Starting phenix.real_space_refine on Thu Feb 22 21:07:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d73_7822/02_2024/6d73_7822.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d73_7822/02_2024/6d73_7822.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d73_7822/02_2024/6d73_7822.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d73_7822/02_2024/6d73_7822.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d73_7822/02_2024/6d73_7822.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d73_7822/02_2024/6d73_7822.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.001 sd= 0.006 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 Ca 4 9.91 5 S 148 5.16 5 C 22892 2.51 5 N 6182 2.21 5 O 6114 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 280": "NH1" <-> "NH2" Residue "B ARG 334": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B ARG 544": "NH1" <-> "NH2" Residue "B ARG 559": "NH1" <-> "NH2" Residue "B ARG 596": "NH1" <-> "NH2" Residue "B ARG 619": "NH1" <-> "NH2" Residue "B ARG 675": "NH1" <-> "NH2" Residue "B ARG 689": "NH1" <-> "NH2" Residue "B ARG 978": "NH1" <-> "NH2" Residue "B ARG 984": "NH1" <-> "NH2" Residue "B PHE 1280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 167": "NH1" <-> "NH2" Residue "A ARG 334": "NH1" <-> "NH2" Residue "A ARG 418": "NH1" <-> "NH2" Residue "A ARG 425": "NH1" <-> "NH2" Residue "A ARG 596": "NH1" <-> "NH2" Residue "A ARG 619": "NH1" <-> "NH2" Residue "A ARG 675": "NH1" <-> "NH2" Residue "A ARG 689": "NH1" <-> "NH2" Residue "A PHE 865": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1179": "NH1" <-> "NH2" Residue "C ARG 167": "NH1" <-> "NH2" Residue "C ARG 334": "NH1" <-> "NH2" Residue "C ARG 418": "NH1" <-> "NH2" Residue "C ARG 425": "NH1" <-> "NH2" Residue "C ARG 596": "NH1" <-> "NH2" Residue "C ARG 619": "NH1" <-> "NH2" Residue "C ARG 675": "NH1" <-> "NH2" Residue "C ARG 689": "NH1" <-> "NH2" Residue "C PHE 865": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1179": "NH1" <-> "NH2" Residue "D ARG 280": "NH1" <-> "NH2" Residue "D ARG 334": "NH1" <-> "NH2" Residue "D ARG 357": "NH1" <-> "NH2" Residue "D ARG 544": "NH1" <-> "NH2" Residue "D ARG 559": "NH1" <-> "NH2" Residue "D ARG 596": "NH1" <-> "NH2" Residue "D ARG 619": "NH1" <-> "NH2" Residue "D ARG 675": "NH1" <-> "NH2" Residue "D ARG 689": "NH1" <-> "NH2" Residue "D ARG 978": "NH1" <-> "NH2" Residue "D ARG 984": "NH1" <-> "NH2" Residue "D PHE 1280": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 35340 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 8892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1256, 8892 Classifications: {'peptide': 1256} Incomplete info: {'truncation_to_alanine': 371} Link IDs: {'PTRANS': 48, 'TRANS': 1207} Chain breaks: 13 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1293 Unresolved non-hydrogen angles: 1612 Unresolved non-hydrogen dihedrals: 1022 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'GLN:plan1': 24, 'UNK:plan-1': 22, 'ASP:plan': 39, 'TYR:plan': 2, 'ASN:plan1': 13, 'TRP:plan': 1, 'HIS:plan': 11, 'PHE:plan': 6, 'GLU:plan': 64, 'ARG:plan': 29} Unresolved non-hydrogen planarities: 789 Chain: "A" Number of atoms: 8776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1227, 8776 Classifications: {'peptide': 1227} Incomplete info: {'truncation_to_alanine': 329} Link IDs: {'PTRANS': 43, 'TRANS': 1183} Chain breaks: 14 Unresolved non-hydrogen bonds: 1178 Unresolved non-hydrogen angles: 1472 Unresolved non-hydrogen dihedrals: 937 Unresolved non-hydrogen chiralities: 60 Planarities with less than four sites: {'GLN:plan1': 26, 'UNK:plan-1': 22, 'ASP:plan': 35, 'TYR:plan': 4, 'ASN:plan1': 20, 'TRP:plan': 3, 'HIS:plan': 6, 'PHE:plan': 4, 'GLU:plan': 55, 'ARG:plan': 29} Unresolved non-hydrogen planarities: 765 Chain: "C" Number of atoms: 8776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1227, 8776 Classifications: {'peptide': 1227} Incomplete info: {'truncation_to_alanine': 329} Link IDs: {'PTRANS': 43, 'TRANS': 1183} Chain breaks: 14 Unresolved non-hydrogen bonds: 1178 Unresolved non-hydrogen angles: 1472 Unresolved non-hydrogen dihedrals: 937 Unresolved non-hydrogen chiralities: 60 Planarities with less than four sites: {'GLN:plan1': 26, 'UNK:plan-1': 22, 'ASP:plan': 35, 'TYR:plan': 4, 'ASN:plan1': 20, 'TRP:plan': 3, 'HIS:plan': 6, 'PHE:plan': 4, 'GLU:plan': 55, 'ARG:plan': 29} Unresolved non-hydrogen planarities: 765 Chain: "D" Number of atoms: 8892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1256, 8892 Classifications: {'peptide': 1256} Incomplete info: {'truncation_to_alanine': 371} Link IDs: {'PTRANS': 48, 'TRANS': 1207} Chain breaks: 13 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1293 Unresolved non-hydrogen angles: 1612 Unresolved non-hydrogen dihedrals: 1022 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'GLN:plan1': 24, 'UNK:plan-1': 22, 'ASP:plan': 39, 'TYR:plan': 2, 'ASN:plan1': 13, 'TRP:plan': 1, 'HIS:plan': 11, 'PHE:plan': 6, 'GLU:plan': 64, 'ARG:plan': 29} Unresolved non-hydrogen planarities: 789 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" N GLU B1272 " occ=0.50 ... (3 atoms not shown) pdb=" CB GLU B1272 " occ=0.50 residue: pdb=" N VAL B1400 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL B1400 " occ=0.50 residue: pdb=" N ARG B1447 " occ=0.50 ... (3 atoms not shown) pdb=" CB ARG B1447 " occ=0.50 residue: pdb=" N GLU A1272 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU A1272 " occ=0.50 residue: pdb=" N VAL A1287 " occ=0.50 ... (3 atoms not shown) pdb=" CB VAL A1287 " occ=0.50 residue: pdb=" N VAL A1400 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL A1400 " occ=0.50 residue: pdb=" N GLU C1272 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU C1272 " occ=0.50 residue: pdb=" N VAL C1287 " occ=0.50 ... (3 atoms not shown) pdb=" CB VAL C1287 " occ=0.50 residue: pdb=" N VAL C1400 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL C1400 " occ=0.50 residue: pdb=" N GLU D1272 " occ=0.50 ... (3 atoms not shown) pdb=" CB GLU D1272 " occ=0.50 residue: pdb=" N VAL D1400 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL D1400 " occ=0.50 residue: pdb=" N ARG D1447 " occ=0.50 ... (3 atoms not shown) pdb=" CB ARG D1447 " occ=0.50 Time building chain proxies: 19.35, per 1000 atoms: 0.55 Number of scatterers: 35340 At special positions: 0 Unit cell: (161, 154.1, 175.95, 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) Ca 4 19.99 S 148 16.00 O 6114 8.00 N 6182 7.00 C 22892 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS B 303 " - pdb=" SG CYS B 326 " distance=2.03 Simple disulfide: pdb=" SG CYS B1012 " - pdb=" SG CYS B1024 " distance=2.04 Simple disulfide: pdb=" SG CYS A 303 " - pdb=" SG CYS A 326 " distance=2.03 Simple disulfide: pdb=" SG CYS A1012 " - pdb=" SG CYS A1024 " distance=2.02 Simple disulfide: pdb=" SG CYS C 303 " - pdb=" SG CYS C 326 " distance=2.03 Simple disulfide: pdb=" SG CYS C1012 " - pdb=" SG CYS C1024 " distance=2.02 Simple disulfide: pdb=" SG CYS D 303 " - pdb=" SG CYS D 326 " distance=2.03 Simple disulfide: pdb=" SG CYS D1012 " - pdb=" SG CYS D1024 " 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: 13.80 Conformation dependent library (CDL) restraints added in 6.6 seconds 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9412 Finding SS restraints... Secondary structure from input PDB file: 200 helices and 14 sheets defined 61.6% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.02 Creating SS restraints... Processing helix chain 'B' and resid 40 through 48 Processing helix chain 'B' and resid 89 through 94 Processing helix chain 'B' and resid 126 through 138 Processing helix chain 'B' and resid 159 through 176 removed outlier: 4.044A pdb=" N THR B 176 " --> pdb=" O LYS B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 205 removed outlier: 3.644A pdb=" N HIS B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 229 Processing helix chain 'B' and resid 273 through 287 removed outlier: 3.611A pdb=" N LEU B 277 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ARG B 280 " --> pdb=" O GLU B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 321 Processing helix chain 'B' and resid 334 through 341 Processing helix chain 'B' and resid 351 through 363 Processing helix chain 'B' and resid 366 through 370 Processing helix chain 'B' and resid 371 through 387 Processing helix chain 'B' and resid 404 through 419 removed outlier: 3.672A pdb=" N ALA B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 439 removed outlier: 4.457A pdb=" N TRP B 428 " --> pdb=" O GLY B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 448 removed outlier: 3.971A pdb=" N ALA B 444 " --> pdb=" O ARG B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 459 Processing helix chain 'B' and resid 460 through 470 removed outlier: 3.555A pdb=" N GLY B 470 " --> pdb=" O SER B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 482 removed outlier: 3.616A pdb=" N VAL B 476 " --> pdb=" O LYS B 472 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG B 477 " --> pdb=" O PRO B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 490 Processing helix chain 'B' and resid 492 through 502 removed outlier: 3.987A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 517 Processing helix chain 'B' and resid 535 through 548 removed outlier: 3.984A pdb=" N VAL B 539 " --> pdb=" O CYS B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 605 Processing helix chain 'B' and resid 607 through 618 Processing helix chain 'B' and resid 620 through 638 Processing helix chain 'B' and resid 644 through 672 removed outlier: 3.703A pdb=" N ASP B 672 " --> pdb=" O CYS B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 681 Processing helix chain 'B' and resid 692 through 699 Processing helix chain 'B' and resid 707 through 720 Processing helix chain 'B' and resid 727 through 737 removed outlier: 3.619A pdb=" N PHE B 737 " --> pdb=" O LEU B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 745 Processing helix chain 'B' and resid 748 through 765 removed outlier: 3.635A pdb=" N GLU B 752 " --> pdb=" O PHE B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 807 Processing helix chain 'B' and resid 808 through 833 Processing helix chain 'B' and resid 840 through 864 removed outlier: 3.839A pdb=" N ASP B 864 " --> pdb=" O GLN B 860 " (cutoff:3.500A) Processing helix chain 'B' and resid 870 through 879 Processing helix chain 'B' and resid 881 through 901 Processing helix chain 'B' and resid 904 through 931 Processing helix chain 'B' and resid 936 through 973 removed outlier: 3.688A pdb=" N ILE B 941 " --> pdb=" O GLY B 937 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ILE B 942 " --> pdb=" O PRO B 938 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 996 removed outlier: 5.794A pdb=" N GLU B 989 " --> pdb=" O GLY B 985 " (cutoff:3.500A) Proline residue: B 990 - end of helix removed outlier: 3.898A pdb=" N GLY B 996 " --> pdb=" O ILE B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1036 through 1071 Processing helix chain 'B' and resid 1073 through 1092 removed outlier: 3.575A pdb=" N ILE B1077 " --> pdb=" O ASN B1073 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS B1079 " --> pdb=" O ASP B1075 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER B1091 " --> pdb=" O LYS B1087 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG B1092 " --> pdb=" O GLU B1088 " (cutoff:3.500A) Processing helix chain 'B' and resid 1096 through 1114 removed outlier: 4.460A pdb=" N LEU B1102 " --> pdb=" O PRO B1098 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL B1112 " --> pdb=" O PHE B1108 " (cutoff:3.500A) Processing helix chain 'B' and resid 1129 through 1157 Processing helix chain 'B' and resid 1158 through 1184 Processing helix chain 'B' and resid 1189 through 1209 Processing helix chain 'B' and resid 1252 through 1256 removed outlier: 3.567A pdb=" N GLN B1256 " --> pdb=" O PHE B1253 " (cutoff:3.500A) Processing helix chain 'B' and resid 1370 through 1381 Processing helix chain 'B' and resid 1427 through 1433 removed outlier: 3.794A pdb=" N MET B1433 " --> pdb=" O ASP B1429 " (cutoff:3.500A) Processing helix chain 'B' and resid 1437 through 1441 removed outlier: 3.574A pdb=" N SER B1440 " --> pdb=" O SER B1437 " (cutoff:3.500A) Processing helix chain 'B' and resid 1456 through 1470 removed outlier: 3.641A pdb=" N ILE B1466 " --> pdb=" O ALA B1462 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA B1467 " --> pdb=" O LEU B1463 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 48 removed outlier: 3.663A pdb=" N ASN A 47 " --> pdb=" O TRP A 43 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE A 48 " --> pdb=" O ILE A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 138 Processing helix chain 'A' and resid 159 through 177 Processing helix chain 'A' and resid 189 through 202 removed outlier: 3.877A pdb=" N HIS A 193 " --> pdb=" O GLY A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 288 Processing helix chain 'A' and resid 309 through 322 removed outlier: 3.819A pdb=" N LEU A 313 " --> pdb=" O GLY A 309 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASN A 314 " --> pdb=" O PRO A 310 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR A 315 " --> pdb=" O GLY A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 344 removed outlier: 3.928A pdb=" N SER A 344 " --> pdb=" O ALA A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 362 Processing helix chain 'A' and resid 363 through 371 removed outlier: 5.058A pdb=" N ASN A 369 " --> pdb=" O GLN A 365 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR A 371 " --> pdb=" O TYR A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 387 Processing helix chain 'A' and resid 404 through 421 removed outlier: 4.164A pdb=" N ALA A 408 " --> pdb=" O ASP A 404 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 439 removed outlier: 4.305A pdb=" N ARG A 430 " --> pdb=" O HIS A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 448 removed outlier: 3.894A pdb=" N ALA A 444 " --> pdb=" O ARG A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 470 removed outlier: 3.582A pdb=" N LEU A 460 " --> pdb=" O THR A 456 " (cutoff:3.500A) Proline residue: A 462 - end of helix removed outlier: 3.780A pdb=" N GLY A 470 " --> pdb=" O SER A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 481 Processing helix chain 'A' and resid 485 through 490 Processing helix chain 'A' and resid 492 through 501 removed outlier: 3.804A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 