Starting phenix.real_space_refine on Sun Aug 4 05:04:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsu_33435/08_2024/7xsu_33435.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsu_33435/08_2024/7xsu_33435.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsu_33435/08_2024/7xsu_33435.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsu_33435/08_2024/7xsu_33435.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsu_33435/08_2024/7xsu_33435.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsu_33435/08_2024/7xsu_33435.cif" } resolution = 3.4 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= 0.005 sd= 0.083 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 68 5.16 5 C 5929 2.51 5 N 1394 2.21 5 O 1576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 172": "OE1" <-> "OE2" Residue "A ASP 192": "OD1" <-> "OD2" Residue "A PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 209": "OE1" <-> "OE2" Residue "A PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 306": "OD1" <-> "OD2" Residue "A PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 368": "NH1" <-> "NH2" Residue "A TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 384": "NH1" <-> "NH2" Residue "A TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 721": "OD1" <-> "OD2" Residue "A PHE 734": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 738": "OE1" <-> "OE2" Residue "A GLU 745": "OE1" <-> "OE2" Residue "A GLU 764": "OE1" <-> "OE2" Residue "A TYR 776": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 785": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 786": "OD1" <-> "OD2" Residue "A PHE 887": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 896": "NH1" <-> "NH2" Residue "A GLU 904": "OE1" <-> "OE2" Residue "A ASP 908": "OD1" <-> "OD2" Residue "A TYR 1201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1227": "OE1" <-> "OE2" Residue "A GLU 1233": "OE1" <-> "OE2" Residue "A TYR 1263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1305": "NH1" <-> "NH2" Residue "A ARG 1311": "NH1" <-> "NH2" Residue "A GLU 1320": "OE1" <-> "OE2" Residue "A PHE 1461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1525": "OD1" <-> "OD2" Residue "A PHE 1569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1576": "OE1" <-> "OE2" Residue "A TYR 1588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1628": "NH1" <-> "NH2" Residue "A ARG 1634": "NH1" <-> "NH2" Residue "A ARG 1637": "NH1" <-> "NH2" Residue "A PHE 1696": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1699": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1731": "OD1" <-> "OD2" Residue "A PHE 1753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1762": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 29": "OE1" <-> "OE2" Residue "B PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 61": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8969 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1085, 8247 Classifications: {'peptide': 1085} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 1058} Chain breaks: 6 Unresolved non-hydrogen bonds: 503 Unresolved non-hydrogen angles: 628 Unresolved non-hydrogen dihedrals: 439 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 7, 'TYR:plan': 8, 'ASN:plan1': 7, 'TRP:plan': 3, 'HIS:plan': 1, 'PHE:plan': 7, 'GLU:plan': 14, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 324 Chain: "B" Number of atoms: 463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 463 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 62} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "A" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 259 Unusual residues: {'6OU': 6, '9Z9': 1, 'BMA': 1, 'NAG': 5} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 173 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'6OU:plan-1': 6, '6OU:plan-2': 2, '6OU:plan-3': 1} Unresolved non-hydrogen planarities: 24 Time building chain proxies: 5.45, per 1000 atoms: 0.61 Number of scatterers: 8969 At special positions: 0 Unit cell: (135.168, 127.776, 104.544, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 68 16.00 P 2 15.00 O 1576 8.00 N 1394 7.00 C 5929 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 336 " distance=2.02 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS A 342 " distance=2.04 Simple disulfide: pdb=" SG CYS A 909 " - pdb=" SG CYS A 918 " distance=2.01 Simple disulfide: pdb=" SG CYS A1730 " - pdb=" SG CYS A1744 " distance=2.03 Simple disulfide: pdb=" SG CYS B 12 " - pdb=" SG CYS B 65 " distance=2.03 Simple disulfide: pdb=" SG CYS B 16 " - pdb=" SG CYS B 37 " distance=2.03 Simple disulfide: pdb=" SG CYS B 27 " - pdb=" SG CYS B 49 " 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=0, symmetry=0 Time building additional restraints: 3.54 Conformation dependent library (CDL) restraints added in 1.5 seconds 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 3 sheets defined 76.6% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 121 through 130 Processing helix chain 'A' and resid 131 through 150 removed outlier: 4.085A pdb=" N SER A 135 " --> pdb=" O HIS A 131 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 160 removed outlier: 3.557A pdb=" N TYR A 160 " --> pdb=" O PRO A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 181 Processing helix chain 'A' and resid 184 through 189 Processing helix chain 'A' and resid 192 through 210 removed outlier: 3.535A pdb=" N TRP A 196 " --> pdb=" O ASP A 192 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP A 198 " --> pdb=" O TRP A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 226 removed outlier: 3.538A pdb=" N ARG A 223 " --> pdb=" O ARG A 220 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL A 224 " --> pdb=" O THR A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 234 removed outlier: 4.211A pdb=" N ILE A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 251 Processing helix chain 'A' and resid 251 through 274 Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 305 through 311 removed outlier: 3.610A pdb=" N ASP A 311 " --> pdb=" O VAL