Starting phenix.real_space_refine on Sun Jul 21 22:05:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tbw_25800/07_2024/7tbw_25800_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tbw_25800/07_2024/7tbw_25800.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/7tbw_25800/07_2024/7tbw_25800.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tbw_25800/07_2024/7tbw_25800.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tbw_25800/07_2024/7tbw_25800_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tbw_25800/07_2024/7tbw_25800_neut.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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 90 5.16 5 C 9895 2.51 5 N 2563 2.21 5 O 2782 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 18": "NH1" <-> "NH2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A ARG 104": "NH1" <-> "NH2" Residue "A ASP 124": "OD1" <-> "OD2" Residue "A ARG 126": "NH1" <-> "NH2" Residue "A ARG 282": "NH1" <-> "NH2" Residue "A ARG 393": "NH1" <-> "NH2" Residue "A ASP 411": "OD1" <-> "OD2" Residue "A GLU 417": "OE1" <-> "OE2" Residue "A GLU 432": "OE1" <-> "OE2" Residue "A ASP 434": "OD1" <-> "OD2" Residue "A ASP 441": "OD1" <-> "OD2" Residue "A ASP 444": "OD1" <-> "OD2" Residue "A ASP 462": "OD1" <-> "OD2" Residue "A ARG 485": "NH1" <-> "NH2" Residue "A GLU 503": "OE1" <-> "OE2" Residue "A GLU 511": "OE1" <-> "OE2" Residue "A GLU 547": "OE1" <-> "OE2" Residue "A ARG 579": "NH1" <-> "NH2" Residue "A GLU 612": "OE1" <-> "OE2" Residue "A GLU 669": "OE1" <-> "OE2" Residue "A TYR 754": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 815": "OE1" <-> "OE2" Residue "A GLU 816": "OE1" <-> "OE2" Residue "A PHE 819": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 891": "OE1" <-> "OE2" Residue "A ASP 917": "OD1" <-> "OD2" Residue "A ARG 1039": "NH1" <-> "NH2" Residue "A ARG 1079": "NH1" <-> "NH2" Residue "A ARG 1082": "NH1" <-> "NH2" Residue "A ARG 1100": "NH1" <-> "NH2" Residue "A TYR 1126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1198": "OE1" <-> "OE2" Residue "A ASP 1199": "OD1" <-> "OD2" Residue "A TYR 1206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1246": "OE1" <-> "OE2" Residue "A GLU 1253": "OE1" <-> "OE2" Residue "A ARG 1336": "NH1" <-> "NH2" Residue "A GLU 1386": "OE1" <-> "OE2" Residue "A GLU 1403": "OE1" <-> "OE2" Residue "A ASP 1411": "OD1" <-> "OD2" Residue "A GLU 1420": "OE1" <-> "OE2" Residue "A ASP 1426": "OD1" <-> "OD2" Residue "A GLU 1435": "OE1" <-> "OE2" Residue "A ARG 1503": "NH1" <-> "NH2" Residue "A ASP 1567": "OD1" <-> "OD2" Residue "A ASP 1571": "OD1" <-> "OD2" Residue "A GLU 1622": "OE1" <-> "OE2" Residue "A ASP 1654": "OD1" <-> "OD2" Residue "A ARG 1680": "NH1" <-> "NH2" Residue "A GLU 1789": "OE1" <-> "OE2" Residue "A ASP 1801": "OD1" <-> "OD2" Residue "A ASP 1847": "OD1" <-> "OD2" Residue "A GLU 1893": "OE1" <-> "OE2" Residue "A ASP 1904": "OD1" <-> "OD2" Residue "A ARG 2004": "NH1" <-> "NH2" Residue "A GLU 2005": "OE1" <-> "OE2" Residue "A PHE 2010": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2039": "OE1" <-> "OE2" Residue "A ARG 2051": "NH1" <-> "NH2" Residue "A ARG 2081": "NH1" <-> "NH2" Residue "A ARG 2095": "NH1" <-> "NH2" Residue "A GLU 2108": "OE1" <-> "OE2" Residue "A ARG 2113": "NH1" <-> "NH2" Residue "A ARG 2123": "NH1" <-> "NH2" Residue "A ASP 2151": "OD1" <-> "OD2" Residue "A PHE 2159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2170": "OE1" <-> "OE2" Residue "A ASP 2205": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 15338 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 15129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1928, 15129 Classifications: {'peptide': 1928} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PCIS': 2, 'PTRANS': 91, 'TRANS': 1834} Chain breaks: 14 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 252 Unresolved non-hydrogen dihedrals: 166 