517 removed outlier: 3.537A pdb=" N ARG A 510 " --> pdb=" O CYS A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 548 Processing helix chain 'A' and resid 593 through 606 removed outlier: 3.634A pdb=" N ASP A 597 " --> pdb=" O ASP A 593 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 598 " --> pdb=" O PRO A 594 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE A 599 " --> pdb=" O GLY A 595 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN A 606 " --> pdb=" O ALA A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 618 Processing helix chain 'A' and resid 620 through 638 Processing helix chain 'A' and resid 643 through 672 Processing helix chain 'A' and resid 673 through 682 removed outlier: 3.551A pdb=" N ARG A 682 " --> pdb=" O LYS A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 699 removed outlier: 3.534A pdb=" N LEU A 695 " --> pdb=" O THR A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 706 removed outlier: 3.584A pdb=" N ILE A 705 " --> pdb=" O ASP A 701 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA A 706 " --> pdb=" O LYS A 702 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 701 through 706' Processing helix chain 'A' and resid 707 through 719 Processing helix chain 'A' and resid 727 through 737 removed outlier: 3.521A pdb=" N PHE A 737 " --> pdb=" O LEU A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 743 removed outlier: 3.749A pdb=" N ILE A 741 " --> pdb=" O PHE A 738 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR A 742 " --> pdb=" O PRO A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 763 Processing helix chain 'A' and resid 799 through 807 Processing helix chain 'A' and resid 808 through 833 Processing helix chain 'A' and resid 840 through 863 Processing helix chain 'A' and resid 868 through 876 removed outlier: 4.012A pdb=" N ARG A 872 " --> pdb=" O SER A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 901 removed outlier: 3.874A pdb=" N LEU A 885 " --> pdb=" O LEU A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 926 removed outlier: 3.616A pdb=" N ILE A 920 " --> pdb=" O CYS A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 929 No H-bonds generated for 'chain 'A' and resid 927 through 929' Processing helix chain 'A' and resid 936 through 973 removed outlier: 3.587A pdb=" N ARG A 945 " --> pdb=" O ILE A 941 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LEU A 948 " --> pdb=" O ARG A 944 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ASP A 949 " --> pdb=" O ARG A 945 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N PHE A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE A 953 " --> pdb=" O ASP A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 996 removed outlier: 4.956A pdb=" N GLU A 989 " --> pdb=" O GLY A 985 " (cutoff:3.500A) Proline residue: A 990 - end of helix removed outlier: 3.538A pdb=" N ILE A 994 " --> pdb=" O PRO A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1002 Processing helix chain 'A' and resid 1036 through 1068 removed outlier: 4.047A pdb=" N TYR A1065 " --> pdb=" O ALA A1061 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR A1066 " --> pdb=" O ILE A1062 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLN A1068 " --> pdb=" O ASN A1064 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1092 removed outlier: 4.485A pdb=" N TYR A1083 " --> pdb=" O LYS A1079 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N GLU A1084 " --> pdb=" O PHE A1080 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG A1092 " --> pdb=" O GLU A1088 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1114 removed outlier: 5.175A pdb=" N LEU A1102 " --> pdb=" O PRO A1098 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER A1103 " --> pdb=" O PHE A1099 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1157 Processing helix chain 'A' and resid 1158 through 1182 Processing helix chain 'A' and resid 1189 through 1208 Processing helix chain 'A' and resid 1270 through 1275 removed outlier: 3.704A pdb=" N SER A1275 " --> pdb=" O GLU A1271 " (cutoff:3.500A) Processing helix chain 'A' and resid 1370 through 1381 Processing helix chain 'A' and resid 1456 through 1467 Processing helix chain 'C' and resid 41 through 48 removed outlier: 3.663A pdb=" N ASN C 47 " --> pdb=" O TRP C 43 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE C 48 " --> pdb=" O ILE C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 138 Processing helix chain 'C' and resid 159 through 177 Processing helix chain 'C' and resid 189 through 202 removed outlier: 3.877A pdb=" N HIS C 193 " --> pdb=" O GLY C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 288 Processing helix chain 'C' and resid 309 through 322 removed outlier: 3.819A pdb=" N LEU C 313 " --> pdb=" O GLY C 309 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASN C 314 " --> pdb=" O PRO C 310 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR C 315 " --> pdb=" O GLY C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 344 removed outlier: 3.929A pdb=" N SER C 344 " --> pdb=" O ALA C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 362 Processing helix chain 'C' and resid 363 through 371 removed outlier: 5.058A pdb=" N ASN C 369 " --> pdb=" O GLN C 365 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR C 371 " --> pdb=" O TYR C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 387 Processing helix chain 'C' and resid 404 through 421 removed outlier: 4.165A pdb=" N ALA C 408 " --> pdb=" O ASP C 404 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU C 421 " --> pdb=" O SER C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 439 removed outlier: 4.305A pdb=" N ARG C 430 " --> pdb=" O HIS C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 448 removed outlier: 3.893A pdb=" N ALA C 444 " --> pdb=" O ARG C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 470 removed outlier: 3.583A pdb=" N LEU C 460 " --> pdb=" O THR C 456 " (cutoff:3.500A) Proline residue: C 462 - end of helix removed outlier: 3.781A pdb=" N GLY C 470 " --> pdb=" O SER C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 481 Processing helix chain 'C' and resid 485 through 490 Processing helix chain 'C' and resid 492 through 501 removed outlier: 3.804A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 517 removed outlier: 3.537A pdb=" N ARG C 510 " --> pdb=" O CYS C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 548 Processing helix chain 'C' and resid 593 through 606 removed outlier: 3.634A pdb=" N ASP C 597 " --> pdb=" O ASP C 593 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU C 598 " --> pdb=" O PRO C 594 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE C 599 " --> pdb=" O GLY C 595 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN C 606 " --> pdb=" O ALA C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 618 Processing helix chain 'C' and resid 620 through 638 Processing helix chain 'C' and resid 643 through 672 Processing helix chain 'C' and resid 673 through 682 removed outlier: 3.551A pdb=" N ARG C 682 " --> pdb=" O LYS C 678 " (cutoff:3.500A) Processing helix chain 'C' and resid 691 through 699 removed outlier: 3.534A pdb=" N LEU C 695 " --> pdb=" O THR C 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 701 through 706 removed outlier: 3.585A pdb=" N ILE C 705 " --> pdb=" O ASP C 701 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA C 706 " --> pdb=" O LYS C 702 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 701 through 706' Processing helix chain 'C' and resid 707 through 719 Processing helix chain 'C' and resid 727 through 737 removed outlier: 3.521A pdb=" N PHE C 737 " --> pdb=" O LEU C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 743 removed outlier: 3.749A pdb=" N ILE C 741 " --> pdb=" O PHE C 738 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR C 742 " --> pdb=" O PRO C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 763 Processing helix chain 'C' and resid 799 through 807 Processing helix chain 'C' and resid 808 through 833 Processing helix chain 'C' and resid 840 through 863 Processing helix chain 'C' and resid 868 through 876 removed outlier: 4.012A pdb=" N ARG C 872 " --> pdb=" O SER C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 881 through 901 removed outlier: 3.875A pdb=" N LEU C 885 " --> pdb=" O LEU C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 904 through 926 removed outlier: 3.615A pdb=" N ILE C 920 " --> pdb=" O CYS C 916 " (cutoff:3.500A) Processing helix chain 'C' and resid 927 through 929 No H-bonds generated for 'chain 'C' and resid 927 through 929' Processing helix chain 'C' and resid 936 through 973 removed outlier: 3.586A pdb=" N ARG C 945 " --> pdb=" O ILE C 941 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LEU C 948 " --> pdb=" O ARG C 944 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ASP C 949 " --> pdb=" O ARG C 945 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N PHE C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE C 953 " --> pdb=" O ASP C 949 " (cutoff:3.500A) Processing helix chain 'C' and resid 979 through 996 removed outlier: 4.955A pdb=" N GLU C 989 " --> pdb=" O GLY C 985 " (cutoff:3.500A) Proline residue: C 990 - end of helix removed outlier: 3.538A pdb=" N ILE C 994 " --> pdb=" O PRO C 990 " (cutoff:3.500A) Processing helix chain 'C' and resid 998 through 1002 Processing helix chain 'C' and resid 1036 through 1068 removed outlier: 4.048A pdb=" N TYR C1065 " --> pdb=" O ALA C1061 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR C1066 " --> pdb=" O ILE C1062 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLN C1068 " --> pdb=" O ASN C1064 " (cutoff:3.500A) Processing helix chain 'C' and resid 1069 through 1092 removed outlier: 4.485A pdb=" N TYR C1083 " --> pdb=" O LYS C1079 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N GLU C1084 " --> pdb=" O PHE C1080 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG C1092 " --> pdb=" O GLU C1088 " (cutoff:3.500A) Processing helix chain 'C' and resid 1096 through 1114 removed outlier: 5.176A pdb=" N LEU C1102 " --> pdb=" O PRO C1098 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER C1103 " --> pdb=" O PHE C1099 " (cutoff:3.500A) Processing helix chain 'C' and resid 1129 through 1157 Processing helix chain 'C' and resid 1158 through 1182 Processing helix chain 'C' and resid 1189 through 1208 Processing helix chain 'C' and resid 1270 through 1275 removed outlier: 3.703A pdb=" N SER C1275 " --> pdb=" O GLU C1271 " (cutoff:3.500A) Processing helix chain 'C' and resid 1370 through 1381 Processing helix chain 'C' and resid 1456 through 1467 Processing helix chain 'D' and resid 41 through 48 Processing helix chain 'D' and resid 89 through 94 Processing helix chain 'D' and resid 126 through 138 Processing helix chain 'D' and resid 159 through 176 removed outlier: 4.044A pdb=" N THR D 176 " --> pdb=" O LYS D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 205 removed outlier: 3.646A pdb=" N HIS D 193 " --> pdb=" O GLY D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 229 Processing helix chain 'D' and resid 273 through 287 removed outlier: 3.611A pdb=" N LEU D 277 " --> pdb=" O VAL D 273 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ARG D 280 " --> pdb=" O GLU D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 321 Processing helix chain 'D' and resid 334 through 341 Processing helix chain 'D' and resid 351 through 363 Processing helix chain 'D' and resid 366 through 370 Processing helix chain 'D' and resid 371 through 387 Processing helix chain 'D' and resid 404 through 419 removed outlier: 3.670A pdb=" N ALA D 408 " --> pdb=" O ASP D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 439 removed outlier: 4.457A pdb=" N TRP D 428 " --> pdb=" O GLY D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 448 removed outlier: 3.972A pdb=" N ALA D 444 " --> pdb=" O ARG D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 459 Processing helix chain 'D' and resid 460 through 470 removed outlier: 3.554A pdb=" N GLY D 470 " --> pdb=" O SER D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 482 removed outlier: 3.617A pdb=" N VAL D 476 " --> pdb=" O LYS D 472 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG D 477 " --> pdb=" O PRO D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 490 Processing helix chain 'D' and resid 492 through 502 removed outlier: 3.987A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 506 through 517 Processing helix chain 'D' and resid 535 through 548 removed outlier: 3.984A pdb=" N VAL D 539 " --> pdb=" O CYS D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 593 through 605 Processing helix chain 'D' and resid 607 through 618 Processing helix chain 'D' and resid 620 through 638 Processing helix chain 'D' and resid 644 through 672 removed outlier: 3.702A pdb=" N ASP D 672 " --> pdb=" O CYS D 668 " (cutoff:3.500A) Processing helix chain 'D' and resid 673 through 681 Processing helix chain 'D' and resid 692 through 699 Processing helix chain 'D' and resid 707 through 720 Processing helix chain 'D' and resid 727 through 737 removed outlier: 3.619A pdb=" N PHE D 737 " --> pdb=" O LEU D 733 " (cutoff:3.500A) Processing helix chain 'D' and resid 737 through 745 Processing helix chain 'D' and resid 748 through 765 removed outlier: 3.636A pdb=" N GLU D 752 " --> pdb=" O PHE D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 798 through 807 Processing helix chain 'D' and resid 808 through 833 Processing helix chain 'D' and resid 840 through 864 removed outlier: 3.839A pdb=" N ASP D 864 " --> pdb=" O GLN D 860 " (cutoff:3.500A) Processing helix chain 'D' and resid 870 through 879 Processing helix chain 'D' and resid 881 through 901 Processing helix chain 'D' and resid 904 through 931 Processing helix chain 'D' and resid 936 through 973 removed outlier: 3.688A pdb=" N ILE D 941 " --> pdb=" O GLY D 937 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ILE D 942 " --> pdb=" O PRO D 938 " (cutoff:3.500A) Processing helix chain 'D' and resid 978 through 996 removed outlier: 5.795A pdb=" N GLU D 989 " --> pdb=" O GLY D 985 " (cutoff:3.500A) Proline residue: D 990 - end of helix removed outlier: 3.897A pdb=" N GLY D 996 " --> pdb=" O ILE D 992 " (cutoff:3.500A) Processing helix chain 'D' and resid 1036 through 1071 Processing helix chain 'D' and resid 1073 through 1092 removed outlier: 3.575A pdb=" N ILE D1077 " --> pdb=" O ASN D1073 