Starting phenix.real_space_refine on Fri Mar 15 05:51:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hw4_35050/03_2024/8hw4_35050_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hw4_35050/03_2024/8hw4_35050.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hw4_35050/03_2024/8hw4_35050_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hw4_35050/03_2024/8hw4_35050_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hw4_35050/03_2024/8hw4_35050_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hw4_35050/03_2024/8hw4_35050.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hw4_35050/03_2024/8hw4_35050.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hw4_35050/03_2024/8hw4_35050_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hw4_35050/03_2024/8hw4_35050_updated.pdb" } resolution = 3.52 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= 0.002 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 59 5.16 5 C 6997 2.51 5 N 1791 2.21 5 O 1899 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 57": "NH1" <-> "NH2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 153": "NH1" <-> "NH2" Residue "A PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 217": "NH1" <-> "NH2" Residue "A TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 232": "NH1" <-> "NH2" Residue "A ARG 248": "NH1" <-> "NH2" Residue "A ARG 261": "NH1" <-> "NH2" Residue "A ARG 391": "NH1" <-> "NH2" Residue "A ARG 402": "NH1" <-> "NH2" Residue "A ASP 416": "OD1" <-> "OD2" Residue "A ARG 487": "NH1" <-> "NH2" Residue "A GLU 493": "OE1" <-> "OE2" Residue "A TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 518": "NH1" <-> "NH2" Residue "A ARG 526": "NH1" <-> "NH2" Residue "A GLU 610": "OE1" <-> "OE2" Residue "A GLU 707": "OE1" <-> "OE2" Residue "A GLU 734": "OE1" <-> "OE2" Residue "A ARG 756": "NH1" <-> "NH2" Residue "A PHE 772": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1011": "NH1" <-> "NH2" Residue "A PHE 1024": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1042": "NH1" <-> "NH2" Residue "A ARG 1054": "NH1" <-> "NH2" Residue "A ARG 1067": "NH1" <-> "NH2" Residue "A GLU 1081": "OE1" <-> "OE2" Residue "A ARG 1138": "NH1" <-> "NH2" Residue "A ARG 1144": "NH1" <-> "NH2" Residue "A ARG 1162": "NH1" <-> "NH2" Residue "A TYR 1164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1166": "NH1" <-> "NH2" Residue "A ARG 1168": "NH1" <-> "NH2" Residue "A ARG 1193": "NH1" <-> "NH2" Residue "A PHE 1201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1281": "OE1" <-> "OE2" Residue "A GLU 1341": "OE1" <-> "OE2" Residue "A GLU 1346": "OE1" <-> "OE2" Residue "A PHE 1387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1400": "OE1" <-> "OE2" Residue "A ARG 1445": "NH1" <-> "NH2" Residue "A TYR 1490": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10746 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 10746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1366, 10746 Unusual residues: {'ZWY': 2} Classifications: {'peptide': 1364, 'undetermined': 2} Link IDs: {'PTRANS': 59, 'TRANS': 1304, None: 2} Not linked: pdbres="MET A1520 " pdbres="ZWY A1601 " Not linked: pdbres="ZWY A1601 " pdbres="ZWY A1602 " Chain breaks: 2 Time building chain proxies: 6.08, per 1000 atoms: 0.57 Number of scatterers: 10746 At special positions: 0 Unit cell: (74.9, 109.14, 153.01, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 59 16.00 O 1899 8.00 N 1791 7.00 C 6997 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.34 Conformation dependent library (CDL) restraints added in 2.0 seconds 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2560 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 68 helices and 5 sheets defined 56.3% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.55 Creating SS restraints... Processing helix chain 'A' and resid 37 through 51 Proline residue: A 41 - end of helix Proline residue: A 50 - end of helix Processing helix chain 'A' and resid 53 through 58 removed outlier: 3.527A pdb=" N ARG A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N HIS A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 53 through 58' Processing helix chain 'A' and resid 70 through 73 No H-bonds generated for 'chain 'A' and resid 70 through 73' Processing helix chain 'A' and resid 76 through 94 removed outlier: 4.239A pdb=" N ALA A 86 " --> pdb=" O CYS A 82 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP A 87 " --> pdb=" O VAL A 83 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU A 88 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N SER A 91 " --> pdb=" O ASP A 87 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLY A 94 " --> pdb=" O TYR A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 127 removed outlier: 3.925A pdb=" N THR A 108 " --> pdb=" O VAL A 104 " (cutoff:3.500A) Proline residue: A 109 - end of helix removed outlier: 4.577A pdb=" N MET A 116 " --> pdb=" O VAL A 112 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 117 " --> pdb=" O GLY A 113 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU A 121 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLN A 124 " --> pdb=" O THR A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 147 Processing helix chain 'A' and resid 149 through 162 removed outlier: 3.632A pdb=" N ILE A 156 " --> pdb=" O PHE A 152 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N LEU A 157 " --> pdb=" O ARG A 153 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 189 removed outlier: 3.502A pdb=" N ALA A 179 " --> pdb=" O TYR A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 218 Processing helix chain 'A' and resid 221 through 232 removed outlier: 3.710A pdb=" N LYS A 225 " --> pdb=" O TRP A 222 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE A 228 " --> pdb=" O LYS A 225 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLY A 230 " --> pdb=" O ALA A 227 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARG A 232 " --> pdb=" O TYR A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 239 No H-bonds generated for 'chain 'A' and resid 237 through 239' Processing helix chain 'A' and resid 254 through 262 removed outlier: 4.096A pdb=" N ALA A 259 " --> pdb=" O GLN A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 306 Processing helix chain 'A' and resid 315 through 339 removed outlier: 4.499A pdb=" N PHE A 326 " --> pdb=" O ASP A 322 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ILE A 327 " --> pdb=" O LEU A 323 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ASN A 328 " --> pdb=" O LEU A 324 " (cutoff:3.500A) Proline residue: A 329 - end of helix Processing helix chain 'A' and resid 346 through 357 removed outlier: 4.506A pdb=" N LEU A 351 " --> pdb=" O TRP A 348 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 355 " --> pdb=" O VAL A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 374 No H-bonds generated for 'chain 'A' and resid 371 through 374' Processing helix chain 'A' and resid 378 through 394 removed outlier: 3.811A pdb=" N MET A 386 " --> pdb=" O ARG A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 403 Processing helix chain 'A' and resid 406 through 412 removed outlier: 4.141A pdb=" N VAL A 410 " --> pdb=" O VAL A 406 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASN A 411 " --> pdb=" O GLY A 407 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 412 " --> pdb=" O GLU A 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 406 through 412' Processing helix chain 'A' and resid 424 through 436 removed outlier: 4.273A pdb=" N ASN A 428 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LEU A 429 " --> pdb=" O PRO A 425 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU A 430 " --> pdb=" O PHE A 426 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N TRP A 431 " --> pdb=" O