Starting phenix.real_space_refine on Mon Mar 11 14:48:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1k_33564/03_2024/7y1k_33564_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1k_33564/03_2024/7y1k_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_33564/03_2024/7y1k_33564.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1k_33564/03_2024/7y1k_33564.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1k_33564/03_2024/7y1k_33564_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1k_33564/03_2024/7y1k_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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 5.18, per 1000 atoms: 0.61 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: 3.64 Conformation dependent library (CDL) restraints added in 1.8 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: 2.60 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: 3.07 Time building geometry restraints manager: 3.83 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: 4981 31.47 - 62.94: 95 62.94 - 94.41: 5 94.41 - 125.88: 2 125.88 - 157.35: 2 Dihedral angle restraints: 5085 sinusoidal: 1703 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 5082 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: 0.000 Normalize map: mean=0, sd=1: 2.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.330 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 27.800 Find NCS groups from input model: 0.250 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.190 ------------------------------------------------------------------------------- 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 : 12.888 157.353 2893 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 507 HIS 0.004 0.001 HIS A 555 PHE 0.008 0.001 PHE A 569 TYR 0.011 0.001 TYR A 290 ARG 0.002 0.000 ARG A1461 *********************** 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 : 1.117 Fit side-chains REVERT: A 239 HIS cc_start: 0.8650 (OUTLIER) cc_final: 0.8248 (m90) REVERT: A 356 PHE cc_start: 0.8518 (t80) cc_final: 0.8278 (t80) REVERT: A 479 LYS cc_start: 0.9225 (tttt) cc_final: 0.8695 (ttmm) REVERT: A 571 SER cc_start: 0.8710 (m) cc_final: 0.8499 (t) REVERT: A 698 MET cc_start: 0.3873 (mtp) cc_final: 0.3274 (ttm) REVERT: A 823 TYR cc_start: 0.6147 (t80) cc_final: 0.5500 (t80) REVERT: A 1050 SER cc_start: 0.9380 (m) cc_final: 0.9167 (p) REVERT: A 1089 LEU cc_start: 0.9183 (tp) cc_final: 0.8953 (tt) REVERT: A 1228 LEU cc_start: 0.9136 (tp) cc_final: 0.8879 (tt) REVERT: A 1271 GLN cc_start: 0.8715 (mt0) cc_final: 0.8465 (mt0) REVERT: A 1317 TYR cc_start: 0.4463 (OUTLIER) cc_final: 0.3633 (p90) REVERT: A 1373 ILE cc_start: 0.8880 (pt) cc_final: 0.8472 (pt) outliers start: 24 outliers final: 5 residues processed: 195 average time/residue: 0.1719 time to fit residues: 48.8705 Evaluate side-chains 123 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 116 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 1186 HIS Chi-restraints excluded: chain A residue 1203 ILE Chi-restraints excluded: chain A residue 1317 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.5980 chunk 87 optimal weight: 0.9990 chunk 48 optimal weight: 0.4980 chunk 30 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 90 optimal weight: 8.9990 chunk 35 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 105 optimal weight: 8.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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: 0.8063 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8678 Z= 0.179 Angle : 0.571 7.620 11884 Z= 0.284 Chirality : 0.040 0.192 1485 Planarity : 0.004 0.049 1452 Dihedral : 10.332 150.196 1300 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.82 % Allowed : 12.07 % Favored : 84.11 % 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: 1.56 (0.25), residues: 1150 helix: 1.56 (0.18), residues: 774 sheet: -1.95 (0.92), residues: 27 loop : 0.27 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 507 HIS 0.003 0.001 HIS A 555 PHE 0.015 0.001 PHE A1281 TYR 0.017 0.001 TYR A1009 ARG 0.008 0.000 ARG A1218 *********************** 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 177 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 146 time to evaluate : 0.842 Fit side-chains REVERT: A 239 HIS cc_start: 0.8628 (OUTLIER) cc_final: 0.8299 (m90) REVERT: A 390 ASN cc_start: 0.8618 (OUTLIER) cc_final: 0.8117 (t0) REVERT: A 407 LEU cc_start: 0.8976 (tt) cc_final: 