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 87 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: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 120 Unusual residues: {' MG': 2, 'ATP': 2, 'CLR': 1, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 8.66, per 1000 atoms: 0.56 Number of scatterers: 15338 At special positions: 0 Unit cell: (105.5, 91.152, 207.624, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 90 16.00 P 6 15.00 Mg 2 11.99 O 2782 8.00 N 2563 7.00 C 9895 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=2.04 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 A2506 " - " ASN A 98 " " NAG A2507 " - " ASN A1637 " " 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: 6.02 Conformation dependent library (CDL) restraints added in 2.5 seconds 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3606 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 10 sheets defined 58.2% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.19 Creating SS restraints... Processing helix chain 'A' and resid 3 through 21 Processing helix chain 'A' and resid 21 through 45 removed outlier: 3.715A pdb=" N LEU A 25 " --> pdb=" O GLN A 21 " (cutoff:3.500A) Proline residue: A 32 - end of helix removed outlier: 4.163A pdb=" N ILE A 35 " --> pdb=" O TRP A 31 " (cutoff:3.500A) removed outlier: 3.529A 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 65 through 76 removed outlier: 3.533A pdb=" N ASN A 76 " --> pdb=" O GLY A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 90 Processing helix chain 'A' and resid 100 through 118 removed outlier: 3.516A pdb=" N ARG A 104 " --> pdb=" O SER A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 136 Processing helix chain 'A' and resid 200 through 210 removed outlier: 3.571A pdb=" N LEU A 206 " --> pdb=" O GLU A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 227 removed outlier: 3.973A pdb=" N GLU A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 234 removed outlier: 3.815A pdb=" N MET A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ASP A 234 " --> pdb=" O ARG A 230 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 229 through 234' Processing helix chain 'A' and resid 235 through 240 removed outlier: 3.959A pdb=" N LEU A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 275 removed outlier: 3.673A pdb=" N GLU A 256 " --> pdb=" O LYS A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 289 removed outlier: 3.537A pdb=" N THR A 289 " --> pdb=" O VAL A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 309 removed outlier: 3.730A pdb=" N GLN A 302 " --> pdb=" O THR A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 364 Processing helix chain 'A' and resid 368 through 380 removed outlier: 3.696A pdb=" N TRP A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) 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: 4.380A pdb=" N PHE A 409 " --> pdb=" O LEU A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 417 Processing helix chain 'A' and resid 418 through 427 removed outlier: 4.513A pdb=" N LYS A 422 " --> pdb=" O GLU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 441 Processing helix chain 'A' and resid 444 through 454 removed outlier: 3.509A pdb=" N ASP A 454 " --> pdb=" O GLU A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 468 Processing helix chain 'A' and resid 483 through 502 removed outlier: 3.581A 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 removed outlier: 3.781A pdb=" N TRP A 590 " --> pdb=" O MET A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 609 Processing helix chain 'A' and resid 630 through 644 removed outlier: 3.578A pdb=" N ARG A 634 " --> pdb=" O ASP A 630 " (cutoff:3.500A) Proline residue: A 641 - end of helix Processing helix chain 'A' and resid 645 through 665 removed outlier: 3.747A pdb=" N SER A 651 " --> pdb=" O ALA A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 675 Processing helix