LEU A 427 " (cutoff:3.500A) Proline residue: A 434 - end of helix Processing helix chain 'A' and resid 440 through 448 removed outlier: 3.523A pdb=" N LEU A 444 " --> pdb=" O ALA A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 464 Proline residue: A 464 - end of helix Processing helix chain 'A' and resid 468 through 472 Processing helix chain 'A' and resid 482 through 495 Processing helix chain 'A' and resid 498 through 503 Processing helix chain 'A' and resid 507 through 526 removed outlier: 3.510A pdb=" N LEU A 524 " --> pdb=" O GLY A 520 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 525 " --> pdb=" O GLU A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 532 No H-bonds generated for 'chain 'A' and resid 530 through 532' Processing helix chain 'A' and resid 542 through 557 Processing helix chain 'A' and resid 565 through 582 removed outlier: 4.160A pdb=" N VAL A 570 " --> pdb=" O GLU A 566 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ASN A 576 " --> pdb=" O VAL A 572 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE A 577 " --> pdb=" O SER A 573 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 580 " --> pdb=" O ASN A 576 " (cutoff:3.500A) Proline residue: A 581 - end of helix Processing helix chain 'A' and resid 584 through 606 removed outlier: 4.391A pdb=" N VAL A 597 " --> pdb=" O THR A 593 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER A 598 " --> pdb=" O GLN A 594 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS A 600 " --> pdb=" O SER A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 675 removed outlier: 3.640A pdb=" N SER A 672 " --> pdb=" O SER A 668 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA A 673 " --> pdb=" O SER A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 710 Processing helix chain 'A' and resid 717 through 726 Processing helix chain 'A' and resid 730 through 735 Processing helix chain 'A' and resid 745 through 747 No H-bonds generated for 'chain 'A' and resid 745 through 747' Processing helix chain 'A' and resid 753 through 766 removed outlier: 3.768A pdb=" N GLN A 757 " --> pdb=" O GLY A 753 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG A 758 " --> pdb=" O GLY A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 780 removed outlier: 4.439A pdb=" N ALA A 780 " --> pdb=" O PRO A 777 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 777 through 780' Processing helix chain 'A' and resid 783 through 792 Processing helix chain 'A' and resid 835 through 840 removed outlier: 4.010A pdb=" N GLN A 840 " --> pdb=" O PRO A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 849 removed outlier: 3.573A pdb=" N LEU A 849 " --> pdb=" O PHE A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 966 removed outlier: 3.664A pdb=" N TRP A 960 " --> pdb=" O LEU A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 996 removed outlier: 3.988A pdb=" N LEU A 977 " --> pdb=" O ALA A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1024 removed outlier: 3.823A pdb=" N SER A1009 " --> pdb=" O ASN A1006 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LEU A1012 " --> pdb=" O SER A1009 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ILE A1020 " --> pdb=" O ALA A1017 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N LEU A1021 " --> pdb=" O LEU A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1052 removed outlier: 4.064A pdb=" N ALA A1032 " --> pdb=" O LEU A1028 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLY A1036 " --> pdb=" O ALA A1032 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLN A1039 " --> pdb=" O ALA A1035 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A1044 " --> pdb=" O ALA A1040 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASN A1051 " --> pdb=" O ALA A1047 " (cutoff:3.500A) Processing helix chain 'A' and resid 1057 through 1062 Processing helix chain 'A' and resid 1067 through 