Starting phenix.real_space_refine on Fri Feb 23 07:24:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pur_20479/02_2024/6pur_20479_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pur_20479/02_2024/6pur_20479.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pur_20479/02_2024/6pur_20479.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pur_20479/02_2024/6pur_20479.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pur_20479/02_2024/6pur_20479_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pur_20479/02_2024/6pur_20479_updated.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 P 16 5.49 5 S 140 5.16 5 C 24072 2.51 5 N 6636 2.21 5 O 6404 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 65": "OE1" <-> "OE2" Residue "A ARG 144": "NH1" <-> "NH2" Residue "A ARG 223": "NH1" <-> "NH2" Residue "A ARG 304": "NH1" <-> "NH2" Residue "A ARG 358": "NH1" <-> "NH2" Residue "A ARG 411": "NH1" <-> "NH2" Residue "A ARG 412": "NH1" <-> "NH2" Residue "A ARG 413": "NH1" <-> "NH2" Residue "A ARG 420": "NH1" <-> "NH2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "A ARG 469": "NH1" <-> "NH2" Residue "A ARG 634": "NH1" <-> "NH2" Residue "A ARG 685": "NH1" <-> "NH2" Residue "A GLU 692": "OE1" <-> "OE2" Residue "A ARG 695": "NH1" <-> "NH2" Residue "A ARG 700": "NH1" <-> "NH2" Residue "A ARG 755": "NH1" <-> "NH2" Residue "A ARG 774": "NH1" <-> "NH2" Residue "A GLU 842": "OE1" <-> "OE2" Residue "A ARG 845": "NH1" <-> "NH2" Residue "A ARG 896": "NH1" <-> "NH2" Residue "A ARG 1077": "NH1" <-> "NH2" Residue "A ARG 1136": "NH1" <-> "NH2" Residue "A ARG 1143": "NH1" <-> "NH2" Residue "A ARG 1310": "NH1" <-> "NH2" Residue "A ARG 1311": "NH1" <-> "NH2" Residue "A ARG 1354": "NH1" <-> "NH2" Residue "A ARG 1356": "NH1" <-> "NH2" Residue "A ARG 1365": "NH1" <-> "NH2" Residue "A ARG 1474": "NH1" <-> "NH2" Residue "B GLU 65": "OE1" <-> "OE2" Residue "B ARG 144": "NH1" <-> "NH2" Residue "B ARG 223": "NH1" <-> "NH2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "B ARG 358": "NH1" <-> "NH2" Residue "B ARG 411": "NH1" <-> "NH2" Residue "B ARG 412": "NH1" <-> "NH2" Residue "B ARG 413": "NH1" <-> "NH2" Residue "B ARG 420": "NH1" <-> "NH2" Residue "B ARG 464": "NH1" <-> "NH2" Residue "B ARG 469": "NH1" <-> "NH2" Residue "B ARG 634": "NH1" <-> "NH2" Residue "B ARG 685": "NH1" <-> "NH2" Residue "B GLU 692": "OE1" <-> "OE2" Residue "B ARG 695": "NH1" <-> "NH2" Residue "B ARG 700": "NH1" <-> "NH2" Residue "B ARG 755": "NH1" <-> "NH2" Residue "B ARG 774": "NH1" <-> "NH2" Residue "B GLU 842": "OE1" <-> "OE2" Residue "B ARG 845": "NH1" <-> "NH2" Residue "B ARG 896": "NH1" <-> "NH2" Residue "B ARG 1077": "NH1" <-> "NH2" Residue "B ARG 1136": "NH1" <-> "NH2" Residue "B ARG 1143": "NH1" <-> "NH2" Residue "B ARG 1310": "NH1" <-> "NH2" Residue "B ARG 1311": "NH1" <-> "NH2" Residue "B ARG 1354": "NH1" <-> "NH2" Residue "B ARG 1356": "NH1" <-> "NH2" Residue "B ARG 1365": "NH1" <-> "NH2" Residue "B ARG 1474": "NH1" <-> "NH2" Residue "C GLU 65": "OE1" <-> "OE2" Residue "C ARG 144": "NH1" <-> "NH2" Residue "C ARG 223": "NH1" <-> "NH2" Residue "C ARG 304": "NH1" <-> "NH2" Residue "C ARG 358": "NH1" <-> "NH2" Residue "C ARG 411": "NH1" <-> "NH2" Residue "C ARG 412": "NH1" <-> "NH2" Residue "C ARG 413": "NH1" <-> "NH2" Residue "C ARG 420": "NH1" <-> "NH2" Residue "C ARG 464": "NH1" <-> "NH2" Residue "C ARG 469": "NH1" <-> "NH2" Residue "C ARG 634": "NH1" <-> "NH2" Residue "C ARG 685": "NH1" <-> "NH2" Residue "C GLU 692": "OE1" <-> "OE2" Residue "C ARG 695": "NH1" <-> "NH2" Residue "C ARG 700": "NH1" <-> "NH2" Residue "C ARG 755": "NH1" <-> "NH2" Residue "C ARG 774": "NH1" <-> "NH2" Residue "C GLU 842": "OE1" <-> "OE2" Residue "C ARG 845": "NH1" <-> "NH2" Residue "C ARG 896": "NH1" <-> "NH2" Residue "C ARG 1077": "NH1" <-> "NH2" Residue "C ARG 1136": "NH1" <-> "NH2" Residue "C ARG 1143": "NH1" <-> "NH2" Residue "C ARG 1310": "NH1" <-> "NH2" Residue "C ARG 1311": "NH1" <-> "NH2" Residue "C ARG 1354": "NH1" <-> "NH2" Residue "C ARG 1356": "NH1" <-> "NH2" Residue "C ARG 1365": "NH1" <-> "NH2" Residue "C ARG 1474": "NH1" <-> "NH2" Residue "D GLU 65": "OE1" <-> "OE2" Residue "D ARG 144": "NH1" <-> "NH2" Residue "D ARG 223": "NH1" <-> "NH2" Residue "D ARG 304": "NH1" <-> "NH2" Residue "D ARG 358": "NH1" <-> "NH2" Residue "D ARG 411": "NH1" <-> "NH2" Residue "D ARG 412": "NH1" <-> "NH2" Residue "D ARG 413": "NH1" <-> "NH2" Residue "D ARG 420": "NH1" <-> "NH2" Residue "D ARG 464": "NH1" <-> "NH2" Residue "D ARG 469": "NH1" <-> "NH2" Residue "D ARG 634": "NH1" <-> "NH2" Residue "D ARG 685": "NH1" <-> "NH2" Residue "D GLU 692": "OE1" <-> "OE2" Residue "D ARG 695": "NH1" <-> "NH2" Residue "D ARG 700": "NH1" <-> "NH2" Residue "D ARG 755": "NH1" <-> "NH2" Residue "D ARG 774": "NH1" <-> "NH2" Residue "D GLU 842": "OE1" <-> "OE2" Residue "D ARG 845": "NH1" <-> "NH2" Residue "D ARG 896": "NH1" <-> "NH2" Residue "D ARG 1077": "NH1" <-> "NH2" Residue "D ARG 1136": "NH1" <-> "NH2" Residue "D ARG 1143": "NH1" <-> "NH2" Residue "D ARG 1310": "NH1" <-> "NH2" Residue "D ARG 1311": "NH1" <-> "NH2" Residue "D ARG 1354": "NH1" <-> "NH2" Residue "D ARG 1356": "NH1" <-> "NH2" Residue "D ARG 1365": "NH1" <-> "NH2" Residue "D ARG 1474": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 37268 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 9245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1306, 9245 Classifications: {'peptide': 1306} Incomplete info: {'truncation_to_alanine': 365} Link IDs: {'PTRANS': 62, 'TRANS': 1243} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 1338 Unresolved non-hydrogen angles: 1689 Unresolved non-hydrogen dihedrals: 1097 Unresolved non-hydrogen chiralities: 84 Planarities with less than four sites: {'GLN:plan1': 24, 'ARG:plan': 23, 'TYR:plan': 7, 'ASN:plan1': 11, 'TRP:plan': 5, 'HIS:plan': 14, 'PHE:plan': 12, 'GLU:plan': 63, 'ASP:plan': 46} Unresolved non-hydrogen planarities: 870 Chain: "B" Number of atoms: 9245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1306, 9245 Classifications: {'peptide': 1306} Incomplete info: {'truncation_to_alanine': 365} Link IDs: {'PTRANS': 62, 'TRANS': 1243} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 1338 Unresolved non-hydrogen angles: 1689 Unresolved non-hydrogen dihedrals: 1097 Unresolved non-hydrogen chiralities: 84 Planarities with less than four sites: {'GLN:plan1': 24, 'ARG:plan': 23, 'TYR:plan': 7, 'ASN:plan1': 11, 'TRP:plan': 5, 'HIS:plan': 14, 'PHE:plan': 12, 'GLU:plan': 63, 'ASP:plan': 46} Unresolved non-hydrogen planarities: 870 Chain: "C" Number of atoms: 9245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1306, 9245 Classifications: {'peptide': 1306} Incomplete info: {'truncation_to_alanine': 365} Link IDs: {'PTRANS': 62, 'TRANS': 1243} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 1338 Unresolved non-hydrogen angles: 1689 Unresolved non-hydrogen dihedrals: 1097 Unresolved non-hydrogen chiralities: 84 Planarities with less than four sites: {'GLN:plan1': 24, 'ARG:plan': 23, 'TYR:plan': 7, 'ASN:plan1': 11, 'TRP:plan': 5, 'HIS:plan': 14, 'PHE:plan': 12, 'GLU:plan': 63, 'ASP:plan': 46} Unresolved non-hydrogen planarities: 870 Chain: "D" Number of atoms: 9245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1306, 9245 Classifications: {'peptide': 1306} Incomplete info: {'truncation_to_alanine': 365} Link IDs: {'PTRANS': 62, 'TRANS': 1243} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 1338 Unresolved non-hydrogen angles: 1689 Unresolved non-hydrogen dihedrals: 1097 Unresolved non-hydrogen chiralities: 84 Planarities with less than four sites: {'GLN:plan1': 24, 'ARG:plan': 23, 'TYR:plan': 7, 'ASN:plan1': 11, 'TRP:plan': 5, 'HIS:plan': 14, 'PHE:plan': 12, 'GLU:plan': 63, 'ASP:plan': 46} Unresolved non-hydrogen planarities: 870 Chain: "A" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 72 Unusual residues: {'APR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 72 Unusual residues: {'APR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 72 Unusual residues: {'APR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 72 Unusual residues: {'APR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 19.63, per 1000 atoms: 0.53 Number of scatterers: 37268 At special positions: 0 Unit cell: (157.878, 157.878, 164.322, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 140 16.00 P 16 15.00 O 6404 8.00 N 6636 7.00 C 24072 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.89 Conformation dependent library (CDL) restraints added in 7.2 seconds 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9856 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 212 helices and 20 sheets defined 48.5% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 11.19 Creating SS restraints... Processing helix chain 'A' and resid 57 through 66 Proline residue: A 64 - end of helix Processing helix chain 'A' and resid 151 through 160 Processing helix chain 'A' and resid 184 through 201 removed outlier: 3.662A pdb=" N ILE A 189 " --> pdb=" O ARG A 185 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU A 194 " --> pdb=" O PHE A 190 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL A 195 " --> pdb=" O ARG A 191 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR A 200 " --> pdb=" O LYS A 196 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N