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS D1079 " --> pdb=" O ASP D1075 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER D1091 " --> pdb=" O LYS D1087 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG D1092 " --> pdb=" O GLU D1088 " (cutoff:3.500A) Processing helix chain 'D' and resid 1096 through 1114 removed outlier: 4.460A pdb=" N LEU D1102 " --> pdb=" O PRO D1098 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL D1112 " --> pdb=" O PHE D1108 " (cutoff:3.500A) Processing helix chain 'D' and resid 1129 through 1157 Processing helix chain 'D' and resid 1158 through 1184 Processing helix chain 'D' and resid 1189 through 1209 Processing helix chain 'D' and resid 1252 through 1256 removed outlier: 3.568A pdb=" N GLN D1256 " --> pdb=" O PHE D1253 " (cutoff:3.500A) Processing helix chain 'D' and resid 1370 through 1381 Processing helix chain 'D' and resid 1427 through 1433 removed outlier: 3.795A pdb=" N MET D1433 " --> pdb=" O ASP D1429 " (cutoff:3.500A) Processing helix chain 'D' and resid 1437 through 1441 removed outlier: 3.573A pdb=" N SER D1440 " --> pdb=" O SER D1437 " (cutoff:3.500A) Processing helix chain 'D' and resid 1456 through 1470 removed outlier: 3.641A pdb=" N ILE D1466 " --> pdb=" O ALA D1462 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA D1467 " --> pdb=" O LEU D1463 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 49 through 52 Processing sheet with id=AA2, first strand: chain 'B' and resid 237 through 240 removed outlier: 6.117A pdb=" N ILE B 181 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N VAL B 217 " --> pdb=" O ILE B 181 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N THR B 183 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ILE B 147 " --> pdb=" O LEU B 182 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N GLY B 184 " --> pdb=" O ILE B 147 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N VAL B 149 " --> pdb=" O GLY B 184 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N CYS B 326 " --> pdb=" O THR B 393 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N PHE B 395 " --> pdb=" O CYS B 326 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N VAL B 328 " --> pdb=" O PHE B 395 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 1324 through 1329 removed outlier: 3.578A pdb=" N HIS B1329 " --> pdb=" O SER B1414 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 1357 through 1358 removed outlier: 3.663A pdb=" N ALA B1357 " --> pdb=" O VAL B1348 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 237 through 240 removed outlier: 3.877A pdb=" N TYR A 240 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LYS A 117 " --> pdb=" O PHE A 260 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N LEU A 262 " --> pdb=" O LYS A 117 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL A 119 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N ASP A 264 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL A 121 " --> pdb=" O ASP A 264 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL A 214 " --> pdb=" O HIS A 259 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N LEU A 261 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N GLY A 216 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N VAL A 263 " --> pdb=" O GLY A 216 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ALA A 218 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ILE A 181 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N VAL A 217 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N THR A 183 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE A 147 " --> pdb=" O LEU A 182 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N GLY A 184 " --> pdb=" O ILE A 147 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N VAL A 149 " --> pdb=" O GLY A 184 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU A 146 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N VAL A 304 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N SER A 148 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N VAL A 327 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N CYS A 303 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N CYS A 326 " --> pdb=" O THR A 393 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1361 through 1362 removed outlier: 5.610A pdb=" N GLY A1323 " --> pdb=" O TRP A1410 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLU A1412 " --> pdb=" O GLY A1323 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ASN A1325 " --> pdb=" O GLU A1412 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N SER A1414 " --> pdb=" O ASN A1325 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE A1327 " --> pdb=" O SER A1414 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ILE A1416 " --> pdb=" O ILE A1327 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N HIS A1329 " --> pdb=" O ILE A1416 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N LEU A1418 " --> pdb=" O HIS A1329 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ILE A1331 " --> pdb=" O LEU A1418 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N VAL A1411 " --> pdb=" O TYR A1399 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N TYR A1399 " --> pdb=" O VAL A1411 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N THR A1413 " --> pdb=" O LYS A1397 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LYS A1397 " --> pdb=" O THR A1413 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE A1415 " --> pdb=" O VAL A1395 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1361 through 1362 removed outlier: 5.990A pdb=" N PHE A1332 " --> pdb=" O LEU A1346 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A1346 " --> pdb=" O PHE A1332 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 237 through 240 removed outlier: 3.877A pdb=" N TYR C 240 " --> pdb=" O SER C 107 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LYS C 117 " --> pdb=" O PHE C 260 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N LEU C 262 " --> pdb=" O LYS C 117 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL C 119 " --> pdb=" O LEU C 262 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N ASP C 264 " --> pdb=" O VAL C 119 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL C 121 " --> pdb=" O ASP C 264 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL C 214 " --> pdb=" O HIS C 259 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N LEU C 261 " --> pdb=" O VAL C 214 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N GLY C 216 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL C 263 " --> pdb=" O GLY C 216 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ALA C 218 " --> pdb=" O VAL C 263 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ILE C 181 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N VAL C 217 " --> pdb=" O ILE C 181 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR C 183 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE C 147 " --> pdb=" O LEU C 182 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N GLY C 184 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 8.839A pdb=" N VAL C 149 " --> pdb=" O GLY C 184 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU C 146 " --> pdb=" O VAL C 302 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N VAL C 304 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N SER C 148 " --> pdb=" O VAL C 304 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N VAL C 327 " --> pdb=" O VAL C 301 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N CYS C 303 " --> pdb=" O VAL C 327 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N CYS C 326 " --> pdb=" O THR C 393 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 1361 through 1362 removed outlier: 5.610A pdb=" N GLY C1323 " --> pdb=" O TRP C1410 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLU C1412 " --> pdb=" O GLY C1323 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ASN C1325 " --> pdb=" O GLU C1412 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N SER C1414 " --> pdb=" O ASN C1325 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE C1327 " --> pdb=" O SER C1414 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ILE C1416 " --> pdb=" O ILE C1327 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N HIS C1329 " --> pdb=" O ILE C1416 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LEU C1418 " --> pdb=" O HIS C1329 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ILE C1331 " --> pdb=" O LEU C1418 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N VAL C1411 " --> pdb=" O TYR C1399 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N TYR C1399 " --> pdb=" O VAL C1411 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR C1413 " --> pdb=" O LYS C1397 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LYS C1397 " --> pdb=" O THR C1413 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE C1415 " --> pdb=" O VAL C1395 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 1361 through 1362 removed outlier: 5.991A pdb=" N PHE C1332 " --> pdb=" O LEU C1346 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU C1346 " --> pdb=" O PHE C1332 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 49 through 52 Processing sheet with id=AB3, first strand: chain 'D' and resid 237 through 240 removed outlier: 6.117A pdb=" N ILE D 181 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N VAL D 217 " --> pdb=" O ILE D 181 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N THR D 183 " --> pdb=" O VAL D 217 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ILE D 147 " --> pdb=" O LEU D 182 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N GLY D 184 " --> pdb=" O ILE D 147 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N VAL D 149 " --> pdb=" O GLY D 184 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N CYS D 326 " --> pdb=" O THR D 393 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N PHE D 395 " --> pdb=" O CYS D 326 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N VAL D 328 " --> pdb=" O PHE D 395 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 1324 through 1329 removed outlier: 3.578A pdb=" N HIS D1329 " --> pdb=" O SER D1414 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 1357 through 1358 removed outlier: 3.663A pdb=" N ALA D1357 " --> pdb=" O VAL D1348 " (cutoff:3.500A) 2165 hydrogen bonds defined for protein. 6369 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: 13.76 Time building geometry restraints manager: 15.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11415 1.34 - 1.46: 8917 1.46 - 1.58: 15624 1.58 - 1.70: 0 1.70 - 1.82: 212 Bond restraints: 36168 Sorted by residual: bond pdb=" C SER A1281 " pdb=" N PRO A1282 " ideal model delta sigma weight residual 1.334 1.403 -0.069 2.34e-02 1.83e+03 8.62e+00 bond pdb=" C SER C1281 " pdb=" N PRO C1282 " ideal model delta sigma weight residual 1.334 1.402 -0.068 2.34e-02 1.83e+03 8.54e+00 bond pdb=" CB VAL C 604 " pdb=" CG1 VAL C 604 " ideal model delta sigma weight residual 1.521 1.447 0.074 3.30e-02 9.18e+02 4.99e+00 bond pdb=" CB VAL A 604 " pdb=" CG1 VAL A 604 " ideal model delta sigma weight residual 1.521 1.448 0.073 3.30e-02 9.18e+02 4.94e+00 bond pdb=" CG LEU A 926 " pdb=" CD1 LEU A 926 " ideal model delta sigma weight residual 1.521 1.453 0.068 3.30e-02 9.18e+02 4.20e+00 ... (remaining 36163 not shown) Histogram of bond angle deviations from ideal: 98.06 - 105.27: 651 105.27 - 112.48: 18771 112.48 - 119.70: 12085 119.70 - 126.91: 17405 126.91 - 134.12: 620 Bond angle restraints: 49532 Sorted by residual: angle pdb=" N GLY D 272 " pdb=" CA GLY D 272 " pdb=" C GLY D 272 " ideal model delta sigma weight residual 113.24 129.48 -16.24 1.31e+00 5.83e-01 1.54e+02 angle pdb=" N GLY B 272 " pdb=" CA GLY B 272 " pdb=" C GLY B 272 " ideal model delta sigma weight residual 113.24 129.42 -16.18 1.31e+00 5.83e-01 1.53e+02 angle pdb=" N HIS B 502 " pdb=" CA HIS B 502 " pdb=" C HIS B 502 " ideal model delta sigma weight residual 112.92 123.83 -10.91 1.23e+00 6.61e-01 7.86e+01 angle pdb=" N HIS D 502 " pdb=" CA HIS D 502 " pdb=" C HIS D 502 " ideal model delta sigma weight residual 112.92 123.80 -10.88 1.23e+00 6.61e-01 7.83e+01 angle pdb=" N VAL D 273 " pdb=" CA VAL D 273 " pdb=" C VAL D 273 " ideal model delta sigma weight residual 110.62 118.08 -7.46 1.02e+00 9.61e-01 5.36e+01 ... (remaining 49527 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.64: 19521 14.64 - 29.27: 1083 29.27 - 43.91: 278 43.91 - 58.54: 34 58.54 - 73.18: 6 Dihedral angle restraints: 20922 sinusoidal: 6470 harmonic: 14452 Sorted by residual: dihedral pdb=" CA SER C1013 " pdb=" C SER C1013 " pdb=" N VAL C1014 " pdb=" CA VAL C1014 " ideal model delta harmonic sigma weight residual -180.00 -122.19 -57.81 0 5.00e+00 4.00e-02 1.34e+02 dihedral pdb=" CA SER A1013 " pdb=" C SER A1013 " pdb=" N VAL A1014 " pdb=" CA VAL A1014 " ideal model delta harmonic sigma weight residual -180.00 -122.19 -57.81 0 5.00e+00 4.00e-02 1.34e+02 dihedral pdb=" CA LYS C1021 " pdb=" C LYS C1021 " pdb=" N PRO C1022 " pdb=" CA PRO C1022 " ideal model delta harmonic sigma weight residual -180.00 -138.99 -41.01 0 5.00e+00 4.00e-02 6.73e+01 ... (remaining 20919 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 4949 0.075 - 0.150: 809 0.150 - 0.225: 100 0.225 - 0.301: 18 0.301 - 0.376: 4 Chirality restraints: 5880 Sorted by residual: chirality pdb=" CA HIS D 502 " pdb=" N HIS D 502 " pdb=" C HIS D 502 " pdb=" CB HIS D 502 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.53e+00 chirality pdb=" CA HIS B 502 " pdb=" N HIS B 502 " pdb=" C HIS B 502 " pdb=" CB HIS B 502 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.53e+00 chirality pdb=" CA LYS B 154 " pdb=" N LYS B 154 " pdb=" C LYS B 154 " pdb=" CB LYS B 154 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.68e+00 ... (remaining 5877 not shown) Planarity restraints: 6272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B1084 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C GLU B1084 " 0.056 2.00e-02 2.50e+03 pdb=" O GLU B1084 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU B1085 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D1084 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.05e+01 pdb=" C GLU D1084 " 0.056 2.00e-02 2.50e+03 pdb=" O GLU D1084 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU D1085 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B1087 " -0.015 2.00e-02 2.50e+03 3.08e-02 9.48e+00 