1070 No H-bonds generated for 'chain 'A' and resid 1067 through 1070' Processing helix chain 'A' and resid 1075 through 1081 removed outlier: 4.078A pdb=" N VAL A1079 " --> pdb=" O ASP A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1107 removed outlier: 3.617A pdb=" N PHE A1095 " --> pdb=" O LEU A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1109 through 1141 removed outlier: 3.714A pdb=" N THR A1112 " --> pdb=" O PRO A1109 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL A1113 " --> pdb=" O LEU A1110 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU A1116 " --> pdb=" O VAL A1113 " (cutoff:3.500A) Proline residue: A1117 - end of helix removed outlier: 5.078A pdb=" N SER A1133 " --> pdb=" O ALA A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1150 Processing helix chain 'A' and resid 1154 through 1161 removed outlier: 5.360A pdb=" N SER A1159 " --> pdb=" O VAL A1155 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N VAL A1160 " --> pdb=" O THR A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1167 through 1204 removed outlier: 4.071A pdb=" N ILE A1173 " --> pdb=" O ASP A1169 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N SER A1174 " --> pdb=" O PHE A1170 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASN A1181 " --> pdb=" O LYS A1177 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N SER A1184 " --> pdb=" O ALA A1180 " (cutoff:3.500A) Proline residue: A1187 - end of helix removed outlier: 3.823A pdb=" N VAL A1202 " --> pdb=" O GLY A1198 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY A1203 " --> pdb=" O VAL A1199 " (cutoff:3.500A) Processing helix chain 'A' and resid 1207 through 1215 Processing helix chain 'A' and resid 1223 through 1233 removed outlier: 4.000A pdb=" N LEU A1228 " --> pdb=" O GLY A1224 " (cutoff:3.500A) Processing helix chain 'A' and resid 1242 through 1247 Processing helix chain 'A' and resid 1255 through 1262 Processing helix chain 'A' and resid 1284 through 1286 No H-bonds generated for 'chain 'A' and resid 1284 through 1286' Processing helix chain 'A' and resid 1330 through 1337 removed outlier: 3.998A pdb=" N LEU A1334 " --> pdb=" O SER A1330 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE A1337 " --> pdb=" O THR A1333 " (cutoff:3.500A) Processing helix chain 'A' and resid 1354 through 1356 No H-bonds generated for 'chain 'A' and resid 1354 through 1356' Processing helix chain 'A' and resid 1359 through 1365 removed outlier: 3.821A pdb=" N SER A1364 " --> pdb=" O HIS A1360 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN A1365 " --> pdb=" O ASP A1361 " (cutoff:3.500A) Processing helix chain 'A' and resid 1380 through 1385 Processing helix chain 'A' and resid 1392 through 1401 Processing helix chain 'A' and resid 1405 through 1409 Processing helix chain 'A' and resid 1414 through 1416 No H-bonds generated for 'chain 'A' and resid 1414 through 1416' Processing helix chain 'A' and resid 1428 through 1442 removed outlier: 4.202A pdb=" N ARG A1442 " --> pdb=" O ARG A1438 " (cutoff:3.500A) Processing helix chain 'A' and resid 1458 through 1471 removed outlier: 3.619A pdb=" N GLN A1471 " --> pdb=" O THR A1467 " (cutoff:3.500A) Processing helix chain 'A' and resid 1507 through 1513 Processing helix chain 'A' and resid 1516 through 1519 No H-bonds generated for 'chain 'A' and resid 1516 through 1519' Processing sheet with id= A, first strand: chain 'A' and resid 820 through 823 Processing sheet with id= B, first strand: chain 'A' and resid 1289 through 1292 removed outlier: 3.683A pdb=" N ARG A1292 " --> pdb=" O GLU A1346 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU A1346 " --> pdb=" O ARG A1292 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1319 through 1323 removed outlier: 7.143A pdb=" N ARG A1492 " --> pdb=" O GLY A1320 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N VAL A1322 " --> pdb=" O ARG A1492 