Starting phenix.real_space_refine on Thu Apr 11 11:03:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jxq_36709/04_2024/8jxq_36709_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jxq_36709/04_2024/8jxq_36709.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jxq_36709/04_2024/8jxq_36709_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jxq_36709/04_2024/8jxq_36709_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jxq_36709/04_2024/8jxq_36709_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jxq_36709/04_2024/8jxq_36709.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jxq_36709/04_2024/8jxq_36709.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jxq_36709/04_2024/8jxq_36709_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jxq_36709/04_2024/8jxq_36709_trim_updated.pdb" } resolution = 3.32 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= 0.045 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: 5 Type Number sf(0) Gaussians S 59 5.16 5 C 7228 2.51 5 N 1829 2.21 5 O 1994 1.98 5 H 11287 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 189": "OE1" <-> "OE2" Residue "A ASP 230": "OD1" <-> "OD2" Residue "A ASP 354": "OD1" <-> "OD2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 611": "OE1" <-> "OE2" Residue "A GLU 614": "OE1" <-> "OE2" Residue "A ASP 630": "OD1" <-> "OD2" Residue "A GLU 641": "OE1" <-> "OE2" Residue "A GLU 687": "OE1" <-> "OE2" Residue "A GLU 689": "OE1" <-> "OE2" Residue "A TYR 703": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 717": "OD1" <-> "OD2" Residue "A GLU 724": "OE1" <-> "OE2" Residue "A GLU 727": "OE1" <-> "OE2" Residue "A GLU 735": "OE1" <-> "OE2" Residue "A ASP 750": "OD1" <-> "OD2" Residue "A TYR 776": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 782": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 785": "OD1" <-> "OD2" Residue "A PHE 1071": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1084": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 1093": "OD1" <-> "OD2" Residue "A GLU 1212": "OE1" <-> "OE2" Residue "A GLU 1263": "OE1" <-> "OE2" Residue "A GLU 1279": "OE1" <-> "OE2" Residue "A ASP 1372": "OD1" <-> "OD2" Residue "A TYR 1401": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1411": "OE1" <-> "OE2" Residue "A GLU 1429": "OE1" <-> "OE2" Residue "A ASP 1502": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 22397 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 22314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1388, 22314 Classifications: {'peptide': 1388} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 1345} Chain breaks: 3 Chain: "A" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 83 Unusual residues: {'CLR': 1, 'FEI': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.99, per 1000 atoms: 0.45 Number of scatterers: 22397 At special positions: 0 Unit cell: (94.16, 123.05, 153.01, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 59 16.00 O 1994 8.00 N 1829 7.00 C 7228 6.00 H 11287 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 6 " - pdb=" SG CYS A 26 " distance=2.03 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: 18.70 Conformation dependent library (CDL) restraints added in 2.4 seconds 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2624 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 76 helices and 6 sheets defined 55.6% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.49 Creating SS restraints... Processing helix chain 'A' and resid 3 through 6 No H-bonds generated for 'chain 'A' and resid 3 through 6' Processing helix chain 'A' and resid 13 through 16 Processing helix chain 'A' and resid 25 through 31 Processing helix chain 'A' and resid 34 through 41 Processing helix chain 'A' and resid 44 through 53 removed outlier: 4.349A pdb=" N VAL A 51 " --> pdb=" O GLN A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 87 removed outlier: 3.783A pdb=" N VAL A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 123 removed outlier: 3.812A pdb=" N ASN A 103 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Proline residue: A 104 - end of helix removed outlier: 3.509A pdb=" N LEU A 108 " --> pdb=" O PRO A 104 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLN A 122 " --> pdb=" O GLN A 118 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N TRP A 123 " --> pdb=" O TYR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 133 No H-bonds generated for 'chain 'A' and resid 130 through 133' Processing helix chain 'A' and resid 135 through 140 Processing helix chain 'A' and resid 145 through 156 removed outlier: 3.570A pdb=" N THR A 149 " --> pdb=" O PHE A 145 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE A 151 " --> pdb=" O PHE A 147 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN A 156 " --> pdb=" O ARG A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 183 removed outlier: 3.787A pdb=" N ILE A 170 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLY A 173 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE A 176 " --> pdb=" O TYR A 172 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU A 177 " --> pdb=" O GLY A 173 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILE A 180 " --> pdb=" O ILE A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 216 Processing helix chain 'A' and resid 235 through 256 removed outlier: 3.664A pdb=" N SER A 240 " --> pdb=" O LYS A 236 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR A 244 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N