Starting phenix.real_space_refine on Mon Aug 5 19:12:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tc0_25803/08_2024/7tc0_25803.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tc0_25803/08_2024/7tc0_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_25803/08_2024/7tc0_25803.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tc0_25803/08_2024/7tc0_25803.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tc0_25803/08_2024/7tc0_25803.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tc0_25803/08_2024/7tc0_25803.cif" } resolution = 3.1 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= 0.002 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 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. 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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 dihedrals: 6 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 dihedrals: 15 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 8.25, per 1000 atoms: 0.60 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: 5.44 Conformation dependent library (CDL) restraints added in 2.6 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... Secondary structure from input PDB file: 79 helices and 10 sheets defined 60.5% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.96 Creating SS restraints... Processing helix chain 'A' and resid 3 through 22 removed outlier: 3.827A pdb=" N GLN A 21 " --> pdb=" O PHE A 17 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N THR A 22 " --> pdb=" O ARG A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 44 Proline residue: A 32 - end of helix 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 65 through 75 Processing helix chain 'A' and resid 86 through 90 Processing helix chain 'A' and resid 100 through 119 removed outlier: 3.547A pdb=" N ARG A 104 " --> pdb=" O SER A 100 " (cutoff:3.500A) 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 120 through 133 Processing helix chain 'A' and resid 252 through 273 removed outlier: 4.061A pdb=" N GLU A 256 " --> pdb=" O LYS A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 289 removed outlier: 3.784A pdb=" N GLN A 283 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR A 289 " --> pdb=" O VAL A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 309 removed outlier: 4.013A pdb=" N TYR A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 364 Processing helix chain 'A' and resid 371 through 380 Proline residue: A 377 - end of helix Processing helix chain 'A' and resid 389 through 405 Processing helix chain 'A' and resid 406 through 410 removed outlier: 4.466A pdb=" N PHE A 409 " --> pdb=" O LEU A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 429 removed outlier: 3.729A pdb=" N MET A 415 " --> pdb=" O ASP A 411 " (cutoff:3.500A) Proline residue: A 421 - end of helix Processing helix chain 'A' and resid 430 through 441 removed outlier: 4.085A pdb=" N ASP A 441 " --> pdb=" O ARG A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 453 removed outlier: 3.861A pdb=" N PHE A 448 " --> pdb=" O ASP A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 467 Processing helix chain 'A' and resid 483 through 503 removed outlier: 3.686A pdb=" N ALA A 487 " --> pdb=" O THR A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 529 Processing helix chain 'A' and resid 586 through 591 Processing helix chain 'A' and resid 592 through 610 Processing helix chain 'A' and resid 630 through 639 Processing helix chain 'A' and resid 639 through 665 removed outlier: 4.371A pdb=" N PHE A 643 " --> pdb=" O SER A 639 " (cutoff:3.500A) 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 666 through 674 Processing helix chain 'A' and resid 677 through 707 removed outlier: 3.649A pdb=" N LEU A 681 " --> pdb=" O ASP A 677 " (cutoff:3.500A) Proline residue: A 692 - end of helix Processing helix chain 'A' and resid 714 through 737 removed outlier: 3.799A pdb=" N VAL A 718 " --> pdb=" O ASP A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 740 No H-bonds generated for 'chain 'A' and resid 738 through 740' Processing helix chain 'A' and resid 742 through 767 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) removed outlier: 4.060A pdb=" N TRP A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 771 removed outlier: 3.840A pdb=" N VAL A 771 " --> pdb=" O ARG A 768 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 768 through 771' Processing helix chain 'A' and resid 772 through 780 Processing helix chain 'A' and resid 782 through 800 removed outlier: 3.649A pdb=" N ALA A 786 " --> pdb=" O LEU A 782 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLN A 800 " --> pdb=" O LEU A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 846 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 948 Processing helix chain 'A' and resid 968 through 973 removed outlier: 3.584A pdb=" N GLN A 973 " --> pdb=" O SER A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1002 Processing helix chain 'A' and resid 1004 through 1020 removed outlier: 3.868A pdb=" N GLY A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1023 through 1028 Processing helix chain 'A' and resid 1034 through 1045 Processing helix chain 'A' and resid 1046 through 1051 removed outlier: 6.705A pdb=" N GLY A1049 " --> pdb=" O ALA A1046 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY A1050 " --> pdb=" O PHE A1047 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER A1051 " --> pdb=" O VAL A1048 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1046 through 1051' Processing helix chain 'A' and resid 1064 through 1078 Processing helix chain 'A' and resid 1090 through 1098 removed outlier: 3.658A pdb=" N ALA A1094 " --> pdb=" O HIS A1090 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1122 removed outlier: 3.862A pdb=" N LEU A1122 " --> pdb=" O LEU A1118 " (cutoff:3.500A) Processing helix chain 'A' and resid 1180 through 1191 removed outlier: 3.511A pdb=" N SER A1184 " --> pdb=" O VAL A1180 " (cutoff:3.500A) Processing helix chain 'A' and resid 1216 through 1228 removed outlier: 3.673A pdb=" N GLU A1220 " --> pdb=" O GLY A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1243 through 1252 removed outlier: 3.735A pdb=" N ILE A1247 " --> pdb=" O THR A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1321 through 1342 removed outlier: 4.125A pdb=" N THR A1325 " --> pdb=" O GLY A1321 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLN A1326 " --> pdb=" O TRP A1322 " (cutoff:3.500A) Processing helix chain 'A' and resid 1348 through 1365 removed outlier: 4.098A pdb=" N VAL A1352 " --> pdb=" O PHE A1348 " (cutoff:3.500A) Proline residue: A1354 - end of helix Processing helix chain 'A' and resid 1380 through 1384 removed outlier: 3.551A pdb=" N MET A1383 " --> pdb=" O GLN A1380 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TYR A1384 " --> pdb=" O PRO A1381 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1380 through 1384' Processing helix chain 'A' and resid 1398 through 1409 Processing helix chain 'A' and resid 1442 through 1451 Processing helix chain 'A' and resid 1504 through 1522 Processing helix chain 'A' and resid 1550 through 1562 Processing helix chain 'A' and resid 1568 through 1583 Processing helix chain 'A' and resid 1600 through 1617 removed outlier: 3.753A pdb=" N SER A1604 " --> pdb=" O HIS A1600 " (cutoff:3.500A) Processing helix chain 'A' and resid 1623 through 1627 Processing helix chain 'A' and resid 1639 through 1649 Processing helix chain 'A' and resid 1650 through 1666 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) Processing helix chain 'A' and resid 1667 through 1681 removed outlier: 4.104A pdb=" N SER A1671 " --> pdb=" O PHE A1667 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE A1672 " --> pdb=" O VAL A1668 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL A1681 " --> pdb=" O ILE A1677 " (cutoff:3.500A) Processing helix chain 'A' and resid 1684 through 1691 removed outlier: 4.226A pdb=" N SER A1691 " --> pdb=" O LEU A1687 " (cutoff:3.500A) Processing helix chain 'A' and resid 1694 through 1724 removed outlier: 3.563A pdb=" N VAL A1712 " --> pdb=" O CYS A1708 " (cutoff:3.500A) Proline residue: A1713 - end of helix removed outlier: 3.896A pdb=" N PHE A1724 " --> pdb=" O ILE A1720 " (cutoff:3.500A) Processing helix chain 'A' and resid 1726 through 1731 removed outlier: 3.724A pdb=" N SER A1731 " --> pdb=" O LYS A1727 " (cutoff:3.500A) Processing helix chain 'A' and resid 1734 through 1753 Proline residue: A1751 - end of helix Processing helix chain 'A' and resid 1754 through 1758 Processing helix chain 'A' and resid 1765 through 1787 removed outlier: 3.945A pdb=" N VAL A1769 " --> pdb=" O THR A1765 " (cutoff:3.500A) Processing helix chain 'A' and resid 1801 through 1807 Processing helix chain 'A' and resid 1810 through 1836 Processing helix chain 'A' and resid 1850 through 1873 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 2002 through 2014 removed outlier: 3.540A pdb=" N HIS A2006 " --> pdb=" O THR A2002 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL A2007 " --> pdb=" O GLY A2003 " (cutoff:3.500A) Processing helix chain 'A' and resid 2020 through 2032 Processing helix chain 'A' and resid 2034 through 2038 Processing helix chain 'A' and resid 2041 through 2045 Processing