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU A1494 " --> pdb=" O VAL A1322 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU A1503 " --> pdb=" O VAL A1495 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ASP A1497 " --> pdb=" O VAL A1501 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N VAL A1501 " --> pdb=" O ASP A1497 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 1446 through 1448 removed outlier: 5.995A pdb=" N THR A1476 " --> pdb=" O LEU A1447 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 625 through 630 removed outlier: 7.085A pdb=" N VAL A 651 " --> pdb=" O ALA A 626 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N THR A 628 " --> pdb=" O ILE A 649 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ILE A 649 " --> pdb=" O THR A 628 " (cutoff:3.500A) 419 hydrogen bonds defined for protein. 1059 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: 3.94 Time building geometry restraints manager: 4.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2066 1.33 - 1.45: 2630 1.45 - 1.57: 6205 1.57 - 1.69: 7 1.69 - 1.81: 93 Bond restraints: 11001 Sorted by residual: bond pdb=" C15 ZWY A1601 " pdb=" C16 ZWY A1601 " ideal model delta sigma weight residual 0.007 1.439 -1.432 2.00e-02 2.50e+03 5.13e+03 bond pdb=" C15 ZWY A1602 " pdb=" C16 ZWY A1602 " ideal model delta sigma weight residual 0.007 1.277 -1.270 2.00e-02 2.50e+03 4.03e+03 bond pdb=" C18 ZWY A1602 " pdb=" C19 ZWY A1602 " ideal model delta sigma weight residual 0.565 1.575 -1.010 2.00e-02 2.50e+03 2.55e+03 bond pdb=" C18 ZWY A1601 " pdb=" C19 ZWY A1601 " ideal model delta sigma weight residual 0.565 1.553 -0.988 2.00e-02 2.50e+03 2.44e+03 bond pdb=" C05 ZWY A1601 " pdb=" C06 ZWY A1601 " ideal model delta sigma weight residual 0.767 1.512 -0.745 2.00e-02 2.50e+03 1.39e+03 ... (remaining 10996 not shown) Histogram of bond angle deviations from ideal: 99.10 - 106.09: 269 106.09 - 113.07: 6110 113.07 - 120.06: 3962 120.06 - 127.05: 4484 127.05 - 134.03: 153 Bond angle restraints: 14978 Sorted by residual: angle pdb=" C13 ZWY A1601 " pdb=" C14 ZWY A1601 " pdb=" C19 ZWY A1601 " ideal model delta sigma weight residual 169.18 125.87 43.31 3.00e+00 1.11e-01 2.08e+02 angle pdb=" C13 ZWY A1602 " pdb=" C14 ZWY A1602 " pdb=" C19 ZWY A1602 " ideal model delta sigma weight residual 169.18 126.35 42.83 3.00e+00 1.11e-01 2.04e+02 angle pdb=" C14 ZWY A1601 " pdb=" C15 ZWY A1601 " pdb=" C25 ZWY A1601 " ideal model delta sigma weight residual 70.53 111.41 -40.88 3.00e+00 1.11e-01 1.86e+02 angle pdb=" C13 ZWY A1601 " pdb=" C14 ZWY A1601 " pdb=" C15 ZWY A1601 " ideal model delta sigma weight residual 80.34 120.69 -40.35 3.00e+00 1.11e-01 1.81e+02 angle pdb=" C14 ZWY A1602 " pdb=" C15 ZWY A1602 " pdb=" C25 ZWY A1602 " ideal model delta sigma weight residual 70.53 110.53 -40.00 3.00e+00 1.11e-01 1.78e+02 ... (remaining 14973 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.04: 6373 33.04 - 66.08: 139 66.08 - 99.12: 16 99.12 - 132.15: 1 132.15 - 165.19: 1 Dihedral angle restraints: 6530 sinusoidal: 2568 harmonic: 3962 Sorted by residual: dihedral pdb=" CD ARG A1245 " pdb=" NE ARG A1245 " pdb=" CZ ARG A1245 " pdb=" NH1 ARG A1245 " ideal model delta sinusoidal sigma weight residual 0.00 -83.40 83.40 1 1.00e+01 1.00e-02 8.50e+01 dihedral pdb=" CA PHE A 196 " pdb=" C PHE A 196 " pdb=" N PHE A 197 " pdb=" CA PHE A 197 " ideal model delta harmonic sigma weight residual -180.00 -150.03 -29.97 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA GLU A 164 " pdb=" C GLU A 164 " pdb=" N ILE A 165 " pdb=" CA ILE A 165 " ideal model delta harmonic sigma weight residual 180.00 -155.96 -24.04 0 5.00e+00 4.00e-02 2.31e+01 ... (remaining 6527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.825: 1741 0.825 - 1.650: 3 1.650 - 2.474: 3 2.474 - 3.299: 0 3.299 - 4.124: 2 Chirality restraints: 1749 Sorted by residual: chirality pdb=" C06 ZWY A1601 " pdb=" C05 ZWY A1601 " pdb=" C07 ZWY A1601 " pdb=" C12 ZWY A1601 " both_signs ideal model delta sigma weight residual False -1.73 2.40 -4.12 2.00e-01 2.50e+01 4.25e+02 chirality pdb=" C06 ZWY A1602 " pdb=" C05 ZWY A1602 " pdb=" C07 ZWY A1602 " pdb=" C12 ZWY A1602 " both_signs ideal model delta sigma weight residual False -1.73 2.21 -3.93 2.00e-01 2.50e+01 3.86e+02 chirality pdb=" C15 ZWY A1601 " pdb=" C05 ZWY A1601 " pdb=" C14 ZWY A1601 " pdb=" C16 ZWY A1601 " both_signs ideal model delta sigma weight residual False -0.02 2.17 -2.19 2.00e-01 2.50e+01 1.20e+02 ... (remaining 1746 not shown) Planarity restraints: 1864 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C12 ZWY A1601 " 0.194 2.00e-02 2.50e+03 1.73e-01 3.76e+02 pdb=" C13 ZWY A1601 " -0.196 2.00e-02 2.50e+03 pdb=" C14 ZWY A1601 " -0.192 2.00e-02 2.50e+03 pdb=" C15 ZWY A1601 " 0.001 2.00e-02 2.50e+03 pdb=" C19 ZWY A1601 " 0.194 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1245 " -1.092 9.50e-02 1.11e+02 4.89e-01 1.44e+02 pdb=" NE ARG A1245 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG A1245 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A1245 " -0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG A1245 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 ZWY A1602 " -0.052 2.00e-02 2.50e+03 9.40e-02 1.10e+02 pdb=" C13 ZWY A1602 " 0.127 2.00e-02 2.50e+03 pdb=" C14 ZWY A1602 " -0.148 2.00e-02 2.50e+03 pdb=" C15 ZWY A1602 " 0.057 2.00e-02 2.50e+03 pdb=" C19 ZWY A1602 " 0.016 2.00e-02 2.50e+03 ... (remaining 1861 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 374 2.69 - 3.25: 11903 3.25 - 3.80: 17273 3.80 - 4.35: 22268 4.35 - 4.90: 35690 Nonbonded interactions: 87508 Sorted by model distance: nonbonded pdb=" OG1 THR A1479 " pdb=" OH TYR A1490 " model vdw 2.142 2.440 nonbonded pdb=" OE2 GLU A 617 " pdb=" ND1 HIS A 686 " model vdw 2.191 2.520 nonbonded pdb=" O GLY A1282 " pdb=" NH1 ARG A1286 " model vdw 2.236 2.520 nonbonded pdb=" O ILE A 396 " pdb=" OG1 THR A 397 " model vdw 2.242 2.440 nonbonded pdb=" OD2 ASP A 247 " pdb=" OH TYR A1186 " model vdw 2.247 2.440 ... (remaining 87503 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 group one per residue 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: 0.830 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: 4.070 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 33.090 Find NCS groups from input model: 0.290 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: 0.000 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 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 : 0.033 1.432 11001 Z= 2.003 Angle : 1.386 43.309 14978 Z= 0.581 Chirality : 0.173 4.124 1749 Planarity : 0.013 0.489 1864 Dihedral : 15.271 165.193 3970 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 0.09 % Allowed : 0.34 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.22), residues: 1358 helix: -1.57 (0.17), residues: 826 sheet: -0.76 (0.61), residues: 65 loop : -1.36 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1194 HIS 0.007 0.001 HIS A 369 PHE 0.030 0.002 PHE A1151 TYR 0.019 0.002 TYR A 207 ARG 0.003 0.000 ARG A1278 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 157 time to evaluate : 1.218 Fit side-chains REVERT: A 361 MET cc_start: 0.7775 (tpt) cc_final: 0.7573 (tpt) REVERT: A 499 LYS cc_start: 0.8863 (ttpt) cc_final: 0.8624 (ttmt) REVERT: A 1115 ILE cc_start: 0.8961 (tp) cc_final: 0.8737 (tp) REVERT: A 1245 ARG cc_start: 0.7268 (OUTLIER) cc_final: 0.6802 (tpp-160) REVERT: A 1272 TRP cc_start: 0.7668 (m-10) cc_final: 0.7427 (m-10) REVERT: A 1432 GLN cc_start: 0.8535 (mp10) cc_final: 0.8328 (mp10) outliers start: 1 outliers final: 0 residues processed: 158 average time/residue: 0.1973 time to fit residues: 47.3574 Evaluate side-chains 134 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 133 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1245 