chain 'A' and resid 677 through 707 removed outlier: 3.913A 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 738 Processing helix chain 'A' and resid 742 through 757 removed outlier: 3.934A pdb=" N ALA A 748 " --> pdb=" O ASN A 744 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N GLY A 751 " --> pdb=" O ALA A 747 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE A 752 " --> pdb=" O ALA A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 768 removed outlier: 3.691A pdb=" N VAL A 762 " --> pdb=" O TYR A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 780 Processing helix chain 'A' and resid 784 through 800 removed outlier: 3.506A pdb=" N GLY A 788 " --> pdb=" O PRO A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 846 Processing helix chain 'A' and resid 939 through 947 Processing helix chain 'A' and resid 967 through 973 removed outlier: 3.582A pdb=" N ILE A 971 " --> pdb=" O GLU A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1000 Processing helix chain 'A' and resid 1004 through 1020 removed outlier: 3.809A pdb=" N GLY A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1033 Processing helix chain 'A' and resid 1034 through 1046 Processing helix chain 'A' and resid 1064 through 1078 removed outlier: 3.553A pdb=" N ARG A1069 " --> pdb=" O PRO A1065 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY A1070 " --> pdb=" O TYR A1066 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1097 Processing helix chain 'A' and resid 1114 through 1122 removed outlier: 3.552A pdb=" N LEU A1122 " --> pdb=" O LEU A1118 " (cutoff:3.500A) Processing helix chain 'A' and resid 1182 through 1191 removed outlier: 3.636A pdb=" N HIS A1190 " --> pdb=" O LEU A1186 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A1191 " --> pdb=" O ILE A1187 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1228 removed outlier: 3.520A pdb=" N ARG A1228 " --> pdb=" O GLU A1224 " (cutoff:3.500A) Processing helix chain 'A' and resid 1243 through 1254 Processing helix chain 'A' and resid 1321 through 1342 Processing helix chain 'A' and resid 1343 through 1351 removed outlier: 3.554A pdb=" N PHE A1347 " --> pdb=" O SER A1343 " (cutoff:3.500A) Processing helix chain 'A' and resid 1351 through 1365 removed outlier: 4.113A pdb=" N ALA A1355 " --> pdb=" O ILE A1351 " (cutoff:3.500A) Processing helix chain 'A' and resid 1400 through 1409 removed outlier: 4.275A pdb=" N LEU A1404 " --> pdb=" O GLY A1400 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR A1409 " --> pdb=" O LEU A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1445 through 1450 Processing helix chain 'A' and resid 1504 through 1523 removed outlier: 3.701A pdb=" N ASN A1523 " --> pdb=" O LYS A1519 " (cutoff:3.500A) Processing helix chain 'A' and resid 1548 through 1561 Processing helix chain 'A' and resid 1570 through 1583 Processing helix chain 'A' and resid 1600 through 1618 removed outlier: 3.500A pdb=" N SER A1604 " --> pdb=" O HIS A1600 " (cutoff:3.500A) Processing helix chain 'A' and resid 1643 through 1668 removed outlier: 3.968A pdb=" N THR A1651 " --> pdb=" O ALA A1647 " (cutoff:3.500A) Processing helix chain 'A' and resid 1671 through 1681 removed outlier: 3.924A pdb=" N PHE A1675 " --> pdb=" O SER A1671 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU A1676 " --> pdb=" O PHE A1672 " (cutoff:3.500A) Processing helix chain 'A' and resid 1683 through 1691 Processing helix chain 'A' and resid 1694 through 1724 Proline residue: A1713 - end of helix Processing helix chain 'A' and resid 1734 through 1754 Proline residue: A1751 - end of helix Processing helix chain 'A' and resid 1762 through 1790 Processing helix chain 'A' and resid 1795 through 1808 removed outlier: 3.910A pdb=" N ILE A1799 " --> pdb=" O LYS A1795 " (cutoff:3.500A) Processing helix chain 'A' and resid 1810 through 1834 Processing helix chain 'A' and resid 1848 through 1872 removed