Starting phenix.real_space_refine on Fri Mar 15 01:35:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bhu_7099/03_2024/6bhu_7099_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bhu_7099/03_2024/6bhu_7099.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bhu_7099/03_2024/6bhu_7099.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bhu_7099/03_2024/6bhu_7099.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bhu_7099/03_2024/6bhu_7099_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bhu_7099/03_2024/6bhu_7099_updated.pdb" } resolution = 3.14 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= 0.008 sd= 0.236 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 6 5.49 5 Mg 2 5.21 5 S 47 5.16 5 C 6616 2.51 5 N 1727 2.21 5 O 1875 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 360": "OE1" <-> "OE2" Residue "A ARG 723": "NH1" <-> "NH2" Residue "A ARG 735": "NH1" <-> "NH2" Residue "A ARG 758": "NH1" <-> "NH2" Residue "A ARG 780": "NH1" <-> "NH2" Residue "A ARG 858": "NH1" <-> "NH2" Residue "A GLU 1009": "OE1" <-> "OE2" Residue "A ARG 1137": "NH1" <-> "NH2" Residue "A ARG 1141": "NH1" <-> "NH2" Residue "A ARG 1262": "NH1" <-> "NH2" Residue "A ARG 1291": "NH1" <-> "NH2" Residue "A ARG 1295": "NH1" <-> "NH2" Residue "A ARG 1302": "NH1" <-> "NH2" Residue "A ARG 1327": "NH1" <-> "NH2" Residue "A ARG 1366": "NH1" <-> "NH2" Residue "A ARG 1384": "NH1" <-> "NH2" Residue "A ARG 1434": "NH1" <-> "NH2" Residue "A ARG 1441": "NH1" <-> "NH2" Residue "A ARG 1495": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10273 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 10273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1335, 10273 Unusual residues: {' MG': 2, 'ATP': 2, 'CLR': 3} Classifications: {'peptide': 1328, 'undetermined': 7} Incomplete info: {'truncation_to_alanine': 120} Link IDs: {'PTRANS': 44, 'TRANS': 1283, None: 7} Not linked: pdbres="VAL A1530 " pdbres="ATP A1601 " Not linked: pdbres="ATP A1601 " pdbres="ATP A1602 " Not linked: pdbres="ATP A1602 " pdbres=" MG A1603 " Not linked: pdbres=" MG A1603 " pdbres=" MG A1604 " Not linked: pdbres=" MG A1604 " pdbres="CLR A1605 " ... (remaining 2 not shown) Chain breaks: 8 Unresolved non-hydrogen bonds: 240 Unresolved non-hydrogen angles: 360 Unresolved non-hydrogen dihedrals: 120 Planarities with less than four sites: {'UNK:plan-1': 120} Unresolved non-hydrogen planarities: 120 Time building chain proxies: 6.23, per 1000 atoms: 0.61 Number of scatterers: 10273 At special positions: 0 Unit cell: (144.609, 98.857, 97.223, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 47 16.00 P 6 15.00 Mg 2 11.99 O 1875 8.00 N 1727 7.00 C 6616 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: 3.95 Conformation dependent library (CDL) restraints added in 1.7 seconds 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2518 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 51 helices and 5 sheets defined 70.3% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.18 Creating SS restraints... Processing helix chain 'A' and resid 31 through 39 Processing helix chain 'A' and resid 43 through 49 Processing helix chain 'A' and resid 76 through 98 Processing helix chain 'A' and resid 106 through 129 Processing helix chain 'A' and resid 140 through 151 removed outlier: 3.519A pdb=" N UNK A 148 " --> pdb=" O UNK A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 157 No H-bonds generated for 'chain 'A' and resid 155 through 157' Processing helix chain 'A' and resid 171 through 193 Processing helix chain 'A' and resid 209 through 212 No H-bonds generated for 'chain 'A' and resid 209 through 212' Processing helix chain 'A' and resid 215 through 220 Processing helix chain 'A' and resid 223 through 233 removed outlier: 3.986A pdb=" N GLY A 226 " --> pdb=" O TRP A 223 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL A 229 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR A 232 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG A 233 " --> pdb=" O GLN A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 240 No H-bonds generated for 'chain 'A' and resid 238 through 240' Processing helix chain 'A' and resid 250 through 267 Proline residue: A 255 - end of helix Processing helix chain 'A' and resid 316 through 319 Processing helix chain 'A' and resid 322 through 354 removed outlier: 5.084A pdb=" N MET A 327 " --> pdb=" O PRO A 323 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N SER A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N PHE A 329 " --> pdb=" O PHE A 325 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LEU A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) Proline residue: A 343 - end of helix removed outlier: 3.629A pdb=" N ASN A 354 " --> pdb=" O ILE A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 407 Processing helix chain 'A' and resid 412 through 417 removed outlier: 3.762A pdb=" N SER A 417 " --> pdb=" O ALA A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 461 removed outlier: 3.967A pdb=" N ASP A 430 " --> pdb=" O LEU A 426 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ALA A 431 " --> pdb=" O MET A 427 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLN A 432 " --> pdb=" O SER A 428 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR A 439 " --> pdb=" O MET A 435 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR A 440 " --> pdb=" O ASP A 436 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ASN A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N MET A 443 " --> pdb=" O THR A 439 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE A 444 " --> pdb=" O TYR A 440 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N TRP A 445 " --> pdb=" O ILE A 441 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER A 446 " --> pdb=" O ASN A 442 " (cutoff:3.500A) Proline residue: A 448 - end of helix removed outlier: 3.534A pdb=" N LEU A 458 " --> pdb=" O ALA A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 518 removed outlier: 3.692A pdb=" N MET A 473 " --> pdb=" O GLY A 469 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A 474 " --> pdb=" O VAL A 470 " (cutoff:3.500A) Proline residue: A 478 - end of helix removed outlier: 