THR A 201 " --> pdb=" O VAL A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 228 removed outlier: 4.385A pdb=" N PHE A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER A 226 " --> pdb=" O VAL A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 252 No H-bonds generated for 'chain 'A' and resid 250 through 252' Processing helix chain 'A' and resid 299 through 311 removed outlier: 3.552A pdb=" N LYS A 307 " --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE A 308 " --> pdb=" O ARG A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 346 removed outlier: 3.628A pdb=" N HIS A 338 " --> pdb=" O PRO A 334 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR A 345 " --> pdb=" O ASP A 341 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASN A 346 " --> pdb=" O ASN A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 366 removed outlier: 4.081A pdb=" N VAL A 366 " --> pdb=" O VAL A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 373 No H-bonds generated for 'chain 'A' and resid 371 through 373' Processing helix chain 'A' and resid 376 through 386 removed outlier: 3.761A pdb=" N VAL A 385 " --> pdb=" O GLN A 381 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE A 386 " --> pdb=" O LYS A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 393 No H-bonds generated for 'chain 'A' and resid 391 through 393' Processing helix chain 'A' and resid 396 through 411 Processing helix chain 'A' and resid 413 through 415 No H-bonds generated for 'chain 'A' and resid 413 through 415' Processing helix chain 'A' and resid 430 through 444 removed outlier: 3.739A pdb=" N GLN A 435 " --> pdb=" O VAL A 431 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA A 440 " --> pdb=" O ALA A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 461 removed outlier: 3.905A pdb=" N LEU A 456 " --> pdb=" O TRP A 452 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS A 457 " --> pdb=" O ASP A 453 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU A 458 " --> pdb=" O HIS A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 470 Processing helix chain 'A' and resid 482 through 493 Proline residue: A 486 - end of helix removed outlier: 4.331A pdb=" N ALA A 490 " --> pdb=" O THR A 487 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE A 493 " --> pdb=" O ALA A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 506 Processing helix chain 'A' and resid 510 through 513 No H-bonds generated for 'chain 'A' and resid 510 through 513' Processing helix chain 'A' and resid 516 through 525 removed outlier: 3.542A pdb=" N ASN A 525 " --> pdb=" O TYR A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 541 Processing helix chain 'A' and resid 558 through 569 Processing helix chain 'A' and resid 621 through 631 Processing helix chain 'A' and resid 635 through 644 removed outlier: 4.449A pdb=" N ALA A 643 " --> pdb=" O GLY A 639 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLN A 644 " --> pdb=" O ILE A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 665 removed outlier: 3.575A pdb=" N LEU A 653 " --> pdb=" O ILE A 649 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS A 664 " --> pdb=" O LYS A 660 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLU A 665 " --> pdb=" O GLU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 696 removed outlier: 3.554A pdb=" N ALA A 679 " --> pdb=" O MET A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 705 removed outlier: 3.709A pdb=" N LYS A 703 " --> pdb=" O GLU A 699 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU A 704 " --> pdb=" O ARG A 700 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU A 705 " --> pdb=" O ALA A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 723 Processing helix chain 'A' and resid 727 through 730 No H-bonds generated for 'chain 'A' and resid 727 through 730' Processing helix chain 'A' and resid 733 through 743 Processing helix chain 'A' and resid 754 through 761 Processing helix chain 'A' and resid 776 through 780 Processing helix chain 'A' and resid 784 through 793 Processing helix chain 'A' and resid 795 through 819 Processing helix chain 'A' and resid 827 through 847 Processing helix chain 'A' and resid 856 through 865 Processing helix chain 'A' and resid 867 through 887 removed outlier: 3.718A pdb=" N THR A 884 " --> pdb=" O VAL A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 912 removed outlier: 3.534A pdb=" N VAL A 897 " --> pdb=" O TYR A 893 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ARG A 909 " --> pdb=" O LEU A 905 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU A 910 " --> pdb=" O PHE A 906 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N MET A 911 " --> pdb=" O CYS A 907 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N HIS A 912 " --> pdb=" O LEU A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 955 removed outlier: 4.542A pdb=" N LYS A 932 " --> pdb=" O LYS A 928 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ASP A 933 " --> pdb=" O ARG A 929 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N PHE A 936 " --> pdb=" O LYS A 932 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU A 940 " --> pdb=" O PHE A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 978 Processing helix chain 'A' and resid 1022 through 1035 Processing helix chain 'A' and resid 1039 through 1053 Processing helix chain 'A' and resid 1059 through 1066 Processing helix chain 'A' and resid 1068 through 1076 Processing helix chain 'A' and resid 1085 through 1098 removed outlier: 3.527A pdb=" N GLN A1091 " --> pdb=" O LEU A1087 " (cutoff:3.500A) Processing helix chain 'A' and resid 1115 through 1142 removed outlier: 4.170A pdb=" N GLU A1130 " --> pdb=" O ILE A1126 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN A1131 " --> pdb=" O TYR A1127 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASN A1135 " --> pdb=" O ASN A1131 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN A1142 " --> pdb=" O PHE A1138 " (cutoff:3.500A) Processing helix chain 'A' and resid 1144 through 1164 Processing helix chain 'A' and resid 1279 through 1281 No H-bonds generated for 'chain 'A' and resid 1279 through 1281' Processing helix chain 'A' and resid 1289 through 1291 No H-bonds generated for 'chain 'A' and resid 1289 through 1291' Processing helix chain 'A' and resid 1398 through 1403 Processing helix chain 'A' and resid 1411 through 1417 Processing helix chain 'A' and resid 1456 through 1463 Processing helix chain 'A' and resid 1486 through 1498 removed outlier: 3.512A pdb=" N LEU A1491 " --> pdb=" O ASN A1487 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ALA A1497 " --> pdb=" O GLN A1493 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N GLU A1498 " --> pdb=" O LYS A1494 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 66 Proline residue: B 64 - end of helix Processing helix chain 'B' and resid 151 through 160 Processing helix chain 'B' and resid 184 through 201 removed outlier: 3.661A pdb=" N ILE B 189 " --> pdb=" O ARG B 185 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU B 194 " --> pdb=" O PHE B 190 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N VAL B 195 " --> pdb=" O ARG B 191 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N THR B 201 " --> pdb=" O VAL B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 228 removed outlier: 4.385A pdb=" N PHE B 225 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER B 226 " --> pdb=" O VAL B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 252 No H-bonds generated for 'chain 'B' and resid 250 through 252' Processing helix chain 'B' and resid 299 through 311 removed outlier: 3.552A pdb=" N LYS B 307 " --> pdb=" O THR B 303 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE B 308 " --> pdb=" O ARG B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 346 removed outlier: 3.627A pdb=" N HIS B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR B 345 " --> pdb=" O ASP B 341 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASN B 346 " --> pdb=" O ASN B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 366 removed outlier: 4.081A pdb=" N VAL B 366 " --> pdb=" O VAL B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 376 through 386 removed outlier: 3.761A pdb=" N VAL B 385 " --> pdb=" O GLN B 381 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE B 386 " --> pdb=" O LYS B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 393 No H-bonds generated for 'chain 'B' and resid 391 through 393' Processing helix chain 'B' and resid 396 through 411 Processing helix chain 'B' and resid 413 through 415 No H-bonds generated for 'chain 'B' and resid 413 through 415' Processing helix chain 'B' and resid 430 through 444 removed outlier: 3.738A pdb=" N GLN B 435 " --> pdb=" O VAL B 431 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA B 440 " --> pdb=" O ALA B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 461 removed outlier: 3.905A pdb=" N LEU B 456 " --> pdb=" O TRP B 452 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS B 457 " --> pdb=" O ASP B 453 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU B 458 " --> pdb=" O HIS B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 470 Processing helix chain 'B' and resid 482 through 493 Proline residue: B 486 - end of helix