A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 315 Processing helix chain 'A' and resid 358 through 372 Processing helix chain 'A' and resid 374 through 387 removed outlier: 4.114A pdb=" N LEU A 378 " --> pdb=" O CYS A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 423 removed outlier: 3.760A pdb=" N PHE A 394 " --> pdb=" O TYR A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 717 removed outlier: 3.580A pdb=" N LYS A 712 " --> pdb=" O LYS A 708 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE A 713 " --> pdb=" O GLN A 709 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL A 714 " --> pdb=" O LYS A 710 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP A 717 " --> pdb=" O PHE A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 737 Processing helix chain 'A' and resid 743 through 772 Processing helix chain 'A' and resid 776 through 779 Processing helix chain 'A' and resid 780 through 798 Processing helix chain 'A' and resid 807 through 821 removed outlier: 3.935A pdb=" N PHE A 811 " --> pdb=" O LEU A 808 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG A 812 " --> pdb=" O ARG A 809 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 814 " --> pdb=" O PHE A 811 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 819 " --> pdb=" O VAL A 816 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS A 821 " --> pdb=" O LYS A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 838 removed outlier: 3.659A pdb=" N VAL A 837 " --> pdb=" O ILE A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 869 removed outlier: 4.941A pdb=" N LYS A 864 " --> pdb=" O GLN A 860 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ASN A 865 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 874 removed outlier: 3.722A pdb=" N ILE A 873 " --> pdb=" O LEU A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 900 Processing helix chain 'A' and resid 901 through 914 removed outlier: 4.492A pdb=" N THR A 905 " --> pdb=" O GLU A 901 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASP A 908 " --> pdb=" O GLU A 904 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL A 912 " --> pdb=" O ASP A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 945 removed outlier: 3.666A pdb=" N CYS A 918 " --> pdb=" O GLY A 914 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 920 " --> pdb=" O SER A 916 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE A 945 " --> pdb=" O LEU A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1206 Processing helix chain 'A' and resid 1206 through 1226 removed outlier: 3.756A pdb=" N LEU A1224 " --> pdb=" O SER A1220 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA A1225 " --> pdb=" O SER A1221 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE A1226 " --> pdb=" O GLY A1222 " (cutoff:3.500A) Processing helix chain 'A' and resid 1234 through 1271 removed outlier: 3.554A pdb=" N LEU A1240 " --> pdb=" O THR A1236 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N PHE A1265 " --> pdb=" O VAL A1261 " (cutoff:3.500A) removed outlier: 9.506A pdb=" N LYS A1266 " --> pdb=" O ALA A1262 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LYS A1267 " --> pdb=" O TYR A1263 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR A1270 " --> pdb=" O LYS A1266 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASN A1271 " --> pdb=" O LYS A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1271 through 1294 Processing helix chain 'A' and resid 1300 through 1307 Processing helix chain 'A' and resid 1310 through 1319 removed outlier: 4.103A pdb=" N ARG A1314 " --> pdb=" O LEU A1310 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ALA A1315 " --> pdb=" O ARG A1311 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU A1316 " --> pdb=" O PRO A1312 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER A1317 " --> pdb=" O LEU A1313 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ARG A1318 " --> pdb=" O ARG A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1319 through 1332 Processing helix chain 'A' and resid 1332 through 1359 removed outlier: 3.597A pdb=" N ASN A1338 " --> pdb=" O PRO A1334 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL A1339 " --> pdb=" O SER A1335 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE A1350 " --> pdb=" O PHE A1346 " (cutoff:3.500A) Processing helix chain 'A' and resid 1382 through 1390 Processing helix chain 'A' and resid 1406 through 1420 Processing helix chain 'A' and resid 1422 through 1432 removed outlier: 3.653A pdb=" N ILE A1426 " --> pdb=" O GLY A1422 " (cutoff:3.500A) Processing helix chain 'A' and resid 1445 through 1447 No H-bonds generated for 'chain 'A' and resid 1445 through 1447' Processing helix chain 'A' and resid 1448 through 1460 removed outlier: 3.625A pdb=" N PHE A1452 " --> pdb=" O MET A1448 " (cutoff:3.500A) Processing helix chain 'A' and resid 1460 through 1482 Processing helix chain 'A' and resid 1518 through 1528 removed outlier: 4.531A pdb=" N THR A1528 " --> pdb=" O PHE A1524 " (cutoff:3.500A) Processing helix chain 'A' and resid 1529 through 1549 removed outlier: 4.218A pdb=" N ASP A1533 " --> pdb=" O LYS A1529 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE A1536 " --> pdb=" O PHE A1532 " (cutoff:3.500A) Processing helix chain 'A' and resid 1555 through 1582 removed outlier: 3.883A pdb=" N ASN A1560 " --> pdb=" O PRO A1556 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ALA A1582 " --> pdb=" O ILE A1578 " (cutoff:3.500A) Processing helix chain 'A' and resid 1586 through 1591 removed outlier: 3.890A pdb=" N ASN A1591 " --> pdb=" O TYR A1587 " (cutoff:3.500A) Processing helix chain 'A' and resid 1591 through 1610 removed outlier: 3.613A pdb=" N ILE A1595 " --> pdb=" O ASN A1591 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A1599 " --> pdb=" O ILE A1595 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A1609 " --> pdb=" O ILE A1605 " (cutoff:3.500A) Processing helix chain 'A' and resid 1610 through 1618 removed outlier: 3.766A pdb=" N GLN A1615 " --> pdb=" O SER A1611 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N