pdb=" C LYS B1087 " 0.053 2.00e-02 2.50e+03 pdb=" O LYS B1087 " -0.020 2.00e-02 2.50e+03 pdb=" N GLU B1088 " -0.018 2.00e-02 2.50e+03 ... (remaining 6269 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.12: 2 2.12 - 2.81: 10123 2.81 - 3.51: 48347 3.51 - 4.20: 78096 4.20 - 4.90: 132713 Nonbonded interactions: 269281 Sorted by model distance: nonbonded pdb=" OG SER C 348 " pdb=" OE1 GLU C1271 " model vdw 1.420 2.440 nonbonded pdb=" OG SER A 348 " pdb=" OE1 GLU A1271 " model vdw 1.421 2.440 nonbonded pdb=" O TYR C 367 " pdb=" CG2 THR C 371 " model vdw 2.179 3.460 nonbonded pdb=" O TYR A 367 " pdb=" CG2 THR A 371 " model vdw 2.180 3.460 nonbonded pdb=" O VAL C 301 " pdb=" OG1 THR C 324 " model vdw 2.221 2.440 ... (remaining 269276 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 40 through 43 or (resid 44 through 46 and (name N or name \ CA or name C or name O or name CB )) or resid 47 or (resid 48 through 50 and (na \ me N or name CA or name C or name O or name CB )) or resid 51 through 131 or (re \ sid 132 through 133 and (name N or name CA or name C or name O or name CB )) or \ resid 134 through 159 or (resid 160 through 162 and (name N or name CA or name C \ or name O or name CB )) or resid 163 through 175 or (resid 176 through 177 and \ (name N or name CA or name C or name O or name CB )) or resid 178 through 198 or \ (resid 199 through 200 and (name N or name CA or name C or name O or name CB )) \ or resid 201 through 229 or (resid 230 and (name N or name CA or name C or name \ O or name CB )) or resid 231 through 241 or (resid 242 through 245 and (name N \ or name CA or name C or name O or name CB )) or (resid 246 through 250 and (name \ N or name CA or name C or name O or name CB )) or resid 251 through 253 or (res \ id 254 and (name N or name CA or name C or name O or name CB )) or resid 255 thr \ ough 264 or (resid 265 and (name N or name CA or name C or name O or name CB )) \ or resid 266 through 275 or (resid 276 and (name N or name CA or name C or name \ O or name CB )) or resid 277 through 282 or (resid 283 and (name N or name CA or \ name C or name O or name CB )) or resid 284 through 286 or (resid 287 and (name \ N or name CA or name C or name O or name CB )) or resid 288 through 289 or (res \ id 290 and (name N or name CA or name C or name O or name CB )) or resid 291 or \ resid 296 through 311 or (resid 312 and (name N or name CA or name C or name O o \ r name CB )) or resid 313 through 323 or (resid 324 and (name N or name CA or na \ me C or name O or name CB )) or resid 325 through 347 or (resid 348 through 349 \ and (name N or name CA or name C or name O or name CB )) or resid 350 through 38 \ 0 or (resid 381 through 384 and (name N or name CA or name C or name O or name C \ B )) or resid 385 through 398 or (resid 399 through 404 and (name N or name CA o \ r name C or name O or name CB )) or resid 405 through 421 or (resid 422 through \ 423 and (name N or name CA or name C or name O or name CB )) or resid 424 or (re \ sid 425 through 427 and (name N or name CA or name C or name O or name CB )) or \ resid 428 or (resid 429 through 430 and (name N or name CA or name C or name O o \ r name CB )) or resid 431 through 446 or (resid 447 and (name N or name CA or na \ me C or name O or name CB )) or resid 448 through 514 or (resid 515 and (name N \ or name CA or name C or name O or name CB )) or resid 516 through 557 or (resid \ 558 through 559 and (name N or name CA or name C or name O or name CB )) or resi \ d 560 or resid 589 through 638 or (resid 639 and (name N or name CA or name C or \ name O or name CB )) or (resid 640 through 643 and (name N or name CA or name C \ or name O or name CB )) or resid 644 or (resid 645 and (name N or name CA or na \ me C or name O or name CB )) or resid 646 through 699 or (resid 700 through 702 \ and (name N or name CA or name C or name O or name CB )) or resid 703 through 73 \ 1 or (resid 732 through 738 and (name N or name CA or name C or name O or name C \ B )) or resid 739 or (resid 740 and (name N or name CA or name C or name O or na \ me CB )) or resid 741 through 744 or (resid 745 and (name N or name CA or name C \ or name O or name CB )) or resid 746 through 762 or (resid 763 through 798 and \ (name N or name CA or name C or name O or name CB )) or resid 799 through 811 or \ (resid 812 and (name N or name CA or name C or name O or name CB or name CG or \ name CD )) or resid 813 through 863 or (resid 864 and (name N or name CA or name \ C or name O or name CB )) or resid 869 through 870 or (resid 871 through 872 an \ d (name N or name CA or name C or name O or name CB )) or resid 873 through 874 \ or (resid 875 through 876 and (name N or name CA or name C or name O or name CB \ )) or resid 877 through 879 or (resid 880 and (name N or name CA or name C or na \ me O or name CB )) or resid 881 through 904 or (resid 905 through 906 and (name \ N or name CA or name C or name O or name CB )) or resid 907 through 911 or (resi \ d 912 and (name N or name CA or name C or name O or name CB )) or resid 913 thro \ ugh 926 or (resid 927 through 928 and (name N or name CA or name C or name O or \ name CB )) or resid 929 through 930 or (resid 931 through 933 and (name N or nam \ e CA or name C or name O or name CB )) or resid 934 through 941 or (resid 942 th \ rough 943 and (name N or name CA or name C or name O or name CB )) or resid 944 \ or (resid 945 through 947 and (name N or name CA or name C or name O or name CB \ )) or resid 948 through 949 or (resid 950 and (name N or name CA or name C or na \ me O or name CB )) or resid 951 through 974 or (resid 975 through 977 and (name \ N or name CA or name C or name O or name CB )) or resid 978 through 981 or (resi \ d 982 through 983 and (name N or name CA or name C or name O or name CB )) or re \ sid 984 through 997 or (resid 998 and (name N or name CA or name C or name O or \ name CB )) or resid 999 through 1042 or (resid 1043 through 1044 and (name N or \ name CA or name C or name O or name CB )) or resid 1045 through 1047 or (resid 1 \ 048 through 1049 and (name N or name CA or name C or name O or name CB )) or res \ id 1050 through 1061 or (resid 1062 and (name N or name CA or name C or name O o \ r name CB )) or resid 1063 through 1071 or (resid 1072 through 1077 and (name N \ or name CA or name C or name O or name CB )) or resid 1078 through 1081 or (resi \ d 1082 and (name N or name CA or name C or name O or name CB )) or resid 1083 th \ rough 1108 or (resid 1109 and (name N or name CA or name C or name O or name CB \ )) or resid 1110 through 1132 or (resid 1133 through 1134 and (name N or name CA \ or name C or name O or name CB )) or resid 1135 through 1181 or (resid 1182 thr \ ough 1183 and (name N or name CA or name C or name O or name CB )) or resid 1184 \ through 1209 or resid 1247 through 1270 or (resid 1271 through 1275 and (name N \ or name CA or name C or name O or name CB )) or resid 1276 through 1305 or (res \ id 1306 and (name N or name CA or name C or name O or name CB )) or resid 1307 t \ hrough 1309 or (resid 1310 through 1311 and (name N or name CA or name C or name \ O or name CB )) or resid 1312 through 1326 or (resid 1327 through 1328 and (nam \ e N or name CA or name C or name O or name CB )) or resid 1329 through 1330 or ( \ resid 1331 and (name N or name CA or name C or name O or name CB )) or resid 133 \ 2 through 1333 or (resid 1334 through 1355 and (name N or name CA or name C or n \ ame O or name CB )) or resid 1356 through 1357 or (resid 1358 through 1359 and ( \ name N or name CA or name C or name O or name CB )) or resid 1360 through 1363 o \ r (resid 1369 through 1376 and (name N or name CA or name C or name O or name CB \ )) or resid 1377 through 1379 or (resid 1380 through 1381 and (name N or name C \ A or name C or name O or name CB )) or resid 1392 or (resid 1393 through 1395 an \ d (name N or name CA or name C or name O or name CB )) or resid 1396 or (resid 1 \ 397 and (name N or name CA or name C or name O or name CB )) or resid 1398 throu \ gh 1419 or (resid 1427 through 1433 and (name N or name CA or name C or name O o \ r name CB )) or resid 1434 through 1444 or (resid 1445 through 1467 and (name N \ or name CA or name C or name O or name CB )) or resid 1601)) selection = (chain 'B' and (resid 40 through 49 or (resid 50 and (name N or name CA or name \ C or name O or name CB )) or resid 51 through 52 or (resid 89 through 91 and (na \ me N or name CA or name C or name O or name CB )) or resid 92 through 104 or (re \ sid 105 and (name N or name CA or name C or name O or name CB )) or resid 106 th \ rough 154 or (resid 155 and (name N or name CA or name C or name O or name CB )) \ or resid 156 through 157 or (resid 158 through 162 and (name N or name CA or na \ me C or name O or name CB )) or resid 163 through 167 or (resid 168 and (name N \ or name CA or name C or name O or name CB )) or resid 169 through 171 or (resid \ 172 and (name N or name CA or name C or name O or name CB )) or resid 173 throug \ h 191 or (resid 192 and (name N or name CA or name C or name O or name CB )) or \ resid 193 through 207 or (resid 208 through 209 and (name N or name CA or name C \ or name O or name CB )) or resid 210 or (resid 211 and (name N or name CA or na \ me C or name O or name CB )) or resid 212 through 334 or (resid 335 through 337 \ and (name N or name CA or name C or name O or name CB )) or resid 338 or (resid \ 339 through 345 and (name N or name CA or name C or name O or name CB )) or resi \ d 346 or (resid 347 through 349 and (name N or name CA or name C or name O or na \ me CB )) or resid 350 through 351 or (resid 352 through 353 and (name N or name \ CA or name C or name O or name CB )) or resid 354 through 355 or (resid 356 and \ (name N or name CA or name C or name O or name CB )) or resid 357 through 369 or \ (resid 370 and (name N or name CA or name C or name O or name CB )) or resid 37 \ 1 through 372 or (resid 373 through 374 and (name N or name CA or name C or name \ O or name CB )) or resid 375 or (resid 376 through 377 and (name N or name CA o \ r name C or name O or name CB )) or resid 378 through 379 or (resid 380 through \ 384 and (name N or name CA or name C or name O or name CB )) or resid 385 throug \ h 386 or (resid 387 and (name N or name CA or name C or name O or name CB )) or \ resid 388 through 392 or (resid 393 and (name N or name CA or name C or name O o \ r name CB )) or resid 394 through 402 or (resid 403 through 404 and (name N or n \ ame CA or name C or name O or name CB )) or resid 405 or (resid 406 and (name N \ or name CA or name C or name O or name CB )) or resid 407 through 410 or (resid \ 411 through 412 and (name N or name CA or name C or name O or name CB )) or resi \ d 413 through 414 or (resid 415 through 417 and (name N or name CA or name C or \ name O or name CB )) or resid 418 through 419 or (resid 420 through 423 and (nam \ e N or name CA or name C or name O or name CB )) or resid 424 through 429 or (re \ sid 430 and (name N or name CA or name C or name O or name CB )) or resid 431 th \ rough 486 or (resid 487 through 488 and (name N or name CA or name C or name O o \ r name CB )) or resid 489 through 495 or (resid 496 through 498 and (name N or n \ ame CA or name C or name O or name CB )) or resid 499 through 513 or (resid 514 \ through 515 and (name N or name CA or name C or name O or name CB )) or resid 51 \ 6 or (resid 517 and (name N or name CA or name C or name O or name CB )) or (res \ id 535 through 536 and (name N or name CA or name C or name O or name CB )) or r \ esid 537 through 558 or (resid 559 and (name N or name CA or name C or name O or \ name CB )) or resid 560 through 592 or (resid 593 and (name N or name CA or nam \ e C or name O or name CB )) or resid 594 through 633 or (resid 634 and (name N o \ r name CA or name C or name O or name CB )) or resid 635 through 657 or (resid 6 \ 58 and (name N or name CA or name C or name O or name CB )) or resid 659 through \ 715 or (resid 716 and (name N or name CA or name C or name O or name CB )) or r \ esid 717 through 749 or (resid 750 through 753 and (name N or name CA or name C \ or name O or name CB )) or resid 754 through 763 or (resid 798 and (name N or na \ me CA or name C or name O or name CB )) or resid 799 through 853 or (resid 854 a \ nd (name N or name CA or name C or name O or name CB )) or resid 855 through 877 \ or (resid 878 through 880 and (name N or name CA or name C or name O or name CB \ )) or resid 881 through 901 or (resid 902 through 906 and (name N or name CA or \ name C or name O or name CB )) or resid 907 through 938 or (resid 939 and (name \ N or name CA or name C or name O or name CB )) or resid 940 or (resid 941 throu \ gh 943 and (name N or name CA or name C or name O or name CB )) or resid 944 thr \ ough 978 or (resid 979 through 980 and (name N or name CA or name C or name O or \ name CB )) or resid 981 through 988 or (resid 989 and (name N or name CA or nam \ e C or name O or name CB )) or resid 990 through 996 or (resid 997 through 998 a \ nd (name N or name CA or name C or name O or name CB )) or resid 999 through 100 \ 0 or (resid 1001 through 1011 and (name N or name CA or name C or name O or name \ CB )) or resid 1012 through 1022 or (resid 1023 and (name N or name CA or name \ C or name O or name CB )) or resid 1024 through 1036 or (resid 1037 and (name N \ or name CA or name C or name O or name CB )) or resid 1038 through 1067 or (resi \ d 1068 through 1077 and (name N or name CA or name C or name O or name CB )) or \ resid 1078 through 1083 or (resid 1084 and (name N or name CA or name C or name \ O or name CB )) or resid 1085 through 1087 or (resid 1088 and (name N or name CA \ or name C or name O or name CB )) or resid 1089 through 1104 or (resid 1105 thr \ ough 1107 and (name N or name CA or name C or name O or name CB )) or resid 1108 \ through 1111 or (resid 1112 and (name N or name CA or name C or name O or name \ CB )) or resid 1113 or (resid 1114 through 1120 and (name N or name CA or name C \ or name O or name CB )) or resid 1121 through 1122 or (resid 1123 and (name N o \ r name CA or name C or name O or name CB )) or resid 1124 through 1179 or (resid \ 1180 through 1183 and (name N or name CA or name C or name O or name CB )) or r \ esid 1184 through 1247 or (resid 1248 through 1249 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1250 through 1251 or (resid 1252 and (name \ N or name CA or name C