3.781A pdb=" N THR A 489 " --> pdb=" O MET A 485 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU A 507 " --> pdb=" O LYS A 503 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY A 511 " --> pdb=" O GLU A 507 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LYS A 513 " --> pdb=" O LEU A 509 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N VAL A 514 " --> pdb=" O ASN A 510 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU A 515 " --> pdb=" O GLY A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 554 Processing helix chain 'A' and resid 556 through 570 removed outlier: 3.992A pdb=" N VAL A 567 " --> pdb=" O SER A 563 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N TYR A 568 " --> pdb=" O THR A 564 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL A 569 " --> pdb=" O PHE A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 590 removed outlier: 3.794A pdb=" N VAL A 584 " --> pdb=" O GLN A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 597 removed outlier: 4.071A pdb=" N LEU A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 620 removed outlier: 3.502A pdb=" N SER A 612 " --> pdb=" O GLN A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 692 removed outlier: 3.676A pdb=" N LEU A 692 " --> pdb=" O LEU A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 727 Processing helix chain 'A' and resid 734 through 743 Processing helix chain 'A' and resid 747 through 752 Processing helix chain 'A' and resid 770 through 784 removed outlier: 3.700A pdb=" N ALA A 781 " --> pdb=" O SER A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 809 Processing helix chain 'A' and resid 832 through 834 No H-bonds generated for 'chain 'A' and resid 832 through 834' Processing helix chain 'A' and resid 852 through 858 Processing helix chain 'A' and resid 861 through 866 Processing helix chain 'A' and resid 959 through 969 removed outlier: 3.679A pdb=" N ILE A 969 " --> pdb=" O TYR A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 999 removed outlier: 3.550A pdb=" N ASN A 992 " --> pdb=" O SER A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1008 through 1057 removed outlier: 3.977A pdb=" N GLN A1012 " --> pdb=" O GLN A1008 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N SER A1016 " --> pdb=" O GLN A1012 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL A1017 " --> pdb=" O VAL A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1060 through 1065 Processing helix chain 'A' and resid 1068 through 1109 removed outlier: 3.662A pdb=" N ARG A1074 " --> pdb=" O ASN A1070 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU A1078 " --> pdb=" O ARG A1074 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LEU A1079 " --> pdb=" O PHE A1075 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ILE A1086 " --> pdb=" O VAL A1082 " (cutoff:3.500A) Proline residue: A1087 - end of helix Processing helix chain 'A' and resid 1116 through 1159 Proline residue: A1120 - end of helix removed outlier: 3.894A pdb=" N TYR A1125 " --> pdb=" O LEU A1121 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE A1127 " --> pdb=" O LEU A1123 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA A1134 " --> pdb=" O ARG A1130 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N SER A1135 " --> pdb=" O PHE A1131 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLN A1138 " --> pdb=" O ALA A1134 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER A1148 " --> pdb=" O SER A1144 " (cutoff:3.500A) Proline residue: A1149 - end of helix removed outlier: 3.652A pdb=" N PHE A1154 " --> pdb=" O VAL A1150 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU A1159 " --> pdb=" O ASN A1155 " (cutoff:3.500A) Processing helix chain 'A' and resid 1161 through 1167 Processing helix chain 'A' and resid 1170 through 1219 removed outlier: 3.696A pdb=" N GLU A1183 " --> pdb=" O LEU A1179 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASN A1184 " --> pdb=" O LYS A1180 " (cutoff:3.500A) Proline residue: A1190 - end of helix Processing helix chain 'A' and resid 1226 through 1266 removed outlier: 3.745A pdb=" N GLY A1230 " --> pdb=" O ALA A1226 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU A1231 " --> pdb=" O GLY A1227 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL A1233 " --> pdb=" O VAL A1229 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER A1234 " --> pdb=" O GLY A1230 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR A1235 " --> pdb=" O LEU A1231 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER A1236 " --> pdb=" O SER A1232 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A1237 " --> pdb=" O VAL A1233 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLN A1238 " --> pdb=" O SER A1234 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR A1240 " --> pdb=" O SER A1236 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A1247 " --> pdb=" O LEU A1243 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG A1248 " --> pdb=" O ASN A1244 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N VAL A1258 " --> pdb=" O GLU A1254 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ALA A1259 " --> pdb=" O THR A1255 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N VAL A1260 " --> pdb=" O ASN A1256 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU A1265 " --> pdb=" O GLU A1261 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N TYR A1266 " --> pdb=" O ARG A1262 " (cutoff:3.500A) Processing helix chain 'A' and resid 1333 through 1339 Processing helix chain 'A' and resid 1362 through 1366 Processing helix chain 'A' and resid 1383 through 1387 removed outlier: 3.552A pdb=" N LEU A1387 " --> pdb=" O LEU A1383 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1383 through 1387' Processing helix chain 'A' and resid 1395 through 1404 Processing helix chain 'A' and resid 1408 through 1413 Processing helix chain 'A' and resid 1431 through 1445 removed outlier: 3.635A pdb=" N LEU A1436 " --> pdb=" O GLY A1432 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG A1445 " --> pdb=" O ARG A1441 " (cutoff:3.500A) Processing helix chain 'A' and resid 1461 through 1474 removed outlier: 3.855A pdb=" N ASP A1465 " --> pdb=" O LEU