LYS A1616 " --> pdb=" O ASP A1612 " (cutoff:3.500A) Processing helix chain 'A' and resid 1621 through 1625 Processing helix chain 'A' and resid 1626 through 1631 removed outlier: 3.970A pdb=" N ALA A1630 " --> pdb=" O VAL A1626 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG A1631 " --> pdb=" O ILE A1627 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1626 through 1631' Processing helix chain 'A' and resid 1632 through 1639 removed outlier: 3.787A pdb=" N LEU A1636 " --> pdb=" O ILE A1632 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG A1637 " --> pdb=" O GLY A1633 " (cutoff:3.500A) Processing helix chain 'A' and resid 1643 through 1655 Processing helix chain 'A' and resid 1655 through 1682 removed outlier: 3.685A pdb=" N PHE A1660 " --> pdb=" O LEU A1656 " (cutoff:3.500A) Processing helix chain 'A' and resid 1698 through 1711 removed outlier: 3.722A pdb=" N LEU A1704 " --> pdb=" O ALA A1700 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N THR A1711 " --> pdb=" O PHE A1707 " (cutoff:3.500A) Processing helix chain 'A' and resid 1714 through 1724 Proline residue: A1721 - end of helix Processing helix chain 'A' and resid 1746 through 1777 Processing helix chain 'B' and resid 23 through 31 Processing sheet with id=AA1, first strand: chain 'A' and resid 280 through 283 Processing sheet with id=AA2, first strand: chain 'B' and resid 7 through 8 Processing sheet with id=AA3, first strand: chain 'B' and resid 37 through 40 602 hydrogen bonds defined for protein. 1749 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: 2.83 Time building geometry restraints manager: 3.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1375 1.30 - 1.43: 2468 1.43 - 1.56: 5200 1.56 - 1.69: 18 1.69 - 1.82: 106 Bond restraints: 9167 Sorted by residual: bond pdb=" C13 9Z9 A3013 " pdb=" C14 9Z9 A3013 " ideal model delta sigma weight residual 1.332 1.670 -0.338 2.00e-02 2.50e+03 2.85e+02 bond pdb=" C07 6OU A3012 " pdb=" C08 6OU A3012 " ideal model delta sigma weight residual 1.524 1.311 0.213 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C07 6OU A3011 " pdb=" C08 6OU A3011 " ideal model delta sigma weight residual 1.524 1.312 0.212 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C73 9Z9 A3013 " pdb=" O72 9Z9 A3013 " ideal model delta sigma weight residual 1.406 1.568 -0.162 2.00e-02 2.50e+03 6.57e+01 bond pdb=" C04 9Z9 A3013 " pdb=" O72 9Z9 A3013 " ideal model delta sigma weight residual 1.420 1.261 0.159 2.00e-02 2.50e+03 6.35e+01 ... (remaining 9162 not shown) Histogram of bond angle deviations from ideal: 76.18 - 90.71: 1 90.71 - 105.25: 152 105.25 - 119.79: 7876 119.79 - 134.33: 4425 134.33 - 148.87: 2 Bond angle restraints: 12456 Sorted by residual: angle pdb=" N PRO A 349 " pdb=" CA PRO A 349 " pdb=" C PRO A 349 " ideal model delta sigma weight residual 112.47 148.87 -36.40 2.06e+00 2.36e-01 3.12e+02 angle pdb=" N THR A1378 " pdb=" CA THR A1378 " pdb=" C THR A1378 " ideal model delta sigma weight residual 112.93 132.06 -19.13 1.33e+00 5.65e-01 2.07e+02 angle pdb=" N ILE A1379 " pdb=" CA ILE A1379 " pdb=" C ILE A1379 " ideal model delta sigma weight residual 111.90 100.95 10.95 8.10e-01 1.52e+00 1.83e+02 angle pdb=" N ASP A 350 " pdb=" CA ASP A 350 " pdb=" C ASP A 350 " ideal model delta sigma weight residual 112.12 95.77 16.35 1.34e+00 5.57e-01 1.49e+02 angle pdb=" C LEU A1373 " pdb=" N PRO A1374 " pdb=" CA PRO A1374 " ideal model delta sigma weight residual 120.52 132.29 -11.77 9.90e-01 1.02e+00 1.41e+02 ... (remaining 12451 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.03: 5264 35.03 - 70.05: 185 70.05 - 105.08: 23 105.08 - 140.11: 18 140.11 - 175.13: 1 Dihedral angle restraints: 5491 sinusoidal: 2158 harmonic: 3333 Sorted by residual: dihedral pdb=" CB CYS A 909 " pdb=" SG CYS A 909 " pdb=" SG CYS A 918 " pdb=" CB CYS A 918 " ideal model delta sinusoidal sigma weight residual -86.00 -170.42 84.42 1 1.00e+01 1.00e-02 8.67e+01 dihedral pdb=" CB CYS A1730 " pdb=" SG CYS A1730 " pdb=" SG CYS A1744 " pdb=" CB CYS A1744 " ideal model delta sinusoidal sigma weight residual -86.00 -148.90 62.90 1 1.00e+01 1.00e-02 5.23e+01 dihedral pdb=" C PHE A 285 " pdb=" N PHE A 285 " pdb=" CA PHE A 285 " pdb=" CB PHE A 285 " ideal model delta harmonic sigma weight residual -122.60 -105.71 -16.89 0 2.50e+00 1.60e-01 4.56e+01 ... (remaining 5488 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.237: 1440 0.237 - 0.474: 46 0.474 - 0.710: 3 0.710 - 0.947: 1 0.947 - 1.184: 1 Chirality restraints: 1491 Sorted by residual: chirality pdb=" CA PRO A 349 " pdb=" N PRO A 349 " pdb=" C PRO A 349 " pdb=" CB PRO A 349 " both_signs ideal model delta sigma weight residual False 2.72 1.53 1.18 2.00e-01 2.50e+01 3.50e+01 chirality pdb=" C02 9Z9 A3013 " pdb=" C03 9Z9 A3013 " pdb=" C06 9Z9 A3013 " pdb=" C10 9Z9 A3013 " both_signs ideal model delta sigma weight residual False 2.92 2.18 0.74 2.00e-01 2.50e+01 1.38e+01 chirality pdb=" CA CYS A1365 " pdb=" N CYS A1365 " pdb=" C CYS A1365 " pdb=" CB CYS A1365 " both_signs ideal model delta sigma weight residual False 2.51 1.86 0.65 2.00e-01 2.50e+01 1.05e+01 ... (remaining 1488 not shown) Planarity restraints: 1510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A3003 " 0.324 2.00e-02 2.50e+03 2.82e-01 9.96e+02 pdb=" C7 NAG A3003 " -0.073 2.00e-02 2.50e+03 pdb=" C8 NAG A3003 " 0.126 2.00e-02 2.50e+03 pdb=" N2 NAG A3003 " -0.505 2.00e-02 2.50e+03 pdb=" O7 NAG A3003 " 0.128 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A3004 " -0.237 2.00e-02 2.50e+03 1.97e-01 4.87e+02 pdb=" C7 NAG A3004 " 0.063 2.00e-02 2.50e+03 pdb=" C8 NAG A3004 " -0.165 2.00e-02 2.50e+03 pdb=" N2 NAG A3004 " 0.327 2.00e-02 2.50e+03 pdb=" O7 NAG A3004 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A3001 " 0.239 2.00e-02 2.50e+03 1.97e-01 4.84e+02 pdb=" C7 NAG A3001 " -0.065 2.00e-02 2.50e+03 pdb=" C8 NAG A3001 " 0.169 2.00e-02 2.50e+03 pdb=" N2 NAG A3001 " -0.322 2.00e-02 2.50e+03 pdb=" O7 NAG A3001 " -0.020 2.00e-02 2.50e+03 ... (remaining 1507 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.13: 4 2.13 - 2.82: 3010 