or name O or name CB )) or resid 1253 through 1254 or (re \ sid 1255 through 1258 and (name N or name CA or name C or name O or name CB )) o \ r resid 1259 through 1263 or (resid 1264 through 1266 and (name N or name CA or \ name C or name O or name CB )) or resid 1267 through 1277 or (resid 1278 through \ 1279 and (name N or name CA or name C or name O or name CB )) or resid 1280 thr \ ough 1286 or (resid 1287 through 1290 and (name N or name CA or name C or name O \ or name CB )) or (resid 1303 through 1306 and (name N or name CA or name C or n \ ame O or name CB )) or resid 1307 through 1319 or (resid 1320 through 1322 and ( \ name N or name CA or name C or name O or name CB )) or resid 1323 through 1334 o \ r (resid 1335 through 1337 and (name N or name CA or name C or name O or name CB \ )) or (resid 1341 through 1349 and (name N or name CA or name C or name O or na \ me CB )) or resid 1355 through 1363 or resid 1369 through 1381 or resid 1392 thr \ ough 1403 or (resid 1404 and (name N or name CA or name C or name O or name CB ) \ ) or resid 1405 through 1419 or (resid 1427 through 1433 and (name N or name CA \ or name C or name O or name CB )) or resid 1434 through 1435 or resid 1444 throu \ gh 1467 or resid 1601)) selection = (chain 'C' and (resid 40 through 43 or (resid 44 through 46 and (name N or name \ CA or name C or name O or name CB )) or resid 47 or (resid 48 through 50 and (na \ me N or name CA or name C or name O or name CB )) or resid 51 through 131 or (re \ sid 132 through 133 and (name N or name CA or name C or name O or name CB )) or \ resid 134 through 159 or (resid 160 through 162 and (name N or name CA or name C \ or name O or name CB )) or resid 163 through 175 or (resid 176 through 177 and \ (name N or name CA or name C or name O or name CB )) or resid 178 through 198 or \ (resid 199 through 200 and (name N or name CA or name C or name O or name CB )) \ or resid 201 through 229 or (resid 230 and (name N or name CA or name C or name \ O or name CB )) or resid 231 through 241 or (resid 242 through 245 and (name N \ or name CA or name C or name O or name CB )) or (resid 246 through 250 and (name \ N or name CA or name C or name O or name CB )) or resid 251 through 253 or (res \ id 254 and (name N or name CA or name C or name O or name CB )) or resid 255 thr \ ough 264 or (resid 265 and (name N or name CA or name C or name O or name CB )) \ or resid 266 through 275 or (resid 276 and (name N or name CA or name C or name \ O or name CB )) or resid 277 through 282 or (resid 283 and (name N or name CA or \ name C or name O or name CB )) or resid 284 through 286 or (resid 287 and (name \ N or name CA or name C or name O or name CB )) or resid 288 through 289 or (res \ id 290 and (name N or name CA or name C or name O or name CB )) or resid 291 or \ resid 296 through 311 or (resid 312 and (name N or name CA or name C or name O o \ r name CB )) or resid 313 through 323 or (resid 324 and (name N or name CA or na \ me C or name O or name CB )) or resid 325 through 347 or (resid 348 through 349 \ and (name N or name CA or name C or name O or name CB )) or resid 350 through 38 \ 0 or (resid 381 through 384 and (name N or name CA or name C or name O or name C \ B )) or resid 385 through 398 or (resid 399 through 404 and (name N or name CA o \ r name C or name O or name CB )) or resid 405 through 421 or (resid 422 through \ 423 and (name N or name CA or name C or name O or name CB )) or resid 424 or (re \ sid 425 through 427 and (name N or name CA or name C or name O or name CB )) or \ resid 428 or (resid 429 through 430 and (name N or name CA or name C or name O o \ r name CB )) or resid 431 through 446 or (resid 447 and (name N or name CA or na \ me C or name O or name CB )) or resid 448 through 514 or (resid 515 and (name N \ or name CA or name C or name O or name CB )) or resid 516 through 557 or (resid \ 558 through 559 and (name N or name CA or name C or name O or name CB )) or resi \ d 560 or resid 589 through 638 or (resid 639 and (name N or name CA or name C or \ name O or name CB )) or (resid 640 through 643 and (name N or name CA or name C \ or name O or name CB )) or resid 644 or (resid 645 and (name N or name CA or na \ me C or name O or name CB )) or resid 646 through 699 or (resid 700 through 702 \ and (name N or name CA or name C or name O or name CB )) or resid 703 through 73 \ 1 or (resid 732 through 738 and (name N or name CA or name C or name O or name C \ B )) or resid 739 or (resid 740 and (name N or name CA or name C or name O or na \ me CB )) or resid 741 through 744 or (resid 745 and (name N or name CA or name C \ or name O or name CB )) or resid 746 through 762 or (resid 763 through 798 and \ (name N or name CA or name C or name O or name CB )) or resid 799 through 811 or \ (resid 812 and (name N or name CA or name C or name O or name CB or name CG or \ name CD )) or resid 813 through 863 or (resid 864 and (name N or name CA or name \ C or name O or name CB )) or resid 869 through 870 or (resid 871 through 872 an \ d (name N or name CA or name C or name O or name CB )) or resid 873 through 874 \ or (resid 875 through 876 and (name N or name CA or name C or name O or name CB \ )) or resid 877 through 879 or (resid 880 and (name N or name CA or name C or na \ me O or name CB )) or resid 881 through 904 or (resid 905 through 906 and (name \ N or name CA or name C or name O or name CB )) or resid 907 through 911 or (resi \ d 912 and (name N or name CA or name C or name O or name CB )) or resid 913 thro \ ugh 926 or (resid 927 through 928 and (name N or name CA or name C or name O or \ name CB )) or resid 929 through 930 or (resid 931 through 933 and (name N or nam \ e CA or name C or name O or name CB )) or resid 934 through 941 or (resid 942 th \ rough 943 and (name N or name CA or name C or name O or name CB )) or resid 944 \ or (resid 945 through 947 and (name N or name CA or name C or name O or name CB \ )) or resid 948 through 949 or (resid 950 and (name N or name CA or name C or na \ me O or name CB )) or resid 951 through 974 or (resid 975 through 977 and (name \ N or name CA or name C or name O or name CB )) or resid 978 through 981 or (resi \ d 982 through 983 and (name N or name CA or name C or name O or name CB )) or re \ sid 984 through 997 or (resid 998 and (name N or name CA or name C or name O or \ name CB )) or resid 999 through 1042 or (resid 1043 through 1044 and (name N or \ name CA or name C or name O or name CB )) or resid 1045 through 1047 or (resid 1 \ 048 through 1049 and (name N or name CA or name C or name O or name CB )) or res \ id 1050 through 1061 or (resid 1062 and (name N or name CA or name C or name O o \ r name CB )) or resid 1063 through 1071 or (resid 1072 through 1077 and (name N \ or name CA or name C or name O or name CB )) or resid 1078 through 1081 or (resi \ d 1082 and (name N or name CA or name C or name O or name CB )) or resid 1083 th \ rough 1108 or (resid 1109 and (name N or name CA or name C or name O or name CB \ )) or resid 1110 through 1132 or (resid 1133 through 1134 and (name N or name CA \ or name C or name O or name CB )) or resid 1135 through 1181 or (resid 1182 thr \ ough 1183 and (name N or name CA or name C or name O or name CB )) or resid 1184 \ through 1209 or resid 1247 through 1270 or (resid 1271 through 1275 and (name N \ or name CA or name C or name O or name CB )) or resid 1276 through 1305 or (res \ id 1306 and (name N or name CA or name C or name O or name CB )) or resid 1307 t \ hrough 1309 or (resid 1310 through 1311 and (name N or name CA or name C or name \ O or name CB )) or resid 1312 through 1326 or (resid 1327 through 1328 and (nam \ e N or name CA or name C or name O or name CB )) or resid 1329 through 1330 or ( \ resid 1331 and (name N or name CA or name C or name O or name CB )) or resid 133 \ 2 through 1333 or (resid 1334 through 1355 and (name N or name CA or name C or n \ ame O or name CB )) or resid 1356 through 1357 or (resid 1358 through 1359 and ( \ name N or name CA or name C or name O or name CB )) or resid 1360 through 1363 o \ r (resid 1369 through 1376 and (name N or name CA or name C or name O or name CB \ )) or resid 1377 through 1379 or (resid 1380 through 1381 and (name N or name C \ A or name C or name O or name CB )) or resid 1392 or (resid 1393 through 1395 an \ d (name N or name CA or name C or name O or name CB )) or resid 1396 or (resid 1 \ 397 and (name N or name CA or name C or name O or name CB )) or resid 1398 throu \ gh 1419 or (resid 1427 through 1433 and (name N or name CA or name C or name O o \ r name CB )) or resid 1434 through 1444 or (resid 1445 through 1467 and (name N \ or name CA or name C or name O or name CB )) or resid 1601)) selection = (chain 'D' and (resid 40 through 49 or (resid 50 and (name N or name CA or name \ C or name O or name CB )) or resid 51 through 52 or (resid 89 through 91 and (na \ me N or name CA or name C or name O or name CB )) or resid 92 through 104 or (re \ sid 105 and (name N or name CA or name C or name O or name CB )) or resid 106 th \ rough 154 or (resid 155 and (name N or name CA or name C or name O or name CB )) \ or resid 156 through 157 or (resid 158 through 162 and (name N or name CA or na \ me C or name O or name CB )) or resid 163 through 167 or (resid 168 and (name N \ or name CA or name C or name O or name CB )) or resid 169 through 171 or (resid \ 172 and (name N or name CA or name C or name O or name CB )) or resid 173 throug \ h 191 or (resid 192 and (name N or name CA or name C or name O or name CB )) or \ resid 193 through 207 or (resid 208 through 209 and (name N or name CA or name C \ or name O or name CB )) or resid 210 or (resid 211 and (name N or name CA or na \ me C or name O or name CB )) or resid 212 through 334 or (resid 335 through 337 \ and (name N or name CA or name C or name O or name CB )) or resid 338 or (resid \ 339 through 345 and (name N or name CA or name C or name O or name CB )) or resi \ d 346 or (resid 347 through 349 and (name N or name CA or name C or name O or na \ me CB )) or resid 350 through 351 or (resid 352 through 353 and (name N or name \ CA or name C or name O or name CB )) or resid 354 through 355 or (resid 356 and \ (name N or name CA or name C or name O or name CB )) or resid 357 through 369 or \ (resid 370 and (name N or name CA or name C or name O or name CB )) or resid 37 \ 1 through 372 or (resid 373 through 374 and (name N or name CA or name C or name \ O or name CB )) or resid 375 or (resid 376 through 377 and (name N or name CA o \ r name C or name O or name CB )) or resid 378 through 379 or (resid 380 through \ 384 and (name N or name CA or name C or name O or name CB )) or resid 385 throug \ h 386 or (resid 387 and (name N or name CA or name C or name O or name CB )) or \ resid 388 through 392 or (resid 393 and (name N or name CA or name C or name O o \ r name CB )) or resid 394 through 402 or (resid 403 through 404 and (name N or n \ ame CA or name C or name O or name CB )) or resid 405 or (resid 406 and (name N \ or name CA or name C or name O or name CB )) or resid 407 through 410 or (resid \ 411 through 412 and (name N or name CA or name C or name O or name CB )) or resi \ d 413 through 414 or (resid 415 through 417 and (name N or name CA or name C or \ name O or name CB )) or resid 418 through 419 or (resid 420 through 423 and (nam \ e N or name CA or name C or name O or name CB )) or resid 424 through 429 or (re \ sid 430 and (name N or name CA or name C or name O or name CB )) or resid 431 th \ rough 486 or (resid 487 through 488 and (name N or name CA or name C or name O o \ r name CB )) or resid 489 through 495 or (resid 496 through 498 and (name N or n \ ame CA or name C or name O or name CB )) or resid 499 through 513 or (resid 514 \ through 515 and (name N or name CA or name C or name O or name CB )) or resid 51 \ 6 or (resid 517 and (name N or name CA or name C or name O or name CB )) or (res \ id 535 through 536 and (name N or name CA or name C or name O or name CB )) or r \ esid 537 through 558 or (resid 559 and (name N or name CA or name C or name O or \ name CB )) or resid 560 through 592 or (resid 593 and (name N or name CA or nam \ e C or name O or name CB )) or resid 594 through 633 or (resid 634 and (name N o \ r name CA or name C or name O or name CB )) or resid 635 through 657 or (resid 6 \ 58 and (name N or name CA or name C or name O or name CB )) or resid 659 through \ 715 or (resid 716 and (name N or name CA or name C or name O or name CB )) or r \ esid 717 through 749 or (resid 750 through 753 and (name N or name CA or name C \ or name O or name CB )) or resid 754 through 763 or (resid 798 and (name N or na \ me CA or name C or name O or name CB )) or resid 799 through 853 or (resid 854 a \ nd (name N or name CA or name C or name O or name CB )) or resid 855 through 877 \ or (resid 878 through 880 and (name N or name CA or name C or name O or name CB \ )) or resid 881 through 901 or (resid 902 through 906 and (name N or name CA or \ name C or name O or name CB )) or resid 907 through 938 or (resid 939 and (name \ N or name CA or name C or name O or name CB )) or resid 940 or (resid 941 throu \ gh 943 and (name N or name CA or name C or name O or name CB )) or resid 944 thr \ ough 978 or (resid 979 through 980 and (name N or name CA or name C or name O or \ name CB )) or resid 981 through 988 or (resid 989 and (name N or name CA or nam \ e C or name O or name CB )) or resid 990 through 996 or (resid 997 through 998 a \ nd (name N or name CA or name C or name O or name CB )) or resid 999 through 100 \ 0 or (resid 1001 through 1011 and (name N or name CA or name C or name O or name \ CB )) or resid 1012 through 1022 or (resid 1023 and (name N or name CA or name \ C or name O or name CB )) or resid 1024 through 1036 or (resid 1037 and (name N \ or name CA or name C or name O or name CB )) or resid 1038 through 1067 or (resi \ d 1068 through 1077 and (name N or name CA or name C or name O or name CB )) or \ resid 1078 through 1083 or (resid 1084 and (name N or name CA or name C or name \ O or name CB )) or resid 1085 through 1087 or (resid 1088 and (name N or name CA \ or name C or name O or name CB )) or resid 1089 through 1104 or (resid 1105 thr \ ough 1107 and (name N or name CA or name C or name O or name CB )) or resid 1108 \ through 1111 or (resid 1112 and (name N or name CA or name C or name O or name \ CB )) or resid 1113 or (resid 1114 through 1120 and (name N or name CA or name C \ or name O or name CB )) or resid 1121 through 1122 or (resid 1123 and (name N o \ r name CA or name C or name O or name CB )) or resid 1124 through 1179 or (resid \ 1180 through 1183 and (name N or name CA or name C or name O or name CB )) or r \ esid 1184 through 1247 or (resid 1248 through 1249 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1250 through 1251 or (resid 1252 and (name \ N or name CA or name C or name O or name CB )) or resid 1253 through 1254 or (re \ sid 1255 through 1258 and (name N or name CA or name C or name O or name CB )) o \ r resid 1259 through 1263 or (resid 1264 through 1266 and (name N or name CA or \ name C or name O or name CB )) or resid 1267 through 1277 or (resid 1278 through \ 1279 and (name N or name CA or name C or name O or name CB )) or resid 1280 thr \ ough 1286 or (resid 1287 through 1290 and (name N or name CA or name C or name O \ or name CB )) or (resid 1303 through 1306 and (name N or name CA or name C or n \ ame O or name CB )) or resid 1307 through 1319 or (resid 1320 through 1322 and ( \ name N or name CA or name C or name O or name CB )) or resid 1323 through 1334 o \ r (resid 1335 through 1337 and (name N or name CA or name C or name O or name CB \ )) or (resid 1341 through 1349 and (name N or name CA or name C or name O or na \ me CB )) or resid 1355 through 1363 or resid 1369 through 1381 or resid 1392 thr \ ough 1403 or (resid 1404 and (name N or name CA or name C or name O or name CB ) \ ) or resid 1405 through 1419 or (resid 1427 through 1433 and (name N or name CA \ or name C or name O or name CB )) or resid 1434 through 1435 or resid 1444 throu \ gh 1467 or resid 1601)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.580 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: 0.050 Extract box with map and model: 9.430 Check model and map are aligned: 0.550 Set scattering table: 0.380 Process input model: 92.140 Find NCS groups from input model: 3.000 Set up NCS constraints: 0.150 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:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 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 0.083 36168 Z= 0.437 Angle : 1.042 16.245 49532 Z= 0.576 Chirality : 0.057 0.376 5880 Planarity : 0.007 0.062 6272 Dihedral : 10.450 73.176 11486 Min Nonbonded Distance : 1.420 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.42 % Favored : 93.50 % Rotamer: Outliers : 0.07 % Allowed : 6.45 % Favored : 93.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.04 % 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: -3.78 (0.10), residues: 4770 helix: -2.25 (0.07), residues: 2734 sheet: -1.36 (0.29), residues: 346 loop : -2.93 (0.13), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP B 815 HIS 0.028 0.002 HIS D 461 PHE 0.033 0.003 PHE A 827 TYR 0.035 0.003 TYR B 847 ARG 0.010 0.001 ARG D1092 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 497 time to evaluate : 3.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 394 VAL cc_start: 0.8546 (t) cc_final: 0.8253 (m) REVERT: B 1176 LEU cc_start: 0.8778 (tt) cc_final: 0.8252 (mm) REVERT: D 394 VAL cc_start: 0.8598 (t) cc_final: 0.8320 (m) outliers start: 2 outliers final: 0 residues processed: 498 average time/residue: 0.4664 time to fit residues: 382.3869 Evaluate side-chains 235 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 235 time to evaluate : 4.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 417 optimal weight: 0.9990 chunk 374 optimal weight: 8.9990 chunk 207 optimal weight: 8.9990 chunk 127 optimal weight: 0.0370 chunk 252 optimal weight: 2.9990 chunk 200 optimal weight: 0.4980 chunk 387 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 chunk 235 optimal weight: 50.0000 chunk 288 optimal weight: 8.9990 chunk 448 optimal weight: 5.9990 overall best weight: 1.7064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 187 HIS B 256 ASN B 259 HIS ** B 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 HIS B 707 HIS B 716 GLN B 816 ASN B1001 ASN B1090 HIS ** B1104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1146 ASN B1161 HIS B1256 GLN B1290 GLN B1405 ASN ** B1431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 129 ASN A 175 GLN A 187 HIS A 256 ASN A 259 HIS A 268 GLN A 314 ASN ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN A 655 ASN A 816 ASN A1073 ASN ** A1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1121 HIS A1146 ASN A1329 HIS C 129 ASN C 175 GLN C 187 HIS C 256 ASN C 259 HIS C 268 GLN C 314 ASN ** C 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN C1073 ASN ** C1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1121 HIS C1146 ASN C1157 GLN ** C1164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 187 HIS D 256 ASN D 259 HIS ** D 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 538 HIS D 707 HIS D 716 GLN ** D 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 816 ASN D1001 ASN D1090 HIS ** D1104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1146 ASN D1161 HIS D1256 GLN D1290 GLN D1405 ASN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 36168 Z= 0.198 Angle : 0.612 10.233 49532 Z= 0.319 Chirality : 0.039 0.163 5880 Planarity : 0.005 0.047 6272 Dihedral : 5.240 33.500 5224 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.35 % Favored : 94.61 % Rotamer: Outliers : 2.63 % Allowed : 10.71 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.55 % Twisted General : 0.04 % 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: -1.57 (0.12), residues: 4770 helix: -0.03 (0.09), residues: 2732 sheet: -1.52 (0.27), residues: 360 loop : -2.60 (0.14), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 687 HIS 0.009 0.001 HIS B1104 PHE 0.019 0.002 PHE C 919 TYR 0.021 0.002 TYR A1089 ARG 0.006 0.000 ARG D 477 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 271 time to evaluate : 4.109 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 394 VAL cc_start: 0.8502 (t) cc_final: 0.8201 (m) REVERT: A 191 MET cc_start: 0.8767 (mpp) cc_final: 0.8432 (mpp) REVERT: A 324 THR cc_start: 0.8778 (OUTLIER) cc_final: 0.8555 (t) REVERT: A 881 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8369 (tt) REVERT: A 946 MET cc_start: 0.7502 (tmm) cc_final: 0.6970 (tmm) REVERT: A 947 MET cc_start: 0.7152 (mmm) cc_final: 0.6882 (mmm) REVERT: C 881 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8399 (tt) REVERT: C 946 MET cc_start: 0.7193 (tmm) cc_final: 0.6716 (tmm) REVERT: D 394 VAL cc_start: 0.8546 (t) cc_final: 0.8211 (m) REVERT: D 475 PHE cc_start: 0.8745 (OUTLIER) cc_final: 0.8126 (t80) REVERT: D 1055 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8938 (tt) outliers start: 79 outliers final: 26 residues processed: 338 average time/residue: 0.4147 time to fit residues: 242.0986 Evaluate side-chains 258 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 227 time to evaluate : 4.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 475 PHE Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 922 PHE Chi-restraints excluded: chain B residue 1060 ILE Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1304 HIS Chi-restraints excluded: chain B residue 1326 HIS Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 1163 ILE Chi-restraints excluded: chain A residue 1329 HIS Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 464 MET Chi-restraints excluded: chain C residue 662 ILE Chi-restraints excluded: chain C residue 881 LEU Chi-restraints excluded: chain C residue 932 ILE Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 1163 ILE Chi-restraints excluded: chain C residue 1329 HIS Chi-restraints excluded: chain C residue 1449 VAL Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 475 PHE Chi-restraints excluded: chain D residue 922 PHE Chi-restraints excluded: chain D residue 1055 LEU Chi-restraints excluded: chain D residue 1105 LEU Chi-restraints excluded: chain D residue 1304 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 249 optimal weight: 6.9990 chunk 139 optimal weight: 0.2980 chunk 373 optimal weight: 6.9990 chunk 305 optimal weight: 0.9990 chunk 123 optimal weight: 50.0000 chunk 449 optimal weight: 1.9990 chunk 485 optimal weight: 3.9990 chunk 400 optimal weight: 7.9990 chunk 445 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 360 optimal weight: 1.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 GLN ** B 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 GLN ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN A 816 ASN ** A1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 GLN ** C 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 816 ASN ** C1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 268 GLN ** D 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 863 HIS ** D1104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 36168 Z= 0.189 Angle : 0.567 17.453 49532 Z= 0.293 Chirality : 0.039 0.168 5880 Planarity : 0.004 0.047 6272 Dihedral : 4.726 29.162 5224 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 3.33 % Allowed : 12.54 % Favored : 84.13 % 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: -0.56 (0.12), residues: 4770 helix: 0.92 (0.10), residues: 2738 sheet: -1.45 (0.28), residues: 360 loop : -2.35 (0.14), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 981 HIS 0.023 0.001 HIS A1329 PHE 0.017 0.001 PHE A 919 TYR 0.019 0.001 TYR D 555 ARG 0.005 0.000 ARG B 477 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 248 time to evaluate : 4.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 394 VAL cc_start: 0.8547 (t) cc_final: 0.8226 (m) REVERT: B 1100 ILE cc_start: 0.8378 (OUTLIER) cc_final: 0.8159 (tp) REVERT: B 1418 LEU cc_start: 0.5461 (OUTLIER) cc_final: 0.5121 (pt) REVERT: A 881 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8362 (tt) REVERT: A 946 MET cc_start: 0.7599 (tmm) cc_final: 0.7031 (tmm) REVERT: A 947 MET cc_start: 0.7197 (mmm) cc_final: 0.6949 (mmm) REVERT: C 946 MET cc_start: 0.7276 (tmm) cc_final: 0.6678 (tmm) REVERT: D 394 VAL cc_start: 0.8552 (t) cc_final: 0.8195 (m) REVERT: D 475 PHE cc_start: 0.8724 (OUTLIER) cc_final: 0.8169 (t80) outliers start: 100 outliers final: 52 residues processed: 328 average time/residue: 0.3967 time to fit residues: 231.8718 Evaluate side-chains 278 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 222 time to evaluate : 4.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 475 PHE Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 922 PHE Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 991 TYR Chi-restraints excluded: chain B residue 1060 ILE Chi-restraints excluded: chain B residue 1100 ILE Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1304 HIS Chi-restraints excluded: chain B residue 1418 LEU Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 1062 ILE Chi-restraints excluded: chain A residue 1163 ILE Chi-restraints excluded: chain A residue 1358 LEU Chi-restraints excluded: chain A residue 1396 TYR Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 326 CYS Chi-restraints excluded: chain C residue 464 MET Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain C residue 616 GLU Chi-restraints excluded: chain C residue 855 CYS Chi-restraints excluded: chain C residue 901 LEU Chi-restraints excluded: chain C residue 932 ILE Chi-restraints excluded: chain C residue 957 LEU Chi-restraints excluded: chain C residue 1048 LEU Chi-restraints excluded: chain C residue 1050 PHE Chi-restraints excluded: chain C residue 1100 ILE Chi-restraints excluded: chain C residue 1163 ILE Chi-restraints excluded: chain C residue 1329 HIS Chi-restraints excluded: chain C residue 1358 LEU Chi-restraints excluded: chain C residue 1396 TYR Chi-restraints excluded: chain C residue 1449 VAL Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 475 PHE Chi-restraints excluded: chain D residue 490 LEU Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain D residue 922 PHE Chi-restraints excluded: chain D residue 956 LEU Chi-restraints excluded: chain D residue 991 TYR Chi-restraints excluded: chain D residue 1105 LEU Chi-restraints excluded: chain D residue 1304 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 444 optimal weight: 8.9990 chunk 337 optimal weight: 1.9990 chunk 233 optimal weight: 0.1980 chunk 49 optimal weight: 5.9990 chunk 214 optimal weight: 1.9990 chunk 301 optimal weight: 0.7980 chunk 451 optimal weight: 0.5980 chunk 477 optimal weight: 10.0000 chunk 235 optimal weight: 30.0000 chunk 427 optimal weight: 5.9990 chunk 128 optimal weight: 9.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 GLN A 390 HIS ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 816 ASN ** A1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1153 GLN A1157 GLN ** C 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 36168 Z= 0.156 Angle : 0.535 13.274 49532 Z= 0.274 Chirality : 0.038 0.172 5880 Planarity : 0.003 0.049 6272 Dihedral : 4.405 26.450 5224 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.76 % Allowed : 14.44 % Favored : 82.80 % 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: -0.03 (0.13), residues: 4770 helix: 1.40 (0.10), residues: 2740 sheet: -1.46 (0.27), residues: 374 loop : -2.16 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 981 HIS 0.007 0.001 HIS D1104 PHE 0.015 0.001 PHE A 919 TYR 0.017 0.001 TYR B 555 ARG 0.004 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 248 time to evaluate : 4.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 394 VAL cc_start: 0.8571 (t) cc_final: 0.8205 (m) REVERT: B 475 PHE cc_start: 0.8671 (OUTLIER) cc_final: 0.8209 (t80) REVERT: B 832 MET cc_start: 0.8083 (mmm) cc_final: 0.7578 (mtt) REVERT: B 1100 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.8104 (tp) REVERT: B 1418 LEU cc_start: 0.5572 (OUTLIER) cc_final: 0.5239 (pt) REVERT: A 881 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8329 (tt) REVERT: A 946 MET cc_start: 0.7650 (tmm) cc_final: 0.7055 (tmm) REVERT: A 947 MET cc_start: 0.7287 (mmm) cc_final: 0.6914 (ttp) REVERT: C 946 MET cc_start: 0.7492 (tmm) cc_final: 0.6807 (tmm) REVERT: D 320 MET cc_start: 0.8618 (tpp) cc_final: 0.8361 (mtt) REVERT: D 475 PHE cc_start: 0.8687 (OUTLIER) cc_final: 0.8225 (t80) REVERT: D 832 MET cc_start: 0.8040 (mmm) cc_final: 0.7652 (mtm) REVERT: D 1136 LEU cc_start: 0.9015 (tp) cc_final: 0.8759 (tp) outliers start: 83 outliers final: 52 residues processed: 319 average time/residue: 0.3978 time to fit residues: 224.9006 Evaluate side-chains 275 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 218 time to evaluate : 4.