helix chain 'A' and resid 2046 through 2058 Processing helix chain 'A' and resid 2079 through 2092 removed outlier: 3.504A pdb=" N LEU A2083 " --> pdb=" O ALA A2079 " (cutoff:3.500A) Processing helix chain 'A' and resid 2103 through 2111 removed outlier: 3.559A pdb=" N CYS A2107 " --> pdb=" O SER A2103 " (cutoff:3.500A) Processing helix chain 'A' and resid 2128 through 2135 Processing helix chain 'A' and resid 2152 through 2163 removed outlier: 3.779A pdb=" N GLN A2156 " --> pdb=" O LEU A2152 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE A2163 " --> pdb=" O PHE A2159 " (cutoff:3.500A) Processing helix chain 'A' and resid 2186 through 2201 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 2212 through 2223 removed outlier: 3.660A pdb=" N VAL A2216 " --> pdb=" O THR A2212 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASP A2223 " --> pdb=" O ASN A2219 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 50 Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.552A pdb=" N GLY A 616 " --> pdb=" O VAL A1590 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N VAL A1592 " --> pdb=" O GLY A 616 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TYR A 618 " --> pdb=" O VAL A1592 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N PHE A1594 " --> pdb=" O TYR A 618 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLN A 620 " --> pdb=" O PHE A1594 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N TYR A1388 " --> pdb=" O GLY A1533 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N PHE A1535 " --> pdb=" O TYR A1388 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N PHE A1390 " --> pdb=" O PHE A1535 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N LEU A1537 " --> pdb=" O PHE A1390 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N SER A1392 " --> pdb=" O LEU A1537 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N VAL A1539 " --> pdb=" O SER A1392 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 511 through 512 removed outlier: 6.485A pdb=" N LEU A 384 " --> pdb=" O ILE A 536 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N PHE A 538 " --> pdb=" O LEU A 384 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N THR A 386 " --> pdb=" O PHE A 538 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LYS A 553 " --> pdb=" O THR A 539 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL A 552 " --> pdb=" O THR A1630 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N PHE A1632 " --> pdb=" O VAL A 552 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N TYR A 554 " --> pdb=" O PHE A1632 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 920 through 924 removed outlier: 3.504A pdb=" N VAL A 899 " --> pdb=" O PHE A 923 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 975 through 978 Processing sheet with id=AA6, 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) Processing sheet with id=AA7, first strand: chain 'A' and resid 1195 through 1200 removed outlier: 5.945A pdb=" N LEU A1196 " --> pdb=" O VAL A1207 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N VAL A1207 " --> pdb=" O LEU A1196 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1942 through 1943 removed outlier: 6.537A pdb=" N ARG A2113 " --> pdb=" O GLY A1943 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 1988 through 1991 removed outlier: 6.260A pdb=" N GLY A1989 " --> pdb=" O PHE A2067 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ASP A2069 " --> pdb=" O GLY A1989 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N CYS A1991 " --> pdb=" O ASP A2069 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N VAL A2066 " --> pdb=" O VAL A2098 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N THR A2100 " --> pdb=" O VAL A2066 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU A2068 " --> pdb=" O THR A2100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 2167 through 2172 removed outlier: 6.314A pdb=" N LEU A2168 " --> pdb=" O GLN A2179 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N GLN A2179 " --> pdb=" O LEU A2168 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU A2170 " --> pdb=" O GLN A2177 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N MET A2175 " --> pdb=" O HIS A2172 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP A2205 " --> pdb=" O ARG A2144 " (cutoff:3.500A) 750 hydrogen bonds defined for protein. 