Starting phenix.real_space_refine on Thu Mar 14 20:24:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uy0_20945/03_2024/6uy0_20945_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uy0_20945/03_2024/6uy0_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_20945/03_2024/6uy0_20945.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uy0_20945/03_2024/6uy0_20945.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uy0_20945/03_2024/6uy0_20945_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uy0_20945/03_2024/6uy0_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 5.66, per 1000 atoms: 0.58 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: 3.76 Conformation dependent library (CDL) restraints added in 1.7 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: 2.55 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: 3.25 Time building geometry restraints manager: 4.11 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: 5670 21.50 - 43.01: 357 43.01 - 64.51: 43 64.51 - 86.02: 5 86.02 - 107.52: 2 Dihedral angle restraints: 6077 sinusoidal: 2550 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 6074 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: 1.890 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: 0.000 Extract box with map and model: 7.400 Check model and map are aligned: 0.140 Set scattering table: 0.110 Process input model: 28.870 Find NCS groups from input model: 0.270 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.690 ------------------------------------------------------------------------------- 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 : 13.733 107.522 3795 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 963 HIS 0.007 0.001 HIS A 382 PHE 0.018 0.002 PHE A1379 TYR 0.021 0.002 TYR A 869 ARG 0.005 0.001 ARG A 775 *********************** 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 : 1.249 Fit side-chains revert: symmetry clash REVERT: A 230 GLN cc_start: 0.7213 (tt0) cc_final: 0.6612 (tp40) REVERT: A 234 GLN cc_start: 0.6526 (mp10) cc_final: 0.6196 (pp30) REVERT: A 361 TRP cc_start: 0.7268 (p-90) cc_final: 0.6908 (p-90) REVERT: A 648 ASN cc_start: 0.7215 (t0) cc_final: 0.6837 (m-40) REVERT: A 670 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7509 (tp30) REVERT: A 679 GLN cc_start: 0.7154 (mm110) cc_final: 0.6709 (mm-40) REVERT: A 733 GLN cc_start: 0.5598 (mp10) cc_final: 0.5224 (mt0) REVERT: A 796 SER cc_start: 0.8245 (t) cc_final: 0.7885 (p) REVERT: A 835 MET cc_start: 0.7563 (mmt) cc_final: 0.7199 (mmt) REVERT: A 851 SER cc_start: 0.6608 (m) cc_final: 0.6387 (t) REVERT: A 864 GLU cc_start: 0.7789 (tt0) cc_final: 0.7488 (tp30) REVERT: A 966 MET cc_start: 0.7429 (mmm) cc_final: 0.7186 (mmt) REVERT: A 993 TYR cc_start: 0.6223 (t80) cc_final: 0.5467 (t80) REVERT: A 1057 ARG cc_start: 0.6949 (tpt-90) cc_final: 0.6686 (mmm160) REVERT: A 1088 GLN cc_start: 0.6431 (tt0) cc_final: 0.6191 (tt0) REVERT: A 1123 LEU cc_start: 0.6189 (tp) cc_final: 0.5941 (mp) REVERT: A 1280 MET cc_start: 0.6847 (mtm) cc_final: 0.6604 (mtm) REVERT: A 1375 ASP cc_start: 0.6861 (p0) cc_final: 0.6554 (p0) REVERT: A 1396 GLU cc_start: 0.7675 (mp0) cc_final: 0.6900 (pt0) REVERT: A 1417 LYS cc_start: 0.7543 (mptt) cc_final: 0.7158 (mmmt) REVERT: A 1465 ASP cc_start: 0.7282 (t70) cc_final: 0.7070 (t0) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.2509 time to fit residues: 63.2657 Evaluate side-chains 128 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.140 ------------------------------------------------------------------------------- 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: 0.9980 chunk 48 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 ASN A 662 HIS A 725 ASN A1010 HIS A1356 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6340 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9892 Z= 0.238 Angle : 0.572 7.137 13450 Z= 0.293 Chirality : 0.040 0.178 