2.82 - 3.52: 13237 3.52 - 4.21: 18933 4.21 - 4.90: 34962 Nonbonded interactions: 70146 Sorted by model distance: nonbonded pdb=" OD1 ASN A1445 " pdb=" CE MET A1448 " model vdw 1.440 3.460 nonbonded pdb=" CG ASN A1445 " pdb=" CE MET A1448 " model vdw 1.598 3.690 nonbonded pdb=" ND2 ASN A1445 " pdb=" CE MET A1448 " model vdw 1.748 3.540 nonbonded pdb=" O3 NAG A3001 " pdb=" O6 NAG A3001 " model vdw 1.809 3.040 nonbonded pdb=" N PHE A 285 " pdb=" O PHE A 285 " model vdw 2.255 2.496 ... (remaining 70141 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: 1.090 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 26.580 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 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 : 0.011 0.338 9167 Z= 0.751 Angle : 1.611 36.397 12456 Z= 1.013 Chirality : 0.106 1.184 1491 Planarity : 0.013 0.282 1510 Dihedral : 19.266 175.133 3314 Min Nonbonded Distance : 1.440 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.46 % Favored : 94.10 % Rotamer: Outliers : 5.06 % Allowed : 18.09 % Favored : 76.85 % Cbeta Deviations : 0.83 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.18 % 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: 1.66 (0.25), residues: 1136 helix: 2.38 (0.18), residues: 731 sheet: -0.35 (2.23), residues: 12 loop : -1.44 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A1715 HIS 0.008 0.002 HIS A 279 PHE 0.020 0.002 PHE A 887 TYR 0.025 0.002 TYR A 379 ARG 0.004 0.001 ARG A 881 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 243 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 MET cc_start: 0.5939 (tpp) cc_final: 0.5328 (tmm) REVERT: A 137 LEU cc_start: 0.8841 (tt) cc_final: 0.8600 (tp) REVERT: A 249 LYS cc_start: 0.6300 (mptt) cc_final: 0.6004 (tttp) REVERT: A 260 PHE cc_start: 0.8580 (t80) cc_final: 0.8278 (t80) REVERT: A 351 HIS cc_start: 0.7222 (OUTLIER) cc_final: 0.6090 (t-90) REVERT: A 379 TYR cc_start: 0.8730 (OUTLIER) cc_final: 0.8035 (t80) REVERT: A 778 PHE cc_start: 0.5588 (t80) cc_final: 0.4781 (t80) REVERT: A 835 ASN cc_start: 0.8744 (OUTLIER) cc_final: 0.8471 (t0) REVERT: A 1197 ARG cc_start: 0.7806 (ttp80) cc_final: 0.7480 (ttm-80) REVERT: A 1202 ARG cc_start: 0.7576 (ttm170) cc_final: 0.7356 (mtp-110) REVERT: A 1209 PHE cc_start: 0.8539 (t80) cc_final: 0.8145 (t80) REVERT: A 1233 GLU cc_start: 0.6449 (tt0) cc_final: 0.6204 (tt0) REVERT: A 1302 LYS cc_start: 0.7936 (pttt) cc_final: 0.7734 (mptt) REVERT: A 1424 MET cc_start: 0.7862 (mmp) cc_final: 0.7588 (mmm) REVERT: A 1538 PHE cc_start: 0.7709 (OUTLIER) cc_final: 0.7324 (t80) REVERT: A 1581 MET cc_start: 0.4007 (ppp) cc_final: 0.3189 (tpp) REVERT: A 1619 PHE cc_start: 0.6115 (OUTLIER) cc_final: 0.5788 (p90) REVERT: A 1664 LEU cc_start: 0.7984 (tp) cc_final: 0.7748 (mt) REVERT: A 1762 PHE cc_start: 0.8989 (t80) cc_final: 0.8611 (t80) outliers start: 45 outliers final: 19 residues processed: 276 average time/residue: 0.1885 time to fit residues: 74.3931 Evaluate side-chains 213 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 189 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 379 TYR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 725 THR Chi-restraints excluded: chain A residue 728 ILE Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 835 ASN Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 1345 ILE Chi-restraints excluded: chain A residue 1402 VAL Chi-restraints excluded: chain A residue 1404 PHE Chi-restraints excluded: chain A residue 1431 VAL Chi-restraints excluded: chain A residue 1474 ASN Chi-restraints excluded: chain A residue 1536 ILE Chi-restraints excluded: chain A residue 1538 PHE Chi-restraints excluded: chain A residue 1619 PHE Chi-restraints excluded: chain A residue 1626 VAL Chi-restraints excluded: chain A residue 1647 THR Chi-restraints excluded: chain B residue 29 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.5980 chunk 86 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 89 optimal weight: 30.0000 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 66 optimal weight: 0.8980 chunk 103 optimal weight: 0.0980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN A 827 ASN A 865 ASN A 889 HIS A1271 ASN A1441 GLN B 8 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 9167 Z= 0.236 Angle : 0.700 8.645 12456 Z= 0.363 Chirality : 0.041 0.220 1491 Planarity : 0.004 0.052 1510 Dihedral : 13.670 149.839 1582 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.17 % Favored : 96.74 % Rotamer: Outliers : 3.93 % Allowed : 20.79 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.18 % 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: 1.16 (0.25), residues: 1136 helix: 1.80 (0.18), residues: 766 sheet: -0.59 (1.93), residues: 12 loop : -1.52 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1715 HIS 0.002 0.001 HIS B 43 PHE 0.019 0.001 PHE A1215 TYR 0.021 0.002 TYR A 379 ARG 0.005 0.000 ARG A1305 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 221 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 HIS cc_start: 0.8344 (t-90) cc_final: 0.7929 (t-90) REVERT: A 136 MET cc_start: 0.6031 (tpp) cc_final: 0.5434 (tmm) REVERT: A 137 LEU cc_start: 0.8700 (tt) cc_final: 0.8418 (tp) REVERT: A 260 PHE cc_start: 0.8639 (t80) cc_final: 0.8328 (t80) REVERT: A 341 ARG cc_start: 0.7408 (OUTLIER) cc_final: 0.5356 (mpt180) REVERT: A 415 MET cc_start: 0.4714 (mmm) cc_final: 0.4316 (mmm) REVERT: A 1197 ARG cc_start: 0.7762 (ttp80) cc_final: 0.7375 (ttm-80) REVERT: A 1202 ARG cc_start: 0.7556 (ttm170) cc_final: 0.7188 (mtp-110) REVERT: A 1209 PHE cc_start: 0.8430 (t80) cc_final: 0.8063 (t80) REVERT: A 1216 MET cc_start: 0.8908 (mmm) cc_final: 0.8661 (tpt) REVERT: A 1302 LYS cc_start: 0.7403 (pttt) cc_final: 0.7125 (tttm) REVERT: A 1364 ARG cc_start: 0.6174 (ptt180) cc_final: 0.5891 (ptm160) REVERT: A 1406 ASN cc_start: 0.7448 (m110) cc_final: 0.7210 (m-40) REVERT: A 1448 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.7456 (mpp) REVERT: A 1538 PHE cc_start: 0.7769 (OUTLIER) cc_final: 0.7465 (t80) REVERT: A 1547 MET cc_start: 0.6334 (mtm) cc_final: 0.6043 (mtm) REVERT: A 1664 LEU cc_start: 0.7869 (tp) cc_final: 0.7623 (tp) REVERT: A 1703 MET cc_start: 0.8019 (mmm) cc_final: 0.7707 (mmt) outliers start: 35 outliers final: 14 residues processed: 246 average time/residue: 0.1888 time to fit residues: 65.8723 Evaluate side-chains 209 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 192 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 728 ILE Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 918 CYS Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 1255 GLU Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1448 MET Chi-restraints excluded: chain A residue 1538 PHE Chi-restraints excluded: chain A residue 1626 VAL Chi-restraints excluded: chain A residue 1662 ILE Chi-restraints excluded: chain B residue 3 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 86 optimal weight: 8.9990 chunk 70 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 112 optimal weight: 9.9990 chunk 92 optimal weight: 3.9990 chunk 102 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.114 9167 Z= 0.218 Angle : 0.605 9.999 12456 Z= 0.317 Chirality : 0.038 0.159 1491 Planarity : 0.004 0.046 1510 Dihedral : 10.234 140.686 1551 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.05 % Favored : 95.86 % Rotamer: Outliers : 4.61 % Allowed : 23.26 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.18 % 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: 0.91 (0.25), residues: 1136 helix: 1.58 (0.18), residues: 783 sheet: -0.96 (1.80), residues: 12 loop : -1.70 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1715 HIS 0.002 0.001 HIS B 43 PHE 0.019 0.001 PHE A 778 TYR 0.017 0.001 TYR A 379 ARG 0.005 0.000 ARG A1305 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 210 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 HIS cc_start: 0.8438 (t-90) cc_final: 0.8227 (t-90) REVERT: A 136 MET cc_start: 0.6422 (tpp) cc_final: 0.5675 (tmm) REVERT: A 137 LEU cc_start: 0.8608 (tt) cc_final: 0.8313 (tp) REVERT: A 238 LYS cc_start: 0.7876 (mtpt) cc_final: 0.7200 (pttm) REVERT: A 260 PHE cc_start: 0.8551 (t80) cc_final: 0.8267 (t80) REVERT: A 1197 ARG cc_start: 0.7704 (ttp80) cc_final: 0.7236 (ttm-80) REVERT: A 1202 ARG cc_start: 0.7414 (ttm170) cc_final: 0.7142 (mtp-110) REVERT: A 1209 PHE cc_start: 0.8490 (t80) cc_final: 0.8092 (t80) REVERT: A 1263 TYR cc_start: 0.7579 (m-80) cc_final: 0.7288 (m-80) REVERT: A 1302 LYS cc_start: 0.7495 (pttt) cc_final: 0.7235 (tttp) REVERT: A 1406 ASN cc_start: 0.7464 (m110) cc_final: 0.7220 (m-40) REVERT: A 1562 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8349 (mm) REVERT: A 1653 MET cc_start: 0.7405 (mmt) cc_final: 0.6804 (mmm) REVERT: A 1664 LEU cc_start: 0.7944 (tp) cc_final: 0.7577 (mt) REVERT: A 1703 MET cc_start: 0.7998 (mmm) cc_final: 0.7732 (mmt) REVERT: B 3 ASP cc_start: 0.4531 (OUTLIER) cc_final: 0.4212 (t70) outliers start: 41 outliers final: 20 residues processed: 240 average time/residue: 0.1691 time to fit residues: 59.8564 Evaluate side-chains 208 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 186 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 728 ILE Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 918 CYS Chi-restraints excluded: chain A residue 1213 ILE Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 1255 GLU Chi-restraints excluded: chain A residue 1330 VAL Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1562 LEU Chi-restraints excluded: chain A residue 1568 LEU Chi-restraints excluded: chain A residue 1635 ILE Chi-restraints excluded: chain A residue 1662 ILE Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 52 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 0.5980 chunk 77 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 110 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1543 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9167 Z= 0.228 Angle : 0.581 7.678 12456 Z= 0.307 Chirality : 0.037 0.169 1491 Planarity : 0.003 0.043 1510 Dihedral : 9.538 135.689 1548 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.23 % Favored : 95.69 % Rotamer: Outliers : 5.39 % Allowed : 23.26 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.18 % 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: 0.82 (0.25), residues: 1136 helix: 1.50 (0.18), residues: 784 sheet: -1.55 (1.72), residues: 12 loop : -1.69 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1715 HIS 0.001 0.000 HIS A 739 PHE 0.028 0.001 PHE A 778 TYR 0.021 0.001 TYR A 379 ARG 0.005 0.000 ARG A1305 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 192 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 MET cc_start: 0.6472 (tpp) cc_final: 0.5754 (tmm) REVERT: A 137 LEU cc_start: 0.8619 (tt) cc_final: 0.8338 (tp) REVERT: A 260 PHE cc_start: 0.8645 (t80) cc_final: 0.8346 (t80) REVERT: A 379 TYR cc_start: 0.8525 (OUTLIER) cc_final: 0.7842 (t80) REVERT: A 904 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7467 (mp0) REVERT: A 1197 ARG cc_start: 0.7721 (ttp80) cc_final: 0.7235 (ttm-80) REVERT: A 1202 ARG cc_start: 0.7352 (ttm170) cc_final: 0.7137 (mtp-110) REVERT: A 1209 PHE cc_start: 0.8485 (t80) cc_final: 0.8101 (t80) REVERT: A 1302 LYS cc_start: 0.7475 (pttt) cc_final: 0.7139 (tttp) REVERT: A 1406 ASN cc_start: 0.7492 (m110) cc_final: 0.7251 (m-40) REVERT: A 1477 GLN cc_start: 0.8696 (mm-40) cc_final: 0.8312 (mm-40) REVERT: A 1562 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8312 (mm) REVERT: A 1664 LEU cc_start: 0.8056 (tp) cc_final: 0.7562 (mt) REVERT: A 1693 MET cc_start: 0.8331 (OUTLIER) cc_final: 0.7895 (ttp) REVERT: A 1703 MET cc_start: 0.8014 (mmm) cc_final: 0.7576 (tpp) REVERT: B 3 ASP cc_start: 0.4993 (OUTLIER) cc_final: 0.4713 (t70) outliers start: 48 outliers final: 34 residues processed: 226 average time/residue: 0.1615 time to fit residues: 54.3517 Evaluate side-chains 224 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 185 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 379 TYR Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 727 CYS Chi-restraints excluded: chain A residue 728 ILE Chi-restraints excluded: chain