removed outlier: 4.331A pdb=" N ALA B 490 " --> pdb=" O THR B 487 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE B 493 " --> pdb=" O ALA B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 506 Processing helix chain 'B' and resid 510 through 513 No H-bonds generated for 'chain 'B' and resid 510 through 513' Processing helix chain 'B' and resid 516 through 525 removed outlier: 3.542A pdb=" N ASN B 525 " --> pdb=" O TYR B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 541 Processing helix chain 'B' and resid 558 through 569 Processing helix chain 'B' and resid 621 through 631 Processing helix chain 'B' and resid 635 through 644 removed outlier: 4.449A pdb=" N ALA B 643 " --> pdb=" O GLY B 639 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLN B 644 " --> pdb=" O ILE B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 665 removed outlier: 3.575A pdb=" N LEU B 653 " --> pdb=" O ILE B 649 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS B 664 " --> pdb=" O LYS B 660 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLU B 665 " --> pdb=" O GLU B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 696 removed outlier: 3.554A pdb=" N ALA B 679 " --> pdb=" O MET B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 698 through 705 removed outlier: 3.709A pdb=" N LYS B 703 " --> pdb=" O GLU B 699 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU B 704 " --> pdb=" O ARG B 700 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU B 705 " --> pdb=" O ALA B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 723 Processing helix chain 'B' and resid 727 through 730 No H-bonds generated for 'chain 'B' and resid 727 through 730' Processing helix chain 'B' and resid 733 through 743 Processing helix chain 'B' and resid 754 through 761 Processing helix chain 'B' and resid 776 through 780 Processing helix chain 'B' and resid 784 through 793 Processing helix chain 'B' and resid 795 through 819 Processing helix chain 'B' and resid 827 through 847 Processing helix chain 'B' and resid 856 through 865 Processing helix chain 'B' and resid 867 through 887 removed outlier: 3.718A pdb=" N THR B 884 " --> pdb=" O VAL B 880 " (cutoff:3.500A) Processing helix chain 'B' and resid 892 through 912 removed outlier: 3.534A pdb=" N VAL B 897 " --> pdb=" O TYR B 893 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ARG B 909 " --> pdb=" O LEU B 905 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU B 910 " --> pdb=" O PHE B 906 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N MET B 911 " --> pdb=" O CYS B 907 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N HIS B 912 " --> pdb=" O LEU B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 920 through 955 removed outlier: 4.542A pdb=" N LYS B 932 " --> pdb=" O LYS B 928 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ASP B 933 " --> pdb=" O ARG B 929 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N PHE B 936 " --> pdb=" O LYS B 932 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU B 940 " --> pdb=" O PHE B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 978 Processing helix chain 'B' and resid 1022 through 1035 Processing helix chain 'B' and resid 1039 through 1053 Processing helix chain 'B' and resid 1059 through 1066 Processing helix chain 'B' and resid 1068 through 1076 Processing helix chain 'B' and resid 1085 through 1098 removed outlier: 3.527A pdb=" N GLN B1091 " --> pdb=" O LEU B1087 " (cutoff:3.500A) Processing helix chain 'B' and resid 1115 through 1142 removed outlier: 4.170A pdb=" N GLU B1130 " --> pdb=" O ILE B1126 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN B1131 " --> pdb=" O TYR B1127 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN B1135 " --> pdb=" O ASN B1131 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN B1142 " --> pdb=" O PHE B1138 " (cutoff:3.500A) Processing helix chain 'B' and resid 1144 through 1164 Processing helix chain 'B' and resid 1279 through 1281 No H-bonds generated for 'chain 'B' and resid 1279 through 1281' Processing helix chain 'B' and resid 1289 through 1291 No H-bonds generated for 'chain 'B' and resid 1289 through 1291' Processing helix chain 'B' and resid 1398 through 1403 Processing helix chain 'B' and resid 1411 through 1417 Processing helix chain 'B' and resid 1456 through 1463 Processing helix chain 'B' and resid 1486 through 1498 removed outlier: 3.512A pdb=" N LEU B1491 " --> pdb=" O ASN B1487 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ALA B1497 " --> pdb=" O GLN B1493 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N GLU B1498 " --> pdb=" O LYS B1494 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 66 Proline residue: C 64 - end of helix Processing helix chain 'C' and resid 151 through 160 Processing helix chain 'C' and resid 184 through 201 removed outlier: 3.661A pdb=" N ILE C 189 " --> pdb=" O ARG C 185 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE C 190 " --> pdb=" O LEU C 186 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU C 194 " --> pdb=" O PHE C 190 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL C 195 " --> pdb=" O ARG C 191 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR C 200 " --> pdb=" O LYS C 196 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N THR C 201 " --> pdb=" O VAL C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 228 removed outlier: 4.385A pdb=" N PHE C 225 " --> pdb=" O ALA C 221 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER C 226 " --> pdb=" O VAL C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 252 No H-bonds generated for 'chain 'C' and resid 250 through 252' Processing helix chain 'C' and resid 299 through 311 removed outlier: 3.552A pdb=" N LYS C 307 " --> pdb=" O THR C 303 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE C 308 " --> pdb=" O ARG C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 346 removed outlier: 3.628A pdb=" N HIS C 338 " --> pdb=" O PRO C 334 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR C 345 " --> pdb=" O ASP C 341 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASN C 346 " --> pdb=" O ASN C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 366 removed outlier: 4.080A pdb=" N VAL C 366 " --> pdb=" O VAL C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 373 No H-bonds generated for 'chain 'C' and resid 371 through 373' Processing helix chain 'C' and resid 376 through 386 removed outlier: 3.761A pdb=" N VAL C 385 " --> pdb=" O GLN C 381 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE C 386 " --> pdb=" O LYS C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 393 No H-bonds generated for 'chain 'C' and resid 391 through 393' Processing helix chain 'C' and resid 396 through 411 Processing helix chain 'C' and resid 413 through 415 No H-bonds generated for 'chain 'C' and resid 413 through 415' Processing helix chain 'C' and resid 430 through 444 removed outlier: 3.739A pdb=" N GLN C 435 " --> pdb=" O VAL C 431 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA C 440 " --> pdb=" O ALA C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 461 removed outlier: 3.904A pdb=" N LEU C 456 " --> pdb=" O TRP C 452 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS C 457 " --> pdb=" O ASP C 453 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU C 458 " --> pdb=" O HIS C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 470 Processing helix chain 'C' and resid 482 through 493 Proline residue: C 486 - end of helix removed outlier: 4.331A pdb=" N ALA C 490 " --> pdb=" O THR C 487 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE C 493 " --> pdb=" O ALA C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 506 Processing helix chain 'C' and resid 510 through 513 No H-bonds generated for 'chain 'C' and resid 510 through 513' Processing helix chain 'C' and resid 516 through 525 removed outlier: 3.542A pdb=" N ASN C 525 " --> pdb=" O TYR C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 531 through 541 Processing helix chain 'C' and resid 558 through 569 Processing helix chain 'C' and resid 621 through 631 Processing helix chain 'C' and resid 635 through 644 removed outlier: 4.449A pdb=" N ALA C 643 " --> pdb=" O GLY C 639 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLN C 644 " --> pdb=" O ILE C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 665 removed outlier: 3.574A pdb=" N LEU C 653 " --> pdb=" O ILE C 649 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS C 664 " --> pdb=" O LYS C 660 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLU C 665 " --> pdb=" O GLU C 661 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 696 removed outlier: 3.555A pdb=" N ALA C 679 " --> pdb=" O MET C 675 " (cutoff:3.500A) Processing helix chain 'C' and resid 698 through 705 removed outlier: 3.708A pdb=" N LYS C 703 " --> pdb=" O GLU C 699 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU C 704 " --> pdb=" O ARG C 700 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU C 705 " --> pdb=" O ALA C 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 717 through 723 Processing helix chain 'C' and resid 727 through 730 No H-bonds generated for 'chain 'C' and resid 727 through 730' Processing helix chain 'C' and resid 733 through 743 Processing helix chain 