Starting phenix.real_space_refine (version: dev) on Wed Mar 15 06:28:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tc0_25803/03_2023/7tc0_25803_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tc0_25803/03_2023/7tc0_25803.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tc0_25803/03_2023/7tc0_25803.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tc0_25803/03_2023/7tc0_25803.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tc0_25803/03_2023/7tc0_25803_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tc0_25803/03_2023/7tc0_25803_updated.pdb" } resolution = 3.1 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A ARG 8": "NH1" <-> "NH2" Residue "A ARG 18": "NH1" <-> "NH2" Residue "A ARG 19": "NH1" <-> "NH2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A ARG 43": "NH1" <-> "NH2" Residue "A ARG 104": "NH1" <-> "NH2" Residue "A ASP 124": "OD1" <-> "OD2" Residue "A ARG 282": "NH1" <-> "NH2" Residue "A GLU 363": "OE1" <-> "OE2" Residue "A ARG 393": "NH1" <-> "NH2" Residue "A ASP 411": "OD1" <-> "OD2" Residue "A ASP 441": "OD1" <-> "OD2" Residue "A ARG 485": "NH1" <-> "NH2" Residue "A GLU 503": "OE1" <-> "OE2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "A GLU 529": "OE1" <-> "OE2" Residue "A ASP 559": "OD1" <-> "OD2" Residue "A ARG 579": "NH1" <-> "NH2" Residue "A GLU 584": "OE1" <-> "OE2" Residue "A GLU 612": "OE1" <-> "OE2" Residue "A ARG 634": "NH1" <-> "NH2" Residue "A ARG 672": "NH1" <-> "NH2" Residue "A PHE 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 742": "NH1" <-> "NH2" Residue "A GLU 792": "OE1" <-> "OE2" Residue "A GLU 799": "OE1" <-> "OE2" Residue "A ASP 807": "OD1" <-> "OD2" Residue "A GLU 891": "OE1" <-> "OE2" Residue "A PHE 950": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 985": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 986": "OD1" <-> "OD2" Residue "A GLU 1011": "OE1" <-> "OE2" Residue "A GLU 1013": "OE1" <-> "OE2" Residue "A ASP 1057": "OD1" <-> "OD2" Residue "A ASP 1064": "OD1" <-> "OD2" Residue "A ARG 1069": "NH1" <-> "NH2" Residue "A GLU 1073": "OE1" <-> "OE2" Residue "A ARG 1082": "NH1" <-> "NH2" Residue "A ASP 1095": "OD1" <-> "OD2" Residue "A ARG 1100": "NH1" <-> "NH2" Residue "A ASP 1179": "OD1" <-> "OD2" Residue "A TYR 1206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1245": "OE1" <-> "OE2" Residue "A ARG 1336": "NH1" <-> "NH2" Residue "A PHE 1347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1386": "OE1" <-> "OE2" Residue "A GLU 1420": "OE1" <-> "OE2" Residue "A ASP 1426": "OD1" <-> "OD2" Residue "A PHE 1449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1503": "NH1" <-> "NH2" Residue "A ASP 1553": "OD1" <-> "OD2" Residue "A ASP 1567": "OD1" <-> "OD2" Residue "A PHE 1605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1654": "OD1" <-> "OD2" Residue "A ARG 1680": "NH1" <-> "NH2" Residue "A TYR 1710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1721": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1801": "OD1" <-> "OD2" Residue "A ASP 1821": "OD1" <-> "OD2" Residue "A GLU 1833": "OE1" <-> "OE2" Residue "A TYR 1872": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1999": "OE1" <-> "OE2" Residue "A ARG 2004": "NH1" <-> "NH2" Residue "A GLU 2005": "OE1" <-> "OE2" Residue "A GLU 2018": "OE1" <-> "OE2" Residue "A TYR 2041": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2051": "NH1" <-> "NH2" Residue "A ASP 2069": "OD1" <-> "OD2" Residue "A GLU 2070": "OE1" <-> "OE2" Residue "A ARG 2081": "NH1" <-> "NH2" Residue "A ARG 2095": "NH1" <-> "NH2" Residue "A ARG 2113": "NH1" <-> "NH2" Residue "A ASP 2137": "OD1" <-> "OD2" Residue "A TYR 2178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2204": "OE1" <-> "OE2" Residue "A ASP 2223": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/chem_data/mon_lib" Total number of atoms: 13809 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 13636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1781, 13636 Classifications: {'peptide': 1781} Incomplete info: {'truncation_to_alanine': 151} Link IDs: {'PCIS': 2, 'PTRANS': 85, 'TRANS': 1693} Chain breaks: 13 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 