HIS A 245 " --> pdb=" O LYS A 241 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG A 248 " --> pdb=" O THR A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 315 Processing helix chain 'A' and resid 326 through 334 removed outlier: 3.627A pdb=" N VAL A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 340 No H-bonds generated for 'chain 'A' and resid 337 through 340' Processing helix chain 'A' and resid 343 through 351 removed outlier: 3.653A pdb=" N SER A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 363 Processing helix chain 'A' and resid 366 through 369 No H-bonds generated for 'chain 'A' and resid 366 through 369' Processing helix chain 'A' and resid 379 through 387 removed outlier: 3.637A pdb=" N GLN A 383 " --> pdb=" O GLN A 379 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU A 384 " --> pdb=" O CYS A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 406 removed outlier: 3.908A pdb=" N SER A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS A 402 " --> pdb=" O ALA A 398 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS A 403 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 405 " --> pdb=" O TYR A 401 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N THR A 406 " --> pdb=" O LYS A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 411 No H-bonds generated for 'chain 'A' and resid 409 through 411' Processing helix chain 'A' and resid 417 through 423 removed outlier: 3.647A pdb=" N VAL A 421 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ASN A 422 " --> pdb=" O GLY A 418 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU A 423 " --> pdb=" O GLU A 419 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 417 through 423' Processing helix chain 'A' and resid 438 through 489 removed outlier: 3.750A pdb=" N LEU A 441 " --> pdb=" O MET A 438 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TRP A 442 " --> pdb=" O HIS A 439 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SER A 443 " --> pdb=" O MET A 440 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N SER A 444 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU A 446 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLN A 447 " --> pdb=" O SER A 444 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE A 448 " --> pdb=" O VAL A 445 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL A 449 " --> pdb=" O LEU A 446 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU A 450 " --> pdb=" O GLN A 447 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER A 451 " --> pdb=" O ILE A 448 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE A 452 " --> pdb=" O VAL A 449 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N PHE A 454 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU A 455 " --> pdb=" O ILE A 452 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG A 457 " --> pdb=" O PHE A 454 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU A 459 " --> pdb=" O TRP A 456 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N GLY A 460 " --> pdb=" O ARG A 457 " (cutoff:3.500A) Proline residue: A 461 - end of helix removed outlier: 4.083A pdb=" N VAL A 471 " --> pdb=" O GLY A 468 " (cutoff:3.500A) Proline residue: A 475 - end of helix removed outlier: 3.861A pdb=" N ILE A 479 " --> pdb=" O ILE A 476 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N LEU A 480 " --> pdb=" O ASN A 477 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER A 481 " --> pdb=" O ALA A 478 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR A 482 " --> pdb=" O ILE A 479 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LYS A 483 " --> pdb=" O LEU A 480 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THR A 486 " --> pdb=" O LYS A 483 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 487 " --> pdb=" O SER A 484 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL A 489 " --> pdb=" O THR A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 506 removed outlier: 3.702A pdb=" N LEU A 499 " --> pdb=" O LYS A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 514 Processing helix chain 'A' and resid 518 through 540 removed outlier: 4.161A pdb=" N LYS A 531 " --> pdb=" O ASN A 527 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ASN A 535 " --> pdb=" O LYS A 531 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE A 539 " --> pdb=" O ASN A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 551 No H-bonds generated for 'chain 'A' and resid 548 through 551' Processing helix chain 'A' and resid 553 through 565 removed outlier: 3.521A pdb=" N SER A 558 " --> pdb=" O PRO A 554 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL A 559 " --> pdb=" O VAL A 555 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE A 562 " --> pdb=" O SER A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 583 removed outlier: 3.664A pdb=" N PHE A 580 " --> pdb=" O ALA A 576 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N THR A 581 " --> pdb=" O GLN A 577 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER A 582 " --> pdb=" O LYS A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 603 Proline residue: A 592 - end of helix removed outlier: 3.893A pdb=" N LEU A 596 " --> pdb=" O PRO A 592 " (cutoff:3.500A) Proline residue: A 597 - end of helix removed outlier: 3.603A pdb=" N SER A 602 " --> pdb=" O MET A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 616 Processing helix chain 'A' and resid 677 through 684 