A1461 " (cutoff:3.500A) Processing helix chain 'A' and resid 1487 through 1490 Processing helix chain 'A' and resid 1510 through 1516 Processing helix chain 'A' and resid 1519 through 1527 Processing sheet with id= A, first strand: chain 'A' and resid 666 through 668 Processing sheet with id= B, first strand: chain 'A' and resid 845 through 848 removed outlier: 7.108A pdb=" N VAL A 840 " --> pdb=" O SER A 847 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL A 837 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ARG A 822 " --> pdb=" O VAL A 674 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N VAL A 676 " --> pdb=" O ARG A 822 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LEU A 824 " --> pdb=" O VAL A 676 " (cutoff:3.500A) removed outlier: 8.932A pdb=" N GLY A 678 " --> pdb=" O LEU A 824 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1292 through 1295 Processing sheet with id= D, first strand: chain 'A' and resid 1495 through 1499 removed outlier: 6.973A pdb=" N THR A1370 " --> pdb=" O VAL A1451 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N ASP A1453 " --> pdb=" O THR A1370 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE A1372 " --> pdb=" O ASP A1453 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 650 through 652 removed outlier: 6.149A pdb=" N THR A 652 " --> pdb=" O LYS A 697 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N LYS A 697 " --> pdb=" O THR A 652 " (cutoff:3.500A) 589 hydrogen bonds defined for protein. 1728 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: 3.55 Time building geometry restraints manager: 4.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1738 1.33 - 1.45: 2600 1.45 - 1.57: 6048 1.57 - 1.69: 10 1.69 - 1.81: 79 Bond restraints: 10475 Sorted by residual: bond pdb=" C4 ATP A1602 " pdb=" C5 ATP A1602 " ideal model delta sigma weight residual 1.388 1.473 -0.085 1.00e-02 1.00e+04 7.20e+01 bond pdb=" C4 ATP A1601 " pdb=" C5 ATP A1601 " ideal model delta sigma weight residual 1.388 1.473 -0.085 1.00e-02 1.00e+04 7.17e+01 bond pdb=" C5 ATP A1601 " pdb=" C6 ATP A1601 " ideal model delta sigma weight residual 1.409 1.485 -0.076 1.00e-02 1.00e+04 5.72e+01 bond pdb=" C5 ATP A1602 " pdb=" C6 ATP A1602 " ideal model delta sigma weight residual 1.409 1.481 -0.072 1.00e-02 1.00e+04 5.25e+01 bond pdb=" C8 ATP A1601 " pdb=" N7 ATP A1601 " ideal model delta sigma weight residual 1.310 1.358 -0.048 1.00e-02 1.00e+04 2.34e+01 ... (remaining 10470 not shown) Histogram of bond angle deviations from ideal: 100.19 - 107.40: 368 107.40 - 114.61: 6069 114.61 - 121.82: 4837 121.82 - 129.03: 2913 129.03 - 136.24: 71 Bond angle restraints: 14258 Sorted by residual: angle pdb=" PB ATP A1602 " pdb=" O3B ATP A1602 " pdb=" PG ATP A1602 " ideal model delta sigma weight residual 139.87 121.41 18.46 1.00e+00 1.00e+00 3.41e+02 angle pdb=" PB ATP A1601 " pdb=" O3B ATP A1601 " pdb=" PG ATP A1601 " ideal model delta sigma weight residual 139.87 121.57 18.30 1.00e+00 1.00e+00 3.35e+02 angle pdb=" PA ATP A1602 " pdb=" O3A ATP A1602 " pdb=" PB ATP A1602 " ideal model delta sigma weight residual 136.83 121.48 15.35 1.00e+00 1.00e+00 2.36e+02 angle pdb=" PA ATP A1601 " pdb=" O3A ATP A1601 " pdb=" PB ATP A1601 " ideal model delta sigma weight residual 136.83 121.79 15.04 1.00e+00 1.00e+00 2.26e+02 angle pdb=" C5 ATP A1602 " pdb=" C4 ATP A1602 " pdb=" N3 ATP A1602 " ideal model delta sigma weight residual 126.80 118.41 8.39 1.00e+00 1.00e+00 7.03e+01 ... (remaining 14253 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.96: 5950 16.96 - 33.91: 394 33.91 - 50.87: 85 50.87 - 67.82: 14 67.82 - 84.77: 6 Dihedral angle restraints: 6449 sinusoidal: 2574 harmonic: 3875 Sorted by residual: dihedral pdb=" CA TYR A 318 " pdb=" C TYR A 318 " pdb=" N LYS A 319 " pdb=" CA LYS A 319 " ideal model delta harmonic sigma weight residual 180.00 154.27 25.73 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA ALA A1110 " pdb=" C ALA A1110 " pdb=" N THR A1111 " pdb=" CA THR A1111 " ideal model delta harmonic sigma weight residual 180.00 -159.78 -20.22 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" C ARG A1486 " pdb=" N ARG A1486 " pdb=" CA ARG A1486 " pdb=" CB ARG A1486 " ideal model delta harmonic sigma weight residual -122.60 -112.59 -10.01 0 2.50e+00 1.60e-01 1.60e+01 ... (remaining 6446 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1438 0.083 - 0.167: 217 0.167 - 0.250: 31 0.250 - 0.334: 4 0.334 - 0.417: 1 Chirality restraints: 1691 Sorted by residual: chirality pdb=" CA CYS A 682 " pdb=" N CYS A 682 " pdb=" C CYS A 682 " pdb=" CB CYS A 682 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.35e+00 chirality pdb=" CA ILE A1483 " pdb=" N ILE A1483 " pdb=" C ILE A1483 " pdb=" CB ILE A1483 " both_signs ideal model delta sigma weight residual False 2.43 2.77 -0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CA LEU A1487 " pdb=" N LEU A1487 " pdb=" C LEU A1487 " pdb=" CB LEU A1487 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.61e+00 ... (remaining 1688 not shown) Planarity restraints: 1766 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 825 " 0.013 2.00e-02 2.50e+03 2.61e-02 6.82e+00 pdb=" C VAL A 825 " -0.045 2.00e-02 2.50e+03 pdb=" O VAL A 825 " 0.017 2.00e-02 2.50e+03 pdb=" N THR A 826 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A1486 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.27e+00 pdb=" C ARG A1486 " -0.031 2.00e-02 2.50e+03 pdb=" O ARG A1486 " 0.012 2.00e-02 2.50e+03 pdb=" N LEU A1487 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 824 " -0.008 2.00e-02 2.50e+03 1.78e-02 3.17e+00 pdb=" C LEU A 824 " 0.031 2.00e-02 2.50e+03 pdb=" O LEU A 824 " -0.012 2.00e-02 2.50e+03 pdb=" N VAL A 825 " -0.010 2.00e-02 2.50e+03 ... (remaining 1763 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 15 2.51 - 3.11: 6654 3.11 - 3.71: 15515 3.71 - 4.30: 20977 4.30 - 4.90: 35663 Nonbonded interactions: 78824 Sorted by model distance: nonbonded pdb=" OG SER A1333 " pdb="MG MG A1604 " model vdw 1.915 2.170 nonbonded pdb=" O1G ATP A1601 " pdb="MG MG A1603 " model vdw 1.988 2.170 nonbonded pdb=" O1B ATP A1601 " pdb="MG MG A1603 " model vdw 2.000 2.170 nonbonded pdb=" OE1 GLN A 713 " pdb="MG MG A1603 " model vdw 2.003 2.170 nonbonded pdb=" OG SER A 685 " pdb="MG MG A1603 " model vdw 2.017 2.170 ... (remaining 78819 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.290 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: 12.120 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 31.610 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 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: 49.