A residue 767 PHE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 904 GLU Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 918 CYS Chi-restraints excluded: chain A residue 1213 ILE Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 1255 GLU Chi-restraints excluded: chain A residue 1330 VAL Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1373 LEU Chi-restraints excluded: chain A residue 1379 ILE Chi-restraints excluded: chain A residue 1460 SER Chi-restraints excluded: chain A residue 1562 LEU Chi-restraints excluded: chain A residue 1568 LEU Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 1626 VAL Chi-restraints excluded: chain A residue 1635 ILE Chi-restraints excluded: chain A residue 1662 ILE Chi-restraints excluded: chain A residue 1693 MET Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 52 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 82 optimal weight: 20.0000 chunk 45 optimal weight: 0.8980 chunk 94 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 56 optimal weight: 0.7980 chunk 98 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1680 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9167 Z= 0.195 Angle : 0.558 8.053 12456 Z= 0.292 Chirality : 0.036 0.185 1491 Planarity : 0.003 0.042 1510 Dihedral : 9.101 130.290 1548 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.58 % Favored : 95.33 % Rotamer: Outliers : 5.51 % Allowed : 22.70 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.18 % 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: 0.85 (0.25), residues: 1136 helix: 1.50 (0.18), residues: 788 sheet: -1.55 (1.66), residues: 12 loop : -1.65 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A1715 HIS 0.004 0.001 HIS A 131 PHE 0.028 0.001 PHE A 778 TYR 0.018 0.001 TYR A 379 ARG 0.006 0.000 ARG A1305 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 198 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 MET cc_start: 0.6540 (tpp) cc_final: 0.5822 (tmm) REVERT: A 137 LEU cc_start: 0.8611 (tt) cc_final: 0.8329 (tp) REVERT: A 260 PHE cc_start: 0.8612 (t80) cc_final: 0.8325 (t80) REVERT: A 379 TYR cc_start: 0.8492 (OUTLIER) cc_final: 0.7889 (t80) REVERT: A 904 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7469 (mp0) REVERT: A 1209 PHE cc_start: 0.8478 (t80) cc_final: 0.8086 (t80) REVERT: A 1302 LYS cc_start: 0.7442 (pttt) cc_final: 0.7155 (tttp) REVERT: A 1406 ASN cc_start: 0.7456 (m110) cc_final: 0.7220 (m-40) REVERT: A 1477 GLN cc_start: 0.8724 (mm-40) cc_final: 0.8361 (mm-40) REVERT: A 1562 LEU cc_start: 0.8558 (mm) cc_final: 0.8351 (mm) REVERT: A 1693 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.7839 (ttp) REVERT: B 3 ASP cc_start: 0.5177 (OUTLIER) cc_final: 0.4951 (t70) outliers start: 49 outliers final: 31 residues processed: 234 average time/residue: 0.1754 time to fit residues: 60.7894 Evaluate side-chains 219 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 184 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 379 TYR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 727 CYS Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 904 GLU Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 918 CYS Chi-restraints excluded: chain A residue 1213 ILE Chi-restraints excluded: chain A residue 1255 GLU Chi-restraints excluded: chain A residue 1330 VAL Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1373 LEU Chi-restraints excluded: chain A residue 1379 ILE Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1424 MET Chi-restraints excluded: chain A residue 1460 SER Chi-restraints excluded: chain A residue 1568 LEU Chi-restraints excluded: chain A residue 1626 VAL Chi-restraints excluded: chain A residue 1635 ILE Chi-restraints excluded: chain A residue 1662 ILE Chi-restraints excluded: chain A residue 1693 MET Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 52 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 51 optimal weight: 0.7980 chunk 9 optimal weight: 20.0000 chunk 36 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 HIS ** A 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1441 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9167 Z= 0.236 Angle : 0.587 8.472 12456 Z= 0.305 Chirality : 0.037 0.184 1491 Planarity : 0.003 0.044 1510 Dihedral : 8.922 122.858 1546 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.23 % Favored : 95.69 % Rotamer: Outliers : 6.29 % Allowed : 22.58 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.18 % 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: 0.78 (0.25), residues: 1136 helix: 1.47 (0.19), residues: 779 sheet: -1.60 (1.63), residues: 12 loop : -1.64 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A1715 HIS 0.004 0.001 HIS A 131 PHE 0.029 0.001 PHE A 778 TYR 0.022 0.002 TYR A 379 ARG 0.006 0.000 ARG A1305 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 183 time to evaluate : 0.994 Fit side-chains revert: symmetry clash REVERT: A 136 MET cc_start: 0.6553 (tpp) cc_final: 0.5825 (tmm) REVERT: A 137 LEU cc_start: 0.8669 (tt) cc_final: 0.8361 (tp) REVERT: A 260 PHE cc_start: 0.8642 (t80) cc_final: 0.8359 (t80) REVERT: A 379 TYR cc_start: 0.8524 (OUTLIER) cc_final: 0.7841 (t80) REVERT: A 901 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7149 (mt-10) REVERT: A 904 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7551 (mp0) REVERT: A 1209 PHE cc_start: 0.8462 (t80) cc_final: 0.8062 (t80) REVERT: A 1302 LYS cc_start: 0.7451 (pttt) cc_final: 0.7188 (tttp) REVERT: A 1406 ASN cc_start: 0.7538 (m110) cc_final: 0.7288 (m-40) REVERT: A 1477 GLN cc_start: 0.8752 (mm-40) cc_final: 0.8396 (mm-40) REVERT: A 1538 PHE cc_start: 0.7773 (OUTLIER) cc_final: 0.7458 (t80) REVERT: A 1653 MET cc_start: 0.5994 (mmt) cc_final: 0.5712 (mmm) REVERT: A 1664 LEU cc_start: 0.7948 (tp) cc_final: 0.7676 (tp) REVERT: A 1693 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.7928 (ttp) outliers start: 56 outliers final: 35 residues processed: 225 average time/residue: 0.1694 time to fit residues: 57.7359 Evaluate side-chains 220 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 180 