531 Unresolved non-hydrogen angles: 663 Unresolved non-hydrogen dihedrals: 451 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 13, 'TYR:plan': 2, 'ASN:plan1': 8, 'TRP:plan': 3, 'HIS:plan': 5, 'PHE:plan': 4, 'GLU:plan': 16, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 285 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Unusual residues: {'CLR': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 7.54, per 1000 atoms: 0.55 Number of scatterers: 13809 At special positions: 0 Unit cell: (82.516, 98.514, 218.078, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 2471 8.00 N 2289 7.00 C 8965 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 81 " distance=2.03 Simple disulfide: pdb=" SG CYS A 75 " - pdb=" SG CYS A 309 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 504 " distance=2.03 Simple disulfide: pdb=" SG CYS A 626 " - pdb=" SG CYS A1465 " distance=2.03 Simple disulfide: pdb=" SG CYS A1418 " - pdb=" SG CYS A1429 " distance=2.03 Simple disulfide: pdb=" SG CYS A1463 " - pdb=" SG CYS A1477 " distance=2.03 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=1, symmetry=0 Links applied BETA1-3 " BMA C 3 " - " BMA C 4 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " BETA1-6 " BMA C 3 " - " BMA C 5 " NAG-ASN " NAG A2502 " - " ASN A1637 " " NAG A2503 " - " ASN A 98 " " NAG B 1 " - " ASN A 400 " " NAG C 1 " - " ASN A1504 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.28 Conformation dependent library (CDL) restraints added in 2.0 seconds 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3326 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 74 helices and 8 sheets defined 53.7% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.48 Creating SS restraints... Processing helix chain 'A' and resid 4 through 21 removed outlier: 3.827A pdb=" N GLN A 21 " --> pdb=" O PHE A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 45 Proline residue: A 32 - end of helix removed outlier: 3.638A pdb=" N SER A 45 " --> pdb=" O SER A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 66 through 74 Processing helix chain 'A' and resid 87 through 89 No H-bonds generated for 'chain 'A' and resid 87 through 89' Processing helix chain 'A' and resid 101 through 118 removed outlier: 3.777A pdb=" N GLN A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS A 118 " --> pdb=" O LEU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 253 through 272 Processing helix chain 'A' and resid 278 through 288 removed outlier: 3.784A pdb=" N GLN A 283 " --> pdb=" O SER A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 308 removed outlier: 4.013A pdb=" N TYR A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 363 Processing helix chain 'A' and resid 372 through 379 Proline residue: A 377 - end of helix Processing helix chain 'A' and resid 390 through 409 removed outlier: 4.762A pdb=" N LEU A 406 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ALA A 407 " --> pdb=" O PHE A 403 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N VAL A 408 " --> pdb=" O GLN A 404 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N PHE A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 428 Proline residue: A 421 - end of helix Processing helix chain 'A' and resid 431 through 440 Processing helix chain 'A' and resid 445 through 453 Processing helix chain 'A' and resid 460 through 466 Processing helix chain 'A' and resid 484 through 504 removed outlier: 4.632A pdb=" N CYS A 504 " --> pdb=" O ARG A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 528 Processing helix chain 'A' and resid 587 through 590 No H-bonds generated for 'chain 'A' and resid 587 through 590' Processing helix chain 'A' and resid 593 through 609 Processing helix chain 'A' and resid 631 through 638 Processing helix chain 'A' and resid 640 through 664 removed outlier: 4.605A pdb=" N ALA A 647 " --> pdb=" O PHE A 643 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N TRP A 648 " --> pdb=" O MET A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 673 Processing helix chain 'A' and resid 678 through 706 Proline residue: A 692 - end of helix