'C' and resid 754 through 761 Processing helix chain 'C' and resid 776 through 780 Processing helix chain 'C' and resid 784 through 793 Processing helix chain 'C' and resid 795 through 819 Processing helix chain 'C' and resid 827 through 847 Processing helix chain 'C' and resid 856 through 865 Processing helix chain 'C' and resid 867 through 887 removed outlier: 3.717A pdb=" N THR C 884 " --> pdb=" O VAL C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 892 through 912 removed outlier: 3.535A pdb=" N VAL C 897 " --> pdb=" O TYR C 893 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ARG C 909 " --> pdb=" O LEU C 905 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU C 910 " --> pdb=" O PHE C 906 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N MET C 911 " --> pdb=" O CYS C 907 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N HIS C 912 " --> pdb=" O LEU C 908 " (cutoff:3.500A) Processing helix chain 'C' and resid 920 through 955 removed outlier: 4.541A pdb=" N LYS C 932 " --> pdb=" O LYS C 928 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ASP C 933 " --> pdb=" O ARG C 929 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N PHE C 936 " --> pdb=" O LYS C 932 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU C 940 " --> pdb=" O PHE C 936 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 978 Processing helix chain 'C' and resid 1022 through 1035 Processing helix chain 'C' and resid 1039 through 1053 Processing helix chain 'C' and resid 1059 through 1066 Processing helix chain 'C' and resid 1068 through 1076 Processing helix chain 'C' and resid 1085 through 1098 removed outlier: 3.527A pdb=" N GLN C1091 " --> pdb=" O LEU C1087 " (cutoff:3.500A) Processing helix chain 'C' and resid 1115 through 1142 removed outlier: 4.170A pdb=" N GLU C1130 " --> pdb=" O ILE C1126 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN C1131 " --> pdb=" O TYR C1127 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN C1135 " --> pdb=" O ASN C1131 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN C1142 " --> pdb=" O PHE C1138 " (cutoff:3.500A) Processing helix chain 'C' and resid 1144 through 1164 Processing helix chain 'C' and resid 1279 through 1281 No H-bonds generated for 'chain 'C' and resid 1279 through 1281' Processing helix chain 'C' and resid 1289 through 1291 No H-bonds generated for 'chain 'C' and resid 1289 through 1291' Processing helix chain 'C' and resid 1398 through 1403 Processing helix chain 'C' and resid 1411 through 1417 Processing helix chain 'C' and resid 1456 through 1463 Processing helix chain 'C' and resid 1486 through 1498 removed outlier: 3.512A pdb=" N LEU C1491 " --> pdb=" O ASN C1487 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ALA C1497 " --> pdb=" O GLN C1493 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N GLU C1498 " --> pdb=" O LYS C1494 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 66 Proline residue: D 64 - end of helix Processing helix chain 'D' and resid 151 through 160 Processing helix chain 'D' and resid 184 through 201 removed outlier: 3.662A pdb=" N ILE D 189 " --> pdb=" O ARG D 185 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE D 190 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU D 194 " --> pdb=" O PHE D 190 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL D 195 " --> pdb=" O ARG D 191 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR D 200 " --> pdb=" O LYS D 196 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N THR D 201 " --> pdb=" O VAL D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 228 removed outlier: 4.385A pdb=" N PHE D 225 " --> pdb=" O ALA D 221 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER D 226 " --> pdb=" O VAL D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 252 No H-bonds generated for 'chain 'D' and resid 250 through 252' Processing helix chain 'D' and resid 299 through 311 removed outlier: 3.552A pdb=" N LYS D 307 " --> pdb=" O THR D 303 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE D 308 " --> pdb=" O ARG D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 346 removed outlier: 3.628A pdb=" N HIS D 338 " --> pdb=" O PRO D 334 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR D 345 " --> pdb=" O ASP D 341 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASN D 346 " --> pdb=" O ASN D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 366 removed outlier: 4.081A pdb=" N VAL D 366 " --> pdb=" O VAL D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 373 No H-bonds generated for 'chain 'D' and resid 371 through 373' Processing helix chain 'D' and resid 376 through 386 removed outlier: 3.761A pdb=" N VAL D 385 " --> pdb=" O GLN D 381 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE D 386 " --> pdb=" O LYS D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 393 No H-bonds generated for 'chain 'D' and resid 391 through 393' Processing helix chain 'D' and resid 396 through 411 Processing helix chain 'D' and resid 413 through 415 No H-bonds generated for 'chain 'D' and resid 413 through 415' Processing helix chain 'D' and resid 430 through 444 removed outlier: 3.738A pdb=" N GLN D 435 " --> pdb=" O VAL D 431 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA D 440 " --> pdb=" O ALA D 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 461 removed outlier: 3.905A pdb=" N LEU D 456 " --> pdb=" O TRP D 452 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS D 457 " --> pdb=" O ASP D 453 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU D 458 " --> pdb=" O HIS D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 470 Processing helix chain 'D' and resid 482 through 493 Proline residue: D 486 - end of helix removed outlier: 4.331A pdb=" N ALA D 490 " --> pdb=" O THR D 487 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE D 493 " --> pdb=" O ALA D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 506 Processing helix chain 'D' and resid 510 through 513 No H-bonds generated for 'chain 'D' and resid 510 through 513' Processing helix chain 'D' and resid 516 through 525 removed outlier: 3.542A pdb=" N ASN D 525 " --> pdb=" O TYR D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 541 Processing helix chain 'D' and resid 558 through 569 Processing helix chain 'D' and resid 621 through 631 Processing helix chain 'D' and resid 635 through 644 removed outlier: 4.449A pdb=" N ALA D 643 " --> pdb=" O GLY D 639 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLN D 644 " --> pdb=" O ILE D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 665 removed outlier: 3.574A pdb=" N LEU D 653 " --> pdb=" O ILE D 649 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS D 664 " --> pdb=" O LYS D 660 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLU D 665 " --> pdb=" O GLU D 661 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 696 removed outlier: 3.555A pdb=" N ALA D 679 " --> pdb=" O MET D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 698 through 705 removed outlier: 3.709A pdb=" N LYS D 703 " --> pdb=" O GLU D 699 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU D 704 " --> pdb=" O ARG D 700 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU D 705 " --> pdb=" O ALA D 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 717 through 723 Processing helix chain 'D' and resid 727 through 730 No H-bonds generated for 'chain 'D' and resid 727 through 730' Processing helix chain 'D' and resid 733 through 743 Processing helix chain 'D' and resid 754 through 761 Processing helix chain 'D' and resid 776 through 780 Processing helix chain 'D' and resid 784 through 793 Processing helix chain 'D' and resid 795 through 819 Processing helix chain 'D' and resid 827 through 847 Processing helix chain 'D' and resid 856 through 865 Processing helix chain 'D' and resid 867 through 887 removed outlier: 3.718A pdb=" N THR D 884 " --> pdb=" O VAL D 880 " (cutoff:3.500A) Processing helix chain 'D' and resid 892 through 912 removed outlier: 3.534A pdb=" N VAL D 897 " --> pdb=" O TYR D 893 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ARG D 909 " --> pdb=" O LEU D 905 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU D 910 " --> pdb=" O PHE D 906 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N MET D 911 " --> pdb=" O CYS D 907 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N HIS D 912 " --> pdb=" O LEU D 908 " (cutoff:3.500A) Processing helix chain 'D' and resid 920 through 955 removed outlier: 4.542A pdb=" N LYS D 932 " --> pdb=" O LYS D 928 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ASP D 933 " --> pdb=" O ARG D 929 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N PHE D 936 " --> pdb=" O LYS D 932 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU D 940 " --> pdb=" O PHE D 936 " (cutoff:3.500A) Processing helix chain 'D' and resid 966 through 978 Processing helix chain 'D' and resid 1022 through 1035 Processing helix chain 'D' and resid 1039 through 1053 Processing helix chain 'D' and resid 1059 through 1066 Processing helix chain 'D' and resid 1068 through 1076 Processing helix chain 'D' and resid 1085 through 1098 removed outlier: 3.527A pdb=" N GLN D1091 " --> pdb=" O LEU D1087 " (cutoff:3.500A) Processing helix chain 'D' and resid 1115 through 1142 removed