Processing helix chain 'A' and resid 715 through 720 Processing helix chain 'A' and resid 727 through 736 Processing helix chain 'A' and resid 740 through 745 Processing helix chain 'A' and resid 749 through 751 No H-bonds generated for 'chain 'A' and resid 749 through 751' Processing helix chain 'A' and resid 756 through 758 No H-bonds generated for 'chain 'A' and resid 756 through 758' Processing helix chain 'A' and resid 763 through 777 Processing helix chain 'A' and resid 793 through 802 Processing helix chain 'A' and resid 825 through 827 No H-bonds generated for 'chain 'A' and resid 825 through 827' Processing helix chain 'A' and resid 845 through 851 Processing helix chain 'A' and resid 854 through 865 Processing helix chain 'A' and resid 965 through 973 Processing helix chain 'A' and resid 976 through 1001 removed outlier: 3.889A pdb=" N PHE A 981 " --> pdb=" O PHE A 977 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE A 982 " --> pdb=" O SER A 978 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA A 985 " --> pdb=" O PHE A 981 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N PHE A 986 " --> pdb=" O ILE A 982 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN A 989 " --> pdb=" O ALA A 985 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE A 994 " --> pdb=" O SER A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1008 Processing helix chain 'A' and resid 1017 through 1030 removed outlier: 4.109A pdb=" N MET A1022 " --> pdb=" O SER A1018 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG A1023 " --> pdb=" O GLN A1019 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL A1024 " --> pdb=" O ARG A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1040 through 1052 removed outlier: 3.798A pdb=" N TRP A1044 " --> pdb=" O ILE A1040 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER A1045 " --> pdb=" O ALA A1041 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS A1051 " --> pdb=" O PHE A1047 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A1052 " --> pdb=" O GLY A1048 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1066 removed outlier: 3.513A pdb=" N LYS A1058 " --> pdb=" O ASN A1054 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLN A1059 " --> pdb=" O ILE A1055 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU A1065 " --> pdb=" O LEU A1061 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ARG A1066 " --> pdb=" O ASN A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1074 Processing helix chain 'A' and resid 1077 through 1080 No H-bonds generated for 'chain 'A' and resid 1077 through 1080' Processing helix chain 'A' and resid 1096 through 1110 removed outlier: 3.700A pdb=" N SER A1101 " --> pdb=" O GLN A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1112 through 1119 removed outlier: 3.738A pdb=" N CYS A1117 " --> pdb=" O LEU A1113 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA A1119 " --> pdb=" O MET A1115 " (cutoff:3.500A) Processing helix chain 'A' and resid 1121 through 1149 removed outlier: 4.074A pdb=" N ILE A1128 " --> pdb=" O ILE A1125 " (cutoff:3.500A) Proline residue: A1129 - end of helix removed outlier: 3.742A pdb=" N ILE A1132 " --> pdb=" O PRO A1129 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A1135 " --> pdb=" O ILE A1132 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER A1136 " --> pdb=" O ILE A1133 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET A1139 " --> pdb=" O SER A1136 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE A1140 " --> pdb=" O VAL A1137 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR A1141 " --> pdb=" O GLN A1138 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL A1142 " --> pdb=" O MET A1139 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER A1143 " --> pdb=" O PHE A1140 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER A1145 " --> pdb=" O VAL A1142 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ARG A1146 " --> pdb=" O SER A1143 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN A1147 " --> pdb=" O THR A1144 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A1148 " --> pdb=" O SER A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1158 through 1168 removed outlier: 3.540A pdb=" N GLU A1165 " --> pdb=" O SER A1161 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1175 Processing helix chain 'A' and resid 1183 through 1186 No H-bonds generated for 'chain 'A' and resid 1183 through 1186' Processing helix chain 'A' and resid 1191 through 1201 removed outlier: 3.540A pdb=" N LYS A1195 " --> pdb=" O ASP A1191 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N CYS A1196 " --> pdb=" O THR A1192 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER A1199 " --> pdb=" O LYS A1195 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TRP A1200 " --> pdb=" O CYS A1196 " (cutoff:3.500A) Processing helix chain 'A' and resid 1205 through 1211 removed outlier: 3.746A pdb=" N ARG A1210 " --> pdb=" O TRP A1206 " (cutoff:3.500A) Processing helix chain 'A' and resid 1215 through 1221 removed outlier: 3.557A pdb=" N VAL A1219 " --> pdb=" O GLY A1215 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE A1220 " --> pdb=" O ASN A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1235 through 1247 removed outlier: 3.775A pdb=" N GLY A1239 " --> pdb=" O GLY A1235 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ASN A1244 " --> pdb=" O PHE A1240 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ASN