1574 Planarity : 0.004 0.036 1654 Dihedral : 7.683 96.933 1541 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.52 % Allowed : 7.40 % Favored : 91.08 % 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: 1.21 (0.18), residues: 741 sheet: -0.82 (0.55), residues: 76 loop : -1.77 (0.28), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 520 HIS 0.007 0.001 HIS A 382 PHE 0.012 0.001 PHE A 651 TYR 0.024 0.001 TYR A1032 ARG 0.004 0.000 ARG A1495 *********************** 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 143 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 127 time to evaluate : 1.096 Fit side-chains revert: symmetry clash REVERT: A 230 GLN cc_start: 0.6635 (tt0) cc_final: 0.6375 (tp40) REVERT: A 338 MET cc_start: 0.6479 (mmp) cc_final: 0.6277 (mmp) REVERT: A 568 TYR cc_start: 0.5877 (m-80) cc_final: 0.5342 (m-80) REVERT: A 623 GLU cc_start: 0.7731 (mm-30) cc_final: 0.6859 (tt0) REVERT: A 648 ASN cc_start: 0.7223 (t0) cc_final: 0.6668 (t0) REVERT: A 742 GLU cc_start: 0.7081 (tm-30) cc_final: 0.6310 (pt0) REVERT: A 835 MET cc_start: 0.7517 (mmt) cc_final: 0.7036 (mmt) REVERT: A 966 MET cc_start: 0.6973 (mmm) cc_final: 0.6673 (mmt) REVERT: A 1393 TYR cc_start: 0.6062 (OUTLIER) cc_final: 0.5324 (p90) REVERT: A 1417 LYS cc_start: 0.7582 (mptt) cc_final: 0.7262 (mmmt) outliers start: 16 outliers final: 10 residues processed: 136 average time/residue: 0.2155 time to fit residues: 42.0994 Evaluate side-chains 124 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 113 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1108 LEU Chi-restraints excluded: chain A residue 1393 TYR Chi-restraints excluded: chain A residue 1429 LEU 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: 1.9990 chunk 110 optimal weight: 5.9990 chunk 118 optimal weight: 7.9990 chunk 98 optimal weight: 0.9990 chunk 109 optimal weight: 0.0870 chunk 37 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 overall best weight: 1.6166 ------------------------------------------------------------------------------- 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 450 GLN ** A 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1138 GLN A1485 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6366 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9892 Z= 0.325 Angle : 0.579 7.428 13450 Z= 0.295 Chirality : 0.041 0.160 1574 Planarity : 0.004 0.043 1654 Dihedral : 7.529 92.088 1541 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.71 % Allowed : 10.91 % Favored : 87.38 % 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: 1.53 (0.19), residues: 748 sheet: -0.31 (0.60), residues: 65 loop : -1.60 (0.29), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 223 HIS 0.007 0.001 HIS A 382 PHE 0.011 0.002 PHE A 524 TYR 0.023 0.002 TYR A1032 ARG 0.004 0.000 ARG A1074 *********************** 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 134 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 116 time to evaluate : 1.137 Fit side-chains REVERT: A 230 GLN cc_start: 0.6569 (tt0) cc_final: 0.6299 (tp40) REVERT: A 249 THR cc_start: 0.5671 (m) cc_final: 0.5461 (p) REVERT: A 568 TYR cc_start: 0.6043 (m-80) cc_final: 0.5595 (m-80) REVERT: A 623 GLU cc_start: 0.7687 (mm-30) cc_final: 0.6876 (tt0) REVERT: A 648 ASN cc_start: 0.7274 (t0) cc_final: 0.6705 (t0) REVERT: A 738 LYS cc_start: 0.6896 (ttmt) cc_final: 0.5732 (pttp) REVERT: A 742 GLU cc_start: 0.7043 (tm-30) cc_final: 0.6226 (pt0) REVERT: A 835 MET cc_start: 0.7534 (mmt) cc_final: 0.7087 (mmt) REVERT: A 966 MET cc_start: 0.7070 (mmm) cc_final: 0.6763 (mmt) REVERT: A 1085 MET cc_start: 0.5860 (OUTLIER) cc_final: 0.5351 (mpp) REVERT: A 1278 GLN cc_start: 0.7756 (pp30) cc_final: 0.7393 (pp30) REVERT: A 1302 ARG cc_start: 0.6593 (mmm-85) cc_final: 0.6264 (mtp85) REVERT: A 1393 TYR cc_start: 0.5742 (OUTLIER) cc_final: 0.4926 (p90) REVERT: A 1417 LYS cc_start: 0.7568 (mptt) cc_final: 0.7194 (mmmt) outliers start: 18 outliers final: 11 residues processed: 129 average time/residue: 0.2427 time to fit residues: 43.8832 Evaluate side-chains 123 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 110 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1085 MET Chi-restraints excluded: chain A residue 1240 THR Chi-restraints excluded: chain A residue 1393 TYR Chi-restraints excluded: chain A residue 1429 LEU Chi-restraints excluded: chain A residue 1494 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 679 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6352 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9892 Z= 0.239 Angle : 0.534 7.262 13450 Z= 0.269 Chirality : 0.039 0.169 1574 Planarity : 0.004 0.044 1654 Dihedral : 7.211 88.779 1541 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.90 % Allowed : 11.48 % Favored : 86.62 % 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: 0.93 (0.24), residues: 1202 helix: 1.73 (0.19), residues: 748 sheet: -0.12 (0.61), residues: 65 loop : -1.51 (0.29), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1197 HIS 0.007 0.001 HIS A 382 PHE 0.011 0.001 PHE A 651 TYR 0.021 0.001 TYR A1032 ARG 0.003 0.000 ARG A 655 *********************** 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 131 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 111 time to evaluate : 1.067 Fit side-chains REVERT: A 230 GLN cc_start: 0.6565 (tt0) cc_final: 0.6292 (tp40) REVERT: A 249 THR cc_start: 0.5725 (m) cc_final: 0.5515 (p) REVERT: A 623 GLU cc_start: 0.7596 (mm-30) cc_final: 0.6759 (tt0) REVERT: A 648 ASN cc_start: 0.7264 (t0) cc_final: 0.6674 (t0) REVERT: A 738 LYS cc_start: 0.6883 (ttmt) cc_final: 0.5709 (pttp) REVERT: A 742 GLU cc_start: 0.7039 (tm-30) cc_final: 0.6236 (pt0) REVERT: A 824 LEU cc_start: 0.6787 (OUTLIER) cc_final: 0.6553 (pp) REVERT: A 835 MET cc_start: 0.7612 (mmt) cc_final: 0.7173 (mmt) REVERT: A 1278 GLN cc_start: 0.7786 (pp30) cc_final: 0.7477 (pp30) REVERT: A 1302 ARG cc_start: 0.6708 (mmm-85) cc_final: 0.6404 (mtp-110) REVERT: A 1393 TYR cc_start: 0.5714 (OUTLIER) cc_final: 0.4801 (p90) REVERT: A 1417 LYS cc_start: 0.7547 (mptt) cc_final: 0.7270 (mmmt) outliers start: 20 outliers final: 16 residues processed: 124 average time/residue: 0.2147 time to fit residues: 38.2571 Evaluate side-chains 124 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 106 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 679 GLN Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1357 ILE Chi-restraints excluded: chain A residue 1393 TYR Chi-restraints excluded: chain A residue 1429 LEU Chi-restraints excluded: chain A residue 1481 LEU Chi-restraints excluded: chain A residue 1494 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 87 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 99 optimal weight: 7.9990 chunk 80 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 590 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6340 moved from start: 0.2590 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= 0.190 Angle : 0.506 7.187 13450 Z= 0.254 Chirality : 0.038 0.162 1574 Planarity : 0.004 0.043 1654 Dihedral : 6.977 84.783 1541 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.18 % Allowed : 12.62 % 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: 1.12 (0.24), residues: 1202 helix: 1.89 (0.19), residues: 755 sheet: -0.53 (0.56), residues: 76 loop : -1.43 (0.30), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1197 HIS 0.007 0.001 HIS A 382 PHE 0.011 0.001 PHE A 651 TYR 0.021 0.001 TYR A1032 ARG 0.002 0.000 ARG A 655 *********************** 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 134 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 111 time to evaluate : 1.002 Fit side-chains revert: symmetry clash REVERT: A 230 GLN cc_start: 0.6543 (tt0) cc_final: 0.6258 (tp40) REVERT: A 623 GLU cc_start: 0.7583 (mm-30) cc_final: 0.6754 (tt0) REVERT: A 648 ASN cc_start: 0.7232 (t0) cc_final: 0.6613 (t0) REVERT: A 738 LYS cc_start: 0.6872 (ttmt) cc_final: 0.5691 (pttp) REVERT: A 742 GLU cc_start: 0.7061 (tm-30) cc_final: 0.6279 (pt0) REVERT: A 824 LEU cc_start: 0.6802 (OUTLIER) cc_final: 0.6576 (pp) REVERT: A 835 MET cc_start: 0.7603 (mmt) cc_final: 0.7192 (mmt) REVERT: A 836 ASP cc_start: 0.6917 (m-30) cc_final: 0.6574 (t0) REVERT: A 966 MET cc_start: 0.7223 (mmm) cc_final: 0.6944 (mmt) REVERT: A 1070 ASN cc_start: 0.7598 (OUTLIER) cc_final: 0.7210 (m-40) REVERT: A 1393 TYR cc_start: 0.5695 (OUTLIER) cc_final: 0.4769 (p90) REVERT: A 1417 LYS cc_start: 0.7585 (mptt) cc_final: 0.7303 (mmmt) REVERT: A 1465 ASP cc_start: 0.7113 (t0) cc_final: 0.6400 (m-30) outliers start: 23 outliers final: 17 residues processed: 127 average time/residue: 0.2135 time to fit residues: 39.0496 Evaluate side-chains 126 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 106 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 679 GLN Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1070 ASN Chi-restraints excluded: chain A residue 1106 ILE Chi-restraints excluded: chain A residue 1240 THR Chi-restraints excluded: chain A residue 1357 ILE Chi-restraints excluded: chain A residue 1393 TYR Chi-restraints excluded: chain A residue 1429 LEU Chi-restraints excluded: chain A residue 1481 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 0.0570 chunk 23 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 117 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 9 optimal weight: 0.0470 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- 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 662 HIS A1176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6320 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9892 Z= 0.160 Angle : 0.480 6.927 13450 Z= 0.241 Chirality : 0.037 0.149 1574 Planarity : 0.004 0.054 1654 Dihedral : 6.635 74.486 1541 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.80 % Allowed : 13.57 % Favored : 84.63 % 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: 1.40 (0.25), residues: 1202 helix: 2.10 (0.19), residues: 754 sheet: -0.40 (0.57), residues: 76 loop : -1.29 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1197 HIS 0.006 0.001 HIS A 382 PHE 0.016 0.001 PHE A1216 TYR 0.021 0.001 TYR A1032 ARG 0.002 0.000 ARG A 655 *********************** 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 136 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 117 time to evaluate : 1.074 Fit side-chains revert: symmetry clash REVERT: A 230 GLN cc_start: 0.6517 (tt0) cc_final: 0.6227 (tp40) REVERT: A 623 GLU cc_start: 0.7583 (mm-30) cc_final: 0.6781 (tt0) REVERT: A 648 ASN cc_start: 0.7177 (t0) cc_final: 0.6541 (t0) REVERT: A 738 LYS cc_start: 0.6867 (ttmt) cc_final: 0.5669 (pttp) REVERT: A 742 GLU cc_start: 0.7065 (tm-30) cc_final: 0.6293 (pt0) REVERT: A 824 LEU cc_start: 0.6706 (OUTLIER) cc_final: 0.6500 (pp) REVERT: A 835 MET cc_start: 0.7538 (mmt) cc_final: 0.7141 (mmt) REVERT: A 836 ASP cc_start: 0.6979 (m-30) cc_final: 0.6629 (t0) REVERT: A 1393 TYR cc_start: 0.5747 (OUTLIER) cc_final: 0.4833 (p90) REVERT: A 1417 LYS cc_start: 0.7549 (mptt) cc_final: 0.7294 (mmmm) outliers start: 19 outliers final: 15 residues processed: 131 average time/residue: 0.1948 time to fit residues: 37.3105 Evaluate side-chains 129 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 112 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1240 THR Chi-restraints excluded: chain A residue 1278 GLN Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain A residue 1357 ILE Chi-restraints excluded: chain A residue 1393 TYR Chi-restraints excluded: chain A residue 1429 LEU Chi-restraints excluded: chain A residue 1481 LEU 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: 2.9990 chunk 98 optimal weight: 0.1980 chunk 65 optimal weight: 0.8980 chunk 116 