outlier: 4.169A pdb=" N GLU D1130 " --> pdb=" O ILE D1126 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN D1131 " --> pdb=" O TYR D1127 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASN D1135 " --> pdb=" O ASN D1131 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN D1142 " --> pdb=" O PHE D1138 " (cutoff:3.500A) Processing helix chain 'D' and resid 1144 through 1164 Processing helix chain 'D' and resid 1279 through 1281 No H-bonds generated for 'chain 'D' and resid 1279 through 1281' Processing helix chain 'D' and resid 1289 through 1291 No H-bonds generated for 'chain 'D' and resid 1289 through 1291' Processing helix chain 'D' and resid 1398 through 1403 Processing helix chain 'D' and resid 1411 through 1417 Processing helix chain 'D' and resid 1456 through 1463 Processing helix chain 'D' and resid 1486 through 1498 removed outlier: 3.512A pdb=" N LEU D1491 " --> pdb=" O ASN D1487 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ALA D1497 " --> pdb=" O GLN D1493 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N GLU D1498 " --> pdb=" O LYS D1494 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 68 through 71 Processing sheet with id= B, first strand: chain 'A' and resid 128 through 130 removed outlier: 6.429A pdb=" N ILE A 205 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N VAL A 241 " --> pdb=" O ILE A 205 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N THR A 207 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 8.858A pdb=" N THR A 243 " --> pdb=" O THR A 207 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 170 through 174 removed outlier: 8.226A pdb=" N VAL A 329 " --> pdb=" O PRO A 349 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N VAL A 351 " --> pdb=" O VAL A 329 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 1303 through 1305 Processing sheet with id= E, first strand: chain 'A' and resid 1472 through 1478 removed outlier: 4.842A pdb=" N LEU A1372 " --> pdb=" O VAL A1478 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU A1375 " --> pdb=" O VAL A1352 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N VAL A1352 " --> pdb=" O LEU A1375 " (cutoff:3.500A) removed outlier: 9.372A pdb=" N VAL A1377 " --> pdb=" O PRO A1350 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU A1441 " --> pdb=" O ASN A1345 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TRP A1355 " --> pdb=" O PHE A1449 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ILE A1440 " --> pdb=" O MET A1429 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TYR A1425 " --> pdb=" O ALA A1444 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N SER A1446 " --> pdb=" O GLU A1423 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N GLU A1423 " --> pdb=" O SER A1446 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 68 through 71 Processing sheet with id= G, first strand: chain 'B' and resid 128 through 130 removed outlier: 6.429A pdb=" N ILE B 205 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N VAL B 241 " --> pdb=" O ILE B 205 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N THR B 207 " --> pdb=" O VAL B 241 " (cutoff:3.500A) removed outlier: 8.858A pdb=" N THR B 243 " --> pdb=" O THR B 207 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 170 through 174 removed outlier: 8.226A pdb=" N VAL B 329 " --> pdb=" O PRO B 349 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N VAL B 351 " --> pdb=" O VAL B 329 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 1303 through 1305 Processing sheet with id= J, first strand: chain 'B' and resid 1472 through 1478 removed outlier: 4.842A pdb=" N LEU B1372 " --> pdb=" O VAL B1478 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU B1375 " --> pdb=" O VAL B1352 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N VAL B1352 " --> pdb=" O LEU B1375 " (cutoff:3.500A) removed outlier: 9.371A pdb=" N VAL B1377 " --> pdb=" O PRO B1350 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU B1441 " --> pdb=" O ASN B1345 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TRP B1355 " --> pdb=" O PHE B1449 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ILE B1440 " --> pdb=" O MET B1429 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TYR B1425 " --> pdb=" O ALA B1444 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N SER B1446 " --> pdb=" O GLU B1423 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N GLU B1423 " --> pdb=" O SER B1446 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 68 through 71 Processing sheet with id= L, first strand: chain 'C' and resid 128 through 130 removed outlier: 6.430A pdb=" N ILE C 205 " --> pdb=" O ILE C 239 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N VAL C 241 " --> pdb=" O ILE C 205 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N THR C 207 " --> pdb=" O VAL C 241 " (cutoff:3.500A) removed outlier: 8.858A pdb=" N THR C 243 " --> pdb=" O THR C 207 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 170 through 174 removed outlier: 8.226A pdb=" N VAL C 329 " --> pdb=" O PRO C 349 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N VAL C 351 " --> pdb=" O VAL C 329 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 1303 through 1305 Processing sheet with id= O, first strand: chain 'C' and resid 1472 through 1478 removed outlier: 4.842A pdb=" N LEU C1372 " --> pdb=" O VAL C1478 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU C1375 " --> pdb=" O VAL C1352 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N VAL C1352 " --> pdb=" O LEU C1375 " (cutoff:3.500A) removed outlier: 9.373A pdb=" N VAL C1377 " --> pdb=" O PRO C1350 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU C1441 " --> pdb=" O ASN C1345 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TRP C1355 " --> pdb=" O PHE C1449 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ILE C1440 " --> pdb=" O MET C1429 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TYR C1425 " --> pdb=" O ALA C1444 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N SER C1446 " --> pdb=" O GLU C1423 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N GLU C1423 " --> pdb=" O SER C1446 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 68 through 71 Processing sheet with id= Q, first strand: chain 'D' and resid 128 through 130 removed outlier: 6.429A pdb=" N ILE D 205 " --> pdb=" O ILE D 239 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N VAL D 241 " --> pdb=" O ILE D 205 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N THR D 207 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 8.857A pdb=" N THR D 243 " --> pdb=" O THR D 207 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 170 through 174 removed outlier: 8.227A pdb=" N VAL D 329 " --> pdb=" O PRO D 349 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N VAL D 351 " --> pdb=" O VAL D 329 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 1303 through 1305 Processing sheet with id= T, first strand: chain 'D' and resid 1472 through 1478 removed outlier: 4.842A pdb=" N LEU D1372 " --> pdb=" O VAL D1478 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU D1375 " --> pdb=" O VAL D1352 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N VAL D1352 " --> pdb=" O LEU D1375 " (cutoff:3.500A) removed outlier: 9.372A pdb=" N VAL D1377 " --> pdb=" O PRO D1350 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU D1441 " --> pdb=" O ASN D1345 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TRP D1355 " --> pdb=" O PHE D1449 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ILE D1440 " --> pdb=" O MET D1429 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TYR D1425 " --> pdb=" O ALA D1444 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N SER D1446 " --> pdb=" O GLU D1423 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N GLU D1423 " --> pdb=" O SER D1446 " (cutoff:3.500A) 1688 hydrogen bonds defined for protein. 