0.8729 (mm) REVERT: A 698 MET cc_start: 0.3397 (mtp) cc_final: 0.2919 (ttm) REVERT: A 823 TYR cc_start: 0.6089 (t80) cc_final: 0.5596 (t80) REVERT: A 993 MET cc_start: 0.8781 (tmm) cc_final: 0.8487 (tmm) REVERT: A 1050 SER cc_start: 0.9435 (m) cc_final: 0.9116 (p) REVERT: A 1259 ASN cc_start: 0.9108 (OUTLIER) cc_final: 0.8658 (t0) REVERT: A 1271 GLN cc_start: 0.8479 (mt0) cc_final: 0.7884 (mp10) REVERT: A 1373 ILE cc_start: 0.8633 (pt) cc_final: 0.8308 (pt) outliers start: 31 outliers final: 17 residues processed: 169 average time/residue: 0.1593 time to fit residues: 40.0990 Evaluate side-chains 126 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 106 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 428 CYS Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1203 ILE Chi-restraints excluded: chain A residue 1259 ASN Chi-restraints excluded: chain A residue 1399 ILE Chi-restraints excluded: chain A residue 1460 VAL Chi-restraints excluded: chain A residue 1529 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 20.0000 chunk 32 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 105 optimal weight: 9.9990 chunk 114 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 104 optimal weight: 0.0980 chunk 35 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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: 0.8094 moved from start: 0.2467 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= 0.205 Angle : 0.558 8.420 11884 Z= 0.272 Chirality : 0.040 0.199 1485 Planarity : 0.004 0.051 1452 Dihedral : 9.215 152.690 1294 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.57 % Allowed : 16.13 % Favored : 80.30 % 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: 1.71 (0.25), residues: 1150 helix: 1.72 (0.19), residues: 765 sheet: -2.14 (0.91), residues: 29 loop : 0.29 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 507 HIS 0.003 0.001 HIS A1001 PHE 0.012 0.001 PHE A 569 TYR 0.011 0.001 TYR A1317 ARG 0.006 0.000 ARG A 256 *********************** 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 156 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 127 time to evaluate : 0.955 Fit side-chains REVERT: A 239 HIS cc_start: 0.8697 (OUTLIER) cc_final: 0.8401 (m90) REVERT: A 390 ASN cc_start: 0.8639 (OUTLIER) cc_final: 0.8252 (t0) REVERT: A 718 MET cc_start: 0.7303 (ptm) cc_final: 0.6933 (ptm) REVERT: A 823 TYR cc_start: 0.5903 (t80) cc_final: 0.5430 (t80) REVERT: A 993 MET cc_start: 0.8780 (tmm) cc_final: 0.8422 (tmm) REVERT: A 1050 SER cc_start: 0.9399 (m) cc_final: 0.9079 (p) REVERT: A 1160 ASP cc_start: 0.8209 (t70) cc_final: 0.7940 (t0) REVERT: A 1259 ASN cc_start: 0.9166 (OUTLIER) cc_final: 0.8759 (t0) REVERT: A 1271 GLN cc_start: 0.8417 (mt0) cc_final: 0.7852 (mp10) REVERT: A 1373 ILE cc_start: 0.8530 (pt) cc_final: 0.8239 (pt) outliers start: 29 outliers final: 24 residues processed: 149 average time/residue: 0.1376 time to fit residues: 32.5588 Evaluate side-chains 141 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 114 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 428 CYS Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1004 ILE Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1146 GLN Chi-restraints excluded: chain A residue 1174 THR Chi-restraints excluded: chain A residue 1203 ILE Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1259 ASN Chi-restraints excluded: chain A residue 1399 ILE Chi-restraints excluded: chain A residue 1426 MET Chi-restraints excluded: chain A residue 1529 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 112 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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: 0.8113 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8678 Z= 0.237 Angle : 0.576 8.042 11884 Z= 0.278 Chirality : 0.041 0.296 1485 Planarity : 0.004 0.052 1452 Dihedral : 8.909 151.278 1293 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 5.79 % Allowed : 17.00 % Favored : 77.22 % 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: 1.78 (0.19), residues: 756 sheet: -1.83 (0.89), residues: 31 loop : 0.32 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 507 HIS 0.004 0.001 HIS A 867 PHE 0.014 0.001 PHE A 569 TYR 0.015 0.001 TYR A1257 ARG 0.003 0.000 ARG A1382 *********************** 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 164 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 117 time to evaluate : 0.838 Fit side-chains