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 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 : 0.008 0.085 10475 Z= 0.532 Angle : 1.220 18.457 14258 Z= 0.862 Chirality : 0.062 0.417 1691 Planarity : 0.004 0.042 1766 Dihedral : 12.533 84.775 3931 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 0.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.21), residues: 1200 helix: -0.39 (0.16), residues: 715 sheet: -1.21 (0.52), residues: 74 loop : -2.45 (0.25), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 520 HIS 0.006 0.001 HIS A 382 PHE 0.012 0.002 PHE A1063 TYR 0.020 0.002 TYR A1032 ARG 0.006 0.001 ARG A1137 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 1.234 Fit side-chains revert: symmetry clash REVERT: A 219 ILE cc_start: 0.8251 (tt) cc_final: 0.8039 (tt) REVERT: A 237 GLU cc_start: 0.7673 (tp30) cc_final: 0.7052 (tt0) REVERT: A 239 THR cc_start: 0.7639 (m) cc_final: 0.7390 (p) REVERT: A 246 LYS cc_start: 0.7523 (mtmt) cc_final: 0.7023 (mmtt) REVERT: A 251 GLU cc_start: 0.8340 (tt0) cc_final: 0.7951 (tp30) REVERT: A 473 MET cc_start: 0.7092 (mtm) cc_final: 0.6836 (mtm) REVERT: A 576 ILE cc_start: 0.8121 (mm) cc_final: 0.7830 (mm) REVERT: A 641 THR cc_start: 0.8021 (p) cc_final: 0.7776 (t) REVERT: A 694 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7172 (mm-30) REVERT: A 696 ASP cc_start: 0.8116 (t70) cc_final: 0.7662 (t0) REVERT: A 864 GLU cc_start: 0.8627 (tt0) cc_final: 0.8211 (mm-30) REVERT: A 946 LEU cc_start: 0.6795 (tp) cc_final: 0.6588 (tp) REVERT: A 993 TYR cc_start: 0.7574 (t80) cc_final: 0.6683 (t80) REVERT: A 1027 ILE cc_start: 0.8173 (mm) cc_final: 0.7918 (mp) REVERT: A 1245 TRP cc_start: 0.7185 (m100) cc_final: 0.6674 (m-10) REVERT: A 1248 ARG cc_start: 0.6464 (mtp-110) cc_final: 0.6137 (mtp85) REVERT: A 1252 GLU cc_start: 0.6828 (mm-30) cc_final: 0.6520 (mm-30) REVERT: A 1280 MET cc_start: 0.9096 (mtm) cc_final: 0.8771 (mtp) REVERT: A 1284 LYS cc_start: 0.8973 (mttt) cc_final: 0.8736 (ptmm) REVERT: A 1303 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8262 (tp30) REVERT: A 1355 ILE cc_start: 0.8037 (mm) cc_final: 0.7811 (tt) REVERT: A 1513 LEU cc_start: 0.8025 (mt) cc_final: 0.7793 (mp) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.2270 time to fit residues: 77.4815 Evaluate side-chains 145 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 67 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN A 956 GLN A1185 GLN A1392 GLN A1454 GLN A1485 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6656 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10475 Z= 0.191 Angle : 0.543 10.068 14258 Z= 0.282 Chirality : 0.039 0.168 1691 Planarity : 0.004 0.063 1766 Dihedral : 7.964 87.986 1676 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.99 % Allowed : 9.50 % Favored : 88.51 % 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: 0.49 (0.24), residues: 1200 helix: 1.64 (0.19), residues: 732 sheet: -1.22 (0.50), residues: 86 loop : -1.98 (0.28), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 459 HIS 0.008 0.001 HIS A 985 PHE 0.016 0.001 PHE A 551 TYR 0.024 0.001 TYR A1032 ARG 0.003 0.000 ARG A 633 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 165 time to evaluate : 1.152 Fit side-chains revert: symmetry clash REVERT: A 219 ILE cc_start: 0.8099 (tt) cc_final: 0.7862 (tt) REVERT: A 237 GLU cc_start: 0.7615 (tp30) cc_final: 0.6812 (tt0) REVERT: A 246 LYS cc_start: 0.7419 (mtmt) cc_final: 0.6962 (mmtt) REVERT: A 251 GLU cc_start: 0.8263 (tt0) cc_final: 0.7876 (tp30) REVERT: A 641 THR cc_start: 0.8224 (p) cc_final: 0.8019 (t) REVERT: A 696 ASP cc_start: 0.8052 (t70) cc_final: 0.7571 (t0) REVERT: A 849 MET cc_start: 0.8940 (mtp) cc_final: 0.8680 (mtm) REVERT: A 864 GLU cc_start: 0.8701 (tt0) cc_final: 0.8302 (mm-30) REVERT: A 964 ASP cc_start: 0.7736 (t0) cc_final: 0.7480 (m-30) REVERT: A 1245 TRP cc_start: 0.7173 (m100) cc_final: 0.6817 (m-10) REVERT: A 1248 ARG cc_start: 0.6353 (mtp-110) cc_final: 0.6092 (mtm180) REVERT: A 1280 MET cc_start: 0.8866 (mtm) cc_final: 0.8662 (mtp) REVERT: A 1303 GLU cc_start: 0.8682 (mt-10) cc_final: 0.8247 (tp30) REVERT: A 1353 ASP cc_start: 0.7999 (OUTLIER) cc_final: 0.7437 (m-30) REVERT: A 1355 ILE cc_start: 0.7750 (mm) cc_final: 0.7501 (tt) outliers start: 21 outliers final: 14 residues processed: 179 average time/residue: 0.2018 time to fit residues: 53.0839 Evaluate side-chains 151 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 136 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 496 LYS Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 1104 CYS Chi-restraints excluded: chain A residue 1325 VAL Chi-restraints excluded: chain A residue 1353 ASP Chi-restraints excluded: chain A residue 1362 LEU Chi-restraints excluded: chain A residue 1429 LEU Chi-restraints excluded: chain A residue 1503 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 67 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 130 optimal weight: 0.0670 chunk 107 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 overall best weight: 1.