outlier: 4.213A pdb=" N ASN A1852 " --> pdb=" O LEU A1848 " (cutoff:3.500A) Processing helix chain 'A' and resid 1892 through 1905 Processing helix chain 'A' and resid 1951 through 1961 Processing helix chain 'A' and resid 1980 through 1986 removed outlier: 3.993A pdb=" N VAL A1984 " --> pdb=" O ASN A1980 " (cutoff:3.500A) Processing helix chain 'A' and resid 2002 through 2015 Processing helix chain 'A' and resid 2017 through 2019 No H-bonds generated for 'chain 'A' and resid 2017 through 2019' Processing helix chain 'A' and resid 2020 through 2031 Processing helix chain 'A' and resid 2041 through 2045 Processing helix chain 'A' and resid 2046 through 2059 removed outlier: 4.171A pdb=" N ARG A2051 " --> pdb=" O GLY A2047 " (cutoff:3.500A) Processing helix chain 'A' and resid 2076 through 2093 Processing helix chain 'A' and resid 2103 through 2110 removed outlier: 3.755A 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 Processing helix chain 'A' and resid 2186 through 2197 removed outlier: 3.723A pdb=" N ILE A2190 " --> pdb=" O SER A2186 " (cutoff:3.500A) Processing helix chain 'A' and resid 2212 through 2224 removed outlier: 3.743A pdb=" N VAL A2216 " --> pdb=" O THR A2212 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN A2224 " --> pdb=" O PHE A2220 " (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 58 through 60 removed outlier: 6.507A pdb=" N GLY A 616 " --> pdb=" O VAL A1590 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N VAL A1592 " --> pdb=" O GLY A 616 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N TYR A 618 " --> pdb=" O VAL A1592 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N PHE A1594 " --> pdb=" O TYR A 618 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N GLN A 620 " --> pdb=" O PHE A1594 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N TYR A1388 " --> pdb=" O GLY A1533 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N PHE A1535 " --> pdb=" O TYR A1388 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N PHE A1390 " --> pdb=" O PHE A1535 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LEU A1537 " --> pdb=" O PHE A1390 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N SER A1392 " --> pdb=" O LEU A1537 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N VAL A1539 " --> pdb=" O SER A1392 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP A1499 " --> pdb=" O PRO A1487 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR A1437 " --> pdb=" O GLN A1488 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 535 through 537 removed outlier: 6.198A pdb=" N VAL A 552 " --> pdb=" O THR A1630 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N PHE A1632 " --> pdb=" O VAL A 552 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N TYR A 554 " --> pdb=" O PHE A1632 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 922 through 923 removed outlier: 4.434A pdb=" N LEU A 904 " --> pdb=" O SER A 954 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N SER A 954 " --> pdb=" O LEU A 904 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 975 through 978 removed outlier: 5.909A pdb=" N SER A 930 " --> pdb=" O ALA A1102 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ILE A1104 " --> pdb=" O SER A 930 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU A 932 " --> pdb=" O ILE A1104 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N SER A1105 " --> pdb=" O LEU A1109 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N LEU A1109 " --> pdb=" O SER A1105 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1195 through 1198 removed outlier: 5.951A pdb=" N LEU A1196 " --> pdb=" O VAL A1207 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL A1207 " --> pdb=" O LEU A1196 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU A1198 " --> pdb=" O THR A1205 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1934 through 1936 removed outlier: 3.655A