REVERT: A 219 PHE cc_start: 0.8099 (OUTLIER) cc_final: 0.7762 (t80) REVERT: A 239 HIS cc_start: 0.8707 (OUTLIER) cc_final: 0.8419 (m90) REVERT: A 390 ASN cc_start: 0.8654 (OUTLIER) cc_final: 0.8292 (t0) REVERT: A 407 LEU cc_start: 0.9012 (tt) cc_final: 0.8735 (mm) REVERT: A 487 GLU cc_start: 0.7721 (tp30) cc_final: 0.7359 (tp30) REVERT: A 823 TYR cc_start: 0.5928 (t80) cc_final: 0.5577 (t80) REVERT: A 993 MET cc_start: 0.8787 (tmm) cc_final: 0.8450 (tmm) REVERT: A 1050 SER cc_start: 0.9420 (m) cc_final: 0.9106 (p) REVERT: A 1259 ASN cc_start: 0.9174 (OUTLIER) cc_final: 0.8772 (t0) REVERT: A 1271 GLN cc_start: 0.8422 (mt0) cc_final: 0.7921 (mp10) REVERT: A 1317 TYR cc_start: 0.4543 (OUTLIER) cc_final: 0.3446 (p90) REVERT: A 1373 ILE cc_start: 0.8594 (pt) cc_final: 0.8316 (pt) outliers start: 47 outliers final: 29 residues processed: 151 average time/residue: 0.1408 time to fit residues: 32.8488 Evaluate side-chains 141 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 107 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 428 CYS Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1146 GLN Chi-restraints excluded: chain A residue 1151 VAL Chi-restraints excluded: chain A residue 1174 THR Chi-restraints excluded: chain A residue 1186 HIS Chi-restraints excluded: chain A residue 1203 ILE Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain A residue 1259 ASN Chi-restraints excluded: chain A residue 1317 TYR Chi-restraints excluded: chain A residue 1399 ILE Chi-restraints excluded: chain A residue 1426 MET Chi-restraints excluded: chain A residue 1460 VAL Chi-restraints excluded: chain A residue 1529 LEU 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: 0.9990 chunk 1 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 100 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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: 0.8097 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8678 Z= 0.213 Angle : 0.562 8.221 11884 Z= 0.269 Chirality : 0.040 0.279 1485 Planarity : 0.003 0.051 1452 Dihedral : 8.689 150.562 1293 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 5.30 % Allowed : 17.98 % 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: 1.83 (0.25), residues: 1150 helix: 1.80 (0.19), residues: 756 sheet: -1.58 (0.92), residues: 31 loop : 0.35 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 507 HIS 0.004 0.001 HIS A1001 PHE 0.013 0.001 PHE A 569 TYR 0.012 0.001 TYR A1317 ARG 0.003 0.000 ARG A1382 *********************** 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 161 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 118 time to evaluate : 1.032 Fit side-chains REVERT: A 219 PHE cc_start: 0.8102 (OUTLIER) cc_final: 0.7768 (t80) REVERT: A 239 HIS cc_start: 0.8701 (OUTLIER) cc_final: 0.8403 (m90) REVERT: A 390 ASN cc_start: 0.8643 (OUTLIER) cc_final: 0.8322 (t0) REVERT: A 487 GLU cc_start: 0.7933 (tp30) cc_final: 0.7581 (tp30) REVERT: A 823 TYR cc_start: 0.6109 (t80) cc_final: 0.5663 (t80) REVERT: A 1050 SER cc_start: 0.9442 (m) cc_final: 0.9126 (p) REVERT: A 1071 LYS cc_start: 0.8312 (tptt) cc_final: 0.8009 (tptt) REVERT: A 1259 ASN cc_start: 0.9173 (OUTLIER) cc_final: 0.8808 (t0) REVERT: A 1271 GLN cc_start: 0.8372 (mt0) cc_final: 0.8147 (mt0) REVERT: A 1317 TYR cc_start: 0.4502 (OUTLIER) cc_final: 0.3616 (p90) REVERT: A 1373 ILE cc_start: 0.8542 (pt) cc_final: 0.8253 (pt) REVERT: A 1418 LEU cc_start: 0.6725 (tp) cc_final: 0.6513 (tp) outliers start: 43 outliers final: 29 residues processed: 150 average time/residue: 0.1368 time to fit residues: 32.0895 Evaluate side-chains 142 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 108 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 428 CYS Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1146 GLN Chi-restraints excluded: chain A residue 1151 VAL Chi-restraints excluded: chain A residue 1174 THR Chi-restraints excluded: chain A residue 1203 ILE Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain A residue 1259 ASN Chi-restraints excluded: chain A residue 1317 TYR Chi-restraints excluded: chain A residue 1387 ILE Chi-restraints excluded: chain A residue 1399 ILE Chi-restraints excluded: chain A residue 1426 MET Chi-restraints excluded: chain A residue 1460 VAL Chi-restraints excluded: chain A residue 1529 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 7.9990 chunk 100 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 112 optimal weight: 9.9990 chunk 93 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 58 optimal weight: 20.0000 chunk 108 optimal weight: 4.