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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: 0.2819 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= 0.218 Angle : 0.512 6.706 13450 Z= 0.258 Chirality : 0.038 0.158 1574 Planarity : 0.004 0.062 1654 Dihedral : 6.669 70.421 1541 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.28 % Allowed : 14.14 % 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: 1.26 (0.24), residues: 1202 helix: 1.94 (0.19), residues: 761 sheet: -0.27 (0.62), residues: 66 loop : -1.33 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1197 HIS 0.006 0.001 HIS A 382 PHE 0.010 0.001 PHE A 651 TYR 0.021 0.001 TYR A1032 ARG 0.002 0.000 ARG A1074 *********************** 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 134 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 110 time to evaluate : 1.060 Fit side-chains REVERT: A 230 GLN cc_start: 0.6416 (tt0) cc_final: 0.6130 (tp40) REVERT: A 623 GLU cc_start: 0.7572 (mm-30) cc_final: 0.6760 (tt0) REVERT: A 648 ASN cc_start: 0.7183 (t0) cc_final: 0.6549 (t0) REVERT: A 738 LYS cc_start: 0.6880 (ttmt) cc_final: 0.5706 (pttp) REVERT: A 742 GLU cc_start: 0.7072 (tm-30) cc_final: 0.6311 (pt0) REVERT: A 835 MET cc_start: 0.7546 (mmt) cc_final: 0.7174 (mmt) REVERT: A 836 ASP cc_start: 0.7007 (m-30) cc_final: 0.6629 (t0) REVERT: A 1070 ASN cc_start: 0.7579 (OUTLIER) cc_final: 0.7215 (m-40) REVERT: A 1393 TYR cc_start: 0.5684 (OUTLIER) cc_final: 0.4698 (p90) REVERT: A 1417 LYS cc_start: 0.7491 (mptt) cc_final: 0.7265 (mmmm) outliers start: 24 outliers final: 20 residues processed: 129 average time/residue: 0.2084 time to fit residues: 38.8321 Evaluate side-chains 129 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 107 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 CYS Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 643 SER Chi-restraints excluded: chain A residue 679 GLN Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1070 ASN Chi-restraints excluded: chain A residue 1240 THR Chi-restraints excluded: chain A residue 1278 GLN Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain A residue 1357 ILE Chi-restraints excluded: chain A residue 1393 TYR Chi-restraints excluded: chain A residue 1429 LEU Chi-restraints excluded: chain A residue 1481 LEU Chi-restraints excluded: chain A residue 1494 THR 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: 2.9990 chunk 74 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 106 optimal weight: 0.8980 chunk 111 optimal weight: 0.6980 chunk 101 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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: 0.6335 moved from start: 0.2904 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= 0.201 Angle : 0.506 7.208 13450 Z= 0.254 Chirality : 0.038 0.151 1574 Planarity : 0.004 0.064 1654 Dihedral : 6.554 68.130 1541 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.37 % Allowed : 14.61 % Favored : 83.02 % 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: 1.31 (0.24), residues: 1202 helix: 1.97 (0.19), residues: 761 sheet: -0.25 (0.58), residues: 76 loop : -1.29 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1197 HIS 0.006 0.001 HIS A 382 PHE 0.015 0.001 PHE A1216 TYR 0.021 0.001 TYR A1032 ARG 0.004 0.000 ARG A 655 *********************** 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 134 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 109 time to evaluate : 1.229 Fit side-chains REVERT: A 230 GLN cc_start: 0.6258 (tt0) cc_final: 0.5965 (tp40) REVERT: A 623 GLU cc_start: 0.7552 (mm-30) cc_final: 0.6816 (tt0) REVERT: A 648 ASN cc_start: 0.7208 (t0) cc_final: 0.6567 (t0) REVERT: A 738 LYS cc_start: 0.6877 (ttmt) cc_final: 0.5704 (pttp) REVERT: A 742 GLU cc_start: 0.7063 (tm-30) cc_final: 0.6265 (pt0) REVERT: A 835 MET cc_start: 0.7582 (mmt) cc_final: 0.7270 (mmt) REVERT: A 836 ASP cc_start: 0.7043 (m-30) cc_final: 0.6652 (t0) REVERT: A 