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN A 533 GLN A 827 HIS A 956 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6672 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10475 Z= 0.222 Angle : 0.526 7.170 14258 Z= 0.271 Chirality : 0.038 0.172 1691 Planarity : 0.004 0.059 1766 Dihedral : 7.160 79.826 1676 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.32 % Allowed : 10.73 % Favored : 85.94 % 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: 0.97 (0.24), residues: 1200 helix: 1.99 (0.19), residues: 735 sheet: -1.02 (0.51), residues: 86 loop : -1.73 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 459 HIS 0.008 0.001 HIS A 985 PHE 0.018 0.002 PHE A 651 TYR 0.021 0.001 TYR A1032 ARG 0.003 0.000 ARG A1065 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 156 time to evaluate : 1.223 Fit side-chains revert: symmetry clash REVERT: A 219 ILE cc_start: 0.8065 (tt) cc_final: 0.7811 (tt) REVERT: A 237 GLU cc_start: 0.7455 (tp30) cc_final: 0.6795 (tt0) REVERT: A 246 LYS cc_start: 0.7504 (mtmt) cc_final: 0.7042 (mmtt) REVERT: A 251 GLU cc_start: 0.8292 (tt0) cc_final: 0.7916 (tp30) REVERT: A 591 ILE cc_start: 0.7429 (tt) cc_final: 0.7098 (mm) REVERT: A 641 THR cc_start: 0.8388 (p) cc_final: 0.8180 (t) REVERT: A 656 ASN cc_start: 0.8908 (m-40) cc_final: 0.8304 (t0) REVERT: A 696 ASP cc_start: 0.7887 (t70) cc_final: 0.7442 (t0) REVERT: A 849 MET cc_start: 0.8833 (mtp) cc_final: 0.8397 (mtm) REVERT: A 864 GLU cc_start: 0.8699 (tt0) cc_final: 0.8308 (mm-30) REVERT: A 964 ASP cc_start: 0.7776 (t0) cc_final: 0.7487 (m-30) REVERT: A 1245 TRP cc_start: 0.7047 (m100) cc_final: 0.6622 (m-10) REVERT: A 1252 GLU cc_start: 0.6271 (mm-30) cc_final: 0.6026 (mm-30) REVERT: A 1303 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8271 (tp30) outliers start: 35 outliers final: 24 residues processed: 180 average time/residue: 0.2060 time to fit residues: 53.8203 Evaluate side-chains 158 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 134 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 TRP Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 496 LYS Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 966 MET Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1104 CYS Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1146 SER Chi-restraints excluded: chain A residue 1325 VAL Chi-restraints excluded: chain A residue 1362 LEU Chi-restraints excluded: chain A residue 1363 HIS Chi-restraints excluded: chain A residue 1375 ASP Chi-restraints excluded: chain A residue 1481 LEU Chi-restraints excluded: chain A residue 1487 LEU Chi-restraints excluded: chain A residue 1496 VAL Chi-restraints excluded: chain A residue 1503 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 119 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 81 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 128 optimal weight: 0.1980 chunk 63 optimal weight: 0.0770 chunk 115 optimal weight: 0.3980 chunk 34 optimal weight: 0.9980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN A 956 GLN A1256 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10475 Z= 0.140 Angle : 0.476 6.530 14258 Z= 0.244 Chirality : 0.036 0.161 1691 Planarity : 0.004 0.050 1766 Dihedral : 6.427 70.048 1676 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.51 % Allowed : 12.16 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.25), residues: 1200 helix: 2.32 (0.19), residues: 737 sheet: -0.71 (0.51), residues: 86 loop : -1.60 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 459 HIS 0.006 0.001 HIS A 985 PHE 0.016 0.001 PHE A 594 TYR 0.021 0.001 TYR A1032 ARG 0.008 0.000 ARG A 593 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 148 time to evaluate : 1.081 Fit side-chains revert: symmetry clash REVERT: A 219 ILE cc_start: 0.8088 (tt) cc_final: 0.7828 (tt) REVERT: A 237 GLU cc_start: 0.7356 (tp30) cc_final: 0.6618 (tt0) REVERT: A 246 LYS cc_start: 0.7526 (mtmt) cc_final: 0.7069 (mmtt) REVERT: A 251 GLU cc_start: 0.8276 (tt0) cc_final: 0.7880 (tp30) REVERT: A 552 THR cc_start: 0.6557 (t) cc_final: 0.6341 (t) REVERT: A 591 ILE cc_start: 0.7391 (tt) cc_final: 0.7029 (mm) REVERT: A 641 THR cc_start: 0.8293 (p) cc_final: 0.8081 (t) REVERT: A 656 ASN cc_start: 0.8969 (m-40) cc_final: 0.8350 (t0) REVERT: A 696 ASP cc_start: 0.7710 (t70) cc_final: 0.7271 (t0) REVERT: A 849 MET cc_start: 0.8612 (mtp) cc_final: 0.8399 (mtm) REVERT: A 864 GLU cc_start: 0.8647 (tt0) cc_final: 0.8252 (mm-30) REVERT: A 960 SER cc_start: 0.6836 (p) cc_final: 0.6491 (t) REVERT: A 964 ASP cc_start: 0.7724 (t0) cc_final: 0.7419 (m-30) REVERT: A 1245 TRP cc_start: 0.6948 (m100) cc_final: 0.6628 (m-10) REVERT: A 1252 GLU cc_start: 0.6214 (mm-30) cc_final: 0.5972 (mm-30) REVERT: A 1303 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8269 (tp30) REVERT: A 1353 ASP cc_start: 0.7914 (OUTLIER) cc_final: 0.7696 (m-30) REVERT: A 1393 TYR cc_start: 0.7453 (OUTLIER) cc_final: 0.6550 (p90) outliers start: 37 outliers final: 23 residues processed: 170 average time/residue: 0.1968 time to fit residues: 49.2066 Evaluate side-chains 165 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 140 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 TRP Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 496 LYS Chi-restraints excluded: chain A residue 626 ASP Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain A residue 820 LYS Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1085 MET Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1325 VAL Chi-restraints excluded: chain A residue 1353 ASP Chi-restraints excluded: chain A residue 1362 LEU Chi-restraints excluded: chain A residue 1363 HIS Chi-restraints excluded: chain A residue 1375 ASP Chi-restraints excluded: chain A residue 1393 TYR Chi-restraints excluded: chain A residue 1487 LEU Chi-restraints excluded: chain A residue 1490 ILE Chi-restraints excluded: chain A residue 1503 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 107 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 95 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 chunk 0 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 725 ASN A 956 GLN A1184 ASN A1435 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6689 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10475 Z= 0.267 Angle : 0.547 8.096 14258 Z= 0.277 Chirality : 0.038 0.160 1691 Planarity : 0.004 0.049 1766 Dihedral : 6.308 67.713 1676 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.61 % Allowed : 14.06 % Favored : 82.34 % 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: 1.27 (0.25), residues: 1200 helix: 2.16 (0.19), residues: 735 sheet: -0.74 (0.50), residues: 86 loop : -1.50 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 459 HIS 0.005 0.001 HIS A 985 PHE 0.022 0.002 PHE A 340 TYR 0.018 0.001 TYR A1032 ARG 0.006 0.000 ARG A 593 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 133 time to evaluate : 1.172 Fit side-chains