 (mm-30) REVERT: A 912 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.8096 (ttmm) REVERT: A 1006 MET cc_start: 0.8654 (mmm) cc_final: 0.8417 (mmm) REVERT: A 1494 ASN cc_start: 0.6681 (OUTLIER) cc_final: 0.6313 (t0) REVERT: A 1512 LYS cc_start: 0.7914 (mttm) cc_final: 0.7615 (mtpp) REVERT: A 1535 LYS cc_start: 0.7983 (tmtt) cc_final: 0.7737 (tptm) REVERT: A 1612 GLU cc_start: 0.6561 (OUTLIER) cc_final: 0.5409 (mp0) REVERT: A 1768 LEU cc_start: 0.6632 (tp) cc_final: 0.6161 (tp) outliers start: 19 outliers final: 12 residues processed: 173 average time/residue: 1.5803 time to fit residues: 298.7685 Evaluate side-chains 176 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 158 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 776 GLU Chi-restraints excluded: chain A residue 816 GLU Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 912 LYS Chi-restraints excluded: chain A residue 936 VAL Chi-restraints excluded: chain A residue 1045 SER Chi-restraints excluded: chain A residue 1494 ASN Chi-restraints excluded: chain A residue 1564 HIS Chi-restraints excluded: chain A residue 1565 VAL Chi-restraints excluded: chain A residue 1597 ILE Chi-restraints excluded: chain A residue 1612 GLU 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: 4.9990 chunk 82 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 183 optimal weight: 10.0000 chunk 168 optimal weight: 20.0000 chunk 145 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 89 optimal weight: 0.4980 chunk 115 optimal weight: 0.7980 overall best weight: 2.2586 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A1494 ASN A1566 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1197 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= 0.215 Angle : 0.533 7.729 21694 Z= 0.277 Chirality : 0.040 0.168 2439 Planarity : 0.004 0.054 2606 Dihedral : 12.218 134.273 2660 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.25 % Allowed : 12.45 % Favored : 86.30 % 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: 0.45 (0.19), residues: 1824 helix: 1.41 (0.17), residues: 871 sheet: -0.24 (0.37), residues: 193 loop : -0.83 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 520 HIS 0.004 0.001 HIS A1245 PHE 0.015 0.002 PHE A 911 TYR 0.016 0.001 TYR A 193 ARG 0.008 0.000 ARG A1766 ********************** 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: 19 poor density : 160 time to evaluate : 1.835 Fit side-chains revert: symmetry clash REVERT: A 26 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.6581 (tm-30) REVERT: A 97 GLU cc_start: 0.6791 (pm20) cc_final: 0.6482 (pt0) REVERT: A 160 MET cc_start: 0.7144 (mtp) cc_final: 0.6846 (mtp) REVERT: A 213 GLU cc_start: 0.6008 (pt0) cc_final: 0.5740 (pt0) REVERT: A 389 ASP cc_start: 0.7233 (m-30) cc_final: 0.6856 (m-30) REVERT: A 654 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7057 (tt0) REVERT: A 776 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6844 (mm-30) REVERT: A 912 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.8082 (ttmm) REVERT: A 1494 ASN cc_start: 0.6495 (OUTLIER) cc_final: 0.6092 (t0) REVERT: A 1512 LYS cc_start: 0.7912 (mttm) cc_final: 0.7613 (mtpp) REVERT: A 1535 LYS cc_start: 0.7979 (tmtt) cc_final: 0.7734 (tptm) REVERT: A 1612 GLU cc_start: 0.6561 (OUTLIER) cc_final: 0.5333 (mp0) REVERT: A 1672 MET cc_start: 0.2403 (ppp) cc_final: 0.2143 (tmm) REVERT: A 1768 LEU cc_start: 0.6630 (tp) cc_final: 0.6158 (tp) outliers start: 19 outliers final: 12 residues processed: 174 average time/residue: 1.5495 time to fit residues: 294.9675 Evaluate side-chains 178 residues out of total 1598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 160 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 776 GLU Chi-restraints excluded: chain A residue 816 GLU Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 912 LYS Chi-restraints excluded: chain A residue 936 VAL Chi-restraints excluded: chain A residue 1045 SER Chi-restraints excluded: chain A residue 1494 ASN Chi-restraints excluded: chain A residue 1564 HIS Chi-restraints excluded: chain A residue 1565 VAL Chi-restraints excluded: chain A residue 1597 ILE Chi-restraints excluded: chain A residue 1612 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 9.9990 chunk 44 optimal weight: 0.1980 chunk 134 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 40 optimal weight: 0.2980 chunk 146 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 150 optimal weight: 5.9990 chunk 18 optimal weight: 0.0370 chunk 26 optimal weight: 10.0000 chunk 128 optimal weight: 0.0020 overall best weight: 0.9068 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A1494 ASN A1566 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.143773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.113759 restraints weight = 45682.784| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 3.27 r_work: 0.2916 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2911 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2911 r_free = 0.2911 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2911 r_free = 0.2911 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2911 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15910 Z= 0.142 Angle : 0.473 7.814 21694 Z= 0.247 Chirality : 0.038 0.183 2439 Planarity : 0.003 0.038 2606 Dihedral : 12.116 132.280 2660 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.68 % Allowed : 12.89 % Favored : 86.43 % 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: 0.68 (0.20), residues: 1824 helix: 1.66 (0.18), residues: 867 sheet: -0.15 (0.37), residues: 193 loop : -0.78 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 520 HIS 0.003 0.001 HIS A1403 PHE 0.016 0.001 PHE A 649 TYR 0.017 0.001 TYR A 193 ARG 0.009 0.000 ARG A1766 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5964.29 seconds wall clock time: 107 minutes 20.92 seconds (6440.92 seconds total)