4932 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: 13.70 Time building geometry restraints manager: 16.23 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: 11142 1.34 - 1.45: 6689 1.45 - 1.57: 20097 1.57 - 1.69: 32 1.69 - 1.81: 208 Bond restraints: 38168 Sorted by residual: bond pdb=" N ASN B1453 " pdb=" CA ASN B1453 " ideal model delta sigma weight residual 1.458 1.488 -0.029 6.30e-03 2.52e+04 2.18e+01 bond pdb=" N ASN C1453 " pdb=" CA ASN C1453 " ideal model delta sigma weight residual 1.458 1.487 -0.029 6.30e-03 2.52e+04 2.12e+01 bond pdb=" N ASN A1453 " pdb=" CA ASN A1453 " ideal model delta sigma weight residual 1.458 1.487 -0.029 6.30e-03 2.52e+04 2.12e+01 bond pdb=" N ASN D1453 " pdb=" CA ASN D1453 " ideal model delta sigma weight residual 1.458 1.487 -0.029 6.30e-03 2.52e+04 2.12e+01 bond pdb=" C4 APR C1602 " pdb=" C5 APR C1602 " ideal model delta sigma weight residual 1.386 1.463 -0.077 2.00e-02 2.50e+03 1.49e+01 ... (remaining 38163 not shown) Histogram of bond angle deviations from ideal: 97.76 - 105.46: 884 105.46 - 113.16: 21559 113.16 - 120.85: 18133 120.85 - 128.55: 11324 128.55 - 136.25: 428 Bond angle restraints: 52328 Sorted by residual: angle pdb=" N PRO B 551 " pdb=" CA PRO B 551 " pdb=" CB PRO B 551 " ideal model delta sigma weight residual 103.25 110.70 -7.45 1.05e+00 9.07e-01 5.03e+01 angle pdb=" N PRO C 551 " pdb=" CA PRO C 551 " pdb=" CB PRO C 551 " ideal model delta sigma weight residual 103.25 110.66 -7.41 1.05e+00 9.07e-01 4.98e+01 angle pdb=" N PRO A 551 " pdb=" CA PRO A 551 " pdb=" CB PRO A 551 " ideal model delta sigma weight residual 103.25 110.66 -7.41 1.05e+00 9.07e-01 4.98e+01 angle pdb=" N PRO D 551 " pdb=" CA PRO D 551 " pdb=" CB PRO D 551 " ideal model delta sigma weight residual 103.25 110.64 -7.39 1.05e+00 9.07e-01 4.95e+01 angle pdb=" N ILE A1270 " pdb=" CA ILE A1270 " pdb=" C ILE A1270 " ideal model delta sigma weight residual 112.90 107.25 5.65 9.60e-01 1.09e+00 3.46e+01 ... (remaining 52323 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 20178 17.22 - 34.43: 1760 34.43 - 51.65: 446 51.65 - 68.87: 157 68.87 - 86.08: 35 Dihedral angle restraints: 22576 sinusoidal: 7400 harmonic: 15176 Sorted by residual: dihedral pdb=" CA ILE A1038 " pdb=" C ILE A1038 " pdb=" N LEU A1039 " pdb=" CA LEU A1039 " ideal model delta harmonic sigma weight residual 180.00 -151.48 -28.52 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA ILE C1038 " pdb=" C ILE C1038 " pdb=" N LEU C1039 " pdb=" CA LEU C1039 " ideal model delta harmonic sigma weight residual -180.00 -151.48 -28.52 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA ILE D1038 " pdb=" C ILE D1038 " pdb=" N LEU D1039 " pdb=" CA LEU D1039 " ideal model delta harmonic sigma weight residual -180.00 -151.48 -28.52 0 5.00e+00 4.00e-02 3.25e+01 ... (remaining 22573 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 4744 0.060 - 0.120: 1197 0.120 - 0.180: 228 0.180 - 0.240: 43 0.240 - 0.301: 12 Chirality restraints: 6224 Sorted by residual: chirality pdb=" CB ILE A 254 " pdb=" CA ILE A 254 " pdb=" CG1 ILE A 254 " pdb=" CG2 ILE A 254 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CB ILE D 254 " pdb=" CA ILE D 254 " pdb=" CG1 ILE D 254 " pdb=" CG2 ILE D 254 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CB ILE C 254 " pdb=" CA ILE C 254 " pdb=" CG1 ILE C 254 " pdb=" CG2 ILE C 254 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.25e+00 ... (remaining 6221 not shown) Planarity restraints: 6640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 420 " 0.015 2.00e-02 2.50e+03 3.08e-02 9.50e+00 pdb=" C ARG C 420 " -0.053 2.00e-02 2.50e+03 pdb=" O ARG C 420 " 0.020 2.00e-02 2.50e+03 pdb=" N GLU C 421 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 420 " 0.015 2.00e-02 2.50e+03 3.06e-02 9.38e+00 pdb=" C ARG B 420 " -0.053 2.00e-02 2.50e+03 pdb=" O ARG B 420 " 0.020 2.00e-02 2.50e+03 pdb=" N GLU B 421 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 420 " -0.015 2.00e-02 2.50e+03 3.05e-02 9.32e+00 pdb=" C ARG A 420 " 0.053 2.00e-02 2.50e+03 pdb=" O ARG A 420 " -0.020 2.00e-02 2.50e+03 pdb=" N GLU A 421 " -0.018 2.00e-02 2.50e+03 ... (remaining 6637 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 9402 2.78 - 3.31: 36519 3.31 - 3.84: 62156 3.84 - 4.37: 67026 4.37 - 4.90: 109840 Nonbonded interactions: 284943 Sorted by model distance: nonbonded pdb=" OG SER C 146 " pdb=" OG1 THR C 149 " model vdw 2.255 2.440 nonbonded pdb=" OG SER B 146 " pdb=" OG1 THR B 149 " model vdw 2.255 2.440 nonbonded pdb=" OG SER A 146 " pdb=" OG1 THR A 149 " model vdw 2.255 2.440 nonbonded pdb=" OG SER D 146 " pdb=" OG1 THR D 149 " model vdw 2.255 2.440 nonbonded pdb=" CE MET A 818 " pdb=" OE1 GLN D 953 " model vdw 2.260 3.460 ... (remaining 284938 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.760 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: 0.040 Extract box with map and model: 7.990 Check model and map are aligned: 0.580 Set scattering table: 0.370 Process input model: 97.860 Find NCS groups from input model: 2.370 Set up NCS constraints: 0.230 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:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.082 38168 Z= 0.543 Angle : 1.074 12.677 52328 Z= 0.617 Chirality : 0.058 0.301 6224 Planarity : 0.008 0.076 6640 Dihedral : 15.801 86.083 12720 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.95 % Favored : 91.59 % Rotamer: Outliers : 1.66 % Allowed : 11.19 % Favored : 87.15 % 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: -3.61 (0.10), residues: 5184 helix: -1.88 (0.08), residues: 2512 sheet: -1.81 (0.24), residues: 440 loop : -3.08 (0.12), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 62 HIS 0.007 0.002 HIS D 156 PHE 0.022 0.002 PHE C 690 TYR 0.010 0.002 TYR C 849 ARG 0.009 0.001 ARG B 250 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 188 time to evaluate : 4.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 ASN cc_start: 0.9210 (OUTLIER) cc_final: 0.8805 (p0) REVERT: A 1115 LYS cc_start: 0.9645 (pptt) cc_final: 0.9440 (mmtm) REVERT: A 1158 MET cc_start: 0.9654 (mmm) cc_final: 0.9269 (mmm) REVERT: B 179 ASN cc_start: 0.9204 (OUTLIER) cc_final: 0.8803 (p0) REVERT: B 215 MET cc_start: 0.9425 (mpp) cc_final: 0.9219 (mpp) REVERT: B 1158 MET cc_start: 0.9653 (mmm) cc_final: 0.9335 (mmm) REVERT: C 179 ASN cc_start: 0.9209 (OUTLIER) cc_final: 0.8817 (p0) REVERT: C 1158 MET cc_start: 0.9653 (mmm) cc_final: 0.9276 (mmm) REVERT: D 179 ASN cc_start: 0.9213 (OUTLIER) cc_final: 0.8815 (p0) REVERT: D 215 MET cc_start: 0.9394 (mpp) cc_final: 0.9193 (mpp) REVERT: D 1158 MET cc_start: 0.9652 (mmm) cc_final: 0.9333 (mmm) outliers start: 52 outliers final: 7 residues processed: 240 average time/residue: 0.4685 time to fit residues: 190.3741 Evaluate side-chains 149 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 138 time to evaluate : 4.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 439 optimal weight: 0.0020 chunk 394 optimal weight: 30.0000 chunk 218 optimal weight: 8.9990 chunk 134 optimal weight: 30.0000 chunk 265 optimal weight: 4.9990 chunk 210 optimal weight: 40.0000 chunk 407 optimal weight: 20.0000 chunk 157 optimal weight: 7.9990 chunk 247 optimal weight: 20.0000 chunk 303 optimal weight: 0.0770 chunk 472 optimal weight: 8.9990 overall best weight: 4.4152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 HIS A 342 ASN A 414 GLN A 525 ASN ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 719 GLN A 736 GLN A 751 ASN A 912 HIS ** A1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1066 GLN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1140 GLN B 147 GLN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 HIS B 342 ASN B 414 GLN B 525 ASN ** B 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 719 GLN B 736 GLN B 751 ASN B 912 HIS ** B1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1066 GLN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1140 GLN B1437 ASN C 147 GLN ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 HIS C 342 ASN C 414 GLN C 525 ASN ** C 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 GLN C 736 GLN C 751 ASN C 912 HIS ** C1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1140 GLN D 147 GLN ** D 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 HIS D 414 GLN D 525 ASN ** D 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 719 GLN D 736 GLN D 751 ASN D 912 HIS ** D1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1066 GLN ** D1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1140 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 38168 Z= 0.196 Angle : 0.579 6.357 52328 Z= 0.299 Chirality : 0.040 0.153 6224 Planarity : 0.005 0.064 6640 Dihedral : 8.337 66.686 5908 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.08 % Favored : 93.77 % Rotamer: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.11), residues: 5184 helix: 0.07 (0.10), residues: 2524 sheet: -1.23 (0.26), residues: 368 loop : -2.67 (0.12), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP D 452 HIS 0.003 0.001 HIS B 732 PHE 0.012 0.001 PHE C 690 TYR 0.009 0.001 TYR B 849 ARG 0.003 0.000 ARG B 442 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 4.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 727 MET cc_start: 0.9260 (mmp) cc_final: 0.8964 (mmm) REVERT: A 844 MET cc_start: 0.8978 (ppp) cc_final: 0.8737 (ppp) REVERT: A 857 MET cc_start: 0.9277 (pmm) cc_final: 0.8744 (tmm) REVERT: B 727 MET cc_start: 0.9268 (mmp) cc_final: 0.8987 (mmm) REVERT: B 844 MET cc_start: 0.8982 (ppp) cc_final: 0.8747 (ppp) REVERT: B 857 MET cc_start: 0.9278 (pmm) cc_final: 0.8750 (tmm) REVERT: B 1351 MET cc_start: 0.8319 (ptp) cc_final: 0.7426 (ppp) REVERT: C 727 MET cc_start: 0.9282 (mmp) cc_final: 0.8986 (mmm) REVERT: C 844 MET cc_start: 0.8971 (ppp) cc_final: 0.8729 (ppp) REVERT: C 857 MET cc_start: 0.9281 (pmm) cc_final: 0.8761 (tmm) REVERT: C 1351 MET cc_start: 0.8306 (ptp) cc_final: 0.7420 (ppp) REVERT: D 727 MET cc_start: 0.9267 (mmp) cc_final: 0.8971 (mmm) REVERT: D 844 MET cc_start: 0.8979 (ppp) cc_final: 0.8738 (ppp) REVERT: D 857 MET cc_start: 0.9274 (pmm) cc_final: 0.8753 (tmm) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.4686 time to fit residues: 126.8322 Evaluate side-chains 126 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 4.