Processing helix chain 'A' and resid 715 through 739 removed outlier: 4.088A pdb=" N THR A 738 " --> pdb=" O PHE A 734 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N LEU A 739 " --> pdb=" O LEU A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 766 removed outlier: 4.349A pdb=" N GLY A 751 " --> pdb=" O ALA A 747 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE A 752 " --> pdb=" O ALA A 748 " (cutoff:3.500A) Proline residue: A 760 - end of helix removed outlier: 3.608A pdb=" N ALA A 766 " --> pdb=" O VAL A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 770 No H-bonds generated for 'chain 'A' and resid 768 through 770' Processing helix chain 'A' and resid 773 through 779 Processing helix chain 'A' and resid 783 through 799 Processing helix chain 'A' and resid 821 through 845 removed outlier: 3.627A pdb=" N ALA A 844 " --> pdb=" O TRP A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 947 Processing helix chain 'A' and resid 969 through 974 removed outlier: 3.584A pdb=" N GLN A 973 " --> pdb=" O SER A 969 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ASN A 974 " --> pdb=" O THR A 970 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 969 through 974' Processing helix chain 'A' and resid 990 through 1001 Processing helix chain 'A' and resid 1005 through 1019 Processing helix chain 'A' and resid 1024 through 1027 No H-bonds generated for 'chain 'A' and resid 1024 through 1027' Processing helix chain 'A' and resid 1035 through 1050 removed outlier: 3.860A pdb=" N ALA A1046 " --> pdb=" O SER A1042 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N PHE A1047 " --> pdb=" O VAL A1043 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N VAL A1048 " --> pdb=" O ALA A1044 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLY A1049 " --> pdb=" O LEU A1045 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N GLY A1050 " --> pdb=" O ALA A1046 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1077 Processing helix chain 'A' and resid 1091 through 1097 Processing helix chain 'A' and resid 1115 through 1121 Processing helix chain 'A' and resid 1181 through 1190 Processing helix chain 'A' and resid 1217 through 1227 Processing helix chain 'A' and resid 1244 through 1251 Processing helix chain 'A' and resid 1322 through 1341 removed outlier: 4.199A pdb=" N GLN A1326 " --> pdb=" O TRP A1322 " (cutoff:3.500A) Processing helix chain 'A' and resid 1349 through 1364 Proline residue: A1354 - end of helix Processing helix chain 'A' and resid 1381 through 1383 No H-bonds generated for 'chain 'A' and resid 1381 through 1383' Processing helix chain 'A' and resid 1399 through 1409 Processing helix chain 'A' and resid 1443 through 1451 Processing helix chain 'A' and resid 1505 through 1521 Processing helix chain 'A' and resid 1550 through 1561 Processing helix chain 'A' and resid 1569 through 1584 removed outlier: 3.998A pdb=" N LEU A1584 " --> pdb=" O PHE A1580 " (cutoff:3.500A) Processing helix chain 'A' and resid 1601 through 1617 Processing helix chain 'A' and resid 1624 through 1626 No H-bonds generated for 'chain 'A' and resid 1624 through 1626' Processing helix chain 'A' and resid 1640 through 1680 removed outlier: 4.064A pdb=" N THR A1650 " --> pdb=" O VAL A1646 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N THR A1651 " --> pdb=" O ALA A1647 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N SER A1652 " --> pdb=" O LEU A1648 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N VAL A1653 " --> pdb=" O MET A1649 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LEU A1656 " --> pdb=" O SER A1652 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A1657 " --> pdb=" O VAL A1653 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N PHE A1667 " --> pdb=" O PHE A1663 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N VAL A1668 " --> pdb=" O ALA A1664 " (cutoff:3.500A) Proline residue: A1669 - end of helix removed outlier: 3.768A pdb=" N PHE A1672 " --> pdb=" O VAL A1668 " (cutoff:3.500A) Processing helix chain 'A' and resid 1685 through 1690 Processing helix chain 'A' and resid 1695 through 1723 removed outlier: 3.563A