A1247 " --> pdb=" O SER A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1264 removed outlier: 3.505A pdb=" N THR A1259 " --> pdb=" O LEU A1255 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER A1260 " --> pdb=" O VAL A1256 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A1262 " --> pdb=" O MET A1258 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU A1263 " --> pdb=" O THR A1259 " (cutoff:3.500A) Processing helix chain 'A' and resid 1267 through 1276 removed outlier: 3.658A pdb=" N THR A1276 " --> pdb=" O ILE A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1340 through 1347 removed outlier: 3.652A pdb=" N THR A1344 " --> pdb=" O LYS A1340 " (cutoff:3.500A) Processing helix chain 'A' and resid 1365 through 1367 No H-bonds generated for 'chain 'A' and resid 1365 through 1367' Processing helix chain 'A' and resid 1370 through 1376 removed outlier: 4.104A pdb=" N LYS A1376 " --> pdb=" O ASP A1372 " (cutoff:3.500A) Processing helix chain 'A' and resid 1391 through 1395 Processing helix chain 'A' and resid 1403 through 1412 Processing helix chain 'A' and resid 1416 through 1421 Processing helix chain 'A' and resid 1425 through 1427 No H-bonds generated for 'chain 'A' and resid 1425 through 1427' Processing helix chain 'A' and resid 1432 through 1434 No H-bonds generated for 'chain 'A' and resid 1432 through 1434' Processing helix chain 'A' and resid 1439 through 1453 Processing helix chain 'A' and resid 1469 through 1482 Processing helix chain 'A' and resid 1495 through 1497 No H-bonds generated for 'chain 'A' and resid 1495 through 1497' Processing helix chain 'A' and resid 1518 through 1523 Processing helix chain 'A' and resid 1527 through 1534 Processing sheet with id= A, first strand: chain 'A' and resid 627 through 629 removed outlier: 6.210A pdb=" N ILE A 695 " --> pdb=" O ARG A 628 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET A 637 " --> pdb=" O ILE A 661 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 838 through 843 removed outlier: 6.914A pdb=" N VAL A 833 " --> pdb=" O VAL A 840 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LYS A 842 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ILE A 831 " --> pdb=" O LYS A 842 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ARG A 815 " --> pdb=" O VAL A 667 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N VAL A 669 " --> pdb=" O ARG A 815 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU A 817 " --> pdb=" O VAL A 669 " (cutoff:3.500A) removed outlier: 8.736A pdb=" N GLY A 671 " --> pdb=" O LEU A 817 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1322 through 1324 Processing sheet with id= D, first strand: chain 'A' and resid 1503 through 1507 removed outlier: 6.162A pdb=" N VAL A1488 " --> pdb=" O ILE A1330 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N VAL A1332 " --> pdb=" O VAL A1488 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N THR A1490 " --> pdb=" O VAL A1332 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N GLY A1334 " --> pdb=" O THR A1490 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 643 through 645 removed outlier: 3.657A pdb=" N HIS A 692 " --> pdb=" O SER A 643 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N THR A 645 " --> pdb=" O ASN A 690 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N ASN A 690 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1305 through 1307 removed outlier: 8.178A pdb=" N VAL A1307 " --> pdb=" O ARG A1318 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ARG A1318 " --> pdb=" O VAL A1307 " (cutoff:3.500A) 386 hydrogen bonds defined for protein. 1035 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: 9.80 Time building geometry restraints manager: 19.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 11269 1.03 - 1.23: 99 1.23 - 1.43: 4579 1.43 - 1.62: 6595 1.62 - 1.82: 96 Bond restraints: 22638 Sorted by residual: bond pdb=" C28 FEI A1602 " pdb=" O29 FEI A1602 " ideal model delta sigma weight residual 1.189 1.400 -0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C50 FEI A1602 " pdb=" O51 FEI A1602 " ideal model delta sigma weight residual 1.189 1.396 -0.207 2.00e-02 2.50e+03 1.07e+02 bond pdb=" C32 FEI A1602 " pdb=" C33 FEI A1602 " ideal model delta sigma weight residual 1.329 1.529 -0.200 2.00e-02 2.50e+03 1.00e+02 bond pdb=" C53 FEI A1602 " pdb=" C54 FEI A1602 " ideal model delta sigma weight residual 1.333 1.528 -0.195 2.00e-02 2.50e+03 9.49e+01 bond pdb=" C20 FEI A1602 " pdb=" C21 FEI A1602 " ideal model delta sigma weight residual 1.355 1.529 -0.174 2.00e-02 2.50e+03 7.56e+01 ... (remaining 22633 not shown) Histogram of bond angle deviations from ideal: 100.14 - 106.93: 337 106.93 - 113.72: 27306 113.72 - 120.51: 7493 120.51 - 127.30: 5724 127.30 - 134.09: 119 Bond angle restraints: 40979 Sorted by residual: angle pdb=" N ILE A 396 " pdb=" CA ILE A 396 " pdb=" C ILE A 396 " ideal model delta sigma weight residual 111.90 108.77 3.13 8.10e-01 1.52e+00 1.49e+01 angle pdb=" C22 FEI A1602 " pdb=" C24 FEI A1602 " pdb=" C25 FEI A1602 " ideal model delta sigma weight residual 120.05 108.83 11.22 3.00e+00 1.11e-01 1.40e+01 angle pdb=" N VAL A1114 " pdb=" CA VAL A1114 " pdb=" C VAL A1114 " ideal model delta sigma weight residual 113.39 108.32 5.07 1.47e+00 4.63e-01 1.19e+01 angle pdb=" N ILE A 347 " pdb=" CA ILE A 347 " pdb=" C ILE A 347 " ideal model delta sigma weight residual 111.58 108.16 3.42 1.06e+00 8.90e-01 1.04e+01 angle pdb=" N ILE A1088 " pdb=" CA ILE A1088 " pdb=" C ILE A1088 " ideal model delta sigma weight residual 113.00 109.11 3.89 1.30e+00 5.92e-01 8.97e+00 ... (remaining 40974 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.05: 9912 22.05 - 44.11: 562 44.11 - 66.16: 129 66.16 - 88.22: 13 88.22 - 110.27: 2 Dihedral angle restraints: 10618 sinusoidal: 5781 harmonic: 4837 Sorted by residual: dihedral pdb=" CB CYS A 6 " pdb=" SG CYS A 6 " pdb=" SG CYS A 26 " pdb=" CB CYS A 26 " ideal model delta sinusoidal sigma weight residual 93.00 55.31 37.69 1 1.00e+01 1.00e-02 2.00e+01 dihedral pdb=" CA SER A 185 " pdb=" C SER A 185 " pdb=" N GLU A 186 " pdb=" CA GLU A 186 " ideal model delta harmonic sigma weight residual 180.00 159.85 20.15 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" C07 FEI A1602 " pdb=" C08 FEI A1602 " pdb=" C09 FEI A1602 " pdb=" O10 FEI A1602 " ideal model delta sinusoidal sigma weight residual -58.07 52.20 -110.27 1 3.00e+01 1.11e-03 1.44e+01 ... (remaining 10615 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1131 0.029 - 0.057: 477 0.057 - 0.086: 115 0.086 - 0.115: 61 0.115 - 0.143: 16 Chirality restraints: 1800 Sorted by residual: chirality pdb=" CA ILE A1491 " pdb=" N ILE A1491 " pdb=" C ILE A1491 " pdb=" CB ILE A1491 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" CA ILE A1380 " pdb=" N ILE A1380 " pdb=" C ILE A1380 " pdb=" CB ILE A1380 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.57e-01 chirality pdb=" CA ILE A1524 " pdb=" N ILE A1524 " pdb=" C ILE A1524 " pdb=" CB ILE A1524 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.54e-01 ... (remaining 1797 not shown) Planarity restraints: 3239 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C03 FEI A1602 " 0.562 2.00e-02 2.50e+03 2.32e-01 1.35e+03 pdb=" C46 FEI A1602 " -0.320 2.00e-02 2.50e+03 pdb=" C47 FEI A1602 " -0.175 2.00e-02 2.50e+03 pdb=" C48 FEI A1602 " -0.118 2.00e-02 2.50e+03 pdb=" C49 FEI A1602 " 0.015 2.00e-02 2.50e+03 pdb=" C50 FEI A1602 " 0.035 2.00e-02 2.50e+03 pdb=" C53 FEI A1602 " 0.118 2.00e-02 2.50e+03 pdb=" C55 FEI A1602 " -0.181 2.00e-02 2.50e+03 pdb=" N52 FEI A1602 " -0.083 2.00e-02 2.50e+03 pdb=" O51 FEI A1602 " 0.149 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C22 FEI A1602 " -0.538 2.00e-02 2.50e+03 2.32e-01 1.35e+03 pdb=" C24 FEI A1602 " 0.343 2.00e-02 2.50e+03 pdb=" C25 FEI A1602 " 0.199 2.00e-02 2.50e+03 pdb=" C26 FEI A1602 " 0.047 2.00e-02 2.50e+03 pdb=" C27 FEI A1602 " -0.052 2.00e-02 2.50e+03 pdb=" C28 FEI A1602 " 0.043 2.00e-02 2.50e+03 pdb=" C31 FEI A1602 " -0.223 2.00e-02 2.50e+03 pdb=" C32 FEI A1602 " -0.001 2.00e-02 2.50e+03 pdb=" N30 FEI A1602 " 0.193 2.00e-02 2.50e+03 pdb=" O29 FEI A1602 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A1128 " -0.031 5.00e-02 4.00e+02 4.78e-02 3.65e+00 pdb=" N PRO A1129 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO A1129 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A1129 " -0.027 5.00e-02 4.00e+02 ... (remaining 3236 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 881 2.17 - 2.78: 44890 2.78 - 3.38: 61736 3.38 - 3.99: 79867 3.99 - 4.60: 126251 Nonbonded interactions: 313625 Sorted by model distance: nonbonded pdb=" O PHE A 800 " pdb=" H GLY A 805 " model vdw 1.559 1.850 nonbonded pdb=" O LEU A 720 " pdb=" HG1 THR A 723 " model vdw 1.611 1.850 nonbonded pdb=" HG1 THR A 235 " pdb=" OD1 ASP A1191 " model vdw 1.615 1.850 nonbonded pdb=" HG SER A 139 " pdb=" OE1 GLN A 175 " model vdw 1.623 1.850 nonbonded pdb=" O GLN A1097 " pdb="HE21 GLN A1097 " model vdw 1.628 1.850 ... (remaining 313620 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: 0.710 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: 0.310 Extract box with map and model: 4.610 Check model and map are aligned: 0.350 Set scattering table: 0.240 Process input model: 76.070 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 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 : 0.007 0.211 11351 Z= 0.491 Angle : 0.601 11.217 15405 Z= 0.344 Chirality : 0.037 0.143 1800 Planarity : 0.008 0.232 1897 Dihedral : 14.814 110.270 4160 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.45 % Favored : 98.48 % Rotamer: Outliers : 0.41 % Allowed : 11.95 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.23), residues: 1380 helix: -2.05 (0.17), residues: 885 sheet: 1.42 (0.56), residues: 75 loop : 0.53 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1206 HIS 0.010 0.001 HIS A1428 PHE 0.009 0.001 PHE A 986 TYR 0.017 0.001 TYR A 101 ARG 0.013 0.000 ARG A1392 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 174 time to evaluate : 1.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 177 average time/residue: 0.5074 time to fit residues: 130.7905 Evaluate side-chains 116 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 114 time to evaluate : 1.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 822 MET Chi-restraints excluded: chain A residue 1053 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 8.9990 chunk 104 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 70 optimal weight: 0.0470 chunk 55 optimal weight: 5.9990 chunk 108 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 chunk 125 optimal weight: 6.9990 overall best weight: 4.