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- 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: 0.8106 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8678 Z= 0.233 Angle : 0.571 7.641 11884 Z= 0.275 Chirality : 0.040 0.241 1485 Planarity : 0.003 0.051 1452 Dihedral : 8.594 150.370 1293 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 5.42 % Allowed : 18.10 % Favored : 76.48 % 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: 1.73 (0.25), residues: 1150 helix: 1.71 (0.19), residues: 763 sheet: -0.17 (0.78), residues: 52 loop : 0.21 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 507 HIS 0.004 0.001 HIS A1065 PHE 0.014 0.001 PHE A 569 TYR 0.012 0.001 TYR A1317 ARG 0.003 0.000 ARG A1218 *********************** 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 153 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 109 time to evaluate : 0.932 Fit side-chains REVERT: A 219 PHE cc_start: 0.8120 (OUTLIER) cc_final: 0.7748 (t80) REVERT: A 239 HIS cc_start: 0.8698 (OUTLIER) cc_final: 0.8394 (m90) REVERT: A 390 ASN cc_start: 0.8634 (OUTLIER) cc_final: 0.8319 (t0) REVERT: A 1050 SER cc_start: 0.9423 (m) cc_final: 0.9123 (p) REVERT: A 1071 LYS cc_start: 0.8411 (tptt) cc_final: 0.7913 (tptt) REVERT: A 1259 ASN cc_start: 0.9170 (OUTLIER) cc_final: 0.8808 (t0) REVERT: A 1271 GLN cc_start: 0.8392 (mt0) cc_final: 0.8146 (mt0) REVERT: A 1317 TYR cc_start: 0.4517 (OUTLIER) cc_final: 0.3628 (p90) REVERT: A 1373 ILE cc_start: 0.8502 (pt) cc_final: 0.8253 (pt) outliers start: 44 outliers final: 30 residues processed: 143 average time/residue: 0.1414 time to fit residues: 31.5896 Evaluate side-chains 142 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 107 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 428 CYS Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1146 GLN Chi-restraints excluded: chain A residue 1174 THR Chi-restraints excluded: chain A residue 1203 ILE Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain A residue 1259 ASN Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1317 TYR Chi-restraints excluded: chain A residue 1399 ILE Chi-restraints excluded: chain A residue 1426 MET Chi-restraints excluded: chain A residue 1460 VAL Chi-restraints excluded: chain A residue 1529 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 94 optimal weight: 20.0000 chunk 62 optimal weight: 0.9980 chunk 111 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 44 optimal weight: 9.9990 chunk 66 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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: 0.8083 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8678 Z= 0.194 Angle : 0.561 9.849 11884 Z= 0.265 Chirality : 0.039 0.199 1485 Planarity : 0.003 0.051 1452 Dihedral : 8.401 150.136 1293 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 4.93 % Allowed : 19.33 % Favored : 75.74 % 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: 1.82 (0.25), residues: 1150 helix: 1.78 (0.19), residues: 764 sheet: 0.21 (0.80), residues: 47 loop : 0.16 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 507 HIS 0.003 0.001 HIS A1001 PHE 0.013 0.001 PHE A 569 TYR 0.010 0.001 TYR A1317 ARG 0.002 0.000 ARG A1218 *********************** 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 158 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 118 time to evaluate : 1.007 Fit side-chains revert: symmetry clash REVERT: A 219 PHE cc_start: 0.8109 (OUTLIER) cc_final: 0.7736 (t80) REVERT: A 239 HIS cc_start: 0.8643 (OUTLIER) cc_final: 0.8369 (m90) REVERT: A 390 ASN cc_start: 0.8634 (OUTLIER) cc_final: 0.8339 (t0) REVERT: A 1050 SER cc_start: 0.9425 (m) cc_final: 0.9159 (p) REVERT: A 1259 ASN cc_start: 0.9170 (OUTLIER) cc_final: 0.8825 (t0) REVERT: A 1271 GLN cc_start: 0.8352 (mt0) cc_final: 0.8111 (mt0) REVERT: A 1317 TYR cc_start: 0.4399 (OUTLIER) cc_final: 0.3494 (p90) REVERT: A 1373 ILE cc_start: 0.8407 (pt) cc_final: 0.8200 (pt) outliers start: 40 outliers final: 29 residues processed: 147 average time/residue: 0.1550 time to fit residues: 35.0745 Evaluate side-chains 146 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 112 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1002 SER Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1174 THR Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain A residue 1259 ASN Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1317 TYR Chi-restraints excluded: chain A residue 1371 ILE Chi-restraints excluded: chain A residue 1399 ILE Chi-restraints excluded: chain A residue 1426 MET Chi-restraints excluded: chain A residue 1460 VAL Chi-restraints excluded: chain A residue 1529 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 55 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 104 optimal weight: 0.0870 overall best weight: 0.9560 ------------------------------------------------------------------------------- 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: 0.8068 moved from start: 0.3385 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= 0.173 Angle : 0.553 10.452 11884 Z= 0.259 Chirality : 0.039 0.211 1485 Planarity : 0.003 0.051 1452 Dihedral : 8.205 150.058 1291 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.80 % Allowed : 20.32 % Favored : 74.88 % 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: 1.92 (0.25), residues: 1150 helix: 1.84 (0.19), residues: 767 sheet: 0.22 (0.80), residues: 47 loop : 0.22 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 677 HIS 0.003 0.001 HIS A1001 PHE 0.011 0.001 PHE A 569 TYR 0.010 0.001 TYR A1257 ARG 0.002 0.000 ARG A1382 *********************** 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 157 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 118 time to evaluate : 0.870 Fit side-chains REVERT: A 219 PHE cc_start: 0.8102 (OUTLIER) cc_final: 0.7722 (t80) REVERT: A 239 HIS cc_start: 0.8636 (OUTLIER) cc_final: 0.8373 (m90) REVERT: A 390 ASN cc_start: 0.8593 (OUTLIER) cc_final: 0.8307 (t0) REVERT: A 407 LEU cc_start: 0.9022 (tt) cc_final: 0.8750 (mm) REVERT: A 675 PHE cc_start: 0.8324 (m-80) cc_final: 0.8081 (m-80) REVERT: A 1050 SER cc_start: 0.9451 (m) cc_final: 0.9158 (p) REVERT: A 1071 LYS cc_start: 0.8436 (tptt) cc_final: 0.8210 (tptt) REVERT: A 1259 ASN cc_start: 0.9183 (OUTLIER) cc_final: 0.8843 (t0) REVERT: A 1317 TYR cc_start: 0.4435 (OUTLIER) cc_final: 0.3455 (p90) outliers start: 39 outliers final: 29 residues processed: 147 average time/residue: 0.1436 time to fit residues: 33.1482 Evaluate side-chains 149 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 115 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1002 SER Chi-restraints excluded: chain A residue 1069 LEU Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1174 THR Chi-restraints excluded: chain A residue 1203 ILE Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain A residue 1259 ASN Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1317 TYR Chi-restraints excluded: chain A residue 1399 ILE Chi-restraints excluded: chain A residue 1426 MET Chi-restraints excluded: chain A residue 1460 VAL Chi-restraints excluded: chain A residue 1529 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 7.9990 chunk 62 optimal weight: 0.5980 chunk 45 optimal weight: 8.9990 chunk 81 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 94 optimal weight: 0.3980 chunk 98 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 110 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.8052 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8678 Z= 0.155 Angle : 0.542 10.707 11884 Z= 0.253 Chirality : 0.039 0.225 1485 Planarity : 0.004 0.059 1452 Dihedral : 8.045 148.893 1291 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.94 % Allowed : 21.06 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.25), residues: 1150 helix: 1.98 (0.19), residues: 764 sheet: 0.18 (0.79), residues: 47 loop : 0.16 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 677 HIS 0.003 0.001 HIS A1001 PHE 0.010 0.001 PHE A 569 TYR 0.008 0.001 TYR A1317 ARG 0.002 0.000 ARG A1382 *********************** 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 155 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 123 time to evaluate : 0.868 Fit side-chains REVERT: A 219 PHE cc_start: 0.8083 (OUTLIER) cc_final: 0.7705 (t80) REVERT: A 239 HIS cc_start: 0.8606 (OUTLIER) cc_final: 0.8313 (m90) REVERT: A 407 LEU cc_start: 0.9004 (tt) cc_final: 0.8739 (mm) REVERT: A 1050 SER cc_start: 0.9439 (m) cc_final: 0.9168 (p) REVERT: A 1195 LEU cc_start: 0.8493 (mt) cc_final: 0.8189 (mt) REVERT: A 1259 ASN cc_start: 0.9198 (OUTLIER) cc_final: 0.8875 (t0) REVERT: A 1317 TYR cc_start: 0.4418 (OUTLIER) cc_final: 0.3438 (p90) outliers start: 32 outliers final: 26 residues processed: 146 