Starting phenix.real_space_refine on Tue Nov 14 21:40:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uy0_20945/11_2023/6uy0_20945_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uy0_20945/11_2023/6uy0_20945.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uy0_20945/11_2023/6uy0_20945.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uy0_20945/11_2023/6uy0_20945.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uy0_20945/11_2023/6uy0_20945_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uy0_20945/11_2023/6uy0_20945_updated.pdb" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 5 5.49 5 Mg 2 5.21 5 S 47 5.16 5 C 6266 2.51 5 N 1607 2.21 5 O 1757 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 210": "OE1" <-> "OE2" Residue "A GLU 237": "OE1" <-> "OE2" Residue "A GLU 251": "OE1" <-> "OE2" Residue "A GLU 507": "OE1" <-> "OE2" Residue "A ARG 632": "NH1" <-> "NH2" Residue "A GLU 699": "OE1" <-> "OE2" Residue "A ARG 723": "NH1" <-> "NH2" Residue "A GLU 734": "OE1" <-> "OE2" Residue "A ARG 735": "NH1" <-> "NH2" Residue "A GLU 751": "OE1" <-> "OE2" Residue "A GLU 763": "OE1" <-> "OE2" Residue "A ARG 780": "NH1" <-> "NH2" Residue "A GLU 854": "OE1" <-> "OE2" Residue "A ARG 858": "NH1" <-> "NH2" Residue "A GLU 942": "OE1" <-> "OE2" Residue "A ARG 1130": "NH1" <-> "NH2" Residue "A ARG 1137": "NH1" <-> "NH2" Residue "A ARG 1141": "NH1" <-> "NH2" Residue "A GLU 1156": "OE1" <-> "OE2" Residue "A GLU 1171": "OE1" <-> "OE2" Residue "A GLU 1252": "OE1" <-> "OE2" Residue "A ARG 1262": "NH1" <-> "NH2" Residue "A ARG 1291": "NH1" <-> "NH2" Residue "A ARG 1295": "NH1" <-> "NH2" Residue "A ARG 1302": "NH1" <-> "NH2" Residue "A GLU 1303": "OE1" <-> "OE2" Residue "A ARG 1327": "NH1" <-> "NH2" Residue "A ARG 1366": "NH1" <-> "NH2" Residue "A ARG 1384": "NH1" <-> "NH2" Residue "A ARG 1434": "NH1" <-> "NH2" Residue "A ARG 1441": "NH1" <-> "NH2" Residue "A ARG 1495": "NH1" <-> "NH2" Residue "A GLU 1503": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 9684 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1217, 9684 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1, 'CLR': 3} Classifications: {'peptide': 1210, 'undetermined': 7} Link IDs: {'PTRANS': 44, 'TRANS': 1165, None: 7} Not linked: pdbres="VAL A1530 " pdbres="ATP A1601 " Not linked: pdbres="ATP A1601 " pdbres="ADP A1602 " Not linked: pdbres="ADP A1602 " pdbres=" MG A1603 " Not linked: pdbres=" MG A1603 " pdbres=" MG A1604 " Not linked: pdbres=" MG A1604 " pdbres="CLR A1605 " ... (remaining 2 not shown) Chain breaks: 3 Time building chain proxies: 5.53, per 1000 atoms: 0.57 Number of scatterers: 9684 At special positions: 0 Unit cell: (143.17, 98.88, 83.43, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 47 16.00 P 5 15.00 Mg 2 11.99 O 1757 8.00 N 1607 7.00 C 6266 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=0, symmetry=0 Time building additional restraints: 4.12 Conformation dependent library (CDL) restraints added in 1.8 seconds 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2282 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 5 sheets defined 61.8% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.56 Creating SS restraints... Processing helix chain 'A' and resid 209 through 212 No H-bonds generated for 'chain 'A' and resid 209 through 212' Processing helix chain 'A' and resid 215 through 220 removed outlier: 3.714A pdb=" N THR A 220 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 233 removed outlier: 4.018A pdb=" N GLY A 226 " --> pdb=" O TRP A 223 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 229 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY A 231 " --> pdb=" O MET A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 248 No H-bonds generated for 'chain 'A' and resid 246 through 248' Processing helix chain 'A' and resid 250 through 267 Proline residue: A 255 - end of helix removed outlier: 3.539A pdb=" N LYS A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 354 removed outlier: 4.582A pdb=" N MET A 327 " --> pdb=" O PRO A 323 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N SER A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N PHE A 329 " --> pdb=" O PHE A 325 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) Proline residue: A 343 - end of helix removed outlier: 3.660A pdb=" N ASN A 354 " --> pdb=" O ILE A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 407 removed outlier: 4.086A pdb=" N TYR A 364 " --> pdb=" O GLU A 360 