pdb=" N VAL A1712 " --> pdb=" O CYS A1708 " (cutoff:3.500A) Proline residue: A1713 - end of helix Processing helix chain 'A' and resid 1727 through 1730 No H-bonds generated for 'chain 'A' and resid 1727 through 1730' Processing helix chain 'A' and resid 1735 through 1752 Proline residue: A1751 - end of helix Processing helix chain 'A' and resid 1755 through 1757 No H-bonds generated for 'chain 'A' and resid 1755 through 1757' Processing helix chain 'A' and resid 1766 through 1786 Processing helix chain 'A' and resid 1801 through 1809 removed outlier: 3.916A pdb=" N LEU A1808 " --> pdb=" O LYS A1804 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ILE A1809 " --> pdb=" O SER A1805 " (cutoff:3.500A) Processing helix chain 'A' and resid 1811 through 1835 Processing helix chain 'A' and resid 1851 through 1872 removed outlier: 3.710A pdb=" N GLN A1871 " --> pdb=" O THR A1867 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR A1872 " --> pdb=" O VAL A1868 " (cutoff:3.500A) Processing helix chain 'A' and resid 2003 through 2013 removed outlier: 3.714A pdb=" N VAL A2007 " --> pdb=" O GLY A2003 " (cutoff:3.500A) Processing helix chain 'A' and resid 2021 through 2031 Processing helix chain 'A' and resid 2035 through 2037 No H-bonds generated for 'chain 'A' and resid 2035 through 2037' Processing helix chain 'A' and resid 2042 through 2044 No H-bonds generated for 'chain 'A' and resid 2042 through 2044' Processing helix chain 'A' and resid 2047 through 2059 removed outlier: 3.567A pdb=" N LEU A2059 " --> pdb=" O THR A2055 " (cutoff:3.500A) Processing helix chain 'A' and resid 2080 through 2093 removed outlier: 3.737A pdb=" N GLU A2093 " --> pdb=" O SER A2089 " (cutoff:3.500A) Processing helix chain 'A' and resid 2104 through 2110 Processing helix chain 'A' and resid 2129 through 2134 Processing helix chain 'A' and resid 2153 through 2162 Processing helix chain 'A' and resid 2187 through 2200 removed outlier: 4.388A pdb=" N LYS A2199 " --> pdb=" O SER A2195 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ARG A2200 " --> pdb=" O GLN A2196 " (cutoff:3.500A) Processing helix chain 'A' and resid 2213 through 2222 Processing sheet with id= A, first strand: chain 'A' and resid 384 through 386 removed outlier: 4.360A pdb=" N LYS A 553 " --> pdb=" O THR A 539 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLY A1628 " --> pdb=" O VAL A 552 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N TYR A 554 " --> pdb=" O GLY A1628 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N THR A1630 " --> pdb=" O TYR A 554 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ILE A 556 " --> pdb=" O THR A1630 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N PHE A1632 " --> pdb=" O ILE A 556 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 615 through 621 removed outlier: 7.185A pdb=" N ASN A1588 " --> pdb=" O GLY A 616 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N TYR A 618 " --> pdb=" O ASN A1588 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL A1590 " --> pdb=" O TYR A 618 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N GLN A 620 " --> pdb=" O VAL A1590 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N VAL A1592 " --> pdb=" O GLN A 620 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLY A1533 " --> pdb=" O TYR A1388 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE A1390 " --> pdb=" O GLY A1533 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE A1496 " --> pdb=" O THR A1389 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N VAL A1391 " --> pdb=" O ILE A1496 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLN A1498 " --> pdb=" O VAL A1391 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ASN A1393 " --> pdb=" O GLN A1498 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 956 through 959 removed outlier: 6.784A pdb=" N PHE A 923 " --> pdb=" O GLY A 898 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N SER A 900 " --> pdb=" O LEU A 921 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU A 921 " --> pdb=" O SER A 900 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 975 through 978 removed