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 118 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 11351 Z= 0.329 Angle : 0.634 7.251 15405 Z= 0.343 Chirality : 0.040 0.166 1800 Planarity : 0.005 0.095 1897 Dihedral : 6.812 92.231 1565 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.88 % Favored : 98.04 % Rotamer: Outliers : 0.89 % Allowed : 14.55 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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 (0.22), residues: 1380 helix: -1.87 (0.16), residues: 899 sheet: 1.34 (0.53), residues: 80 loop : 0.47 (0.32), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1254 HIS 0.005 0.001 HIS A1428 PHE 0.021 0.001 PHE A 639 TYR 0.010 0.001 TYR A 319 ARG 0.007 0.000 ARG A1149 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 115 time to evaluate : 1.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 122 average time/residue: 0.4739 time to fit residues: 87.6919 Evaluate side-chains 113 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 105 time to evaluate : 1.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 728 LYS Chi-restraints excluded: chain A residue 822 MET Chi-restraints excluded: chain A residue 1206 TRP Chi-restraints excluded: chain A residue 1261 GLU Chi-restraints excluded: chain A residue 1454 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 69 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 125 optimal weight: 6.9990 chunk 135 optimal weight: 30.0000 chunk 111 optimal weight: 4.9990 chunk 124 optimal weight: 6.9990 chunk 42 optimal weight: 0.6980 chunk 100 optimal weight: 4.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 694 HIS ** A 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 11351 Z= 0.225 Angle : 0.560 7.462 15405 Z= 0.295 Chirality : 0.038 0.154 1800 Planarity : 0.004 0.045 1897 Dihedral : 6.438 93.642 1564 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.96 % Favored : 97.97 % Rotamer: Outliers : 1.14 % Allowed : 14.80 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -1.46 (0.22), residues: 1380 helix: -1.48 (0.17), residues: 900 sheet: 0.92 (0.52), residues: 86 loop : 0.50 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1254 HIS 0.005 0.001 HIS A1428 PHE 0.023 0.001 PHE A 639 TYR 0.009 0.001 TYR A 319 ARG 0.003 0.000 ARG A1149 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 109 time to evaluate : 1.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 684 MET cc_start: 0.8708 (mmm) cc_final: 0.8492 (mmm) REVERT: A 1069 MET cc_start: 0.8361 (mmm) cc_final: 0.7894 (tpp) outliers start: 14 outliers final: 12 residues processed: 116 average time/residue: 0.5120 time to fit residues: 92.4421 Evaluate side-chains 113 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 101 time to evaluate : 2.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain A residue 1053 SER Chi-restraints excluded: chain A residue 1116 ILE Chi-restraints excluded: chain A residue 1206 TRP Chi-restraints excluded: chain A residue 1371 HIS Chi-restraints excluded: chain A residue 1454 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 124 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 chunk 133 optimal weight: 7.9990 chunk 119 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1185 HIS A1303 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 11351 Z= 0.410 Angle : 0.642 7.596 15405 Z= 0.344 Chirality : 0.040 0.151 1800 Planarity : 0.004 0.042 1897 Dihedral : 6.080 92.875 1561 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.97 % Favored : 96.96 % Rotamer: Outliers : 2.11 % Allowed : 14.63 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -1.49 (0.22), residues: 1380 helix: -1.41 (0.16), residues: 902 sheet: 0.73 (0.53), residues: 84 loop : 0.27 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1206 HIS 0.004 0.001 HIS A 692 PHE 0.015 0.001 PHE A 639 TYR 0.009 0.001 TYR A 319 ARG 0.004 0.000 ARG A1392 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 99 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1069 MET cc_start: 0.8354 (mmm) cc_final: 0.7898 (tpp) REVERT: A 1225 MET cc_start: 0.7055 (mmm) cc_final: 0.6717 (mmm) outliers start: 26 outliers final: 21 residues processed: 117 average time/residue: 0.4744 time to fit residues: 84.4272 Evaluate side-chains 115 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 94 time to evaluate : 1.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 639 PHE Chi-restraints excluded: chain A residue 822 MET Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1117 CYS Chi-restraints excluded: chain A residue 1157 SER Chi-restraints excluded: chain A residue 1206 TRP Chi-restraints excluded: chain A residue 1371 HIS Chi-restraints excluded: chain A residue 1454 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 75 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 113 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 68 optimal weight: 7.9990 chunk 119 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11351 Z= 0.289 Angle : 0.571 6.899 15405 Z= 0.302 Chirality : 0.038 0.154 1800 Planarity : 0.003 0.043 1897 Dihedral : 6.033 97.259 1561 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.75 % Favored : 97.17 % Rotamer: Outliers : 1.79 % Allowed : 15.61 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -1.18 (0.22), residues: 1380 helix: -1.13 (0.17), residues: 904 sheet: 0.67 (0.52), residues: 84 loop : 0.32 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1206 HIS 0.004 0.001 HIS A 692 PHE 0.015 0.001 PHE A 639 TYR 0.011 0.001 TYR A 319 ARG 0.004 0.000 ARG A1210 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 98 time to evaluate : 1.