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE A 365 " --> pdb=" O TRP A 361 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR A 366 " --> pdb=" O GLN A 362 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR A 367 " --> pdb=" O GLY A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 417 removed outlier: 3.591A pdb=" N SER A 417 " --> pdb=" O ALA A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 461 removed outlier: 3.819A pdb=" N ASP A 430 " --> pdb=" O LEU A 426 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ALA A 431 " --> pdb=" O MET A 427 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN A 432 " --> pdb=" O SER A 428 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N THR A 439 " --> pdb=" O MET A 435 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N TYR A 440 " --> pdb=" O ASP A 436 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ASN A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N MET A 443 " --> pdb=" O THR A 439 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ILE A 444 " --> pdb=" O TYR A 440 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N TRP A 445 " --> pdb=" O ILE A 441 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER A 446 " --> pdb=" O ASN A 442 " (cutoff:3.500A) Proline residue: A 448 - end of helix removed outlier: 3.593A pdb=" N LEU A 457 " --> pdb=" O LEU A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 510 removed outlier: 3.573A pdb=" N VAL A 477 " --> pdb=" O MET A 473 " (cutoff:3.500A) Proline residue: A 478 - end of helix removed outlier: 3.783A pdb=" N THR A 489 " --> pdb=" O MET A 485 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR A 490 " --> pdb=" O LYS A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 518 Processing helix chain 'A' and resid 521 through 554 Processing helix chain 'A' and resid 556 through 571 removed outlier: 3.684A pdb=" N VAL A 567 " --> pdb=" O SER A 563 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR A 568 " --> pdb=" O THR A 564 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL A 569 " --> pdb=" O PHE A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 589 Processing helix chain 'A' and resid 592 through 620 removed outlier: 4.006A pdb=" N LEU A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE A 598 " --> pdb=" O PHE A 594 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU A 599 " --> pdb=" O PRO A 595 " (cutoff:3.500A) Proline residue: A 600 - end of helix Processing helix chain 'A' and resid 627 through 629 No H-bonds generated for 'chain 'A' and resid 627 through 629' Processing helix chain 'A' and resid 684 through 691 Processing helix chain 'A' and resid 722 through 727 Processing helix chain 'A' and resid 734 through 743 Processing helix chain 'A' and resid 747 through 752 Processing helix chain 'A' and resid 770 through 784 removed outlier: 3.636A pdb=" N ALA A 781 " --> pdb=" O SER A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 809 Processing helix chain 'A' and resid 832 through 834 No H-bonds generated for 'chain 'A' and resid 832 through 834' Processing helix chain 'A' and resid 852 through 857 Processing helix chain 'A' and resid 861 through 869 removed outlier: 3.632A pdb=" N THR A 868 " --> pdb=" O GLU A 864 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR A 869 " --> pdb=" O PHE A 865 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 969 Processing helix chain 'A' and resid 971 through 999 Processing helix chain 'A' and resid 1010 through 1057 removed outlier: 3.988A pdb=" N SER A1016 " --> pdb=" O GLN A1012 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL A1017 " --> pdb=" O VAL A1013 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER A1037 " --> pdb=" O SER A1033 " (cutoff:3.500A) Processing helix chain 'A' and resid 1060 through 1065 Processing helix chain 'A' and resid 1068 through 1110 removed outlier: 3.902A pdb=" N ARG A1074 " --> pdb=" O ASN A1070 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLU A1078 " --> pdb=" O ARG A1074 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N LEU A1079 " --> pdb=" O PHE A1075 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ILE A1086 " --> pdb=" O VAL A1082 " (cutoff:3.500A) Proline residue: A1087 - end of helix removed outlier: 3.568A pdb=" N ILE A1106 " --> pdb=" O GLY A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1112 through 1146 removed outlier: 3.787A pdb=" N ALA A1115 " --> pdb=" O PRO A1112 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL A1116 " --> pdb=" O MET A1113 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE A1118 " --> pdb=" O ALA A1115 " (cutoff:3.500A) Proline residue: A1119 - end of helix removed outlier: 3.607A pdb=" N LEU A1123 " --> pdb=" O PRO A1120 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE A1124 " --> pdb=" O LEU A1121 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE A1127 " --> pdb=" O ILE A1124 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG A1130 " --> pdb=" O PHE A1127 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR A1132 " --> pdb=" O GLN A1129 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N VAL A1133 " --> pdb=" O ARG A1130 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA A1134 " --> pdb=" O PHE A1131 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ARG A1137 " --> pdb=" O ALA A1134 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A1142 " --> pdb=" O LEU A1139 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU A1143 " --> pdb=" O LYS A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1148 through 1167 removed outlier: 3.736A pdb=" N LEU A1159 " --> pdb=" O ASN A1155 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY A1160 " --> pdb=" O GLU A1156 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N SER A1162 " --> pdb=" O LEU A1158 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL A1163 " --> pdb=" O LEU A1159 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1219 removed outlier: 3.778A pdb=" N GLU A1183 " --> pdb=" O LEU A1179 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASN A1184 " --> pdb=" O LYS A1180 " (cutoff:3.500A) Proline residue: A1190 - end of helix Processing helix chain 'A' and resid 1226 through 1256 removed outlier: 3.688A pdb=" N GLY A1230 " --> pdb=" O ALA A1226 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LEU A1231 " --> pdb=" O GLY A1227 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER A1232 " --> pdb=" O LEU A1228 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N VAL A1233 " --> pdb=" O VAL A1229 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N SER A1234 " --> pdb=" O GLY A1230 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR A1235 " --> pdb=" O LEU A1231 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN A1238 " --> pdb=" O SER A1234 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR A1240 " --> pdb=" O SER A1236 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG A1248 " --> pdb=" O ASN A1244 " (cutoff:3.500A) Processing helix chain 'A' and resid 1258 through 1266 removed outlier: 3.556A pdb=" N GLU A1265 " --> pdb=" O GLU A1261 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N TYR A1266 " --> pdb=" O ARG A1262 " (cutoff:3.500A) Processing helix chain 'A' and resid 1333 through 1339 Processing helix chain 'A' and resid 1362 through 1366 Processing helix chain 'A' and resid 1383 through 1387 removed outlier: 3.548A pdb=" N LEU A1387 " --> pdb=" O LEU A1383 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1383 through 1387' Processing helix chain 'A' and resid 1395 through 1404 Processing helix chain 'A' and resid 1408 through 1412 Processing helix chain 'A' and resid 1431 through 1445 removed outlier: 3.596A pdb=" N LEU A1436 " --> pdb=" O GLY A1432 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG A1445 " --> pdb=" O ARG A1441 " (cutoff:3.500A) Processing helix chain 'A' and resid 1461 through 1474 Processing helix chain 'A' and resid 1487 through 1489 No H-bonds generated for 'chain 'A' and resid 1487 through 1489' Processing helix chain 'A' and resid 1510 through 1516 Processing helix chain 'A' and resid 1520 through 1527 Processing sheet with id= A, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.876A pdb=" N VAL A 668 " --> pdb=" O SER A 643 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N THR A 645 " --> pdb=" O PHE A 666 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N PHE A 666 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 845 through 848 removed outlier: 3.818A pdb=" N LYS A 845 " --> pdb=" O SER A 842 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N VAL A 840 " --> pdb=" O SER A 847 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL A 837 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ARG A 822 " --> pdb=" O VAL A 674 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N VAL A 676 " --> pdb=" O ARG A 822 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LEU A 824 " --> pdb=" O