2187 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: 5.76 Time building geometry restraints manager: 5.98 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 - 23.45: 8047 23.45 - 46.90: 412 46.90 - 70.35: 64 70.35 - 93.80: 30 93.80 - 117.25: 18 Dihedral angle restraints: 8571 sinusoidal: 3421 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 8568 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: 8475 3.05 - 3.67: 20241 3.67 - 4.28: 29095 4.28 - 4.90: 48625 Nonbonded interactions: 106471 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 3.120 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 3.040 ... (remaining 106466 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 41.470 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 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= 0.167 Angle : 0.594 16.477 19219 Z= 0.334 Chirality : 0.044 0.529 2242 Planarity : 0.006 0.225 2400 Dihedral : 15.733 117.246 5227 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 % Allowed : 9.87 % Favored : 87.64 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.000 TRP A1705 HIS 0.001 0.000 HIS A 894 PHE 0.006 0.000 PHE A1449 TYR 0.007 0.000 TYR A1698 ARG 0.001 0.000 ARG A2173 *********************** 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 : 1.609 Fit side-chains revert: symmetry clash REVERT: A 17 PHE cc_start: 0.8219 (m-80) cc_final: 0.7997 (t80) REVERT: A 99 LYS cc_start: 0.7189 (mmtt) cc_final: 0.6198 (tmmt) REVERT: A 662 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7616 (tm-30) REVERT: A 982 ASN cc_start: 0.7514 (p0) cc_final: 0.7311 (p0) REVERT: A 1128 LEU cc_start: 0.8084 (pt) cc_final: 0.7794 (pt) REVERT: A 1180 VAL cc_start: 0.9163 (m) cc_final: 0.8934 (t) REVERT: A 1245 GLU cc_start: 0.8416 (tm-30) cc_final: 0.8209 (tt0) REVERT: A 1363 VAL cc_start: 0.8689 (OUTLIER) cc_final: 0.8481 (m) REVERT: A 1656 LEU cc_start: 0.8922 (tt) cc_final: 0.8570 (mm) outliers start: 35 outliers final: 22 residues processed: 302 average time/residue: 0.2769 time to fit residues: 118.8124 Evaluate side-chains 212 residues out of total 1559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 189 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1363 VAL Chi-restraints excluded: chain A residue 1427 THR Chi-restraints excluded: chain A residue 1537 LEU Chi-restraints excluded: chain A residue 1551 VAL Chi-restraints excluded: chain A residue 1602 ILE Chi-restraints excluded: chain A residue 1713 PRO Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1841 VAL Chi-restraints excluded: chain A residue 2065 VAL Chi-restraints excluded: chain A residue 2073 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 6.9990 chunk 134 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 72 optimal weight: 0.0970 chunk 139 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 161 optimal weight: 0.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 283 GLN A 302 GLN A 452 GLN A 820 ASN A 894 HIS A1600 HIS ** A1634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1688 GLN A2179 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 14129 Z= 0.309 Angle : 0.672 11.229 19219 Z= 0.332 Chirality : 0.045 0.209 2242 Planarity : 0.005 0.059 2400 Dihedral : 9.460 85.141 2238 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.84 % Allowed : 12.86 % Favored : 83.31 % Cbeta Deviations : 0.00 % 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: -0.47 (0.20), residues: 1753 helix: 1.10 (0.17), residues: 979 sheet: -0.58 (0.42), residues: 163 loop : -2.68 (0.22), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1747 HIS 0.011 0.002 HIS A 470 PHE 0.025 0.002 PHE A1605 TYR 0.023 0.002 TYR A1210 ARG 0.012 0.001 ARG A2200 *********************** REFINEMENT MACRO_CYCLE 2 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 255 residues out of total 1559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 201 time to evaluate : 1.621 Fit side-chains revert: symmetry clash REVERT: A 276 ARG cc_start: 0.8407 (ttm110) cc_final: 0.8092 (tpp80) REVERT: A 601 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7319 (mt-10) REVERT: A 644 MET cc_start: 0.8256 (tpp) cc_final: 0.7854 (tpt) REVERT: A 662 GLU cc_start: 0.8528 (tm-30) cc_final: 0.8034 (tm-30) REVERT: A 1015 MET cc_start: 0.7299 (mtt) cc_final: 0.7084 (ttm) REVERT: A 1180 VAL cc_start: 0.9140 (m) cc_final: 0.8906 (t) REVERT: A 1245 GLU cc_start: 0.8469 (tm-30) cc_final: 0.8048 (tt0) REVERT: A 1357 PHE cc_start: 0.7422 (OUTLIER) cc_final: 0.5950 (t80) REVERT: A 1363 VAL cc_start: 0.8810 (OUTLIER) cc_final: 0.8601 (m) REVERT: A 1380 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8313 (pt0) outliers start: 54 outliers final: 32 residues processed: 245 average time/residue: 0.2327 time to fit residues: 86.0792 Evaluate side-chains 213 residues out of total 1559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 178 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 