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1069 MET cc_start: 0.8343 (mmm) cc_final: 0.7927 (tpp) outliers start: 22 outliers final: 21 residues processed: 111 average time/residue: 0.4543 time to fit residues: 77.7928 Evaluate side-chains 113 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 92 time to evaluate : 1.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 639 PHE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 822 MET Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1053 SER Chi-restraints excluded: chain A residue 1206 TRP Chi-restraints excluded: chain A residue 1246 LEU Chi-restraints excluded: chain A residue 1371 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 120 optimal weight: 0.1980 chunk 26 optimal weight: 3.9990 chunk 78 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 133 optimal weight: 10.0000 chunk 110 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 70 optimal weight: 0.0870 chunk 128 optimal weight: 5.9990 overall best weight: 2.4564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11351 Z= 0.208 Angle : 0.536 7.399 15405 Z= 0.277 Chirality : 0.037 0.156 1800 Planarity : 0.003 0.041 1897 Dihedral : 5.931 98.007 1561 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.46 % Favored : 97.46 % Rotamer: Outliers : 1.87 % Allowed : 15.77 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.77 (0.23), residues: 1380 helix: -0.74 (0.17), residues: 904 sheet: 0.53 (0.52), residues: 84 loop : 0.36 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1254 HIS 0.003 0.001 HIS A 692 PHE 0.016 0.001 PHE A 639 TYR 0.009 0.001 TYR A 319 ARG 0.003 0.000 ARG A1210 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 97 time to evaluate : 1.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1069 MET cc_start: 0.8313 (mmm) cc_final: 0.7903 (tpp) outliers start: 23 outliers final: 21 residues processed: 112 average time/residue: 0.4427 time to fit residues: 77.4787 Evaluate side-chains 115 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 94 time to evaluate : 1.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 639 PHE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 822 MET Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1053 SER Chi-restraints excluded: chain A residue 1206 TRP Chi-restraints excluded: chain A residue 1246 LEU Chi-restraints excluded: chain A residue 1371 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 97 optimal weight: 8.9990 chunk 75 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 74 optimal weight: 0.6980 chunk 133 optimal weight: 9.9990 chunk 83 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 82 optimal weight: 0.6980 overall best weight: 2.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11351 Z= 0.220 Angle : 0.531 6.841 15405 Z= 0.274 Chirality : 0.037 0.154 1800 Planarity : 0.003 0.041 1897 Dihedral : 5.840 98.157 1561 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.87 % Allowed : 15.77 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.44 (0.23), residues: 1380 helix: -0.46 (0.17), residues: 905 sheet: 0.54 (0.53), residues: 84 loop : 0.44 (0.33), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 646 HIS 0.003 0.001 HIS A 692 PHE 0.014 0.001 PHE A 639 TYR 0.007 0.001 TYR A 319 ARG 0.003 0.000 ARG A1210 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 95 time to evaluate : 1.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 662 MET cc_start: 0.8679 (mmm) cc_final: 0.8358 (mmm) REVERT: A 1069 MET cc_start: 0.8312 (mmm) cc_final: 0.7900 (tpp) outliers start: 23 outliers final: 22 residues processed: 109 average time/residue: 0.4342 time to fit residues: 72.9161 Evaluate side-chains 115 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 93 time to evaluate : 1.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 393 ARG Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 639 PHE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 822 MET Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1206 TRP Chi-restraints excluded: chain A residue 1246 LEU Chi-restraints excluded: chain A residue 1371 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 53 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 120 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 524 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11351 Z= 0.267 Angle : 0.556 8.363 15405 Z= 0.288 Chirality : 0.037 0.152 1800 Planarity : 0.003 0.041 1897 Dihedral : 5.754 98.042 1561 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.20 % Allowed : 15.53 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.30 (0.23), residues: 1380 helix: -0.31 (0.17), residues: 899 sheet: 0.51 (0.53), residues: 84 loop : 0.40 (0.33), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1206 HIS 0.004 0.001 HIS A 692 PHE 0.011 0.001 PHE A 639 TYR 0.008 0.001 TYR A 319 ARG 0.003 0.000 ARG A1210 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 91 time to evaluate : 1.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 662 MET cc_start: 0.8708 (mmm) cc_final: 0.8379 (mmm) REVERT: A 1069 MET cc_start: 0.8388 (mmm) cc_final: 0.7999 (tpp) outliers start: 27 outliers final: 23 residues processed: 108 average time/residue: 0.4742 time to fit residues: 78.2701 Evaluate side-chains 110 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 87 time to evaluate : 1.