VAL A 676 " (cutoff:3.500A) removed outlier: 9.188A pdb=" N GLY A 678 " --> pdb=" O LEU A 824 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1349 through 1352 removed outlier: 3.625A pdb=" N VAL A1314 " --> pdb=" O PHE A1294 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N ILE A1312 " --> pdb=" O ASP A1296 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 1495 through 1498 removed outlier: 3.584A pdb=" N ARG A1495 " --> pdb=" O LYS A1321 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL A1480 " --> pdb=" O VAL A1322 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N ILE A1324 " --> pdb=" O VAL A1480 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N THR A1482 " --> pdb=" O ILE A1324 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 650 through 652 removed outlier: 6.393A pdb=" N THR A 652 " --> pdb=" O LYS A 697 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N LYS A 697 " --> pdb=" O THR A 652 " (cutoff:3.500A) 511 hydrogen bonds defined for protein. 1455 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: 3.02 Time building geometry restraints manager: 4.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 1820 1.34 - 1.46: 2296 1.46 - 1.58: 5689 1.58 - 1.70: 8 1.70 - 1.82: 79 Bond restraints: 9892 Sorted by residual: bond pdb=" C4 ATP A1601 " pdb=" C5 ATP A1601 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.91e+01 bond pdb=" C5 ATP A1601 " pdb=" C6 ATP A1601 " ideal model delta sigma weight residual 1.409 1.477 -0.068 1.00e-02 1.00e+04 4.61e+01 bond pdb=" C8 ATP A1601 " pdb=" N7 ATP A1601 " ideal model delta sigma weight residual 1.310 1.356 -0.046 1.00e-02 1.00e+04 2.12e+01 bond pdb=" N VAL A 668 " pdb=" CA VAL A 668 " ideal model delta sigma weight residual 1.456 1.496 -0.040 8.70e-03 1.32e+04 2.11e+01 bond pdb=" N VAL A 711 " pdb=" CA VAL A 711 " ideal model delta sigma weight residual 1.456 1.494 -0.038 8.60e-03 1.35e+04 1.96e+01 ... (remaining 9887 not shown) Histogram of bond angle deviations from ideal: 99.76 - 107.04: 309 107.04 - 114.33: 5690 114.33 - 121.62: 4569 121.62 - 128.90: 2813 128.90 - 136.19: 69 Bond angle restraints: 13450 Sorted by residual: angle pdb=" C5 ATP A1601 " pdb=" C4 ATP A1601 " pdb=" N3 ATP A1601 " ideal model delta sigma weight residual 126.80 118.75 8.05 1.00e+00 1.00e+00 6.48e+01 angle pdb=" PB ATP A1601 " pdb=" O3B ATP A1601 " pdb=" PG ATP A1601 " ideal model delta sigma weight residual 139.87 131.94 7.93 1.00e+00 1.00e+00 6.30e+01 angle pdb=" PA ATP A1601 " pdb=" O3A ATP A1601 " pdb=" PB ATP A1601 " ideal model delta sigma weight residual 136.83 129.85 6.98 1.00e+00 1.00e+00 4.87e+01 angle pdb=" N3 ATP A1601 " pdb=" C4 ATP A1601 " pdb=" N9 ATP A1601 " ideal model delta sigma weight residual 127.04 134.79 -7.75 1.15e+00 7.59e-01 4.56e+01 angle pdb=" CA GLY A 762 " pdb=" C GLY A 762 " pdb=" O GLY A 762 " ideal model delta sigma weight residual 122.23 117.85 4.38 6.90e-01 2.10e+00 4.03e+01 ... (remaining 13445 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.50: 5487 21.50 - 43.01: 343 43.01 - 64.51: 41 64.51 - 86.02: 5 86.02 - 107.52: 2 Dihedral angle restraints: 5878 sinusoidal: 2351 harmonic: 3527 Sorted by residual: dihedral pdb=" O1B ADP A1602 " pdb=" O3A ADP A1602 " pdb=" PB ADP A1602 " pdb=" PA ADP A1602 " ideal model delta sinusoidal sigma weight residual -60.00 -167.52 107.52 1 2.00e+01 2.50e-03 3.12e+01 dihedral pdb=" C5' ADP A1602 " pdb=" O5' ADP A1602 " pdb=" PA ADP A1602 " pdb=" O2A ADP A1602 " ideal model delta sinusoidal sigma weight residual -60.00 -163.32 103.32 1 2.00e+01 2.50e-03 2.95e+01 dihedral pdb=" CA ASN A 575 " pdb=" C ASN A 575 " pdb=" N ILE A 576 " pdb=" CA ILE A 576 " ideal model delta harmonic sigma weight residual -180.00 -157.68 -22.32 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 5875 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 559 0.045 - 0.090: 515 0.090 - 0.134: 365 0.134 - 0.179: 114 0.179 - 0.224: 21 Chirality restraints: 1574 Sorted by residual: chirality pdb=" CA ILE A1483 " pdb=" N ILE A1483 " pdb=" C ILE A1483 " pdb=" CB ILE A1483 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA PRO A1119 " pdb=" N PRO A1119 " pdb=" C PRO A1119 " pdb=" CB PRO A1119 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA VAL A1451 " pdb=" N VAL A1451 " pdb=" C VAL A1451 " pdb=" CB VAL A1451 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 1571 not shown) Planarity restraints: 1654 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 869 " -0.021 2.00e-02 