revert: symmetry clash REVERT: A 219 ILE cc_start: 0.8044 (tt) cc_final: 0.7755 (tt) REVERT: A 237 GLU cc_start: 0.7318 (tp30) cc_final: 0.6659 (mt-10) REVERT: A 246 LYS cc_start: 0.7524 (mtmt) cc_final: 0.7054 (mmtt) REVERT: A 656 ASN cc_start: 0.8975 (m-40) cc_final: 0.8566 (m-40) REVERT: A 696 ASP cc_start: 0.7916 (t70) cc_final: 0.7614 (t0) REVERT: A 864 GLU cc_start: 0.8654 (tt0) cc_final: 0.8269 (mm-30) REVERT: A 964 ASP cc_start: 0.7732 (t0) cc_final: 0.7416 (m-30) REVERT: A 1245 TRP cc_start: 0.7021 (m100) cc_final: 0.6708 (m-10) REVERT: A 1278 GLN cc_start: 0.8853 (tp40) cc_final: 0.8600 (tp40) REVERT: A 1303 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8322 (tp30) REVERT: A 1383 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7519 (tt) REVERT: A 1393 TYR cc_start: 0.7612 (OUTLIER) cc_final: 0.6717 (p90) REVERT: A 1447 THR cc_start: 0.6647 (t) cc_final: 0.6401 (t) outliers start: 38 outliers final: 28 residues processed: 157 average time/residue: 0.1927 time to fit residues: 45.1727 Evaluate side-chains 158 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 128 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 496 LYS Chi-restraints excluded: chain A residue 707 SER Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 841 MET Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 966 MET Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1085 MET Chi-restraints excluded: chain A residue 1104 CYS Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1146 SER Chi-restraints excluded: chain A residue 1325 VAL Chi-restraints excluded: chain A residue 1363 HIS Chi-restraints excluded: chain A residue 1375 ASP Chi-restraints excluded: chain A residue 1383 LEU Chi-restraints excluded: chain A residue 1393 TYR Chi-restraints excluded: chain A residue 1429 LEU Chi-restraints excluded: chain A residue 1481 LEU Chi-restraints excluded: chain A residue 1487 LEU Chi-restraints excluded: chain A residue 1496 VAL Chi-restraints excluded: chain A residue 1503 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 43 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 75 optimal weight: 0.0570 chunk 31 optimal weight: 0.7980 chunk 128 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 HIS A 597 ASN A 956 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6651 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10475 Z= 0.158 Angle : 0.485 8.777 14258 Z= 0.246 Chirality : 0.036 0.158 1691 Planarity : 0.003 0.049 1766 Dihedral : 6.041 66.109 1676 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.32 % Allowed : 14.43 % Favored : 82.24 % 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: 1200 helix: 2.41 (0.19), residues: 730 sheet: -0.53 (0.50), residues: 86 loop : -1.35 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 459 HIS 0.006 0.001 HIS A 985 PHE 0.018 0.001 PHE A1212 TYR 0.020 0.001 TYR A1032 ARG 0.006 0.000 ARG A 593 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 137 time to evaluate : 1.252 Fit side-chains revert: symmetry clash REVERT: A 219 ILE cc_start: 0.8026 (tt) cc_final: 0.7733 (tt) REVERT: A 237 GLU cc_start: 0.7250 (tp30) cc_final: 0.6551 (mt-10) REVERT: A 246 LYS cc_start: 0.7503 (mtmt) cc_final: 0.7047 (mmtt) REVERT: A 591 ILE cc_start: 0.7312 (tt) cc_final: 0.7032 (mm) REVERT: A 656 ASN cc_start: 0.8973 (m-40) cc_final: 0.8578 (m-40) REVERT: A 696 ASP cc_start: 0.7992 (t70) cc_final: 0.7592 (t0) REVERT: A 757 ASP cc_start: 0.7729 (t70) cc_final: 0.7240 (t0) REVERT: A 864 GLU cc_start: 0.8671 (tt0) cc_final: 0.8277 (mm-30) REVERT: A 964 ASP cc_start: 0.7692 (t0) cc_final: 0.7438 (m-30) REVERT: A 1245 TRP cc_start: 0.6992 (m100) cc_final: 0.6706 (m-10) REVERT: A 1278 GLN cc_start: 0.8840 (tp40) cc_final: 0.8589 (tp40) REVERT: A 1303 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8312 (tp30) REVERT: A 1353 ASP cc_start: 0.7930 (OUTLIER) cc_final: 0.7668 (m-30) REVERT: A 1383 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7523 (tt) REVERT: A 1393 TYR cc_start: 0.7567 (OUTLIER) cc_final: 0.6804 (p90) REVERT: A 1447 THR cc_start: 0.6595 (t) cc_final: 0.6342 (t) outliers start: 35 outliers final: 28 residues processed: 161 average time/residue: 0.1862 time to fit residues: 45.0340 Evaluate side-chains 162 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 131 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 TRP Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 496 LYS Chi-restraints excluded: chain A residue 707 SER Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1034 MET Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1085 MET Chi-restraints excluded: chain A residue 1104 CYS Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1146 SER Chi-restraints excluded: chain A residue 1325 VAL Chi-restraints excluded: chain A residue 1353 ASP Chi-restraints excluded: chain A residue 1362 LEU Chi-restraints excluded: chain A residue 1363 HIS Chi-restraints excluded: chain A residue 1375 ASP Chi-restraints excluded: chain A residue 1383 LEU Chi-restraints excluded: chain A residue 1393 TYR Chi-restraints excluded: chain A residue 1429 LEU Chi-restraints excluded: chain A residue 1487 LEU Chi-restraints excluded: chain A residue 1503 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 124 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 108 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 80 optimal weight: 0.0770 chunk 78 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6643 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10475 Z= 0.155 Angle : 0.487 10.205 14258 Z= 0.245 Chirality : 0.036 0.160 1691 Planarity : 0.004 0.049 1766 Dihedral : 5.910 63.524 1676 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.70 % Allowed : 14.91 % Favored : 81.39 % 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: 1.64 (0.25), residues: 1200 helix: 2.45 (0.20), residues: 731 sheet: -0.42 (0.50), residues: 86 loop : -1.33 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 459 HIS 0.006 0.001 HIS A 985 PHE 0.017 0.001 PHE A1030 TYR 0.020 0.001 TYR A1032 ARG 0.009 0.000 ARG A 593 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 138 time to evaluate : 1.102 Fit side-chains revert: symmetry