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 9.9990 chunk 103 optimal weight: 0.6980 chunk 57 optimal weight: 20.0000 chunk 35 optimal weight: 0.8980 chunk 69 optimal weight: 10.0000 chunk 55 optimal weight: 8.9990 chunk 106 optimal weight: 0.0270 chunk 41 optimal weight: 0.1980 chunk 64 optimal weight: 0.4980 chunk 79 optimal weight: 4.9990 chunk 123 optimal weight: 0.6980 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 792 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.0366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.194 11001 Z= 0.509 Angle : 1.148 24.479 14978 Z= 0.511 Chirality : 0.094 2.224 1749 Planarity : 0.012 0.465 1864 Dihedral : 10.111 109.529 1511 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 23.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 1.29 % Allowed : 7.03 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.22), residues: 1358 helix: -1.54 (0.17), residues: 831 sheet: -0.78 (0.61), residues: 65 loop : -1.37 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 636 HIS 0.007 0.001 HIS A1403 PHE 0.024 0.002 PHE A 105 TYR 0.025 0.002 TYR A 720 ARG 0.009 0.000 ARG A1245 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 132 time to evaluate : 1.207 Fit side-chains revert: symmetry clash REVERT: A 1115 ILE cc_start: 0.8933 (tp) cc_final: 0.8678 (tp) REVERT: A 1245 ARG cc_start: 0.7270 (OUTLIER) cc_final: 0.6784 (tpp-160) REVERT: A 1263 TYR cc_start: 0.8057 (m-10) cc_final: 0.7415 (m-10) REVERT: A 1272 TRP cc_start: 0.7660 (m-10) cc_final: 0.7403 (m-10) REVERT: A 1432 GLN cc_start: 0.8480 (mp10) cc_final: 0.8279 (mp10) outliers start: 15 outliers final: 12 residues processed: 139 average time/residue: 0.1912 time to fit residues: 40.6475 Evaluate side-chains 136 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 123 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1245 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 102 optimal weight: 0.5980 chunk 84 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 123 optimal weight: 0.0010 chunk 133 optimal weight: 10.0000 chunk 110 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 chunk 99 optimal weight: 0.5980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 792 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.0378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.194 11001 Z= 0.509 Angle : 1.148 24.466 14978 Z= 0.511 Chirality : 0.094 2.224 1749 Planarity : 0.012 0.465 1864 Dihedral : 10.117 109.529 1511 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 25.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 1.11 % Allowed : 7.97 % Favored : 90.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.22), residues: 1358 helix: -1.54 (0.17), residues: 831 sheet: -0.78 (0.61), residues: 65 loop : -1.37 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 636 HIS 0.007 0.001 HIS A1403 PHE 0.024 0.002 PHE A 105 TYR 0.025 0.002 TYR A 720 ARG 0.009 0.000 ARG A1245 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 123 time to evaluate : 1.253 Fit side-chains revert: symmetry clash REVERT: A 1115 ILE cc_start: 0.8933 (tp) cc_final: 0.8678 (tp) REVERT: A 1245 ARG cc_start: 0.7268 (OUTLIER) cc_final: 0.6784 (tpp-160) REVERT: A 1263 TYR cc_start: 0.8056 (m-10) cc_final: 0.7415 (m-10) REVERT: A 1272 TRP cc_start: 0.7666 (m-10) cc_final: 0.7403 (m-10) REVERT: A 1432 GLN cc_start: 0.8483 (mp10) cc_final: 0.8279 (mp10) outliers start: 13 outliers final: 12 residues processed: 130 average time/residue: 0.1891 time to fit residues: 38.1277 Evaluate side-chains 135 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 122 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1245 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 64 optimal weight: 0.3980 chunk 13 optimal weight: 0.0070 chunk 59 optimal weight: 9.9990 chunk 83 optimal weight: 0.5980 chunk 124 optimal weight: 7.9990 chunk 131 optimal weight: 1.9990 chunk 117 optimal weight: 8.9990 chunk 35 optimal weight: 0.0050 chunk 109 optimal weight: 0.9980 overall best weight: 0.3412 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 792 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.0378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.194 11001 Z= 0.508 Angle : 1.145 23.717 14978 Z= 0.511 Chirality : 0.094 2.224 1749 Planarity : 0.012 0.465 1864 Dihedral : 10.082 109.499 1511 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 25.