outlier: 6.821A pdb=" N VAL A1053 " --> pdb=" O GLY A 976 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N CYS A 978 " --> pdb=" O VAL A1053 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE A1055 " --> pdb=" O CYS A 978 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 1236 through 1240 removed outlier: 6.356A pdb=" N VAL A1207 " --> pdb=" O LEU A1196 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N LEU A1196 " --> pdb=" O VAL A1207 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1988 through 1991 removed outlier: 6.931A pdb=" N VAL A2065 " --> pdb=" O GLY A1989 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N CYS A1991 " --> pdb=" O VAL A2065 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N PHE A2067 " --> pdb=" O CYS A1991 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 2203 through 2209 removed outlier: 6.954A pdb=" N ARG A2144 " --> pdb=" O GLU A2204 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N TYR A2206 " --> pdb=" O VAL A2142 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL A2142 " --> pdb=" O TYR A2206 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL A2208 " --> pdb=" O THR A2140 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N THR A2140 " --> pdb=" O VAL A2208 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N MET A2175 " --> pdb=" O HIS A2172 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU A2170 " --> pdb=" O GLN A2177 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N GLN A2179 " --> pdb=" O LEU A2168 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU A2168 " --> pdb=" O GLN A2179 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 1101 through 1105 removed outlier: 6.035A pdb=" N SER A1105 " --> pdb=" O LEU A1109 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LEU A1109 " --> pdb=" O SER A1105 " (cutoff:3.500A) 652 hydrogen bonds defined for protein. 1935 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.80 Time building geometry restraints manager: 6.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4331 1.34 - 1.46: 3159 1.46 - 1.58: 6503 1.58 - 1.70: 0 1.70 - 1.82: 136 Bond restraints: 14129 Sorted by residual: bond pdb=" C VAL A1737 " pdb=" N LEU A1738 " ideal model delta sigma weight residual 1.335 1.555 -0.221 1.27e-02 6.20e+03 3.02e+02 bond pdb=" C LEU A1738 " pdb=" N ALA A1739 " ideal model delta sigma weight residual 1.334 1.413 -0.079 1.33e-02 5.65e+03 3.52e+01 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.487 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.57e+01 bond pdb=" C VAL A1712 " pdb=" N PRO A1713 " ideal model delta sigma weight residual 1.335 1.358 -0.023 1.36e-02 5.41e+03 2.82e+00 ... (remaining 14124 not shown) Histogram of bond angle deviations from ideal: 99.92 - 106.73: 444 106.73 - 113.55: 7805 113.55 - 120.36: 5221 120.36 - 127.18: 5590 127.18 - 134.00: 159 Bond angle restraints: 19219 Sorted by residual: angle pdb=" CA PRO A1713 " pdb=" N PRO A1713 " pdb=" CD PRO A1713 " ideal model delta sigma weight residual 112.00 102.02 9.98 1.40e+00 5.10e-01 5.08e+01 angle pdb=" C SER A2127 " pdb=" CA SER A2127 " pdb=" CB SER A2127 " ideal model delta sigma weight residual 116.63 108.52 8.11 1.16e+00 7.43e-01 4.89e+01 angle pdb=" C VAL A1712 " pdb=" N PRO A1713 " pdb=" CA PRO A1713 " ideal model delta sigma weight residual 119.05 111.77 7.28 1.11e+00 8.12e-01 4.30e+01 angle pdb=" C VAL A1737 " pdb=" N LEU A1738 " pdb=" CA LEU A1738 " ideal model delta sigma weight residual 120.82 129.27 -8.45 1.50e+00 4.44e-01 3.18e+01 angle pdb=" CA VAL A1712 " pdb=" C VAL A1712 " pdb=" N PRO A1713 " ideal model delta sigma weight residual 120.83 117.41 3.42 6.10e-01 2.69e+00 3.15e+01 ... (remaining 19214 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 7539 17.39 - 34.78: 560 34.78 - 52.17: 143 52.17 - 69.56: 22 69.56 - 86.95: 12 Dihedral angle restraints: 8276 sinusoidal: 3126 harmonic: 5150 Sorted by residual: dihedral pdb=" CB CYS A1418 " pdb=" SG CYS A1418 " pdb=" SG CYS A1429 " pdb=" CB CYS A1429 " ideal model delta sinusoidal sigma weight residual -86.00 0.95 -86.95 1 1.00e+01 1.00e-02 9.09e+01 dihedral pdb=" CB CYS