pdb=" N LEU A1912 " --> pdb=" O ILE A1936 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU A1917 " --> pdb=" O ARG A1967 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ARG A1967 " --> pdb=" O LEU A1917 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1989 through 1991 removed outlier: 6.282A pdb=" N GLY A1989 " --> pdb=" O PHE A2067 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ASP A2069 " --> pdb=" O GLY A1989 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N CYS A1991 " --> pdb=" O ASP A2069 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N PHE A1942 " --> pdb=" O LEU A2099 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N CYS A1941 " --> pdb=" O ARG A2113 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ALA A2115 " --> pdb=" O CYS A1941 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLY A1943 " --> pdb=" O ALA A2115 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N MET A2117 " --> pdb=" O GLY A1943 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU A1945 " --> pdb=" O MET A2117 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1989 through 1991 removed outlier: 6.282A pdb=" N GLY A1989 " --> pdb=" O PHE A2067 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ASP A2069 " --> pdb=" O GLY A1989 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N CYS A1991 " --> pdb=" O ASP A2069 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N PHE A1942 " --> pdb=" O LEU A2099 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N CYS A1941 " --> pdb=" O ARG A2113 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ALA A2115 " --> pdb=" O CYS A1941 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLY A1943 " --> pdb=" O ALA A2115 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N MET A2117 " --> pdb=" O GLY A1943 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU A1945 " --> pdb=" O MET A2117 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 2168 through 2169 removed outlier: 3.994A pdb=" N GLN A2177 " --> pdb=" O LYS A2169 " (cutoff:3.500A) 815 hydrogen bonds defined for protein. 2382 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: 6.35 Time building geometry restraints manager: 6.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4830 1.34 - 1.46: 3558 1.46 - 1.58: 7146 1.58 - 1.70: 10 1.70 - 1.81: 146 Bond restraints: 15690 Sorted by residual: bond pdb=" C4 ATP A2503 " pdb=" C5 ATP A2503 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.93e+01 bond pdb=" C4 ATP A2502 " pdb=" C5 ATP A2502 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.71e+01 bond pdb=" C5 ATP A2502 " pdb=" C6 ATP A2502 " ideal model delta sigma weight residual 1.409 1.483 -0.074 1.00e-02 1.00e+04 5.42e+01 bond pdb=" C5 ATP A2503 " pdb=" C6 ATP A2503 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.32e+01 bond pdb=" C8 ATP A2502 " pdb=" N7 ATP A2502 " ideal model delta sigma weight residual 1.310 1.358 -0.048 1.00e-02 1.00e+04 2.34e+01 ... (remaining 15685 not shown) Histogram of bond angle deviations from ideal: 100.60 - 107.72: 674 107.72 - 114.85: 9327 114.85 - 121.97: 8319 121.97 - 129.10: 2852 129.10 - 136.22: 129 Bond angle restraints: 21301 Sorted by residual: angle pdb=" PB ATP A2503 " pdb=" O3B ATP A2503 " pdb=" PG ATP A2503 " ideal model delta sigma weight residual 139.87 120.48 19.39 1.00e+00 1.00e+00 3.76e+02 angle pdb=" PB ATP A2502 " pdb=" O3B ATP A2502 " pdb=" PG ATP A2502 " ideal model delta sigma weight residual 139.87 121.15 18.72 1.00e+00 1.00e+00 3.50e+02 angle pdb=" PA ATP A2502 " pdb=" O3A ATP A2502 " pdb=" PB ATP A2502 " ideal model delta sigma weight residual 136.83 121.34 15.49 1.00e+00 1.00e+00 2.40e+02 angle pdb=" PA ATP A2503 " pdb=" O3A ATP A2503 " pdb=" PB ATP A2503 " ideal model delta sigma weight residual 136.83 122.51 14.32 1.00e+00 1.00e+00 2.05e+02 angle pdb=" C5 ATP A2503 " pdb=" C4 ATP A2503 " pdb=" N3 ATP A2503 " ideal model