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 262 optimal weight: 50.0000 chunk 146 optimal weight: 5.9990 chunk 393 optimal weight: 0.6980 chunk 321 optimal weight: 8.9990 chunk 130 optimal weight: 30.0000 chunk 473 optimal weight: 2.9990 chunk 511 optimal weight: 0.0270 chunk 421 optimal weight: 30.0000 chunk 469 optimal weight: 20.0000 chunk 161 optimal weight: 20.0000 chunk 379 optimal weight: 40.0000 overall best weight: 3.7444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 719 GLN ** A1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 ASN ** B 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 719 GLN ** B1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN ** C 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 GLN ** C1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 ASN ** D 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 719 GLN ** D1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 38168 Z= 0.169 Angle : 0.535 9.291 52328 Z= 0.270 Chirality : 0.039 0.160 6224 Planarity : 0.004 0.064 6640 Dihedral : 6.819 58.495 5908 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.25 % Favored : 93.60 % Rotamer: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % 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: -0.86 (0.12), residues: 5184 helix: 0.98 (0.11), residues: 2528 sheet: -1.06 (0.25), residues: 372 loop : -2.38 (0.12), residues: 2284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 462 HIS 0.003 0.001 HIS C 732 PHE 0.010 0.001 PHE D 690 TYR 0.010 0.001 TYR A1074 ARG 0.009 0.000 ARG D 302 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 4.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 MET cc_start: 0.9393 (mpp) cc_final: 0.8590 (mtt) REVERT: A 727 MET cc_start: 0.9227 (mmp) cc_final: 0.8949 (mmm) REVERT: A 857 MET cc_start: 0.9257 (pmm) cc_final: 0.8713 (tmm) REVERT: A 1158 MET cc_start: 0.9732 (mmm) cc_final: 0.9074 (mmm) REVERT: A 1351 MET cc_start: 0.8363 (ptp) cc_final: 0.7492 (ppp) REVERT: B 215 MET cc_start: 0.9398 (mpp) cc_final: 0.8633 (mtt) REVERT: B 727 MET cc_start: 0.9227 (mmp) cc_final: 0.8953 (mmm) REVERT: B 857 MET cc_start: 0.9257 (pmm) cc_final: 0.8719 (tmm) REVERT: B 1158 MET cc_start: 0.9725 (mmm) cc_final: 0.9102 (mmm) REVERT: B 1351 MET cc_start: 0.8361 (ptp) cc_final: 0.7491 (ppp) REVERT: C 215 MET cc_start: 0.9381 (mpp) cc_final: 0.8539 (mtt) REVERT: C 727 MET cc_start: 0.9251 (mmp) cc_final: 0.8969 (mmm) REVERT: C 857 MET cc_start: 0.9256 (pmm) cc_final: 0.8722 (tmm) REVERT: C 1158 MET cc_start: 0.9725 (mmm) cc_final: 0.9103 (mmm) REVERT: C 1351 MET cc_start: 0.8368 (ptp) cc_final: 0.7496 (ppp) REVERT: D 215 MET cc_start: 0.9349 (mpp) cc_final: 0.8537 (mtt) REVERT: D 727 MET cc_start: 0.9226 (mmp) cc_final: 0.8952 (mmm) REVERT: D 857 MET cc_start: 0.9257 (pmm) cc_final: 0.8716 (tmm) REVERT: D 1158 MET cc_start: 0.9725 (mmm) cc_final: 0.9096 (mmm) REVERT: D 1351 MET cc_start: 0.8337 (ptp) cc_final: 0.7462 (ppp) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.4412 time to fit residues: 123.1810 Evaluate side-chains 127 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 4.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 467 optimal weight: 9.9990 chunk 355 optimal weight: 7.9990 chunk 245 optimal weight: 40.0000 chunk 52 optimal weight: 0.9980 chunk 225 optimal weight: 0.0570 chunk 317 optimal weight: 6.9990 chunk 474 optimal weight: 30.0000 chunk 502 optimal weight: 20.0000 chunk 248 optimal weight: 20.0000 chunk 449 optimal weight: 10.0000 chunk 135 optimal weight: 0.0010 overall best weight: 3.2108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 719 GLN A 736 GLN A 953 GLN ** A1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 719 GLN B 736 GLN ** B1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 GLN C 736 GLN ** C1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 719 GLN D 736 GLN D 953 GLN ** D1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 38168 Z= 0.159 Angle : 0.525 6.484 52328 Z= 0.264 Chirality : 0.039 0.163 6224 Planarity : 0.004 0.075 6640 Dihedral : 6.373 57.601 5908 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.42 % Favored : 94.44 % Rotamer: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.12), residues: 5184 helix: 1.27 (0.11), residues: 2540 sheet: -0.55 (0.28), residues: 308 loop : -2.26 (0.12), residues: 2336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 462 HIS 0.006 0.001 HIS B1089 PHE 0.009 0.001 PHE A 937 TYR 0.011 0.001 TYR A 682 ARG 0.002 0.000 ARG B1356 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 4.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 MET cc_start: 0.9440 (mpp) cc_final: 0.8671 (mtt) REVERT: A 675 MET cc_start: 0.9596 (mtm) cc_final: 0.9304 (mtm) REVERT: A 857 MET cc_start: 0.9270 (pmm) cc_final: 0.8739 (tmm) REVERT: A 1158 MET cc_start: 0.9694 (mmm) cc_final: 0.9058 (mmm) REVERT: A 1351 MET cc_start: 0.8291 (ptp) cc_final: 0.7517 (ppp) REVERT: B 215 MET cc_start: 0.9447 (mpp) cc_final: 0.8671 (mtt) REVERT: B 675 MET cc_start: 0.9598 (mtm) cc_final: 0.9308 (mtm) REVERT: B 857 MET cc_start: 0.9266 (pmm) cc_final: 0.8726 (tmm) REVERT: B 1158 MET cc_start: 0.9701 (mmm) cc_final: 0.9078 (mmm) REVERT: B 1351 MET cc_start: 0.8300 (ptp) cc_final: 0.7512 (ppp) REVERT: C 215 MET cc_start: 0.9423 (mpp) cc_final: 0.9103 (mpp) REVERT: C 675 MET cc_start: 0.9605 (mtm) cc_final: 0.9304 (mtm) REVERT: C 857 MET cc_start: 0.9273 (pmm) cc_final: 0.8750 (tmm) REVERT: C 1158 MET cc_start: 0.9701 (mmm) cc_final: 0.9072 (mmm) REVERT: C 1351 MET cc_start: 0.8279 (ptp) cc_final: 0.7477 (ppp) REVERT: D 215 MET cc_start: 0.9426 (mpp) cc_final: 0.8638 (mtt) REVERT: D 675 MET cc_start: 0.9600 (mtm) cc_final: 0.9305 (mtm) REVERT: D 857 MET cc_start: 0.9267 (pmm) cc_final: 0.8743 (tmm) REVERT: D 1158 MET cc_start: 0.9702 (mmm) cc_final: 0.9073 (mmm) REVERT: D 1351 MET cc_start: 0.8292 (ptp) cc_final: 0.7507 (ppp) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.4394 time to fit residues: 123.8011 Evaluate side-chains 131 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 4.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 418 optimal weight: 20.0000 chunk 285 optimal weight: 9.9990 chunk 7 optimal weight: 20.0000 chunk 374 optimal weight: 50.0000 chunk 207 optimal weight: 7.9990 chunk 428 optimal weight: 10.0000 chunk 347 optimal weight: 50.0000 chunk 0 optimal weight: 20.0000 chunk 256 optimal weight: 3.9990 chunk 451 optimal weight: 0.0060 chunk 126 optimal weight: 0.8980 overall best weight: 4.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 HIS A 525 ASN ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 719 GLN ** A1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 HIS ** B 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 719 GLN ** B1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 HIS C 525 ASN ** C 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 GLN ** C1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 HIS D 525 ASN ** D 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 719 GLN ** D1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 38168 Z= 0.191 Angle : 0.538 7.161 52328 Z= 0.269 Chirality : 0.039 0.172 6224 Planarity : 0.004 0.060 6640 Dihedral : 6.233 64.007 5908 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.96 % Favored : 92.96 % Rotamer: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % 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: -0.33 (0.12), residues: 5184 helix: 1.43 (0.11), residues: 2536 sheet: -0.98 (0.25), residues: 380 loop : -2.09 (0.13), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 944 HIS 0.004 0.001 HIS A 283 PHE 0.012 0.001 PHE D 690 TYR 0.009 0.001 TYR A 682 ARG 0.002 0.000 ARG B 469 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 4.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 MET cc_start: 0.9530 (mpp) cc_final: 0.9096 (mpp) REVERT: A 675 MET cc_start: 0.9599 (mtm) cc_final: 0.8796 (ptm) REVERT: A 727 MET cc_start: 0.9401 (mmp) cc_final: 0.9164 (mmm) REVERT: A 857 MET cc_start: 0.9278 (pmm) cc_final: 0.8750 (tmm) REVERT: A 1158 MET cc_start: 0.9680 (mmm) cc_final: 0.9169 (mmm) REVERT: A 1351 MET cc_start: 0.8279 (ptp) cc_final: 0.7488 (ppp) REVERT: B 215 MET cc_start: 0.9548 (mpp) cc_final: 0.8677 (mtm) REVERT: B 675 MET cc_start: 0.9614 (mtm) cc_final: 0.8838 (ptm) REVERT: B 727 MET cc_start: 0.9409 (mmp) cc_final: 0.9163 (mmm) REVERT: B 857 MET cc_start: 0.9283 (pmm) cc_final: 0.8764 (tmm) REVERT: B 1158 MET cc_start: 0.9684 (mmm) cc_final: 0.9185 (mmm) REVERT: B 1351 MET cc_start: 0.8267 (ptp) cc_final: 0.7394 (ppp) REVERT: C 215 MET cc_start: 0.9519 (mpp) cc_final: 0.9086 (mpp) REVERT: C 675 MET cc_start: 0.9617 (mtm) cc_final: 0.8839 (ptm) REVERT: C 727 MET cc_start: 0.9405 (mmp) cc_final: 0.9188 (mmm) REVERT: C 857 MET cc_start: 0.9285 (pmm) cc_final: 0.8769 (tmm) REVERT: C 1158 MET cc_start: 0.9685 (mmm) cc_final: 0.9179 (mmm) REVERT: C 1351 MET cc_start: 0.8289 (ptp) cc_final: 0.7484 (ppp) REVERT: D 215 MET cc_start: 0.9537 (mpp) cc_final: 0.8666 (mtm) REVERT: D 675 MET cc_start: 0.9614 (mtm) cc_final: 0.8841 (ptm) REVERT: D 727 MET cc_start: 0.9405 (mmp) cc_final: 0.9165 (mmm) REVERT: D 857 MET cc_start: 0.9285 (pmm) cc_final: 0.8762 (tmm) REVERT: D 1158 MET cc_start: 0.9686 (mmm) cc_final: 0.9180 (mmm) REVERT: D 1351 MET cc_start: 0.8277 (ptp) cc_final: 0.7498 (ppp) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.4333 time to fit residues: 115.6253 Evaluate side-chains 128 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 4.