712 TYR Chi-restraints excluded: chain A residue 754 TYR Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1357 PHE Chi-restraints excluded: chain A residue 1363 VAL Chi-restraints excluded: chain A residue 1380 GLN Chi-restraints excluded: chain A residue 1414 PHE Chi-restraints excluded: chain A residue 1427 THR Chi-restraints excluded: chain A residue 1463 CYS Chi-restraints excluded: chain A residue 1551 VAL Chi-restraints excluded: chain A residue 1720 ILE Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1841 VAL Chi-restraints excluded: chain A residue 1865 LEU Chi-restraints excluded: chain A residue 2029 ILE Chi-restraints excluded: chain A residue 2032 LEU Chi-restraints excluded: chain A residue 2065 VAL Chi-restraints excluded: chain A residue 2066 VAL Chi-restraints excluded: chain A residue 2073 THR Chi-restraints excluded: chain A residue 2099 LEU Chi-restraints excluded: chain A residue 2170 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 89 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 134 optimal weight: 0.8980 chunk 110 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 161 optimal weight: 0.1980 chunk 174 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 160 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 HIS ** A1634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2174 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14129 Z= 0.165 Angle : 0.551 11.008 19219 Z= 0.271 Chirality : 0.042 0.209 2242 Planarity : 0.004 0.057 2400 Dihedral : 7.376 70.599 2222 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.05 % Allowed : 14.91 % Favored : 82.03 % Cbeta Deviations : 0.00 % 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: 0.10 (0.21), residues: 1753 helix: 1.55 (0.17), residues: 979 sheet: -0.39 (0.42), residues: 163 loop : -2.37 (0.23), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1705 HIS 0.004 0.001 HIS A 470 PHE 0.019 0.001 PHE A1530 TYR 0.016 0.001 TYR A1210 ARG 0.004 0.000 ARG A1572 *********************** REFINEMENT MACRO_CYCLE 3 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 227 residues out of total 1559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 184 time to evaluate : 1.449 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 378 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8912 (tt) REVERT: A 662 GLU cc_start: 0.8427 (tm-30) cc_final: 0.7963 (tm-30) REVERT: A 1128 LEU cc_start: 0.8054 (pt) cc_final: 0.7792 (tt) REVERT: A 1180 VAL cc_start: 0.9119 (m) cc_final: 0.8896 (t) REVERT: A 1245 GLU cc_start: 0.8469 (tm-30) cc_final: 0.8030 (tt0) REVERT: A 1357 PHE cc_start: 0.7493 (OUTLIER) cc_final: 0.5964 (t80) REVERT: A 1552 ASN cc_start: 0.8517 (t0) cc_final: 0.8275 (m-40) REVERT: A 2131 LEU cc_start: 0.8663 (mt) cc_final: 0.8456 (mt) outliers start: 43 outliers final: 29 residues processed: 217 average time/residue: 0.2459 time to fit residues: 83.3202 Evaluate side-chains 205 residues out of total 1559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 174 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 754 TYR Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain A residue 1357 PHE Chi-restraints excluded: chain A residue 1427 THR Chi-restraints excluded: chain A residue 1463 CYS Chi-restraints excluded: chain A residue 1551 VAL Chi-restraints excluded: chain A residue 1693 VAL Chi-restraints excluded: chain A residue 1786 PHE Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1812 HIS Chi-restraints excluded: chain A residue 1841 VAL Chi-restraints excluded: chain A residue 2029 ILE Chi-restraints excluded: chain A residue 2065 VAL Chi-restraints excluded: chain A residue 2066 VAL Chi-restraints excluded: chain A residue 2073 THR Chi-restraints excluded: chain A residue 2097 VAL Chi-restraints excluded: chain A residue 2099 LEU Chi-restraints excluded: chain A residue 2174 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 159 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 84 optimal weight: 0.0270 chunk 17 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 chunk 154 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 overall best weight: 1.7442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 ASN ** A1634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2174 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 14129 Z= 0.278 Angle : 0.599 9.777 19219 Z= 0.302 Chirality : 0.044 0.198 2242 Planarity : 0.004 0.049 2400 Dihedral : 6.393 58.950 2220 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.84 % Allowed : 15.70 % Favored : 80.47 % Cbeta Deviations : 0.00 % 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: 