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 475 PHE Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain B residue 922 PHE Chi-restraints excluded: chain B residue 991 TYR Chi-restraints excluded: chain B residue 1060 ILE Chi-restraints excluded: chain B residue 1100 ILE Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1304 HIS Chi-restraints excluded: chain B residue 1418 LEU Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 1163 ILE Chi-restraints excluded: chain A residue 1358 LEU Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 166 PHE Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 326 CYS Chi-restraints excluded: chain C residue 464 MET Chi-restraints excluded: chain C residue 616 GLU Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 855 CYS Chi-restraints excluded: chain C residue 901 LEU Chi-restraints excluded: chain C residue 932 ILE Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 957 LEU Chi-restraints excluded: chain C residue 1050 PHE Chi-restraints excluded: chain C residue 1062 ILE Chi-restraints excluded: chain C residue 1163 ILE Chi-restraints excluded: chain C residue 1329 HIS Chi-restraints excluded: chain C residue 1358 LEU Chi-restraints excluded: chain C residue 1396 TYR Chi-restraints excluded: chain C residue 1449 VAL Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 448 ILE Chi-restraints excluded: chain D residue 475 PHE Chi-restraints excluded: chain D residue 490 LEU Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 691 THR Chi-restraints excluded: chain D residue 863 HIS Chi-restraints excluded: chain D residue 922 PHE Chi-restraints excluded: chain D residue 956 LEU Chi-restraints excluded: chain D residue 991 TYR Chi-restraints excluded: chain D residue 1105 LEU Chi-restraints excluded: chain D residue 1304 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 397 optimal weight: 10.0000 chunk 271 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 355 optimal weight: 1.9990 chunk 197 optimal weight: 9.9990 chunk 407 optimal weight: 0.0570 chunk 330 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 243 optimal weight: 8.9990 chunk 428 optimal weight: 6.9990 chunk 120 optimal weight: 8.9990 overall best weight: 3.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 47 ASN A 175 GLN A 231 HIS ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN A 816 ASN ** A1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1157 GLN ** D1431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 36168 Z= 0.281 Angle : 0.613 12.457 49532 Z= 0.317 Chirality : 0.040 0.165 5880 Planarity : 0.004 0.047 6272 Dihedral : 4.555 29.667 5224 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.71 % Favored : 93.27 % Rotamer: Outliers : 3.89 % Allowed : 14.67 % Favored : 81.44 % 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: 0.09 (0.13), residues: 4770 helix: 1.46 (0.10), residues: 2762 sheet: -1.38 (0.27), residues: 364 loop : -2.09 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP C 981 HIS 0.006 0.001 HIS C 461 PHE 0.020 0.002 PHE D 599 TYR 0.025 0.002 TYR D 555 ARG 0.008 0.000 ARG D1179 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 203 time to evaluate : 3.875 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 156 PHE cc_start: 0.8549 (OUTLIER) cc_final: 0.8335 (p90) REVERT: B 394 VAL cc_start: 0.8578 (t) cc_final: 0.8265 (m) REVERT: B 475 PHE cc_start: 0.8868 (OUTLIER) cc_final: 0.8373 (t80) REVERT: B 832 MET cc_start: 0.8263 (mmm) cc_final: 0.7840 (mtt) REVERT: B 1418 LEU cc_start: 0.5605 (OUTLIER) cc_final: 0.5269 (pt) REVERT: A 946 MET cc_start: 0.7716 (tmm) cc_final: 0.7349 (tmm) REVERT: A 991 TYR cc_start: 0.7731 (OUTLIER) cc_final: 0.7399 (t80) REVERT: C 946 MET cc_start: 0.7601 (tmm) cc_final: 0.7144 (tmm) REVERT: D 475 PHE cc_start: 0.8873 (OUTLIER) cc_final: 0.8216 (t80) REVERT: D 832 MET cc_start: 0.8151 (mmm) cc_final: 0.7687 (mtm) REVERT: D 1176 LEU cc_start: 0.8976 (tt) cc_final: 0.8281 (mm) outliers start: 117 outliers final: 63 residues processed: 305 average time/residue: 0.3847 time to fit residues: 208.4893 Evaluate side-chains 266 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 198 time to evaluate : 4.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 156 PHE Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 475 PHE Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain B residue 922 PHE Chi-restraints excluded: chain B residue 924 LEU Chi-restraints excluded: chain B residue 991 TYR Chi-restraints excluded: chain B residue 1060 ILE Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1151 THR Chi-restraints excluded: chain B residue 1400 VAL Chi-restraints excluded: chain B residue 1418 LEU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 991 TYR Chi-restraints excluded: chain A residue 1062 ILE Chi-restraints excluded: chain A residue 1163 ILE Chi-restraints excluded: chain A residue 1358 LEU Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 166 PHE Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 326 CYS Chi-restraints excluded: chain C residue 464 MET Chi-restraints excluded: chain C residue 616 GLU Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 855 CYS Chi-restraints excluded: chain C residue 901 LEU Chi-restraints excluded: chain C residue 932 ILE Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 1048 LEU Chi-restraints excluded: chain C residue 1049 LEU Chi-restraints excluded: chain C residue 1062 ILE Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1163 ILE Chi-restraints excluded: chain C residue 1329 HIS Chi-restraints excluded: chain C residue 1449 VAL Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 445 GLU Chi-restraints excluded: chain D residue 448 ILE Chi-restraints excluded: chain D residue 475 PHE Chi-restraints excluded: chain D residue 490 LEU Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 691 THR Chi-restraints excluded: chain D residue 922 PHE Chi-restraints excluded: chain D residue 924 LEU Chi-restraints excluded: chain D residue 991 TYR Chi-restraints excluded: chain D residue 1105 LEU Chi-restraints excluded: chain D residue 1304 HIS Chi-restraints excluded: chain D residue 1400 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 160 optimal weight: 1.9990 chunk 430 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 280 optimal weight: 0.9990 chunk 117 optimal weight: 40.0000 chunk 477 optimal weight: 7.9990 chunk 396 optimal weight: 10.0000 chunk 221 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 158 optimal weight: 0.9980 chunk 250 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1052 ASN ** B1104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 816 ASN ** A1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 431 GLN ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1052 ASN ** D1104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 36168 Z= 0.186 Angle : 0.554 12.854 49532 Z= 0.283 Chirality : 0.038 0.188 5880 Planarity : 0.003 0.048 6272 Dihedral : 4.356 27.026 5224 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.56 % Allowed : 14.84 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.13), residues: 4770 helix: 1.65 (0.10), residues: 2762 sheet: -1.46 (0.27), residues: 378 loop : -2.02 (0.15), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 981 HIS 0.006 0.001 HIS B1104 PHE 0.019 0.001 PHE C 930 TYR 0.019 0.001 TYR D 555 ARG 0.003 0.000 ARG D 334 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 211 time to evaluate : 4.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 394 VAL cc_start: 0.8530 (t) cc_final: 0.8182 (m) REVERT: B 475 PHE cc_start: 0.8786 (OUTLIER) cc_final: 0.8367 (t80) REVERT: B 832 MET cc_start: 0.8235 (mmm) cc_final: 0.7822 (mtt) REVERT: B 1418 LEU cc_start: 0.5578 (OUTLIER) cc_final: 0.5247 (pt) REVERT: A 946 MET cc_start: 0.7627 (tmm) cc_final: 0.6992 (tmm) REVERT: C 946 MET cc_start: 0.7643 (tmm) cc_final: 0.7268 (tmm) REVERT: D 475 PHE cc_start: 0.8728 (OUTLIER) cc_final: 0.8224 (t80) REVERT: D 832 MET cc_start: 0.8180 (mmm) cc_final: 0.7713 (mtm) REVERT: D 1136 LEU cc_start: 0.9093 (tp) cc_final: 0.8847 (tp) outliers start: 107 outliers final: 70 residues processed: 311 average time/residue: 0.3753 time to fit residues: 208.7808 Evaluate side-chains 277 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 204 time to evaluate : 4.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 475 PHE Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 920 ILE Chi-restraints excluded: chain B residue 922 PHE Chi-restraints excluded: chain B residue 1060 ILE Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1400 VAL Chi-restraints excluded: chain B residue 1418 LEU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1062 ILE Chi-restraints excluded: chain A residue 1100 ILE Chi-restraints excluded: chain A residue 1163 ILE Chi-restraints excluded: chain A residue 1358 LEU Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 166 PHE Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 326 CYS Chi-restraints excluded: chain C residue 464 MET Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 855 CYS Chi-restraints excluded: chain C residue 901 LEU Chi-restraints excluded: chain C residue 932 ILE Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 1048 LEU Chi-restraints excluded: chain C residue 1049 LEU Chi-restraints excluded: chain C residue 1062 ILE Chi-restraints excluded: chain C residue 1163 ILE Chi-restraints excluded: chain C residue 1329 HIS Chi-restraints excluded: chain C residue 1358 LEU Chi-restraints excluded: chain C residue 1359 LEU Chi-restraints excluded: chain C residue 1449 VAL Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 475 PHE Chi-restraints excluded: chain D residue 490 LEU Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 691 THR Chi-restraints excluded: chain D residue 862 TYR Chi-restraints excluded: chain D residue 922 PHE Chi-restraints excluded: chain D residue 924 LEU Chi-restraints excluded: chain D residue 956 LEU Chi-restraints excluded: chain D residue 1056 LEU Chi-restraints excluded: chain D residue 1105 LEU Chi-restraints excluded: chain D residue 1304 HIS Chi-restraints excluded: chain D residue 1400 VAL Chi-restraints excluded: chain D residue 1418 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 460 optimal weight: 0.9980 chunk 53 optimal weight: 8.9990 chunk 272 optimal weight: 10.0000 chunk 349 optimal weight: 30.0000 chunk 270 optimal weight: 5.9990 chunk 402 optimal weight: 6.9990 chunk 266 optimal weight: 10.0000 chunk 476 optimal weight: 7.9990 chunk 297 optimal weight: 7.9990 chunk 290 optimal weight: 2.9990 chunk 219 optimal weight: 2.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 431 GLN ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 816 ASN ** A1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN C 231 HIS ** C 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1052 ASN ** D1104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 36168 Z= 0.300 Angle : 0.627 12.801 49532 Z= 0.323 Chirality : 0.040 0.199 5880 Planarity : 0.004 0.047 6272 Dihedral : 4.560 29.850 5224 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.30 % Favored : 92.68 % Rotamer: Outliers : 3.79 % Allowed : 15.47 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.13), residues: 4770 helix: 1.53 (0.10), residues: 2770 sheet: -1.44 (0.27), residues: 364 loop : -2.05 (0.15), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 981 HIS 0.005 0.001 HIS B1104 PHE 0.018 0.002 PHE C 953 TYR 0.025 0.002 TYR D 555 ARG 0.008 0.001 ARG D1179 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 196 time to evaluate : 4.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 394 VAL cc_start: 0.8711 (t) cc_final: 0.8418 (m) REVERT: B 475 PHE cc_start: 0.8894 (OUTLIER) cc_final: 0.8388 (t80) REVERT: B 832 MET cc_start: 0.8293 (mmm) cc_final: 0.7866 (mtt) REVERT: B 1143 MET cc_start: 0.8524 (mmt) cc_final: 0.8147 (mmt) REVERT: A 946 MET cc_start: 0.7514 (tmm) cc_final: 0.7187 (tmm) REVERT: A 947 MET cc_start: 0.7309 (mmm) cc_final: 0.7069 (mmm) REVERT: A 991 TYR cc_start: 0.7813 (OUTLIER) cc_final: 0.7479 (t80) REVERT: C 946 MET cc_start: 0.7555 (tmm) cc_final: 0.7207 (tmm) REVERT: D 475 PHE cc_start: 0.8898 (OUTLIER) cc_final: 0.8247 (t80) REVERT: D 832 MET cc_start: 0.8333 (mmm) cc_final: 0.7816 (mtm) REVERT: D 1006 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7392 (pp) outliers start: 114 outliers final: 78 residues processed: 297 average time/residue: 0.3846 time to fit residues: 205.2386 Evaluate side-chains 274 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 192 time to evaluate : 4.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 475 PHE Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 897 LEU Chi-restraints excluded: chain B residue 920 ILE Chi-restraints excluded: chain B residue 922 PHE Chi-restraints excluded: chain B residue 924 LEU Chi-restraints excluded: chain B residue 995 PHE Chi-restraints excluded: chain B residue 1060 ILE Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1304 HIS Chi-restraints excluded: chain B residue 1326 HIS Chi-restraints excluded: chain B residue 1400 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 991 TYR Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1062 ILE Chi-restraints excluded: chain A residue 1163 ILE Chi-restraints excluded: chain A residue 1358 LEU Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 166 PHE Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 326 CYS Chi-restraints excluded: chain C residue 464 MET Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 855 CYS Chi-restraints excluded: chain C residue 920 ILE Chi-restraints excluded: chain C residue 932 ILE Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 957 LEU Chi-restraints excluded: chain C residue 1012 CYS Chi-restraints excluded: chain C residue 1048 LEU Chi-restraints excluded: chain C residue 1049 LEU Chi-restraints excluded: chain C residue 1062 ILE Chi-restraints excluded: chain C residue 1163 ILE Chi-restraints excluded: chain C residue 1329 HIS Chi-restraints excluded: chain C residue 1449 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 445 GLU Chi-restraints excluded: chain D residue 448 ILE Chi-restraints excluded: chain D residue 475 PHE Chi-restraints excluded: chain D residue 490 LEU Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 691 THR Chi-restraints excluded: chain D residue 863 HIS Chi-restraints excluded: chain D residue 920 ILE Chi-restraints excluded: chain D residue 922 PHE Chi-restraints excluded: chain D residue 924 LEU Chi-restraints excluded: chain D residue 1006 LEU Chi-restraints excluded: chain D residue 1056 LEU Chi-restraints excluded: chain D residue 1105 LEU Chi-restraints excluded: chain D residue 1304 HIS Chi-restraints excluded: chain D residue 1400 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 294 optimal weight: 5.9990 chunk 190 optimal weight: 6.9990 chunk 284 optimal weight: 4.9990 chunk 143 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 92 optimal weight: 0.9980 chunk 302 optimal weight: 5.9990 chunk 324 optimal weight: 0.0980 chunk 235 optimal weight: 0.6980 chunk 44 optimal weight: 5.9990 chunk 374 optimal weight: 6.9990 overall best weight: 2.