clash REVERT: A 219 ILE cc_start: 0.8024 (tt) cc_final: 0.7728 (tt) REVERT: A 237 GLU cc_start: 0.7243 (tp30) cc_final: 0.6560 (mt-10) REVERT: A 246 LYS cc_start: 0.7497 (mtmt) cc_final: 0.7122 (mmtt) REVERT: A 591 ILE cc_start: 0.7292 (tt) cc_final: 0.7017 (mm) REVERT: A 656 ASN cc_start: 0.8977 (m-40) cc_final: 0.8585 (m-40) REVERT: A 696 ASP cc_start: 0.7966 (t70) cc_final: 0.7596 (t0) REVERT: A 757 ASP cc_start: 0.7730 (t70) cc_final: 0.7238 (t0) REVERT: A 864 GLU cc_start: 0.8653 (tt0) cc_final: 0.8269 (mm-30) REVERT: A 960 SER cc_start: 0.6841 (p) cc_final: 0.6496 (t) REVERT: A 964 ASP cc_start: 0.7679 (t0) cc_final: 0.7406 (m-30) REVERT: A 1245 TRP cc_start: 0.6977 (m100) cc_final: 0.6704 (m-10) REVERT: A 1278 GLN cc_start: 0.8776 (tp40) cc_final: 0.8553 (tp40) REVERT: A 1303 GLU cc_start: 0.8727 (mt-10) cc_final: 0.8301 (tp30) REVERT: A 1383 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7556 (tt) REVERT: A 1447 THR cc_start: 0.6628 (t) cc_final: 0.6366 (t) outliers start: 39 outliers final: 28 residues processed: 162 average time/residue: 0.1922 time to fit residues: 46.5656 Evaluate side-chains 162 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 133 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 496 LYS Chi-restraints excluded: chain A residue 626 ASP Chi-restraints excluded: chain A residue 707 SER Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 841 MET Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1034 MET Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1085 MET Chi-restraints excluded: chain A residue 1104 CYS Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1325 VAL Chi-restraints excluded: chain A residue 1362 LEU Chi-restraints excluded: chain A residue 1363 HIS Chi-restraints excluded: chain A residue 1375 ASP Chi-restraints excluded: chain A residue 1383 LEU Chi-restraints excluded: chain A residue 1429 LEU Chi-restraints excluded: chain A residue 1487 LEU Chi-restraints excluded: chain A residue 1496 VAL Chi-restraints excluded: chain A residue 1503 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 79 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 63 optimal weight: 0.0770 chunk 11 optimal weight: 10.0000 chunk 100 optimal weight: 1.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 956 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6640 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10475 Z= 0.163 Angle : 0.488 11.463 14258 Z= 0.245 Chirality : 0.036 0.161 1691 Planarity : 0.003 0.049 1766 Dihedral : 5.864 62.195 1676 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.51 % Allowed : 15.10 % Favored : 81.39 % 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: 1.69 (0.25), residues: 1200 helix: 2.47 (0.20), residues: 730 sheet: -0.27 (0.50), residues: 86 loop : -1.31 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 459 HIS 0.005 0.001 HIS A 985 PHE 0.023 0.001 PHE A 365 TYR 0.019 0.001 TYR A1032 ARG 0.004 0.000 ARG A 593 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 138 time to evaluate : 1.213 Fit side-chains revert: symmetry clash REVERT: A 219 ILE cc_start: 0.8020 (tt) cc_final: 0.7719 (tt) REVERT: A 246 LYS cc_start: 0.7550 (mtmt) cc_final: 0.7063 (mmtt) REVERT: A 338 MET cc_start: 0.7975 (mmm) cc_final: 0.7568 (mtm) REVERT: A 591 ILE cc_start: 0.7339 (tt) cc_final: 0.7099 (mm) REVERT: A 656 ASN cc_start: 0.8962 (m-40) cc_final: 0.8580 (m-40) REVERT: A 696 ASP cc_start: 0.7960 (t70) cc_final: 0.7573 (t0) REVERT: A 757 ASP cc_start: 0.7744 (t70) cc_final: 0.7244 (t0) REVERT: A 864 GLU cc_start: 0.8629 (tt0) cc_final: 0.8288 (mm-30) REVERT: A 960 SER cc_start: 0.6849 (p) cc_final: 0.6493 (t) REVERT: A 964 ASP cc_start: 0.7675 (t0) cc_final: 0.7404 (m-30) REVERT: A 1245 TRP cc_start: 0.6932 (m100) cc_final: 0.6667 (m-10) REVERT: A 1278 GLN cc_start: 0.8783 (tp40) cc_final: 0.8568 (tp40) REVERT: A 1303 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8280 (tp30) REVERT: A 1383 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7541 (tt) REVERT: A 1447 THR cc_start: 0.6659 (t) cc_final: 0.6403 (t) outliers start: 37 outliers final: 30 residues processed: 160 average time/residue: 0.1840 time to fit residues: 44.4476 Evaluate side-chains 168 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 137 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 626 ASP Chi-restraints excluded: chain A residue 707 SER Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 841 MET Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1034 MET Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1085 MET Chi-restraints excluded: chain A residue 1104 CYS Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1146 SER Chi-restraints excluded: chain A residue 1325 VAL Chi-restraints excluded: chain A residue 1362 LEU Chi-restraints excluded: chain A residue 1363 HIS Chi-restraints excluded: chain A residue 1375 ASP Chi-restraints excluded: chain A residue 1383 LEU Chi-restraints excluded: chain A residue 1429 LEU Chi-restraints excluded: chain A residue 1459 VAL Chi-restraints excluded: chain A residue 1487 LEU Chi-restraints excluded: chain A residue 1496 VAL Chi-restraints excluded: chain A residue 1503 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 116 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 956 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 10475 Z= 0.176 Angle : 0.500 12.744 14258 Z= 0.250 Chirality : 0.036 0.159 1691 Planarity : 0.004 0.049 1766 Dihedral : 5.847 61.454 1676 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.42 % Allowed : 15.00 % Favored : 81.58 % 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: 1.70 (0.25), residues: 1200 helix: 2.45 (0.19), residues: 735 sheet: -0.33 (0.50), residues: 88 loop : -1.27 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 459 HIS 0.005 0.001 HIS A 985 PHE 0.029 0.001 PHE A 365 TYR 0.019 0.001 TYR A1032 ARG 0.009 0.000 ARG A 593 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 136 time to evaluate : 1.254 Fit side-chains revert: symmetry clash REVERT: A 219 ILE cc_start: 0.8018 (tt) cc_final: 0.7715 (tt) REVERT: A 246 LYS cc_start: 0.7533 (mtmt) cc_final: 0.7047 (mmtt) REVERT: A 338 MET cc_start: 