1070 ASN cc_start: 0.7557 (OUTLIER) cc_final: 0.7186 (m-40) REVERT: A 1302 ARG cc_start: 0.6402 (mmm160) cc_final: 0.6096 (mtm180) REVERT: A 1315 THR cc_start: 0.8599 (OUTLIER) cc_final: 0.8385 (t) REVERT: A 1393 TYR cc_start: 0.5686 (OUTLIER) cc_final: 0.4713 (p90) REVERT: A 1417 LYS cc_start: 0.7507 (mptt) cc_final: 0.7280 (mmmm) outliers start: 25 outliers final: 21 residues processed: 129 average time/residue: 0.2170 time to fit residues: 40.1978 Evaluate side-chains 129 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 105 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 CYS Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 476 MET Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 643 SER Chi-restraints excluded: chain A residue 679 GLN Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1070 ASN Chi-restraints excluded: chain A residue 1106 ILE Chi-restraints excluded: chain A residue 1240 THR Chi-restraints excluded: chain A residue 1278 GLN Chi-restraints excluded: chain A residue 1315 THR Chi-restraints excluded: chain A residue 1357 ILE Chi-restraints excluded: chain A residue 1393 TYR Chi-restraints excluded: chain A residue 1429 LEU Chi-restraints excluded: chain A residue 1481 LEU Chi-restraints excluded: chain A residue 1494 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 33 optimal weight: 0.0040 chunk 98 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.7994 ------------------------------------------------------------------------------- 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 679 GLN A1515 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6330 moved from start: 0.2979 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= 0.190 Angle : 0.502 6.944 13450 Z= 0.252 Chirality : 0.038 0.151 1574 Planarity : 0.004 0.065 1654 Dihedral : 6.486 67.358 1541 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.28 % Allowed : 15.18 % Favored : 82.54 % 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: 1.34 (0.24), residues: 1202 helix: 1.99 (0.19), residues: 759 sheet: -0.17 (0.61), residues: 66 loop : -1.24 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1245 HIS 0.006 0.001 HIS A 382 PHE 0.010 0.001 PHE A 651 TYR 0.021 0.001 TYR A1032 ARG 0.005 0.000 ARG A 655 *********************** 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 133 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 109 time to evaluate : 1.097 Fit side-chains revert: symmetry clash REVERT: A 230 GLN cc_start: 0.6256 (tt0) cc_final: 0.5963 (tp40) REVERT: A 623 GLU cc_start: 0.7542 (mm-30) cc_final: 0.6813 (tt0) REVERT: A 648 ASN cc_start: 0.7213 (t0) cc_final: 0.6565 (t0) REVERT: A 738 LYS cc_start: 0.6876 (ttmt) cc_final: 0.5705 (pttp) REVERT: A 742 GLU cc_start: 0.7064 (tm-30) cc_final: 0.6266 (pt0) REVERT: A 835 MET cc_start: 0.7568 (mmt) cc_final: 0.7226 (mmt) REVERT: A 836 ASP cc_start: 0.7023 (m-30) cc_final: 0.6640 (t0) REVERT: A 1070 ASN cc_start: 0.7482 (OUTLIER) cc_final: 0.7133 (m-40) REVERT: A 1393 TYR cc_start: 0.5679 (OUTLIER) cc_final: 0.4708 (p90) REVERT: A 1417 LYS cc_start: 0.7505 (mptt) cc_final: 0.7271 (mmmm) outliers start: 24 outliers final: 21 residues processed: 128 average time/residue: 0.2101 time to fit residues: 38.5370 Evaluate side-chains 130 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 107 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 476 MET Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 643 SER Chi-restraints excluded: chain A residue 679 GLN Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1070 ASN Chi-restraints excluded: chain A residue 1106 ILE Chi-restraints excluded: chain A residue 1240 THR Chi-restraints excluded: chain A residue 1278 GLN Chi-restraints excluded: chain A residue 1357 ILE Chi-restraints excluded: chain A residue 1393 TYR Chi-restraints excluded: chain A residue 1429 LEU Chi-restraints excluded: chain A residue 1481 LEU 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: 0.9990 chunk 120 optimal weight: 0.1980 chunk 110 optimal weight: 4.9990 chunk 95 optimal weight: 0.4980 chunk 9 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.6326 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9892 Z= 0.176 Angle : 0.495 6.060 13450 Z= 0.249 Chirality : 0.038 0.150 1574 Planarity : 0.004 0.064 1654 Dihedral : 6.471 66.695 1541 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.28 % Allowed : 14.99 % Favored : 82.73 % 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: 1.40 (0.24), residues: 1202 helix: 2.03 (0.19), residues: 759 sheet: -0.15 (0.61), residues: 66 loop : -1.22 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1197 HIS 0.006 0.001 HIS A 382 PHE 0.014 0.001 PHE A1216 TYR 0.021 0.001 TYR A1032 ARG 0.005 0.000 ARG A 655 ********************** 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 131 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 107 time to evaluate : 1.103 Fit side-chains revert: symmetry clash REVERT: A 230 GLN cc_start: 0.6253 (tt0) cc_final: 0.5959 (tp40) REVERT: A 623 GLU cc_start: 0.7540 (mm-30) cc_final: 0.6811 (tt0) REVERT: A 648 ASN cc_start: 0.7205 (t0) cc_final: 0.6550 (t0) REVERT: A 738 LYS cc_start: 0.6873 (ttmt) cc_final: 0.5702 (pttp) REVERT: A 742 GLU cc_start: 0.7061 (tm-30) cc_final: 0.6276 (pt0) REVERT: A 835 MET cc_start: 0.7583 (mmt) cc_final: 0.7303 (mmt) REVERT: A 836 ASP cc_start: 0.7022 (m-30) cc_final: 0.6643 (t0) REVERT: A 1315 THR cc_start: 0.8633 (OUTLIER) cc_final: 0.8417 (t) REVERT: A 1375 ASP cc_start: 0.6664 (p0) cc_final: 0.6433 (t0) REVERT: A 1393 TYR cc_start: 0.5721 (OUTLIER) cc_final: 0.4748 (p90) REVERT: A 1417 LYS cc_start: 0.7505 (mptt) cc_final: 0.7266 (mmmm) outliers start: 24 outliers final: 21 residues processed: 126 average time/residue: 0.2148 time to fit residues: 39.1789 Evaluate side-chains 129 residues out of total 1054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 106 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 476 MET Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 643 SER Chi-restraints excluded: chain A residue 679 GLN Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1106 ILE Chi-restraints excluded: chain A residue 1240 THR Chi-restraints excluded: chain A residue 1278 GLN Chi-restraints excluded: chain A residue 1315 THR Chi-restraints excluded: chain A residue 1357 ILE Chi-restraints excluded: chain A residue 1393 TYR Chi-restraints excluded: chain A residue 1429 LEU Chi-restraints excluded: chain A residue 1481 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 98 optimal weight: 0.0050 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 0.0770 chunk 84 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 69 optimal weight: 5.9990 overall best weight: 0.7354 ------------------------------------------------------------------------------- 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 = 0.3336 r_free = 0.3336 target = 0.121502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.100050 restraints weight = 12686.748| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.47 r_work: 0.2963 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9892 Z= 0.179 Angle : 0.494 5.950 13450 Z= 0.249 Chirality : 0.038 0.148 1574 Planarity : 0.004 0.064 1654 Dihedral : 6.430 65.305 1541 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.28 % Allowed : 15.28 % Favored : 82.45 % 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: 1.42 (0.24), residues: 1202 helix: 2.05 (0.19), residues: 753 sheet: -0.13 (0.61), residues: 66 loop : -1.18 (0.29), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1197 HIS 0.006 0.001 HIS A 382 PHE 0.010 0.001 PHE A 651 TYR 0.021 0.001 TYR A1032 ARG 0.005 0.000 ARG A 655 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2123.95 seconds wall clock time: 39 minutes 8.66 seconds (2348.66 seconds total)