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 431 GLN ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 HIS ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN A 816 ASN ** A1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 431 GLN ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 36168 Z= 0.216 Angle : 0.577 12.932 49532 Z= 0.295 Chirality : 0.039 0.163 5880 Planarity : 0.004 0.048 6272 Dihedral : 4.451 32.345 5224 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.95 % Favored : 94.00 % Rotamer: Outliers : 3.29 % Allowed : 15.93 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.55 % 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: 0.37 (0.13), residues: 4770 helix: 1.71 (0.10), residues: 2748 sheet: -1.34 (0.27), residues: 362 loop : -1.97 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 981 HIS 0.004 0.001 HIS C 461 PHE 0.018 0.001 PHE C 930 TYR 0.020 0.001 TYR D 555 ARG 0.003 0.000 ARG D1179 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 202 time to evaluate : 4.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 475 PHE cc_start: 0.8836 (OUTLIER) cc_final: 0.8372 (t80) REVERT: B 832 MET cc_start: 0.8262 (mmm) cc_final: 0.7844 (mtt) REVERT: A 946 MET cc_start: 0.7569 (tmm) cc_final: 0.7100 (tmm) REVERT: A 991 TYR cc_start: 0.7778 (OUTLIER) cc_final: 0.7452 (t80) REVERT: C 946 MET cc_start: 0.7531 (tmm) cc_final: 0.7066 (tmm) REVERT: C 991 TYR cc_start: 0.7728 (OUTLIER) cc_final: 0.7430 (t80) REVERT: D 105 ASP cc_start: 0.8092 (OUTLIER) cc_final: 0.7783 (p0) REVERT: D 475 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.8168 (t80) REVERT: D 832 MET cc_start: 0.8285 (mmm) cc_final: 0.7757 (mtm) REVERT: D 1006 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7404 (pp) REVERT: D 1136 LEU cc_start: 0.9120 (tp) cc_final: 0.8884 (tp) outliers start: 99 outliers final: 76 residues processed: 291 average time/residue: 0.3813 time to fit residues: 199.5911 Evaluate side-chains 280 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 198 time to evaluate : 3.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 475 PHE Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain B residue 897 LEU Chi-restraints excluded: chain B residue 920 ILE Chi-restraints excluded: chain B residue 922 PHE Chi-restraints excluded: chain B residue 924 LEU Chi-restraints excluded: chain B residue 995 PHE Chi-restraints excluded: chain B residue 1060 ILE Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1304 HIS Chi-restraints excluded: chain B residue 1326 HIS Chi-restraints excluded: chain B residue 1400 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 991 TYR Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1062 ILE Chi-restraints excluded: chain A residue 1163 ILE Chi-restraints excluded: chain A residue 1358 LEU Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 166 PHE Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 326 CYS Chi-restraints excluded: chain C residue 464 MET Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 855 CYS Chi-restraints excluded: chain C residue 884 ILE Chi-restraints excluded: chain C residue 901 LEU Chi-restraints excluded: chain C residue 932 ILE Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 957 LEU Chi-restraints excluded: chain C residue 991 TYR Chi-restraints excluded: chain C residue 1012 CYS Chi-restraints excluded: chain C residue 1048 LEU Chi-restraints excluded: chain C residue 1049 LEU Chi-restraints excluded: chain C residue 1062 ILE Chi-restraints excluded: chain C residue 1163 ILE Chi-restraints excluded: chain C residue 1329 HIS Chi-restraints excluded: chain C residue 1359 LEU Chi-restraints excluded: chain C residue 1449 VAL Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 448 ILE Chi-restraints excluded: chain D residue 475 PHE Chi-restraints excluded: chain D residue 490 LEU Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 691 THR Chi-restraints excluded: chain D residue 863 HIS Chi-restraints excluded: chain D residue 922 PHE Chi-restraints excluded: chain D residue 924 LEU Chi-restraints excluded: chain D residue 995 PHE Chi-restraints excluded: chain D residue 1006 LEU Chi-restraints excluded: chain D residue 1056 LEU Chi-restraints excluded: chain D residue 1105 LEU Chi-restraints excluded: chain D residue 1400 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 433 optimal weight: 9.9990 chunk 456 optimal weight: 10.0000 chunk 416 optimal weight: 8.9990 chunk 443 optimal weight: 0.9990 chunk 267 optimal weight: 8.9990 chunk 193 optimal weight: 4.9990 chunk 348 optimal weight: 1.9990 chunk 136 optimal weight: 0.0010 chunk 400 optimal weight: 0.0470 chunk 419 optimal weight: 1.9990 chunk 442 optimal weight: 0.9980 overall best weight: 0.8088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 816 ASN ** A1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1325 ASN ** C 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1081 GLN ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 36168 Z= 0.142 Angle : 0.535 12.434 49532 Z= 0.269 Chirality : 0.038 0.189 5880 Planarity : 0.003 0.050 6272 Dihedral : 4.136 24.489 5224 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.13 % Allowed : 17.17 % Favored : 80.71 % 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: 0.63 (0.13), residues: 4770 helix: 2.00 (0.10), residues: 2710 sheet: -1.25 (0.28), residues: 368 loop : -1.91 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 981 HIS 0.005 0.001 HIS D1164 PHE 0.018 0.001 PHE A 919 TYR 0.015 0.001 TYR D 555 ARG 0.004 0.000 ARG D1179 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 222 time to evaluate : 4.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 475 PHE cc_start: 0.8663 (OUTLIER) cc_final: 0.8305 (t80) REVERT: B 832 MET cc_start: 0.8214 (mmm) cc_final: 0.7813 (mtt) REVERT: B 1143 MET cc_start: 0.8409 (mmt) cc_final: 0.8026 (mmt) REVERT: A 946 MET cc_start: 0.7511 (tmm) cc_final: 0.7069 (tmm) REVERT: C 946 MET cc_start: 0.7448 (tmm) cc_final: 0.7081 (tmm) REVERT: C 991 TYR cc_start: 0.7681 (OUTLIER) cc_final: 0.7419 (t80) REVERT: D 475 PHE cc_start: 0.8632 (OUTLIER) cc_final: 0.8207 (t80) REVERT: D 832 MET cc_start: 0.8335 (mmm) cc_final: 0.7825 (mtm) REVERT: D 1136 LEU cc_start: 0.9043 (tp) cc_final: 0.8728 (tp) REVERT: D 1176 LEU cc_start: 0.8844 (tt) cc_final: 0.8100 (mm) outliers start: 64 outliers final: 45 residues processed: 277 average time/residue: 0.3942 time to fit residues: 195.5155 Evaluate side-chains 255 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 207 time to evaluate : 4.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 475 PHE Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain B residue 862 TYR Chi-restraints excluded: chain B residue 897 LEU Chi-restraints excluded: chain B residue 920 ILE Chi-restraints excluded: chain B residue 922 PHE Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 1089 TYR Chi-restraints excluded: chain A residue 1358 LEU Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 326 CYS Chi-restraints excluded: chain C residue 464 MET Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 855 CYS Chi-restraints excluded: chain C residue 901 LEU Chi-restraints excluded: chain C residue 932 ILE Chi-restraints excluded: chain C residue 957 LEU Chi-restraints excluded: chain C residue 991 TYR Chi-restraints excluded: chain C residue 1050 PHE Chi-restraints excluded: chain C residue 1329 HIS Chi-restraints excluded: chain C residue 1359 LEU Chi-restraints excluded: chain C residue 1449 VAL Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 448 ILE Chi-restraints excluded: chain D residue 475 PHE Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain D residue 691 THR Chi-restraints excluded: chain D residue 920 ILE Chi-restraints excluded: chain D residue 922 PHE Chi-restraints excluded: chain D residue 995 PHE Chi-restraints excluded: chain D residue 1105 LEU Chi-restraints excluded: chain D residue 1400 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 291 optimal weight: 6.9990 chunk 469 optimal weight: 6.9990 chunk 286 optimal weight: 0.8980 chunk 222 optimal weight: 0.8980 chunk 326 optimal weight: 1.9990 chunk 492 optimal weight: 50.0000 chunk 452 optimal weight: 2.9990 chunk 391 optimal weight: 0.9980 chunk 40 optimal weight: 0.0010 chunk 302 optimal weight: 10.0000 chunk 240 optimal weight: 8.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.4279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 36168 Z= 0.151 Angle : 0.544 11.940 49532 Z= 0.271 Chirality : 0.038 0.177 5880 Planarity : 0.003 0.049 6272 Dihedral : 4.044 25.380 5224 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.80 % Allowed : 17.80 % Favored : 80.41 % 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: 0.72 (0.13), residues: 4770 helix: 2.03 (0.10), residues: 2724 sheet: -1.10 (0.28), residues: 356 loop : -1.87 (0.15), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 981 HIS 0.006 0.001 HIS B1326 PHE 0.013 0.001 PHE A 475 TYR 0.017 0.001 TYR D 555 ARG 0.008 0.000 ARG B1179 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9540 Ramachandran restraints generated. 4770 Oldfield, 0 Emsley, 4770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 216 time to evaluate : 4.790 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 475 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.8398 (t80) REVERT: B 832 MET cc_start: 0.8276 (mmm) cc_final: 0.7805 (mtm) REVERT: A 946 MET cc_start: 0.7427 (tmm) cc_final: 0.6708 (tmm) REVERT: C 946 MET cc_start: 0.7399 (tmm) cc_final: 0.6750 (tmm) REVERT: C 991 TYR cc_start: 0.7710 (OUTLIER) cc_final: 0.7434 (t80) REVERT: C 1026 MET cc_start: 0.7471 (mmt) cc_final: 0.7232 (mmt) REVERT: D 475 PHE cc_start: 0.8717 (OUTLIER) cc_final: 0.8257 (t80) REVERT: D 832 MET cc_start: 0.8333 (mmm) cc_final: 0.7827 (mtm) REVERT: D 1136 LEU cc_start: 0.9021 (tp) cc_final: 0.8723 (tp) outliers start: 54 outliers final: 49 residues processed: 264 average time/residue: 0.3944 time to fit residues: 187.6913 Evaluate side-chains 260 residues out of total 4320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 208 time to evaluate : 4.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 475 PHE Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain B residue 862 TYR Chi-restraints excluded: chain B residue 897 LEU Chi-restraints excluded: chain B residue 920 ILE Chi-restraints excluded: chain B residue 922 PHE Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1400 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 920 ILE Chi-restraints excluded: chain A residue 1067 PHE Chi-restraints excluded: chain A residue 1358 LEU Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 326 CYS Chi-restraints excluded: chain C residue 464 MET Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 855 CYS Chi-restraints excluded: chain C residue 901 LEU Chi-restraints excluded: chain C residue 932 ILE Chi-restraints excluded: chain C residue 957 LEU Chi-restraints excluded: chain C residue 991 TYR Chi-restraints excluded: chain C residue 1050 PHE Chi-restraints excluded: chain C residue 1329 HIS Chi-restraints excluded: chain C residue 1359 LEU Chi-restraints excluded: chain C residue 1449 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 448 ILE Chi-restraints excluded: chain D residue 475 PHE Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain D residue 691 THR Chi-restraints excluded: chain D residue 920 ILE Chi-restraints excluded: chain D residue 922 PHE Chi-restraints excluded: chain D residue 995 PHE Chi-restraints excluded: chain D residue 1105 LEU Chi-restraints excluded: chain D residue 1400 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 311 optimal weight: 10.0000 chunk 417 optimal weight: 3.9990 chunk 120 optimal weight: 30.0000 chunk 361 optimal weight: 50.0000 chunk 57 optimal weight: 0.5980 chunk 108 optimal weight: 10.0000 chunk 392 optimal weight: 1.9990 chunk 164 optimal weight: 0.8980 chunk 403 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 72 optimal weight: 0.0770 overall best weight: 1.5142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1104 HIS ** 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 = 0.3792 r_free = 0.3792 target = 0.082456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.066434 restraints weight = 186904.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.067892 restraints weight = 102289.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.068805 restraints weight = 67686.271| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3459 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3459 r_free = 0.3459 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3457 r_free = 0.3457 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3457 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.4367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 36168 Z= 0.167 Angle : 0.546 12.028 49532 Z= 0.273 Chirality : 0.038 0.166 5880 Planarity : 0.003 0.049 6272 Dihedral : 3.992 24.632 5224 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.96 % Allowed : 17.50 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.13), residues: 4770 helix: 2.07 (0.10), residues: 2722 sheet: -1.11 (0.28), residues: 356 loop : -1.84 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 981 HIS 0.016 0.001 HIS A1161 PHE 0.015 0.001 PHE D1099 TYR 0.018 0.001 TYR D 555 ARG 0.008 0.000 ARG B1179 =============================================================================== Job complete usr+sys time: 5850.25 seconds wall clock time: 107 minutes 42.35 seconds (6462.35 seconds total)