2.50e+03 1.11e-02 2.47e+00 pdb=" CG TYR A 869 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR A 869 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR A 869 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR A 869 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 869 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 869 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 869 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1481 " 0.006 2.00e-02 2.50e+03 1.27e-02 1.62e+00 pdb=" C LEU A1481 " -0.022 2.00e-02 2.50e+03 pdb=" O LEU A1481 " 0.008 2.00e-02 2.50e+03 pdb=" N THR A1482 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A1277 " -0.006 2.00e-02 2.50e+03 1.26e-02 1.59e+00 pdb=" C ILE A1277 " 0.022 2.00e-02 2.50e+03 pdb=" O ILE A1277 " -0.008 2.00e-02 2.50e+03 pdb=" N GLN A1278 " -0.008 2.00e-02 2.50e+03 ... (remaining 1651 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 10 2.47 - 3.08: 5542 3.08 - 3.68: 14797 3.68 - 4.29: 19660 4.29 - 4.90: 35723 Nonbonded interactions: 75732 Sorted by model distance: nonbonded pdb=" OG SER A1333 " pdb="MG MG A1604 " model vdw 1.861 2.170 nonbonded pdb=" OG SER A 685 " pdb="MG MG A1603 " model vdw 1.863 2.170 nonbonded pdb=" O1G ATP A1601 " pdb="MG MG A1603 " model vdw 1.912 2.170 nonbonded pdb=" O2B ADP A1602 " pdb="MG MG A1604 " model vdw 1.982 2.170 nonbonded pdb=" O1B ATP A1601 " pdb="MG MG A1603 " model vdw 2.028 2.170 ... (remaining 75727 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.520 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: 0.020 Extract box with map and model: 7.470 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 29.030 Find NCS groups from input model: 0.250 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6357 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 : 0.014 0.077 9892 Z= 0.904 Angle : 1.845 8.902 13450 Z= 1.415 Chirality : 0.083 0.224 1574 Planarity : 0.003 0.013 1654 Dihedral : 13.824 107.522 3596 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % 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: -2.56 (0.19), residues: 1202 helix: -1.20 (0.16), residues: 716 sheet: -1.37 (0.52), residues: 76 loop : -2.44 (0.25), residues: 410 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 1.122 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.2817 time to fit residues: 71.0798 Evaluate side-chains 118 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 1.323 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 109 optimal weight: 0.6980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 ASN A 725 ASN A1356 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6335 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9892 Z= 0.230 Angle : 0.572 7.122 13450 Z= 0.292 Chirality : 0.039 0.177 1574 Planarity : 0.004 0.036 1654 Dihedral : 7.076 97.342 1342 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.42 % Allowed : 8.35 % Favored : 90.23 % 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: 0.22 (0.23), residues: 1202 helix: 1.22 (0.18), residues: 739 sheet: -0.84 (0.55), residues: 76 loop : -1.76 (0.28), residues: 387 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 121 time to evaluate : 1.095 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 129 average time/residue: 0.2147 time to fit residues: 40.2707 Evaluate side-chains 118 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 109 time to evaluate : 1.003 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0963 time to fit residues: 3.2827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN A 412 ASN ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 GLN A 662 HIS A1010 HIS A1138 GLN A1356 ASN A1485 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6377 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 9892 Z= 0.383 Angle : 0.632 7.423 13450 Z= 0.321 Chirality : 0.043 0.177 1574 Planarity : 0.005 0.046 1654 Dihedral : 7.180 90.831 1342 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.80 % Allowed : 11.39 % Favored : 86.81 % 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: 0.45 (0.24), residues: 1202 helix: 1.34 (0.19), residues: 740 sheet: -0.17 (0.66), residues: 55 loop : -1.61 (0.28), residues: 407 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 113 time to evaluate : 2.204 Fit side-chains outliers start: 19 outliers final: 12 residues processed: 128 average time/residue: 0.3120 time to fit residues: 56.4817 Evaluate side-chains 114 