0.7993 (mmm) cc_final: 0.7561 (mtm) REVERT: A 591 ILE cc_start: 0.7356 (tt) cc_final: 0.7124 (mm) REVERT: A 656 ASN cc_start: 0.8971 (m-40) cc_final: 0.8601 (m-40) REVERT: A 694 GLU cc_start: 0.7371 (mm-30) cc_final: 0.7153 (mm-30) REVERT: A 696 ASP cc_start: 0.7921 (t70) cc_final: 0.7557 (t0) REVERT: A 757 ASP cc_start: 0.7737 (t70) cc_final: 0.7249 (t0) REVERT: A 864 GLU cc_start: 0.8633 (tt0) cc_final: 0.8295 (mm-30) REVERT: A 960 SER cc_start: 0.6862 (p) cc_final: 0.6500 (t) REVERT: A 964 ASP cc_start: 0.7665 (t0) cc_final: 0.7389 (m-30) REVERT: A 1245 TRP cc_start: 0.6934 (m100) cc_final: 0.6674 (m-10) REVERT: A 1278 GLN cc_start: 0.8779 (tp40) cc_final: 0.8558 (tp40) REVERT: A 1303 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8286 (tp30) REVERT: A 1383 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7513 (tt) REVERT: A 1447 THR cc_start: 0.6619 (t) cc_final: 0.6366 (t) outliers start: 36 outliers final: 31 residues processed: 158 average time/residue: 0.1773 time to fit residues: 43.1357 Evaluate side-chains 166 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 134 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 707 SER Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 841 MET Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 966 MET Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1034 MET Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1085 MET Chi-restraints excluded: chain A residue 1104 CYS Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1146 SER Chi-restraints excluded: chain A residue 1325 VAL Chi-restraints excluded: chain A residue 1363 HIS Chi-restraints excluded: chain A residue 1375 ASP Chi-restraints excluded: chain A residue 1383 LEU Chi-restraints excluded: chain A residue 1429 LEU Chi-restraints excluded: chain A residue 1459 VAL Chi-restraints excluded: chain A residue 1487 LEU Chi-restraints excluded: chain A residue 1490 ILE Chi-restraints excluded: chain A residue 1496 VAL Chi-restraints excluded: chain A residue 1503 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 10 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1053 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 10475 Z= 0.200 Angle : 0.518 13.187 14258 Z= 0.258 Chirality : 0.037 0.160 1691 Planarity : 0.004 0.049 1766 Dihedral : 5.868 60.964 1676 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.23 % Allowed : 15.57 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.25), residues: 1200 helix: 2.40 (0.19), residues: 729 sheet: -0.09 (0.52), residues: 81 loop : -1.19 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 459 HIS 0.005 0.001 HIS A 985 PHE 0.030 0.001 PHE A 365 TYR 0.018 0.001 TYR A1032 ARG 0.008 0.000 ARG A 593 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 133 time to evaluate : 1.142 Fit side-chains revert: symmetry clash REVERT: A 219 ILE cc_start: 0.8040 (tt) cc_final: 0.7739 (tt) REVERT: A 246 LYS cc_start: 0.7492 (mtmt) cc_final: 0.7026 (mmtt) REVERT: A 338 MET cc_start: 0.8033 (mmm) cc_final: 0.7684 (mtm) REVERT: A 656 ASN cc_start: 0.8972 (m-40) cc_final: 0.8713 (m-40) REVERT: A 694 GLU cc_start: 0.7387 (mm-30) cc_final: 0.7173 (mm-30) REVERT: A 696 ASP cc_start: 0.7901 (t70) cc_final: 0.7504 (t0) REVERT: A 757 ASP cc_start: 0.7758 (t70) cc_final: 0.7275 (t0) REVERT: A 864 GLU cc_start: 0.8583 (tt0) cc_final: 0.8252 (mm-30) REVERT: A 964 ASP cc_start: 0.7676 (t0) cc_final: 0.7409 (m-30) REVERT: A 1245 TRP cc_start: 0.6979 (m100) cc_final: 0.6712 (m-10) REVERT: A 1303 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8275 (tp30) REVERT: A 1383 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7525 (tt) REVERT: A 1447 THR cc_start: 0.6634 (t) cc_final: 0.6362 (t) outliers start: 34 outliers final: 30 residues processed: 154 average time/residue: 0.1815 time to fit residues: 43.3096 Evaluate side-chains 162 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 131 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 707 SER Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 966 MET Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1034 MET Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1085 MET Chi-restraints excluded: chain A residue 1104 CYS Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1146 SER Chi-restraints excluded: chain A residue 1325 VAL Chi-restraints excluded: chain A residue 1363 HIS Chi-restraints excluded: chain A residue 1375 ASP Chi-restraints excluded: chain A residue 1383 LEU Chi-restraints excluded: chain A residue 1429 LEU Chi-restraints excluded: chain A residue 1459 VAL Chi-restraints excluded: chain A residue 1487 LEU Chi-restraints excluded: chain A residue 1490 ILE Chi-restraints excluded: chain A residue 1496 VAL Chi-restraints excluded: chain A residue 1503 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 32 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 15 optimal weight: 0.0470 chunk 29 optimal weight: 0.7980 chunk 105 optimal weight: 0.5980 chunk 44 optimal weight: 0.0670 chunk 108 optimal weight: 0.3980 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 0.0970 chunk 92 optimal weight: 0.9980 chunk 6 optimal weight: 10.0000 overall best weight: 0.2414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.135647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.109248 restraints weight = 17383.257| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.62 r_work: 0.3349 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.4365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.073 10475 Z= 0.135 Angle : 0.496 13.022 14258 Z= 0.247 Chirality : 0.036 0.161 1691 Planarity : 0.004 0.049 1766 Dihedral : 5.712 60.784 1676 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.09 % Allowed : 16.71 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.25), residues: 1200 helix: 2.63 (0.20), residues: 735 sheet: 0.06 (0.52), residues: 86 loop : -1.12 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 459 HIS 0.005 0.001 HIS A 985 PHE 0.029 0.001 PHE A 365 TYR 0.020 0.001 TYR A1032 ARG 0.009 0.000 ARG A 593 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2335.51 seconds wall clock time: 42 minutes 34.77 seconds (2554.77 seconds total)