average time/residue: 0.1437 time to fit residues: 32.3814 Evaluate side-chains 148 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 118 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1002 SER Chi-restraints excluded: chain A residue 1069 LEU Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1174 THR Chi-restraints excluded: chain A residue 1203 ILE Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain A residue 1259 ASN Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1317 TYR Chi-restraints excluded: chain A residue 1357 ARG Chi-restraints excluded: chain A residue 1399 ILE Chi-restraints excluded: chain A residue 1426 MET Chi-restraints excluded: chain A residue 1460 VAL Chi-restraints excluded: chain A residue 1529 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 3.9990 chunk 76 optimal weight: 0.5980 chunk 115 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 chunk 92 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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: 0.8049 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8678 Z= 0.159 Angle : 0.553 10.716 11884 Z= 0.259 Chirality : 0.040 0.235 1485 Planarity : 0.003 0.054 1452 Dihedral : 7.962 148.538 1291 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.57 % Allowed : 21.92 % Favored : 74.51 % 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: 1.97 (0.25), residues: 1150 helix: 1.95 (0.19), residues: 774 sheet: 0.09 (0.77), residues: 47 loop : 0.04 (0.34), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 677 HIS 0.003 0.001 HIS A1001 PHE 0.011 0.001 PHE A 569 TYR 0.008 0.001 TYR A 290 ARG 0.002 0.000 ARG A1218 ********************** 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 149 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 120 time to evaluate : 1.065 Fit side-chains REVERT: A 219 PHE cc_start: 0.8086 (OUTLIER) cc_final: 0.7710 (t80) REVERT: A 239 HIS cc_start: 0.8586 (OUTLIER) cc_final: 0.8304 (m90) REVERT: A 407 LEU cc_start: 0.9029 (tt) cc_final: 0.8767 (mm) REVERT: A 1050 SER cc_start: 0.9418 (m) cc_final: 0.9124 (p) REVERT: A 1259 ASN cc_start: 0.9207 (OUTLIER) cc_final: 0.8888 (t0) REVERT: A 1317 TYR cc_start: 0.4433 (OUTLIER) cc_final: 0.3443 (p90) REVERT: A 1418 LEU cc_start: 0.6419 (tp) cc_final: 0.6195 (tp) outliers start: 29 outliers final: 22 residues processed: 142 average time/residue: 0.1527 time to fit residues: 33.3979 Evaluate side-chains 145 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 119 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1002 SER Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1174 THR Chi-restraints excluded: chain A residue 1203 ILE Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain A residue 1259 ASN Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1317 TYR Chi-restraints excluded: chain A residue 1357 ARG Chi-restraints excluded: chain A residue 1399 ILE Chi-restraints excluded: chain A residue 1426 MET Chi-restraints excluded: chain A residue 1460 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 92 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 94 optimal weight: 0.0870 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 5 optimal weight: 0.4980 chunk 66 optimal weight: 0.5980 overall best weight: 0.5560 ------------------------------------------------------------------------------- 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 = 0.3874 r_free = 0.3874 target = 0.132825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.107254 restraints weight = 18032.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.110022 restraints weight = 8590.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.111821 restraints weight = 5081.997| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8678 Z= 0.145 Angle : 0.581 13.709 11884 Z= 0.263 Chirality : 0.039 0.231 1485 Planarity : 0.003 0.052 1452 Dihedral : 7.898 150.177 1289 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.83 % Allowed : 23.03 % 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: 2.03 (0.25), residues: 1150 helix: 1.93 (0.19), residues: 777 sheet: 0.11 (0.77), residues: 47 loop : 0.22 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 677 HIS 0.003 0.000 HIS A1001 PHE 0.021 0.001 PHE A 675 TYR 0.007 0.001 TYR A 290 ARG 0.003 0.000 ARG A1193 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1734.18 seconds wall clock time: 32 minutes 19.02 seconds (1939.02 seconds total)