0.32 (0.21), residues: 1753 helix: 1.73 (0.17), residues: 978 sheet: -0.42 (0.40), residues: 166 loop : -2.23 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1705 HIS 0.005 0.001 HIS A 470 PHE 0.020 0.002 PHE A1605 TYR 0.012 0.001 TYR A 924 ARG 0.005 0.001 ARG A 276 *********************** REFINEMENT MACRO_CYCLE 4 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 234 residues out of total 1559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 180 time to evaluate : 1.628 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 378 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8735 (mp) REVERT: A 662 GLU cc_start: 0.8469 (tm-30) cc_final: 0.8244 (tt0) REVERT: A 1180 VAL cc_start: 0.9122 (m) cc_final: 0.8903 (t) REVERT: A 1245 GLU cc_start: 0.8522 (tm-30) cc_final: 0.8055 (tt0) REVERT: A 1357 PHE cc_start: 0.7641 (OUTLIER) cc_final: 0.6088 (t80) REVERT: A 1693 VAL cc_start: 0.6624 (OUTLIER) cc_final: 0.6381 (t) REVERT: A 1721 PHE cc_start: 0.7643 (OUTLIER) cc_final: 0.5732 (t80) REVERT: A 2059 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8223 (pp) outliers start: 54 outliers final: 34 residues processed: 221 average time/residue: 0.2485 time to fit residues: 85.1049 Evaluate side-chains 210 residues out of total 1559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 171 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 754 TYR Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1197 VAL Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain A residue 1208 LEU Chi-restraints excluded: chain A residue 1352 VAL Chi-restraints excluded: chain A residue 1357 PHE Chi-restraints excluded: chain A residue 1414 PHE Chi-restraints excluded: chain A residue 1427 THR Chi-restraints excluded: chain A residue 1551 VAL Chi-restraints excluded: chain A residue 1693 VAL Chi-restraints excluded: chain A residue 1721 PHE Chi-restraints excluded: chain A residue 1762 ILE Chi-restraints excluded: chain A residue 1786 PHE Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1841 VAL Chi-restraints excluded: chain A residue 2029 ILE Chi-restraints excluded: chain A residue 2032 LEU Chi-restraints excluded: chain A residue 2059 LEU Chi-restraints excluded: chain A residue 2065 VAL Chi-restraints excluded: chain A residue 2066 VAL Chi-restraints excluded: chain A residue 2097 VAL Chi-restraints excluded: chain A residue 2099 LEU Chi-restraints excluded: chain A residue 2174 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 66.58 > 50: distance: 13 - 20: 13.298 distance: 21 - 22: 19.004 distance: 21 - 24: 14.951 distance: 22 - 23: 25.905 distance: 22 - 27: 7.236 distance: 24 - 25: 7.684 distance: 24 - 26: 10.185 distance: 27 - 28: 7.925 distance: 28 - 29: 19.065 distance: 28 - 31: 11.821 distance: 29 - 30: 14.381 distance: 29 - 33: 23.214 distance: 33 - 34: 23.188 distance: 34 - 35: 13.036 distance: 34 - 37: 17.322 distance: 35 - 36: 33.790 distance: 35 - 42: 21.704 distance: 36 - 66: 37.412 distance: 37 - 38: 19.144 distance: 38 - 39: 8.723 distance: 39 - 40: 13.139 distance: 39 - 41: 9.981 distance: 42 - 43: 8.927 distance: 43 - 44: 55.795 distance: 44 - 45: 38.951 distance: 44 - 50: 8.368 distance: 45 - 75: 36.301 distance: 46 - 47: 15.101 distance: 47 - 48: 6.866 distance: 50 - 51: 8.701 distance: 51 - 52: 31.967 distance: 51 - 54: 26.527 distance: 52 - 53: 20.955 distance: 52 - 58: 17.516 distance: 53 - 82: 38.616 distance: 54 - 55: 30.307 distance: 55 - 56: 16.530 distance: 55 - 57: 20.231 distance: 58 - 59: 9.953 distance: 59 - 60: 10.737 distance: 59 - 62: 10.759 distance: 60 - 61: 7.615 distance: 60 - 66: 5.421 distance: 61 - 87: 21.618 distance: 62 - 63: 9.019 distance: 63 - 64: 4.612 distance: 63 - 65: 7.137 distance: 66 - 67: 6.897 distance: 67 - 68: 8.107 distance: 67 - 70: 11.984 distance: 68 - 69: 14.759 distance: 68 - 75: 5.712 distance: 70 - 71: 16.612 distance: 71 - 72: 10.477 distance: 72 - 73: 4.053 distance: 72 - 74: 5.109 distance: 75 - 76: 7.982 distance: 76 - 77: 24.297 distance: 76 - 79: 12.042 distance: 77 - 78: 16.079 distance: 77 - 82: 15.288 distance: 79 - 80: 8.505 distance: 79 - 81: 13.303 distance: 82 - 83: 23.645 distance: 83 - 84: 40.083 distance: 84 - 85: 22.998 distance: 84 - 87: 3.046 distance: 87 - 88: 6.527 distance: 88 - 89: 24.243 distance: 89 - 90: 9.081 distance: 89 - 101: 30.984 distance: 90 - 123: 29.706 distance: 91 - 92: 8.110 distance: 92 - 93: 7.257 distance: 92 - 94: 6.872 distance: 93 - 95: 9.040 distance: 94 - 96: 11.627 distance: 94 - 97: 9.855 distance: 95 - 96: 7.994 distance: 96 - 98: 11.576 distance: 97 - 99: 13.162 distance: 98 - 100: 10.610 distance: 99 - 100: 11.904 distance: 135 - 145: 3.056