delta sigma weight residual 126.80 118.68 8.12 1.00e+00 1.00e+00 6.60e+01 ... (remaining 21296 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.46: 9038 23.46 - 46.93: 402 46.93 - 70.39: 51 70.39 - 93.85: 33 93.85 - 117.32: 18 Dihedral angle restraints: 9542 sinusoidal: 3963 harmonic: 5579 Sorted by residual: 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 -150.28 64.28 1 1.00e+01 1.00e-02 5.43e+01 dihedral pdb=" CA SER A 783 " pdb=" C SER A 783 " pdb=" N PRO A 784 " pdb=" CA PRO A 784 " ideal model delta harmonic sigma weight residual 180.00 147.82 32.18 0 5.00e+00 4.00e-02 4.14e+01 dihedral pdb=" CA LEU A2180 " pdb=" C LEU A2180 " pdb=" N PRO A2181 " pdb=" CA PRO A2181 " ideal model delta harmonic sigma weight residual -180.00 -157.26 -22.74 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 9539 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2244 0.071 - 0.142: 190 0.142 - 0.212: 1 0.212 - 0.283: 4 0.283 - 0.354: 2 Chirality restraints: 2441 Sorted by residual: 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 -2.67 0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" C5 BMA C 4 " pdb=" C4 BMA C 4 " pdb=" C6 BMA C 4 " pdb=" O5 BMA C 4 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.88e+00 ... (remaining 2438 not shown) Planarity restraints: 2663 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 783 " 0.044 5.00e-02 4.00e+02 6.59e-02 6.95e+00 pdb=" N PRO A 784 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 784 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 784 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 386 " 0.034 5.00e-02 4.00e+02 5.11e-02 4.19e+00 pdb=" N PRO A 387 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 387 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 387 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 759 " -0.027 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO A 760 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 760 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 760 " -0.023 5.00e-02 4.00e+02 ... (remaining 2660 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 188 2.66 - 3.22: 14627 3.22 - 3.78: 24311 3.78 - 4.34: 32517 4.34 - 4.90: 52827 Nonbonded interactions: 124470 Sorted by model distance: nonbonded pdb=" O2B ATP A2503 " pdb="MG MG A2504 " model vdw 2.101 2.170 nonbonded pdb=" OG SER A1953 " pdb="MG MG A2504 " model vdw 2.149 2.170 nonbonded pdb=" O2G ATP A2503 " pdb="MG MG A2504 " model vdw 2.204 2.170 nonbonded pdb=" OE1 GLN A1993 " pdb="MG MG A2504 " model vdw 2.209 2.170 nonbonded pdb=" OD1 ASN A 820 " pdb=" OG1 THR A 822 " model vdw 2.254 2.440 ... (remaining 124465 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 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: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 43.160 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 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 0.083 15690 Z= 0.195 Angle : 0.625 19.392 21301 Z= 0.393 Chirality : 0.041 0.354 2441 Planarity : 0.003 0.066 2659 Dihedral : 14.879 117.319 5918 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.23 % Allowed : 7.24 % Favored : 91.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 1.09 % 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: -2.02 (0.18), residues: 1898 helix: -0.18 (0.15), residues: 1070 sheet: -1.14 (0.40), residues: 154 loop : -3.31 (0.20), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1334 HIS 0.002 0.000 HIS A1626 PHE 0.009 0.001 PHE A1663 TYR 0.006 0.001 TYR A1698 ARG 0.002 0.000 ARG A 437 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 334 time to evaluate : 1.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 575 ASP cc_start: 0.7278 (p0) cc_final: 0.6916 (p0) REVERT: A 601 GLU cc_start: 0.6987 (mm-30) cc_final: 0.6701 (mm-30) REVERT: A 815 GLU cc_start: 0.5963 (mm-30) cc_final: 0.5509 (mm-30) REVERT: A 827 MET cc_start: 0.7791 (tpp) cc_final: 0.7489 (tpt) REVERT: A 831 ASP cc_start: 0.6880 (m-30) cc_final: 0.6565 (m-30) REVERT: A 984 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7622 (pp) REVERT: A 1430 GLN cc_start: 0.6846 (mp10) cc_final: 0.6071 (tm-30) REVERT: A 1720 ILE cc_start: 0.7638 (mt) cc_final: 0.7131 (mt) REVERT: A 1799 ILE cc_start: 0.5837 (mp) cc_final: 0.5529 (mt) REVERT: A 1802 ILE cc_start: 0.7494 (mp) cc_final: 0.7245 (mt) REVERT: A 1861 VAL cc_start: 0.8118 (t) cc_final: 0.7869 (t) REVERT: A 2180 LEU cc_start: 0.6528 (OUTLIER) cc_final: 0.5640 (mm) outliers start: 20 outliers final: 11 residues processed: 351 average time/residue: 0.3122 time to fit residues: 157.1450 Evaluate side-chains 216 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 203 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 858 PHE Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1441 VAL Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1602 ILE Chi-restraints excluded: chain A residue 1812 HIS Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 2110 LEU Chi-restraints excluded: chain A residue 2180 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 4.9990 chunk 145 optimal weight: 0.0170 chunk 80 optimal weight: 0.3980 chunk 49 optimal weight: 1.9990 chunk 98 optimal weight: 0.4980 chunk 77 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 174 optimal weight: 3.9990 overall best weight: 0.5220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN A 302 GLN A 356 ASN A 508 ASN A 551 HIS A 621 GLN A 732 GLN A 744 ASN ** A 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 973 GLN A1038 GLN A1185 ASN A1326 GLN A1393 ASN A1610 ASN ** A1633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1678 GLN A1702 ASN A1800 ASN A1871 GLN A1948 ASN ** A2049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2172 HIS A2177 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15690 Z= 0.173 Angle : 0.593 9.973 21301 Z= 0.279 Chirality : 0.041 0.230 2441 Planarity : 0.004 0.088 2659 Dihedral : 10.563 91.038 2398 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.46 % Allowed : 11.79 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 1.09 % 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: -0.66 (0.19), residues: 1898 helix: 0.92 (0.16), residues: 1094 sheet: -0.90 (0.40), residues: 152 loop : -2.76 (0.22), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 278 HIS 0.004 0.001 HIS A1223 PHE 0.018 0.001 PHE A1786 TYR 0.013 0.001 TYR A 115 ARG 0.007 0.000 ARG A2030 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 218 time to evaluate : 1.647 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 415 MET cc_start: 0.8103 (tmm) cc_final: 0.7497 (tmm) REVERT: A 575 ASP cc_start: 0.7328 (p0) cc_final: 0.7004 (p0) REVERT: A 601 GLU cc_start: 0.7091 (mm-30) cc_final: 0.6699 (mm-30) REVERT: A 622 MET cc_start: 0.7385 (mtt) cc_final: 0.7164 (mtt) REVERT: A 640 MET cc_start: 0.8145 (tpp) cc_final: 0.7697 (tpp) REVERT: A 815 GLU cc_start: 0.6304 (mm-30) cc_final: 0.6042 (mm-30) REVERT: A 984 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7709 (pp) REVERT: A 1078 TYR cc_start: 0.8536 (m-10) cc_final: 0.8193 (m-10) REVERT: A 1126 TYR cc_start: 0.6679 (m-80) cc_final: 0.6459 (m-80) REVERT: A 1127 TYR cc_start: 0.8243 (m-80) cc_final: 0.8001 (m-80) REVERT: A 1190 HIS cc_start: 0.5299 (m-70) cc_final: 0.4348 (m170) REVERT: A 1245 GLU cc_start: 0.7934 (tt0) cc_final: 0.7666 (tt0) REVERT: A 1430 GLN cc_start: 0.6829 (mp10) cc_final: 0.5964 (tm-30) REVERT: A 1802 ILE cc_start: 0.7607 (OUTLIER) cc_final: 0.7356 (mt) REVERT: A 1813 PHE cc_start: 0.8047 (t80) cc_final: 0.7832 (t80) REVERT: A 2000 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8346 (mt) outliers start: 40 outliers final: 24 residues processed: 248 average time/residue: 0.2731 time to fit residues: 101.7360 Evaluate side-chains 218 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 191 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1441 VAL Chi-restraints excluded: chain A residue 1476 VAL Chi-restraints excluded: chain A residue 1496 ILE Chi-restraints excluded: chain A residue 1602 ILE Chi-restraints excluded: chain A residue 1630 THR Chi-restraints excluded: chain A residue 1802 ILE Chi-restraints excluded: chain A residue 1812 HIS Chi-restraints excluded: chain A residue 1833 GLU Chi-restraints excluded: chain A residue 1865 LEU Chi-restraints excluded: chain A residue 1929 VAL Chi-restraints excluded: chain A residue 2000 LEU Chi-restraints excluded: chain A residue 2046 SER Chi-restraints excluded: chain A residue 2110 LEU Chi-restraints excluded: chain A residue 2118 VAL Chi-restraints excluded: chain A residue 2167 VAL Chi-restraints excluded: chain A residue 2176 LEU Chi-restraints excluded: chain A residue 2180 LEU Chi-restraints excluded: chain A residue 2203 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/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-5388/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-5388/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-5388/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-5388/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-5388/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-5388/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-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/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-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.2445 > 50: distance: 28 - 151: 14.057 distance: 31 - 148: 24.599 distance: 42 - 134: 21.656 distance: 45 - 131: 22.999 distance: 100 - 142: 35.884 distance: 125 - 131: 22.952 distance: 131 - 132: 17.811 distance: 132 - 133: 27.598 distance: 132 - 135: 15.292 distance: 133 - 134: 7.812 distance: 133 - 139: 25.877 distance: 135 - 136: 46.438 distance: 136 - 137: 32.381 distance: 136 - 138: 9.768 distance: 139 - 140: 11.779 distance: 140 - 141: 19.013 distance: 140 - 143: 23.117 distance: 141 - 142: 6.338 distance: 141 - 148: 8.423 distance: 143 - 144: 30.038 distance: 144 - 145: 33.175 distance: 145 - 146: 15.283 distance: 145 - 147: 6.397 distance: 148 - 149: 23.985 distance: 149 - 150: 20.033 distance: 149 - 152: 26.647 distance: 150 - 151: 22.950 distance: 150 - 160: 14.510 distance: 152 - 153: 19.744 distance: 153 - 154: 7.443 distance: 153 - 155: 9.495 distance: 154 - 156: 10.646 distance: 155 - 157: 23.212 distance: 156 - 158: 12.933 distance: 157 - 158: 9.852 distance: 158 - 159: 18.146 distance: 160 - 161: 8.959 distance: 161 - 162: 15.682 distance: 161 - 164: 41.241 distance: 162 - 163: 39.210 distance: 164 - 165: 19.342 distance: 165 - 166: 38.772 distance: 166 - 167: 20.207 distance: 166 - 168: 10.754 distance: 169 - 170: 8.235 distance: 170 - 171: 9.286 distance: 170 - 173: 9.216 distance: 171 - 172: 7.153 distance: 171 - 177: 42.270 distance: 173 - 174: 18.040 distance: 174 - 175: 30.919 distance: 174 - 176: 30.941 distance: 177 - 178: 8.016 distance: 177 - 183: 26.332 distance: 178 - 179: 33.664 distance: 178 - 181: 23.854 distance: 179 - 180: 17.330 distance: 179 - 184: 44.323 distance: 181 - 182: 9.280 distance: 182 - 183: 7.085 distance: 184 - 185: 19.593 distance: 185 - 186: 31.430 distance: 185 - 188: 44.234 distance: 186 - 187: 21.380 distance: 186 - 190: 12.875 distance: 188 - 189: 27.680 distance: 190 - 191: 25.808 distance: 191 - 192: 12.633 distance: 191 - 194: 29.511 distance: 192 - 193: 23.564 distance: 192 - 196: 18.538 distance: 194 - 195: 31.394 distance: 196 - 197: 15.017 distance: 197 - 200: 31.547 distance: 198 - 204: 19.298 distance: 200 - 201: 27.622 distance: 201 - 202: 30.262 distance: 201 - 203: 18.983 distance: 204 - 205: 30.561 distance: 205 - 206: 13.590 distance: 205 - 208: 17.542 distance: 206 - 207: 12.118 distance: 206 - 210: 20.720 distance: 208 - 209: 14.300