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 379 TYR Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 904 GLU Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 918 CYS Chi-restraints excluded: chain A residue 1231 LEU Chi-restraints excluded: chain A residue 1255 GLU Chi-restraints excluded: chain A residue 1330 VAL Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1373 LEU Chi-restraints excluded: chain A residue 1379 ILE Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1424 MET Chi-restraints excluded: chain A residue 1460 SER Chi-restraints excluded: chain A residue 1538 PHE Chi-restraints excluded: chain A residue 1568 LEU Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 1626 VAL Chi-restraints excluded: chain A residue 1635 ILE Chi-restraints excluded: chain A residue 1662 ILE Chi-restraints excluded: chain A residue 1693 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 chunk 92 optimal weight: 0.0870 chunk 61 optimal weight: 0.9990 chunk 109 optimal weight: 20.0000 chunk 68 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 50 optimal weight: 0.0070 chunk 67 optimal weight: 0.9980 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1543 ASN A1767 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9167 Z= 0.161 Angle : 0.568 8.393 12456 Z= 0.292 Chirality : 0.036 0.194 1491 Planarity : 0.003 0.042 1510 Dihedral : 8.321 115.304 1546 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.05 % Favored : 95.86 % Rotamer: Outliers : 4.83 % Allowed : 24.83 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.18 % 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: 0.95 (0.26), residues: 1136 helix: 1.59 (0.19), residues: 781 sheet: -1.59 (1.54), residues: 12 loop : -1.57 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A1715 HIS 0.002 0.000 HIS A 883 PHE 0.030 0.001 PHE A 778 TYR 0.017 0.001 TYR A1201 ARG 0.007 0.000 ARG A1305 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 195 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 MET cc_start: 0.6557 (tpp) cc_final: 0.5823 (tmm) REVERT: A 137 LEU cc_start: 0.8690 (tt) cc_final: 0.8397 (tp) REVERT: A 196 TRP cc_start: 0.7661 (m-10) cc_final: 0.7400 (m-10) REVERT: A 260 PHE cc_start: 0.8623 (t80) cc_final: 0.8383 (t80) REVERT: A 379 TYR cc_start: 0.8550 (OUTLIER) cc_final: 0.7901 (t80) REVERT: A 901 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.6993 (mt-10) REVERT: A 904 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7445 (mp0) REVERT: A 1209 PHE cc_start: 0.8459 (t80) cc_final: 0.8090 (t80) REVERT: A 1263 TYR cc_start: 0.7687 (m-80) cc_final: 0.7372 (m-80) REVERT: A 1302 LYS cc_start: 0.7378 (pttt) cc_final: 0.7137 (tttp) REVERT: A 1406 ASN cc_start: 0.7332 (m110) cc_final: 0.7095 (m-40) REVERT: A 1448 MET cc_start: 0.8386 (mmt) cc_final: 0.7860 (mmm) REVERT: A 1477 GLN cc_start: 0.8759 (mm-40) cc_final: 0.8400 (mm-40) REVERT: A 1653 MET cc_start: 0.5985 (mmt) cc_final: 0.5732 (mmm) REVERT: A 1693 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7800 (ttp) outliers start: 43 outliers final: 32 residues processed: 225 average time/residue: 0.1565 time to fit residues: 52.8765 Evaluate side-chains 221 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 185 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 379 TYR Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 904 GLU Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 918 CYS Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 1241 LEU Chi-restraints excluded: chain A residue 1242 GLU Chi-restraints excluded: chain A residue 1255 GLU Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1373 LEU Chi-restraints excluded: chain A residue 1379 ILE Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1460 SER Chi-restraints excluded: chain A residue 1568 LEU Chi-restraints excluded: chain A residue 1626 VAL Chi-restraints excluded: chain A residue 1635 ILE Chi-restraints excluded: chain A residue 1662 ILE Chi-restraints excluded: chain A residue 1693 MET Chi-restraints excluded: chain B residue 52 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 33 optimal weight: 0.0980 chunk 21 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 86 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 883 HIS ** A1445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9167 Z= 0.186 Angle : 0.585 8.500 12456 Z= 0.298 Chirality : 0.036 0.197 1491 Planarity : 0.003 0.040 1510 Dihedral : 8.090 114.629 1546 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.14 % Favored : 95.77 % Rotamer: Outliers : 5.06 % Allowed : 25.17 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.18 % 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: 0.93 (0.26), residues: 1136 helix: 1.58 (0.19), residues: 781 sheet: -1.83 (1.47), residues: 12 loop : -1.59 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1715 HIS 0.003 0.000 HIS A 883 PHE 0.030 0.001 PHE A 778 TYR 0.018 0.001 TYR A1201 ARG 0.007 0.000 ARG A1305 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 186 time to evaluate : 0.980 Fit side-chains revert: symmetry clash REVERT: A 136 MET cc_start: 0.6746 (tpp) cc_final: 0.5951 (tmm) REVERT: A 137 LEU cc_start: 0.8681 (tt) cc_final: 0.8396 (tp) REVERT: A 196 TRP cc_start: 0.7634 (m-10) cc_final: 0.7383 (m-10) REVERT: A 260 PHE cc_start: 0.8631 (t80) cc_final: 0.8372 (t80) REVERT: A 379 TYR cc_start: 0.8580 (OUTLIER) cc_final: 0.7939 (t80) REVERT: A 749 MET cc_start: 0.9141 (tmm) cc_final: 0.8908 (tmm) REVERT: A 904 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7424 (mp0) REVERT: A 1209 PHE cc_start: 0.8434 (t80) cc_final: 0.8086 (t80) REVERT: A 1263 TYR cc_start: 0.7626 (m-80) cc_final: 0.7296 (m-80) REVERT: A 1302 LYS cc_start: 0.7303 (pttt) cc_final: 0.7055 (tttp) REVERT: A 1406 ASN cc_start: 0.7489 (m110) cc_final: 0.7239 (m-40) REVERT: A 1448 MET cc_start: 0.8390 (mmt) cc_final: 0.7835 (mmm) REVERT: A 1477 GLN cc_start: 0.8774 (mm-40) cc_final: 0.8456 (mm-40) REVERT: A 1538 PHE cc_start: 0.7640 (OUTLIER) cc_final: 0.7316 (t80) REVERT: A 1653 MET cc_start: 0.5946 (mmt) cc_final: 0.5586 (mmm) REVERT: A 1693 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.7841 (ttp) outliers start: 45 outliers final: 31 residues processed: 221 average time/residue: 0.1600 time to fit residues: 53.0766 Evaluate side-chains 215 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 180 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 379 TYR Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 904 GLU Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 918 CYS Chi-restraints excluded: chain A residue 1241 LEU Chi-restraints excluded: chain A residue 1242 GLU Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1373 LEU Chi-restraints excluded: chain A residue 1379 ILE Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1460 SER Chi-restraints excluded: chain A residue 1538 PHE Chi-restraints excluded: chain A residue 1568 LEU Chi-restraints excluded: chain A residue 1626 VAL Chi-restraints excluded: chain A residue 1635 ILE Chi-restraints excluded: chain A residue 1693 MET Chi-restraints excluded: chain B residue 52 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 6.9990 chunk 102 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 61 optimal weight: 0.3980 chunk 44 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 92 optimal weight: 0.2980 chunk 67 optimal weight: 4.9990 chunk 108 optimal weight: 7.9990 chunk 66 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.4519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 9167 Z= 0.184 Angle : 0.601 9.753 12456 Z= 0.306 Chirality : 0.037 0.208 1491 Planarity : 0.003 0.040 1510 Dihedral : 7.862 113.821 1544 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.70 % Favored : 96.13 % Rotamer: Outliers : 5.17 % Allowed : 24.83 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.18 % 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: 0.98 (0.26), residues: 1136 helix: 1.61 (0.19), residues: 779 sheet: -1.93 (1.43), residues: 12 loop : -1.53 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A1715 HIS 0.003 0.000 HIS A 279 PHE 0.030 0.001 PHE A 778 TYR 0.018 0.001 TYR A1201 ARG 0.007 0.000 ARG A1305 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 189 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 MET cc_start: 0.6765 (tpp) cc_final: 0.5964 (tmm) REVERT: A 137 LEU cc_start: 0.8678 (tt) cc_final: 0.8392 (tp) REVERT: A 260 PHE cc_start: 0.8625 (t80) cc_final: 0.8372 (t80) REVERT: A 379 TYR cc_start: 0.8569 (OUTLIER) cc_final: 0.8013 (t80) REVERT: A 749 MET cc_start: 0.9138 (tmm) cc_final: 0.8888 (tmm) REVERT: A 901 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.6976 (mt-10) REVERT: A 904 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7466 (mp0) REVERT: A 926 MET cc_start: 0.7895 (ttt) cc_final: 0.7671 (mtp) REVERT: A 1209 PHE cc_start: 0.8428 (t80) cc_final: 0.7892 (t80) REVERT: A 1263 TYR cc_start: 0.7626 (m-80) cc_final: 0.7321 (m-80) REVERT: A 1302 LYS cc_start: 0.7286 (pttt) cc_final: 0.7013 (tttp) REVERT: A 1406 ASN cc_start: 0.7444 (m110) cc_final: 0.7186 (m-40) REVERT: A 1448 MET cc_start: 0.8384 (mmt) cc_final: 0.7877 (mmm) REVERT: A 1477 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.8410 (mm-40) REVERT: A 1538 PHE cc_start: 0.7654 (OUTLIER) cc_final: 0.7317 (t80) REVERT: A 1693 MET cc_start: 0.8294 (OUTLIER) cc_final: 0.7826 (ttp) outliers start: 46 outliers final: 32 residues processed: 224 average time/residue: 0.1610 time to fit residues: 54.9192 Evaluate side-chains 220 residues out of total 1007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 182 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 379 TYR Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 901 GLU Chi-restraints excluded: chain A residue 904 GLU Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 918 CYS Chi-restraints excluded: chain A residue 1229 ILE Chi-restraints excluded: chain A residue 1241 LEU Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1373 LEU Chi-restraints excluded: chain A residue 1379 ILE Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1424 MET Chi-restraints excluded: chain A residue 1460 SER Chi-restraints excluded: chain A residue 1477 GLN Chi-restraints excluded: chain A residue 1538 PHE Chi-restraints excluded: chain A residue 1568 LEU Chi-restraints excluded: chain A residue 1626 VAL Chi-restraints excluded: chain A residue 1635 ILE Chi-restraints excluded: chain A residue 1656 LEU Chi-restraints excluded: chain A residue 1693 MET Chi-restraints excluded: chain B residue 52 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- 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: 70.5779 > 50: distance: 19 - 25: 33.593 distance: 25 - 26: 17.046 distance: 26 - 27: 33.937 distance: 26 - 29: 3.603 distance: 27 - 28: 12.867 distance: 27 - 30: 44.258 distance: 31 - 32: 10.509 distance: 31 - 34: 22.661 distance: 32 - 33: 5.975 distance: 32 - 37: 29.434 distance: 34 - 35: 41.070 distance: 34 - 36: 30.843 distance: 37 - 38: 29.014 distance: 38 - 39: 38.055 distance: 38 - 41: 42.604 distance: 39 - 40: 24.123 distance: 42 - 43: 10.134 distance: 43 - 44: 35.092 distance: 44 - 45: 23.597 distance: 44 - 46: 39.860 distance: 46 - 47: 10.234 distance: 47 - 48: 40.611 distance: 47 - 50: 41.435 distance: 48 - 49: 33.445 distance: 48 - 54: 40.239 distance: 50 - 51: 29.405 distance: 51 - 52: 10.249 distance: 51 - 53: 9.456 distance: 54 - 55: 38.725 distance: 55 - 56: 43.714 distance: 56 - 57: 45.182 distance: 56 - 62: 27.678 distance: 58 - 59: 14.233 distance: 59 - 60: 42.737 distance: 59 - 61: 23.581 distance: 62 - 63: 46.019 distance: 62 - 68: 44.509 distance: 63 - 64: 32.311 distance: 63 - 66: 49.908 distance: 64 - 65: 13.389 distance: 64 - 69: 27.648 distance: 66 - 67: 28.331 distance: 67 - 68: 46.363 distance: 69 - 70: 25.559 distance: 70 - 71: 37.874 distance: 70 - 73: 40.707 distance: 71 - 72: 31.097 distance: 71 - 74: 29.861 distance: 74 - 75: 25.458 distance: 75 - 76: 31.698 distance: 75 - 78: 22.154 distance: 76 - 77: 10.789 distance: 76 - 79: 55.073 distance: 79 - 80: 51.440 distance: 80 - 81: 17.099 distance: 80 - 83: 5.488 distance: 81 - 84: 35.457