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 102 time to evaluate : 1.044 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1469 time to fit residues: 4.3987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 73 optimal weight: 0.5980 chunk 110 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 GLN ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6362 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9892 Z= 0.289 Angle : 0.570 7.724 13450 Z= 0.285 Chirality : 0.040 0.159 1574 Planarity : 0.004 0.045 1654 Dihedral : 6.931 87.586 1342 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.95 % Allowed : 13.85 % Favored : 85.20 % 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: 0.68 (0.24), residues: 1202 helix: 1.52 (0.19), residues: 742 sheet: -0.07 (0.67), residues: 55 loop : -1.52 (0.28), residues: 405 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 105 time to evaluate : 1.073 Fit side-chains outliers start: 10 outliers final: 3 residues processed: 112 average time/residue: 0.2560 time to fit residues: 40.0354 Evaluate side-chains 105 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 102 time to evaluate : 1.099 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1048 time to fit residues: 2.0348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 39 optimal weight: 0.0770 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 590 ASN A 662 HIS A1176 GLN A1356 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6327 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9892 Z= 0.167 Angle : 0.494 7.008 13450 Z= 0.247 Chirality : 0.038 0.148 1574 Planarity : 0.004 0.043 1654 Dihedral : 6.568 79.221 1342 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.57 % Allowed : 15.84 % Favored : 83.59 % 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: 1.04 (0.25), residues: 1202 helix: 1.81 (0.19), residues: 760 sheet: -0.55 (0.57), residues: 76 loop : -1.48 (0.30), residues: 366 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 115 time to evaluate : 1.127 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 119 average time/residue: 0.2271 time to fit residues: 38.6928 Evaluate side-chains 103 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 102 time to evaluate : 1.128 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1347 time to fit residues: 1.7991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 117 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 chunk 9 optimal weight: 0.3980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 112 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6330 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9892 Z= 0.181 Angle : 0.505 6.790 13450 Z= 0.250 Chirality : 0.038 0.151 1574 Planarity : 0.004 0.057 1654 Dihedral : 6.386 77.717 1342 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.23 % Allowed : 15.84 % Favored : 82.92 % 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: 1.14 (0.25), residues: 1202 helix: 1.89 (0.19), residues: 758 sheet: -0.53 (0.61), residues: 66 loop : -1.40 (0.30), residues: 378 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 109 time to evaluate : 1.166 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 117 average time/residue: 0.2205 time to fit residues: 37.3135 Evaluate side-chains 113 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 104 time to evaluate : 1.106 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1000 time to fit residues: 3.1814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 98 optimal weight: 0.0970 chunk 65 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6339 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9892 Z= 0.208 Angle : 0.521 6.672 13450 Z= 0.259 Chirality : 0.038 0.159 1574 Planarity : 0.004 0.063 1654 Dihedral : 6.259 76.983 1342 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.76 % Allowed : 17.08 % Favored : 82.16 % 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: 1.13 (0.24), residues: 1202 helix: 1.86 (0.19), residues: 755 sheet: -0.43 (0.62), residues: 66 loop : -1.34 (0.30), residues: 381 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 110 time to evaluate : 1.092 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 115 average time/residue: 0.2297 time to fit residues: 37.8604 Evaluate side-chains 109 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 106 time to evaluate : 1.129 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1022 time to fit residues: 2.0998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 74 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 106 optimal weight: 0.2980 chunk 111 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 108 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6330 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9892 Z= 0.183 Angle : 0.516 7.859 13450 Z= 0.256 Chirality : 0.038 0.151 1574 Planarity : 0.004 0.063 1654 Dihedral : 6.061 75.880 1342 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.66 % Allowed : 17.65 % Favored : 81.69 % 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: 1.23 (0.25), residues: 1202 helix: 1.92 (0.19), residues: 761 sheet: -0.38 (0.61), residues: 66 loop : -1.33 (0.30), residues: 375 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 109 time to evaluate : 1.043 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 111 average time/residue: 0.2056 time to fit residues: 33.7609 Evaluate side-chains 110 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 107 time to evaluate : 0.988 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1106 time to fit residues: 2.0334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 33 optimal weight: 0.0060 chunk 98 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 108 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 114 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1515 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6322 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9892 Z= 0.169 Angle : 0.504 7.711 13450 Z= 0.251 Chirality : 0.037 0.168 1574 Planarity : 0.004 0.064 1654 Dihedral : 5.882 74.521 1342 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.19 % Allowed : 18.03 % Favored : 81.78 % 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: 1.32 (0.25), residues: 1202 helix: 1.97 (0.19), residues: 762 sheet: -0.27 (0.61), residues: 66 loop : -1.26 (0.30), residues: 374 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 112 time to evaluate : 1.187 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 113 average time/residue: 0.2102 time to fit residues: 35.1701 Evaluate side-chains 112 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 111 time to evaluate : 1.181 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0935 time to fit residues: 1.7345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 120 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 95 optimal weight: 0.4980 chunk 9 optimal weight: 0.6980 chunk 74 optimal weight: 0.0010 chunk 58 optimal weight: 1.9990 chunk 76 optimal weight: 0.0370 chunk 102 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.3664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1515 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6297 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9892 Z= 0.141 Angle : 0.488 7.350 13450 Z= 0.243 Chirality : 0.037 0.137 1574 Planarity : 0.004 0.063 1654 Dihedral : 5.674 71.225 1342 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.00 % Allowed : 18.60 % Favored : 81.40 % 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: 1.66 (0.25), residues: 1202 helix: 2.25 (0.19), residues: 753 sheet: 0.26 (0.62), residues: 66 loop : -1.16 (0.30), residues: 383 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 1.034 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.2341 time to fit residues: 38.6044 Evaluate side-chains 109 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 1.037 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 98 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 84 optimal weight: 0.0570 chunk 5 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1515 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.122266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.100585 restraints weight = 12738.019| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.49 r_work: 0.2974 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9892 Z= 0.183 Angle : 0.505 7.980 13450 Z= 0.252 Chirality : 0.037 0.150 1574 Planarity : 0.004 0.063 1654 Dihedral : 5.702 72.217 1342 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.19 % Allowed : 18.50 % Favored : 81.31 % 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: 1.50 (0.24), residues: 1202 helix: 2.10 (0.19), residues: 760 sheet: 0.01 (0.60), residues: 66 loop : -1.17 (0.30), residues: 376 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2210.05 seconds wall clock time: 41 minutes 5.85 seconds (2465.85 seconds total)