A1463 " pdb=" SG CYS A1463 " pdb=" SG CYS A1477 " pdb=" CB CYS A1477 " ideal model delta sinusoidal sigma weight residual -86.00 -8.54 -77.46 1 1.00e+01 1.00e-02 7.52e+01 dihedral pdb=" C PRO A1713 " pdb=" N PRO A1713 " pdb=" CA PRO A1713 " pdb=" CB PRO A1713 " ideal model delta harmonic sigma weight residual -120.70 -131.27 10.57 0 2.50e+00 1.60e-01 1.79e+01 ... (remaining 8273 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 2191 0.106 - 0.212: 40 0.212 - 0.318: 8 0.318 - 0.423: 2 0.423 - 0.529: 1 Chirality restraints: 2242 Sorted by residual: chirality pdb=" CA PRO A1713 " pdb=" N PRO A1713 " pdb=" C PRO A1713 " pdb=" CB PRO A1713 " both_signs ideal model delta sigma weight residual False 2.72 2.19 0.53 2.00e-01 2.50e+01 7.00e+00 chirality pdb=" C14 CLR A2504 " pdb=" C13 CLR A2504 " pdb=" C15 CLR A2504 " pdb=" C8 CLR A2504 " both_signs ideal model delta sigma weight residual False -2.32 -2.66 0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" C14 CLR A2501 " pdb=" C13 CLR A2501 " pdb=" C15 CLR A2501 " pdb=" C8 CLR A2501 " both_signs ideal model delta sigma weight residual False -2.32 -2.66 0.34 2.00e-01 2.50e+01 2.91e+00 ... (remaining 2239 not shown) Planarity restraints: 2404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A1712 " 0.149 5.00e-02 4.00e+02 2.25e-01 8.09e+01 pdb=" N PRO A1713 " -0.389 5.00e-02 4.00e+02 pdb=" CA PRO A1713 " 0.124 5.00e-02 4.00e+02 pdb=" CD PRO A1713 " 0.117 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1738 " 0.013 2.00e-02 2.50e+03 2.49e-02 6.19e+00 pdb=" C LEU A1738 " -0.043 2.00e-02 2.50e+03 pdb=" O LEU A1738 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA A1739 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A1710 " 0.012 2.00e-02 2.50e+03 2.38e-02 5.66e+00 pdb=" C TYR A1710 " -0.041 2.00e-02 2.50e+03 pdb=" O TYR A1710 " 0.015 2.00e-02 2.50e+03 pdb=" N VAL A1711 " 0.014 2.00e-02 2.50e+03 ... (remaining 2401 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.43: 35 2.43 - 3.05: 8514 3.05 - 3.67: 20326 3.67 - 4.28: 29306 4.28 - 4.90: 48682 Nonbonded interactions: 106863 Sorted by model distance: nonbonded pdb=" CE1 PHE A2158 " pdb=" NH2 ARG A2200 " model vdw 1.817 3.420 nonbonded pdb=" CD1 PHE A2158 " pdb=" NH2 ARG A2200 " model vdw 1.992 3.420 nonbonded pdb=" OE2 GLU A2070 " pdb=" ND1 HIS A2102 " model vdw 2.141 2.520 nonbonded pdb=" CZ PHE A2158 " pdb=" NH2 ARG A2200 " model vdw 2.217 3.420 nonbonded pdb=" OD2 ASP A1706 " pdb=" OH TYR A1754 " model vdw 2.231 2.440 ... (remaining 106858 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 8965 2.51 5 N 2289 2.21 5 O 2471 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.840 Check model and map are aligned: 0.190 Process input model: 38.910 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.140 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.221 14129 Z= 0.187 Angle : 0.594 16.477 19219 Z= 0.334 Chirality : 0.044 0.529 2242 Planarity : 0.006 0.225 2400 Dihedral : 13.324 79.583 4932 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer Outliers : 2.49 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 2.33 % 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: -1.78 (0.19), residues: 1753 helix: 0.11 (0.16), residues: 966 sheet: -1.33 (0.39), residues: 174 loop : -3.26 (0.21), residues: 613 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 273 time to evaluate : 1.679 Fit side-chains revert: symmetry clash outliers start: 35 outliers final: 22 residues processed: 302 average time/residue: 0.2852 time to fit residues: 122.9779 Evaluate side-chains 210 residues out of total 1559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 188 time to evaluate : 1.716 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 1 residues processed: 22 average time/residue: 0.1039 time to fit residues: 6.3997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 7.9990 chunk 134 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 72 optimal weight: 0.0670 chunk 139 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 161 optimal weight: 0.5980 overall best weight: 1.1122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: