Starting phenix.real_space_refine (version: 1.21rc1) on Wed Oct 4 03:23:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1k_33564/10_2023/7y1k_33564_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1k_33564/10_2023/7y1k_33564.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1k_33564/10_2023/7y1k_33564.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1k_33564/10_2023/7y1k_33564.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1k_33564/10_2023/7y1k_33564_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1k_33564/10_2023/7y1k_33564_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.068 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 38 5.16 5 C 5528 2.51 5 N 1413 2.21 5 O 1524 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 8510 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 8510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1169, 8510 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1, 'BJX': 1} Classifications: {'peptide': 1164, 'undetermined': 5} Incomplete info: {'truncation_to_alanine': 193} Link IDs: {'PTRANS': 34, 'TRANS': 1129, None: 5} Not linked: pdbres="MET A1542 " pdbres="ATP A1601 " Not linked: pdbres="ATP A1601 " pdbres=" MG A1602 " Not linked: pdbres=" MG A1602 " pdbres=" MG A1603 " Not linked: pdbres=" MG A1603 " pdbres="BJX A1604 " Not linked: pdbres="BJX A1604 " pdbres="ADP A1605 " Chain breaks: 6 Unresolved non-hydrogen bonds: 762 Unresolved non-hydrogen angles: 934 Unresolved non-hydrogen dihedrals: 634 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 6, 'TYR:plan': 3, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 26, 'PHE:plan': 8, 'GLU:plan': 33, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 489 Time building chain proxies: 4.82, per 1000 atoms: 0.57 Number of scatterers: 8510 At special positions: 0 Unit cell: (71.724, 100.08, 133.44, 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 38 16.00 P 5 15.00 Mg 2 11.99 O 1524 8.00 N 1413 7.00 C 5528 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: 3.84 Conformation dependent library (CDL) restraints added in 1.5 seconds 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2192 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 49 helices and 8 sheets defined 66.0% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.27 Creating SS restraints... Processing helix chain 'A' and resid 218 through 227 Processing helix chain 'A' and resid 229 through 240 removed outlier: 4.153A pdb=" N THR A 233 " --> pdb=" O TRP A 229 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LEU A 234 " --> pdb=" O TRP A 230 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N HIS A 239 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG A 240 " --> pdb=" O ILE A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 273 Processing helix chain 'A' and resid 285 through 324 removed outlier: 6.399A pdb=" N ARG A 295 " --> pdb=" O ARG A 291 " (cutoff:3.500A) Proline residue: A 296 - end of helix removed outlier: 3.822A pdb=" N ALA A 313 " --> pdb=" O LEU A 309 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLY A 314 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Proline residue: A 315 - end of helix Processing helix chain 'A' and resid 348 through 393 removed outlier: 3.700A pdb=" N THR A 373 " --> pdb=" O SER A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 415 removed outlier: 3.547A pdb=" N GLY A 408 " --> pdb=" O GLU A 404 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN A 409 " --> pdb=" O MET A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 426 Processing helix chain 'A' and resid 429 through 448 removed outlier: 5.253A pdb=" N MET A 434 " --> pdb=" O LEU A 431 " (cutoff:3.500A) Proline residue: A 435 - end of helix removed outlier: 3.544A pdb=" N VAL A 442 " --> pdb=" O ILE A 439 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR A 446 " --> pdb=" O ILE A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 496 removed outlier: 3.529A pdb=" N GLY A 456 " --> pdb=" O SER A 452 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 463 " --> pdb=" O VAL A 459 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA A 464 " --> pdb=" O ILE A 460 " (cutoff:3.500A) Proline residue: A 465 - end of helix removed outlier: 3.516A pdb=" N GLU A 487 " --> pdb=" O ASP A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 505 Processing helix chain 'A' and resid 508 through 558 removed outlier: 3.535A pdb=" N SER A 514 " --> pdb=" O ILE A 510 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL A 515 " --> pdb=" O PHE A 511 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR A 518 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS A 521 " --> pdb=" O GLU A 517 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THR A 528 " --> pdb=" O SER A 524 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE A 543 " --> pdb=" O MET A 539 " (cutoff:3.500A) Proline residue: A 544 - end of helix removed outlier: 3.566A pdb=" N VAL A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR A 557 " --> pdb=" O VAL A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 606 removed outlier: 3.682A pdb=" N HIS A 576 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N THR A 580 " --> pdb=" O HIS A 576 " (cutoff:3.500A) Proline residue: A 581 - end of helix removed outlier: 4.454A pdb=" N SER A 586 " --> pdb=" O LEU A 582 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N THR A 587 " --> pdb=" O PHE A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 714 removed outlier: 4.413A pdb=" N LEU A 711 " --> pdb=" O LYS A 707 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 714 " --> pdb=" O LEU A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 767 Processing helix chain 'A' and resid 774 through 783 Processing helix chain 'A' and resid 787 through 792 removed outlier: 3.521A pdb=" N ASP A 791 " --> pdb=" O GLN A 787 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU A 792 " --> pdb=" O PRO A 788 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 787 through 792' Processing helix chain 'A' and resid 796 through 798 No H-bonds generated for 'chain 'A' and resid 796 through 798' Processing helix chain 'A' and resid 810 through 823 removed outlier: 3.570A pdb=" N ARG A 815 " --> pdb=" O GLY A 811 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE A 816 " --> pdb=" O GLN A 812 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N CYS A 817 " --> pdb=" O ARG A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 837 removed outlier: 4.450A pdb=" N ALA A 837 " --> pdb=" O PRO A 834 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 834 through 837' Processing helix chain 'A' and resid 840 through 848 Processing helix chain 'A' and resid 853 through 858 removed outlier: 3.502A pdb=" N ASP A 857 " --> pdb=" O LYS A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 871 No H-bonds generated for 'chain 'A' and resid 869 through 871' Processing helix chain 'A' and resid 892 through 898 Processing helix chain 'A' and resid 900 through 911 Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 987 through 1017 removed outlier: 3.679A pdb=" N ALA A1012 " --> pdb=" O ASP A1008 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLU A1017 " --> pdb=" O THR A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1074 removed outlier: 3.940A pdb=" N VAL A1053 " --> pdb=" O THR A1049 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU A1054 " --> pdb=" O SER A1050 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR A1059 " --> pdb=" O TRP A1055 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A1064 " --> pdb=" O ALA A1060 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASN A1070 " --> pdb=" O HIS A1066 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1082 Processing helix chain 'A' and resid 1085 through 1093 removed outlier: 3.658A pdb=" N ARG A1091 " --> pdb=" O LEU A1087 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N PHE A1092 " --> pdb=" O ILE A1088 " (cutoff:3.500A) Processing helix chain 'A' and resid 1095 through 1101 Processing helix chain 'A' and resid 1103 through 1127 Processing helix chain 'A' and resid 1129 through 1175 removed outlier: 3.526A pdb=" N ALA A1136 " --> pdb=" O ILE A1133 " (cutoff:3.500A) Proline residue: A1137 - end of helix removed outlier: 3.751A pdb=" N TYR A1148 " --> pdb=" O ILE A1145 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N PHE A1149 " --> pdb=" O GLN A1146 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG A1150 " --> pdb=" O LYS A1147 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER A1153 " --> pdb=" O ARG A1150 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS A1154 " --> pdb=" O VAL A1151 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP A1155 " --> pdb=" O ALA A1152 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A1156 " --> pdb=" O SER A1153 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR A1163 " --> pdb=" O ASP A1160 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU A1165 " --> pdb=" O SER A1162 " (cutoff:3.500A) Proline residue: A1166 - end of helix Processing helix chain 'A' and resid 1178 through 1183 Processing helix chain 'A' and resid 1187 through 1236 removed outlier: 3.694A pdb=" N ALA A1204 " --> pdb=" O THR A1200 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU A1222 " --> pdb=" O ARG A1218 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N CYS A1225 " --> pdb=" O TYR A1221 " (cutoff:3.500A) Processing helix chain 'A' and resid 1241 through 1257 removed outlier: 3.630A pdb=" N LEU A1248 " --> pdb=" O VAL A1244 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR A1255 " --> pdb=" O ALA A1251 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN A1256 " --> pdb=" O LEU A1252 " (cutoff:3.500A) Processing helix chain 'A' and resid 1260 through 1284 removed outlier: 3.621A pdb=" N LEU A1265 " --> pdb=" O VAL A1261 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY A1273 " --> pdb=" O GLU A1269 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA A1274 " --> pdb=" O VAL A1270 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL A1275 " --> pdb=" O GLN A1271 " (cutoff:3.500A) Processing helix chain 'A' and resid 1295 through 1297 No H-bonds generated for 'chain 'A' and resid 1295 through 1297' Processing helix chain 'A' and resid 1302 through 1304 No H-bonds generated for 'chain 'A' and resid 1302 through 1304' Processing helix chain 'A' and resid 1350 through 1356 removed outlier: 3.723A pdb=" N PHE A1356 " --> pdb=" O SER A1352 " (cutoff:3.500A) Processing helix chain 'A' and resid 1378 through 1383 Processing helix chain 'A' and resid 1399 through 1403 Processing helix chain 'A' and resid 1411 through 1420 removed outlier: 3.541A pdb=" N TRP A1415 " --> pdb=" O ASP A1411 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU A1418 " --> pdb=" O LEU A1414 " (cutoff:3.500A) Processing helix chain 'A' and resid 1424 through 1429 removed outlier: 3.977A pdb=" N SER A1429 " --> pdb=" O ASN A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1440 through 1442 No H-bonds generated for 'chain 'A' and resid 1440 through 1442' Processing helix chain 'A' and resid 1447 through 1460 removed outlier: 3.587A pdb=" N LEU A1452 " --> pdb=" O GLY A1448 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N CYS A1454 " --> pdb=" O ARG A1450 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A1455 " --> pdb=" O GLN A1451 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL A1460 " --> pdb=" O ALA A1456 " (cutoff:3.500A) Processing helix chain 'A' and resid 1477 through 1490 removed outlier: 3.826A pdb=" N ILE A1482 " --> pdb=" O ALA A1478 " (cutoff:3.500A) Processing helix chain 'A' and resid 1503 through 1508 removed outlier: 4.246A pdb=" N ASP A1508 " --> pdb=" O SER A1505 " (cutoff:3.500A) Processing helix chain 'A' and resid 1526 through 1532 removed outlier: 3.526A pdb=" N LEU A1530 " --> pdb=" O GLY A1526 " (cutoff:3.500A) Processing helix chain 'A' and resid 1536 through 1541 Processing sheet with id= A, first strand: chain 'A' and resid 689 through 691 removed outlier: 3.576A pdb=" N THR A 671 " --> pdb=" O LYS A 724 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS A 724 " --> pdb=" O THR A 671 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 697 through 700 removed outlier: 5.856A pdb=" N TRP A 877 " --> pdb=" O MET A 698 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N VAL A 700 " --> pdb=" O TRP A 877 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ILE A 879 " --> pdb=" O VAL A 700 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N LYS A 882 " --> pdb=" O VAL A 886 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N VAL A 886 " --> pdb=" O LYS A 882 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 830 through 832 removed outlier: 6.155A pdb=" N VAL A 863 " --> pdb=" O LEU A 831 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 1308 through 1311 Processing sheet with id= E, first strand: chain 'A' and resid 1339 through 1342 removed outlier: 6.858A pdb=" N SER A1516 " --> pdb=" O LEU A1520 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N LEU A1520 " --> pdb=" O SER A1516 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1386 through 1388 removed outlier: 6.252A pdb=" N THR A1495 " --> pdb=" O LEU A1466 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N MET A1468 " --> pdb=" O THR A1495 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL A1497 " --> pdb=" O MET A1468 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 674 through 676 removed outlier: 3.722A pdb=" N TYR A 674 " --> pdb=" O GLU A 722 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU A 722 " --> pdb=" O TYR A 674 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N SER A 676 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N THR A 720 " --> pdb=" O SER A 676 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'A' and resid 1313 through 1315 removed outlier: 7.318A pdb=" N VAL A1315 " --> pdb=" O LYS A1326 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N LYS A1326 " --> pdb=" O VAL A1315 " (cutoff:3.500A) 504 hydrogen bonds defined for protein. 1371 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: 3.03 Time building geometry restraints manager: 4.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1317 1.31 - 1.43: 2306 1.43 - 1.56: 4988 1.56 - 1.69: 8 1.69 - 1.81: 59 Bond restraints: 8678 Sorted by residual: bond pdb=" C16 BJX A1604 " pdb=" N1 BJX A1604 " ideal model delta sigma weight residual 1.344 1.452 -0.108 2.00e-02 2.50e+03 2.93e+01 bond pdb=" C21 BJX A1604 " pdb=" O1 BJX A1604 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.16e+00 bond pdb=" N SER A1349 " pdb=" CA SER A1349 " ideal model delta sigma weight residual 1.458 1.484 -0.026 1.28e-02 6.10e+03 4.29e+00 bond pdb=" N ALA A 558 " pdb=" CA ALA A 558 " ideal model delta sigma weight residual 1.459 1.434 0.025 1.28e-02 6.10e+03 3.73e+00 bond pdb=" CA ALA A 558 " pdb=" C ALA A 558 " ideal model delta sigma weight residual 1.523 1.497 0.025 1.35e-02 5.49e+03 3.56e+00 ... (remaining 8673 not shown) Histogram of bond angle deviations from ideal: 99.93 - 107.87: 304 107.87 - 115.81: 5491 115.81 - 123.75: 5904 123.75 - 131.69: 160 131.69 - 139.63: 25 Bond angle restraints: 11884 Sorted by residual: angle pdb=" N MET A1284 " pdb=" CA MET A1284 " pdb=" C MET A1284 " ideal model delta sigma weight residual 111.07 120.80 -9.73 1.07e+00 8.73e-01 8.28e+01 angle pdb=" N LYS A1348 " pdb=" CA LYS A1348 " pdb=" C LYS A1348 " ideal model delta sigma weight residual 111.14 119.97 -8.83 1.08e+00 8.57e-01 6.69e+01 angle pdb=" N GLU A1285 " pdb=" CA GLU A1285 " pdb=" C GLU A1285 " ideal model delta sigma weight residual 108.42 116.14 -7.72 1.54e+00 4.22e-01 2.51e+01 angle pdb=" N SER A1346 " pdb=" CA SER A1346 " pdb=" C SER A1346 " ideal model delta sigma weight residual 110.80 118.15 -7.35 2.13e+00 2.20e-01 1.19e+01 angle pdb=" N SER A 559 " pdb=" CA SER A 559 " pdb=" C SER A 559 " ideal model delta sigma weight residual 109.07 114.53 -5.46 1.61e+00 3.86e-01 1.15e+01 ... (remaining 11879 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.47: 4961 31.47 - 62.94: 77 62.94 - 94.41: 2 94.41 - 125.88: 2 125.88 - 157.35: 2 Dihedral angle restraints: 5044 sinusoidal: 1662 harmonic: 3382 Sorted by residual: dihedral pdb=" O1B ADP A1605 " pdb=" O3A ADP A1605 " pdb=" PB ADP A1605 " pdb=" PA ADP A1605 " ideal model delta sinusoidal sigma weight residual -60.00 -169.59 109.59 1 2.00e+01 2.50e-03 3.20e+01 dihedral pdb=" O2A ADP A1605 " pdb=" O3A ADP A1605 " pdb=" PA ADP A1605 " pdb=" PB ADP A1605 " ideal model delta sinusoidal sigma weight residual -60.00 43.72 -103.72 1 2.00e+01 2.50e-03 2.97e+01 dihedral pdb=" O BJX A1604 " pdb=" C16 BJX A1604 " pdb=" C17 BJX A1604 " pdb=" C18 BJX A1604 " ideal model delta sinusoidal sigma weight residual 10.31 167.66 -157.35 1 3.00e+01 1.11e-03 2.05e+01 ... (remaining 5041 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1222 0.050 - 0.099: 214 0.099 - 0.149: 46 0.149 - 0.198: 0 0.198 - 0.248: 3 Chirality restraints: 1485 Sorted by residual: chirality pdb=" CA LYS A1348 " pdb=" N LYS A1348 " pdb=" C LYS A1348 " pdb=" CB LYS A1348 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CA MET A1284 " pdb=" N MET A1284 " pdb=" C MET A1284 " pdb=" CB MET A1284 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA SER A1346 " pdb=" N SER A1346 " pdb=" C SER A1346 " pdb=" CB SER A1346 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 1482 not shown) Planarity restraints: 1452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A1104 " 0.030 5.00e-02 4.00e+02 4.56e-02 3.33e+00 pdb=" N PRO A1105 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A1105 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A1105 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A1345 " 0.009 2.00e-02 2.50e+03 1.82e-02 3.31e+00 pdb=" C GLY A1345 " -0.031 2.00e-02 2.50e+03 pdb=" O GLY A1345 " 0.012 2.00e-02 2.50e+03 pdb=" N SER A1346 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A1103 " -0.028 5.00e-02 4.00e+02 4.28e-02 2.93e+00 pdb=" N PRO A1104 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A1104 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A1104 " -0.024 5.00e-02 4.00e+02 ... (remaining 1449 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 72 2.59 - 3.17: 7988 3.17 - 3.74: 13599 3.74 - 4.32: 17926 4.32 - 4.90: 29214 Nonbonded interactions: 68799 Sorted by model distance: nonbonded pdb="MG MG A1603 " pdb=" O2B ADP A1605 " model vdw 2.011 2.170 nonbonded pdb=" O2B ATP A1601 " pdb="MG MG A1602 " model vdw 2.021 2.170 nonbonded pdb=" O1G ATP A1601 " pdb="MG MG A1602 " model vdw 2.077 2.170 nonbonded pdb=" O3B ATP A1601 " pdb="MG MG A1602 " model vdw 2.121 2.170 nonbonded pdb="MG MG A1603 " pdb=" O1B ADP A1605 " model vdw 2.159 2.170 ... (remaining 68794 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.440 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: 7.350 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 27.720 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 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 : 0.005 0.108 8678 Z= 0.300 Angle : 0.606 9.734 11884 Z= 0.318 Chirality : 0.041 0.248 1485 Planarity : 0.004 0.046 1452 Dihedral : 12.265 157.353 2852 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.96 % Allowed : 7.39 % Favored : 89.66 % 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: 0.96 (0.25), residues: 1150 helix: 0.93 (0.19), residues: 745 sheet: -1.05 (0.84), residues: 37 loop : 0.49 (0.34), residues: 368 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 174 time to evaluate : 0.947 Fit side-chains outliers start: 24 outliers final: 5 residues processed: 195 average time/residue: 0.1710 time to fit residues: 48.5943 Evaluate side-chains 116 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 111 time to evaluate : 0.953 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0828 time to fit residues: 2.0326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 48 optimal weight: 0.4980 chunk 30 optimal weight: 0.9990 chunk 59 optimal weight: 7.9990 chunk 46 optimal weight: 0.9990 chunk 90 optimal weight: 8.9990 chunk 35 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 105 optimal weight: 8.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8678 Z= 0.183 Angle : 0.568 7.384 11884 Z= 0.284 Chirality : 0.040 0.196 1485 Planarity : 0.004 0.049 1452 Dihedral : 8.515 152.753 1246 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.45 % Allowed : 12.56 % Favored : 83.99 % 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: 1.61 (0.25), residues: 1150 helix: 1.59 (0.18), residues: 772 sheet: -1.54 (0.89), residues: 28 loop : 0.29 (0.34), residues: 350 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 141 time to evaluate : 0.936 Fit side-chains outliers start: 28 outliers final: 15 residues processed: 161 average time/residue: 0.1583 time to fit residues: 38.3921 Evaluate side-chains 117 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 102 time to evaluate : 0.879 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0785 time to fit residues: 3.4047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 0.0570 chunk 32 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 overall best weight: 1.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 HIS ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1271 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8678 Z= 0.228 Angle : 0.568 8.439 11884 Z= 0.279 Chirality : 0.040 0.184 1485 Planarity : 0.004 0.051 1452 Dihedral : 8.016 154.861 1246 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.97 % Allowed : 16.26 % Favored : 81.77 % 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: 1.68 (0.25), residues: 1150 helix: 1.66 (0.19), residues: 766 sheet: -1.36 (0.94), residues: 28 loop : 0.28 (0.34), residues: 356 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 116 time to evaluate : 0.921 Fit side-chains outliers start: 16 outliers final: 13 residues processed: 129 average time/residue: 0.1477 time to fit residues: 29.5381 Evaluate side-chains 114 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 101 time to evaluate : 0.952 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0857 time to fit residues: 3.3141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 54 optimal weight: 0.0070 chunk 11 optimal weight: 1.9990 chunk 50 optimal weight: 9.9990 chunk 70 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 112 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 100 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 overall best weight: 1.7404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8678 Z= 0.254 Angle : 0.569 7.558 11884 Z= 0.279 Chirality : 0.040 0.171 1485 Planarity : 0.004 0.051 1452 Dihedral : 7.935 156.465 1246 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.97 % Allowed : 18.47 % Favored : 79.56 % 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: 1.58 (0.25), residues: 1150 helix: 1.61 (0.19), residues: 767 sheet: -1.47 (0.94), residues: 29 loop : 0.18 (0.33), residues: 354 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 114 time to evaluate : 0.891 Fit side-chains outliers start: 16 outliers final: 7 residues processed: 125 average time/residue: 0.1510 time to fit residues: 29.1408 Evaluate side-chains 108 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 101 time to evaluate : 0.959 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0790 time to fit residues: 2.2844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 7.9990 chunk 63 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 83 optimal weight: 0.0980 chunk 46 optimal weight: 0.9990 chunk 95 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 100 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1186 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8678 Z= 0.175 Angle : 0.545 7.028 11884 Z= 0.262 Chirality : 0.040 0.347 1485 Planarity : 0.003 0.050 1452 Dihedral : 7.726 157.621 1246 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.09 % Allowed : 19.33 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.25), residues: 1150 helix: 1.79 (0.19), residues: 754 sheet: -0.69 (0.83), residues: 42 loop : 0.35 (0.34), residues: 354 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 125 time to evaluate : 0.957 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 7 residues processed: 135 average time/residue: 0.1601 time to fit residues: 33.1213 Evaluate side-chains 116 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 109 time to evaluate : 0.987 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0974 time to fit residues: 2.4569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 112 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 9 optimal weight: 0.9980 chunk 58 optimal weight: 8.9990 chunk 108 optimal weight: 3.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8678 Z= 0.334 Angle : 0.637 8.695 11884 Z= 0.311 Chirality : 0.043 0.319 1485 Planarity : 0.004 0.053 1452 Dihedral : 7.802 159.013 1246 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.09 % Allowed : 21.55 % Favored : 76.35 % 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 (0.25), residues: 1150 helix: 1.48 (0.19), residues: 770 sheet: -1.71 (0.89), residues: 31 loop : -0.05 (0.33), residues: 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 109 time to evaluate : 0.894 Fit side-chains outliers start: 17 outliers final: 11 residues processed: 120 average time/residue: 0.1503 time to fit residues: 28.3587 Evaluate side-chains 118 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 107 time to evaluate : 1.059 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0834 time to fit residues: 3.0633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 94 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 44 optimal weight: 9.9990 chunk 66 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1186 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8678 Z= 0.174 Angle : 0.555 8.575 11884 Z= 0.263 Chirality : 0.039 0.237 1485 Planarity : 0.003 0.052 1452 Dihedral : 7.549 159.976 1246 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.86 % Allowed : 21.31 % Favored : 77.83 % 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: 1.76 (0.25), residues: 1150 helix: 1.71 (0.19), residues: 760 sheet: -0.37 (0.75), residues: 52 loop : 0.32 (0.35), residues: 338 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 117 time to evaluate : 1.051 Fit side-chains outliers start: 7 outliers final: 1 residues processed: 121 average time/residue: 0.1509 time to fit residues: 28.6286 Evaluate side-chains 113 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 112 time to evaluate : 0.908 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4655 time to fit residues: 1.8747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 87 optimal weight: 0.7980 chunk 101 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 104 optimal weight: 0.0570 overall best weight: 1.1300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8678 Z= 0.202 Angle : 0.563 8.999 11884 Z= 0.269 Chirality : 0.040 0.251 1485 Planarity : 0.003 0.052 1452 Dihedral : 7.460 160.790 1246 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.35 % Allowed : 22.04 % Favored : 76.60 % 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: 1.78 (0.25), residues: 1150 helix: 1.74 (0.19), residues: 758 sheet: -0.19 (0.76), residues: 52 loop : 0.28 (0.35), residues: 340 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 111 time to evaluate : 0.847 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 119 average time/residue: 0.1491 time to fit residues: 28.1443 Evaluate side-chains 116 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 111 time to evaluate : 0.889 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0842 time to fit residues: 1.9708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 10.0000 chunk 62 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8678 Z= 0.179 Angle : 0.573 9.157 11884 Z= 0.268 Chirality : 0.039 0.267 1485 Planarity : 0.003 0.052 1452 Dihedral : 7.384 161.954 1246 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.62 % Allowed : 22.66 % Favored : 76.72 % 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: 1.86 (0.25), residues: 1150 helix: 1.81 (0.19), residues: 760 sheet: -0.13 (0.75), residues: 52 loop : 0.26 (0.35), residues: 338 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 117 time to evaluate : 0.955 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 118 average time/residue: 0.1477 time to fit residues: 27.3409 Evaluate side-chains 116 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 111 time to evaluate : 0.945 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0801 time to fit residues: 2.0354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 0.0370 chunk 76 optimal weight: 0.9990 chunk 115 optimal weight: 6.9990 chunk 106 optimal weight: 0.3980 chunk 92 optimal weight: 0.1980 chunk 9 optimal weight: 1.9990 chunk 71 optimal weight: 0.3980 chunk 56 optimal weight: 0.0370 chunk 73 optimal weight: 4.9990 chunk 98 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.2136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1186 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8678 Z= 0.138 Angle : 0.566 11.151 11884 Z= 0.262 Chirality : 0.040 0.297 1485 Planarity : 0.004 0.061 1452 Dihedral : 7.192 162.424 1246 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.12 % Allowed : 23.65 % Favored : 76.23 % 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: 1.88 (0.25), residues: 1150 helix: 1.84 (0.19), residues: 771 sheet: -0.55 (0.69), residues: 59 loop : 0.27 (0.35), residues: 320 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 136 time to evaluate : 0.866 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 137 average time/residue: 0.1436 time to fit residues: 30.4713 Evaluate side-chains 119 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.856 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 94 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 80 optimal weight: 2.9990 chunk 5 optimal weight: 0.0000 chunk 66 optimal weight: 0.9980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.132659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.106741 restraints weight = 17865.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.109467 restraints weight = 8668.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.111217 restraints weight = 5205.348| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8678 Z= 0.179 Angle : 0.585 11.545 11884 Z= 0.270 Chirality : 0.039 0.238 1485 Planarity : 0.004 0.054 1452 Dihedral : 7.161 160.897 1246 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.37 % Allowed : 25.49 % Favored : 74.14 % 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: 1.95 (0.25), residues: 1150 helix: 1.89 (0.19), residues: 772 sheet: -0.67 (0.68), residues: 59 loop : 0.33 (0.35), residues: 319 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1684.09 seconds wall clock time: 31 minutes 24.15 seconds (1884.15 seconds total)