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 393 ARG Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 639 PHE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 822 MET Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1053 SER Chi-restraints excluded: chain A residue 1083 ARG Chi-restraints excluded: chain A residue 1206 TRP Chi-restraints excluded: chain A residue 1371 HIS Chi-restraints excluded: chain A residue 1393 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 20.0000 chunk 116 optimal weight: 10.0000 chunk 123 optimal weight: 0.0040 chunk 74 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 chunk 117 optimal weight: 20.0000 chunk 81 optimal weight: 7.9990 chunk 131 optimal weight: 5.9990 overall best weight: 1.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11351 Z= 0.164 Angle : 0.511 8.826 15405 Z= 0.259 Chirality : 0.037 0.156 1800 Planarity : 0.003 0.040 1897 Dihedral : 5.709 97.850 1561 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.95 % Allowed : 15.61 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 0.19 (0.23), residues: 1380 helix: 0.09 (0.18), residues: 904 sheet: 0.47 (0.52), residues: 89 loop : 0.60 (0.34), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 517 HIS 0.003 0.001 HIS A1371 PHE 0.013 0.001 PHE A 639 TYR 0.008 0.001 TYR A 319 ARG 0.002 0.000 ARG A1308 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 92 time to evaluate : 1.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 662 MET cc_start: 0.8711 (mmm) cc_final: 0.8453 (mmm) REVERT: A 1069 MET cc_start: 0.8352 (mmm) cc_final: 0.7964 (tpp) REVERT: A 1460 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.9223 (tt) outliers start: 24 outliers final: 20 residues processed: 109 average time/residue: 0.4803 time to fit residues: 80.0457 Evaluate side-chains 110 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 89 time to evaluate : 2.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 393 ARG Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 639 PHE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 822 MET Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1053 SER Chi-restraints excluded: chain A residue 1155 THR Chi-restraints excluded: chain A residue 1206 TRP Chi-restraints excluded: chain A residue 1371 HIS Chi-restraints excluded: chain A residue 1460 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 79 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 137 optimal weight: 6.9990 chunk 126 optimal weight: 10.0000 chunk 109 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 67 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 chunk 116 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 11351 Z= 0.362 Angle : 0.604 9.699 15405 Z= 0.317 Chirality : 0.039 0.150 1800 Planarity : 0.003 0.038 1897 Dihedral : 5.677 97.754 1561 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.87 % Allowed : 16.02 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.25 (0.22), residues: 1380 helix: -0.25 (0.17), residues: 905 sheet: 0.33 (0.52), residues: 89 loop : 0.40 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1206 HIS 0.004 0.001 HIS A 692 PHE 0.015 0.001 PHE A1163 TYR 0.010 0.001 TYR A 319 ARG 0.004 0.000 ARG A1210 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 86 time to evaluate : 2.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 662 MET cc_start: 0.8746 (mmm) cc_final: 0.8434 (mmm) REVERT: A 1069 MET cc_start: 0.8412 (mmm) cc_final: 0.8049 (tpp) REVERT: A 1460 LEU cc_start: 0.9512 (OUTLIER) cc_final: 0.9242 (tt) outliers start: 23 outliers final: 21 residues processed: 104 average time/residue: 0.4978 time to fit residues: 77.8247 Evaluate side-chains 106 residues out of total 1230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 84 time to evaluate : 1.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 393 ARG Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 544 CYS Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 639 PHE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 822 MET Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1053 SER Chi-restraints excluded: chain A residue 1083 ARG Chi-restraints excluded: chain A residue 1206 TRP Chi-restraints excluded: chain A residue 1246 LEU Chi-restraints excluded: chain A residue 1371 HIS Chi-restraints excluded: chain A residue 1460 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 3.9990 chunk 100 optimal weight: 0.2980 chunk 16 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 chunk 112 optimal weight: 0.0980 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 6 optimal weight: 5.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1097 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 = 0.3591 r_free = 0.3591 target = 0.064238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.045122 restraints weight = 150528.058| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 4.57 r_work: 0.2844 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11351 Z= 0.154 Angle : 0.525 9.813 15405 Z= 0.261 Chirality : 0.037 0.156 1800 Planarity : 0.003 0.041 1897 Dihedral : 5.666 97.952 1561 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.63 % Allowed : 16.10 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 0.42 (0.23), residues: 1380 helix: 0.26 (0.18), residues: 916 sheet: 0.41 (0.52), residues: 89 loop : 0.76 (0.35), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 517 HIS 0.003 0.001 HIS A1371 PHE 0.012 0.001 PHE A 639 TYR 0.010 0.001 TYR A 319 ARG 0.003 0.000 ARG A1308 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4485.72 seconds wall clock time: 81 minutes 17.27 seconds (4877.27 seconds total)