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 1.11 % Allowed : 7.88 % Favored : 91.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.22), residues: 1358 helix: -1.54 (0.17), residues: 831 sheet: -0.78 (0.61), residues: 65 loop : -1.37 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 636 HIS 0.007 0.001 HIS A1403 PHE 0.023 0.002 PHE A 105 TYR 0.025 0.002 TYR A 720 ARG 0.009 0.000 ARG A1245 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 122 time to evaluate : 1.214 Fit side-chains revert: symmetry clash REVERT: A 1115 ILE cc_start: 0.8933 (tp) cc_final: 0.8678 (tp) REVERT: A 1245 ARG cc_start: 0.7268 (OUTLIER) cc_final: 0.6784 (tpp-160) REVERT: A 1263 TYR cc_start: 0.8056 (m-10) cc_final: 0.7414 (m-10) REVERT: A 1272 TRP cc_start: 0.7666 (m-10) cc_final: 0.7403 (m-10) REVERT: A 1432 GLN cc_start: 0.8483 (mp10) cc_final: 0.8279 (mp10) outliers start: 13 outliers final: 12 residues processed: 129 average time/residue: 0.1909 time to fit residues: 38.0270 Evaluate side-chains 135 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 122 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1245 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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: 68.3805 > 50: distance: 21 - 25: 12.923 distance: 25 - 26: 17.421 distance: 25 - 31: 20.295 distance: 26 - 27: 9.643 distance: 26 - 29: 20.866 distance: 27 - 32: 12.156 distance: 29 - 30: 30.517 distance: 30 - 31: 16.699 distance: 32 - 33: 7.739 distance: 33 - 34: 15.797 distance: 33 - 36: 15.526 distance: 34 - 35: 5.923 distance: 34 - 41: 17.348 distance: 35 - 69: 15.954 distance: 36 - 37: 20.254 distance: 37 - 38: 20.324 distance: 38 - 39: 17.586 distance: 38 - 40: 20.531 distance: 41 - 42: 15.040 distance: 42 - 43: 19.920 distance: 42 - 45: 6.507 distance: 43 - 44: 8.753 distance: 43 - 47: 17.731 distance: 44 - 77: 25.173 distance: 45 - 46: 18.866 distance: 47 - 48: 28.132 distance: 48 - 49: 41.751 distance: 48 - 51: 21.120 distance: 49 - 50: 33.717 distance: 49 - 58: 16.083 distance: 51 - 52: 11.142 distance: 52 - 53: 26.122 distance: 52 - 54: 13.508 distance: 53 - 55: 16.115 distance: 54 - 56: 15.461 distance: 55 - 57: 19.792 distance: 56 - 57: 21.671 distance: 58 - 59: 24.097 distance: 59 - 60: 11.293 distance: 59 - 62: 14.299 distance: 60 - 61: 14.510 distance: 60 - 69: 4.206 distance: 62 - 63: 11.026 distance: 63 - 65: 3.366 distance: 64 - 66: 5.797 distance: 65 - 67: 7.854 distance: 66 - 68: 13.007 distance: 67 - 68: 12.111 distance: 69 - 70: 3.126 distance: 70 - 71: 28.758 distance: 70 - 73: 12.843 distance: 71 - 72: 16.946 distance: 71 - 77: 43.249 distance: 73 - 74: 9.617 distance: 74 - 75: 21.809 distance: 74 - 76: 15.346 distance: 77 - 78: 32.424 distance: 78 - 79: 52.613 distance: 78 - 81: 22.582 distance: 79 - 80: 56.194 distance: 81 - 82: 9.742 distance: 81 - 83: 59.565 distance: 85 - 86: 40.911 distance: 85 - 88: 38.761 distance: 86 - 87: 20.317 distance: 86 - 91: 21.422 distance: 88 - 89: 19.505 distance: 88 - 90: 23.486 distance: 91 - 92: 13.363 distance: 91 - 97: 14.054 distance: 92 - 93: 11.309 distance: 92 - 95: 11.376 distance: 93 - 94: 4.308 distance: 93 - 98: 16.260 distance: 95 - 96: 6.229 distance: 96 - 97: 27.994 distance: 98 - 99: 20.229 distance: 99 - 100: 19.789 distance: 99 - 102: 12.607 distance: 100 - 101: 11.853 distance: 100 - 104: 8.443 distance: 102 - 103: 8.205