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 169 optimal weight: 10.0000 chunk 452 optimal weight: 0.0070 chunk 99 optimal weight: 7.9990 chunk 295 optimal weight: 20.0000 chunk 124 optimal weight: 9.9990 chunk 503 optimal weight: 10.0000 chunk 417 optimal weight: 20.0000 chunk 232 optimal weight: 10.0000 chunk 41 optimal weight: 0.7980 chunk 166 optimal weight: 0.8980 chunk 264 optimal weight: 40.0000 overall best weight: 3.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 719 GLN ** A1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1437 ASN ** B 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 719 GLN ** B1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 GLN ** C1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1437 ASN D 342 ASN ** D 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 719 GLN ** D1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1437 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 38168 Z= 0.168 Angle : 0.520 6.760 52328 Z= 0.260 Chirality : 0.038 0.145 6224 Planarity : 0.004 0.060 6640 Dihedral : 6.004 72.211 5908 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.21 % Favored : 93.71 % Rotamer: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % 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: -0.10 (0.12), residues: 5184 helix: 1.58 (0.11), residues: 2564 sheet: -0.81 (0.26), residues: 356 loop : -1.99 (0.13), residues: 2264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 944 HIS 0.004 0.001 HIS B1502 PHE 0.010 0.001 PHE D1048 TYR 0.009 0.001 TYR B 849 ARG 0.001 0.000 ARG D1433 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 4.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 MET cc_start: 0.9536 (mpp) cc_final: 0.8436 (mtm) REVERT: A 675 MET cc_start: 0.9637 (mtm) cc_final: 0.8881 (ptp) REVERT: A 727 MET cc_start: 0.9403 (mmp) cc_final: 0.9157 (mmm) REVERT: A 857 MET cc_start: 0.9274 (pmm) cc_final: 0.8746 (tmm) REVERT: A 1158 MET cc_start: 0.9673 (mmm) cc_final: 0.9185 (mmm) REVERT: A 1351 MET cc_start: 0.8256 (ptp) cc_final: 0.7523 (ppp) REVERT: B 215 MET cc_start: 0.9545 (mpp) cc_final: 0.8459 (mtm) REVERT: B 675 MET cc_start: 0.9645 (mtm) cc_final: 0.8895 (ptp) REVERT: B 727 MET cc_start: 0.9416 (mmp) cc_final: 0.9184 (mmm) REVERT: B 857 MET cc_start: 0.9277 (pmm) cc_final: 0.8745 (tmm) REVERT: B 1158 MET cc_start: 0.9676 (mmm) cc_final: 0.9195 (mmm) REVERT: B 1351 MET cc_start: 0.8258 (ptp) cc_final: 0.7522 (ppp) REVERT: C 215 MET cc_start: 0.9534 (mpp) cc_final: 0.8432 (mtm) REVERT: C 675 MET cc_start: 0.9647 (mtm) cc_final: 0.8900 (ptp) REVERT: C 727 MET cc_start: 0.9412 (mmp) cc_final: 0.9188 (mmm) REVERT: C 857 MET cc_start: 0.9279 (pmm) cc_final: 0.8749 (tmm) REVERT: C 1158 MET cc_start: 0.9678 (mmm) cc_final: 0.9195 (mmm) REVERT: C 1351 MET cc_start: 0.8262 (ptp) cc_final: 0.7526 (ppp) REVERT: D 215 MET cc_start: 0.9541 (mpp) cc_final: 0.8441 (mtm) REVERT: D 675 MET cc_start: 0.9638 (mtm) cc_final: 0.8877 (ptp) REVERT: D 727 MET cc_start: 0.9416 (mmp) cc_final: 0.9181 (mmm) REVERT: D 857 MET cc_start: 0.9276 (pmm) cc_final: 0.8750 (tmm) REVERT: D 1158 MET cc_start: 0.9674 (mmm) cc_final: 0.9185 (mmm) REVERT: D 1351 MET cc_start: 0.8260 (ptp) cc_final: 0.7532 (ppp) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.4223 time to fit residues: 110.7802 Evaluate side-chains 132 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 3.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 485 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 286 optimal weight: 6.9990 chunk 367 optimal weight: 30.0000 chunk 284 optimal weight: 5.9990 chunk 423 optimal weight: 40.0000 chunk 280 optimal weight: 30.0000 chunk 501 optimal weight: 40.0000 chunk 313 optimal weight: 10.0000 chunk 305 optimal weight: 10.0000 chunk 231 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 719 GLN A 736 GLN A1042 ASN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 GLN ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 719 GLN B 736 GLN B1042 ASN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 GLN C 736 GLN C1042 ASN ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 719 GLN D1042 ASN ** D1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 38168 Z= 0.217 Angle : 0.546 7.192 52328 Z= 0.278 Chirality : 0.039 0.207 6224 Planarity : 0.004 0.059 6640 Dihedral : 6.020 60.265 5908 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.77 % Favored : 92.15 % Rotamer: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % 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 (0.12), residues: 5184 helix: 1.63 (0.11), residues: 2560 sheet: -0.82 (0.26), residues: 356 loop : -1.93 (0.13), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 944 HIS 0.006 0.001 HIS C 283 PHE 0.028 0.001 PHE D 499 TYR 0.009 0.001 TYR C 523 ARG 0.002 0.000 ARG A1357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 4.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 MET cc_start: 0.9575 (mpp) cc_final: 0.8786 (mtt) REVERT: A 675 MET cc_start: 0.9658 (mtm) cc_final: 0.8832 (ptm) REVERT: A 727 MET cc_start: 0.9454 (mmp) cc_final: 0.9195 (mmm) REVERT: A 857 MET cc_start: 0.9282 (pmm) cc_final: 0.8721 (tmm) REVERT: A 1158 MET cc_start: 0.9662 (mmm) cc_final: 0.9185 (mmm) REVERT: A 1351 MET cc_start: 0.8269 (ptp) cc_final: 0.7551 (ppp) REVERT: B 215 MET cc_start: 0.9576 (mpp) cc_final: 0.8706 (mtm) REVERT: B 675 MET cc_start: 0.9656 (mtm) cc_final: 0.8829 (ptm) REVERT: B 727 MET cc_start: 0.9457 (mmp) cc_final: 0.9203 (mmm) REVERT: B 857 MET cc_start: 0.9280 (pmm) cc_final: 0.8728 (tmm) REVERT: B 1158 MET cc_start: 0.9665 (mmm) cc_final: 0.9191 (mmm) REVERT: B 1351 MET cc_start: 0.8222 (ptp) cc_final: 0.7507 (ppp) REVERT: C 215 MET cc_start: 0.9561 (mpp) cc_final: 0.8463 (mtm) REVERT: C 675 MET cc_start: 0.9658 (mtm) cc_final: 0.8834 (ptm) REVERT: C 727 MET cc_start: 0.9455 (mmp) cc_final: 0.9202 (mmm) REVERT: C 857 MET cc_start: 0.9285 (pmm) cc_final: 0.8732 (tmm) REVERT: C 1158 MET cc_start: 0.9665 (mmm) cc_final: 0.9189 (mmm) REVERT: C 1351 MET cc_start: 0.8230 (ptp) cc_final: 0.7515 (ppp) REVERT: D 215 MET cc_start: 0.9579 (mpp) cc_final: 0.8497 (mtm) REVERT: D 675 MET cc_start: 0.9656 (mtm) cc_final: 0.8826 (ptm) REVERT: D 727 MET cc_start: 0.9456 (mmp) cc_final: 0.9199 (mmm) REVERT: D 857 MET cc_start: 0.9283 (pmm) cc_final: 0.8725 (tmm) REVERT: D 1158 MET cc_start: 0.9665 (mmm) cc_final: 0.9186 (mmm) REVERT: D 1351 MET cc_start: 0.8242 (ptp) cc_final: 0.7518 (ppp) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.4508 time to fit residues: 118.5828 Evaluate side-chains 133 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 4.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 310 optimal weight: 5.9990 chunk 200 optimal weight: 1.9990 chunk 299 optimal weight: 20.0000 chunk 150 optimal weight: 20.0000 chunk 98 optimal weight: 10.0000 chunk 97 optimal weight: 30.0000 chunk 318 optimal weight: 30.0000 chunk 341 optimal weight: 20.0000 chunk 247 optimal weight: 40.0000 chunk 46 optimal weight: 0.9990 chunk 393 optimal weight: 50.0000 overall best weight: 7.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 GLN ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 719 GLN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 GLN ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 719 GLN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 GLN C 414 GLN ** C 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 GLN ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 GLN D 342 ASN D 414 GLN ** D 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 719 GLN D 736 GLN ** D1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 38168 Z= 0.277 Angle : 0.599 8.532 52328 Z= 0.305 Chirality : 0.040 0.181 6224 Planarity : 0.004 0.057 6640 Dihedral : 6.188 73.074 5908 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.39 % Favored : 92.53 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % 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: -0.08 (0.12), residues: 5184 helix: 1.49 (0.10), residues: 2584 sheet: -0.89 (0.26), residues: 356 loop : -1.82 (0.13), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 944 HIS 0.004 0.001 HIS B1068 PHE 0.019 0.002 PHE A 690 TYR 0.012 0.001 TYR D 849 ARG 0.007 0.000 ARG C 845 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 4.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 MET cc_start: 0.9584 (mpp) cc_final: 0.8691 (mtm) REVERT: A 675 MET cc_start: 0.9668 (mtm) cc_final: 0.8796 (ptm) REVERT: A 727 MET cc_start: 0.9431 (mmp) cc_final: 0.9182 (mmm) REVERT: A 857 MET cc_start: 0.9262 (pmm) cc_final: 0.9021 (pmm) REVERT: A 1158 MET cc_start: 0.9646 (mmm) cc_final: 0.9266 (mmm) REVERT: B 215 MET cc_start: 0.9586 (mpp) cc_final: 0.8707 (mtm) REVERT: B 675 MET cc_start: 0.9658 (mtm) cc_final: 0.8684 (ptm) REVERT: B 727 MET cc_start: 0.9432 (mmp) cc_final: 0.9187 (mmm) REVERT: B 857 MET cc_start: 0.9262 (pmm) cc_final: 0.9026 (pmm) REVERT: B 1158 MET cc_start: 0.9645 (mmm) cc_final: 0.9183 (mmm) REVERT: C 215 MET cc_start: 0.9584 (mpp) cc_final: 0.8690 (mtm) REVERT: C 675 MET cc_start: 0.9660 (mtm) cc_final: 0.8776 (ptm) REVERT: C 727 MET cc_start: 0.9418 (mmp) cc_final: 0.9168 (mmm) REVERT: C 857 MET cc_start: 0.9271 (pmm) cc_final: 0.9040 (pmm) REVERT: C 1158 MET cc_start: 0.9648 (mmm) cc_final: 0.9181 (mmm) REVERT: D 215 MET cc_start: 0.9584 (mpp) cc_final: 0.8693 (mtm) REVERT: D 675 MET cc_start: 0.9659 (mtm) cc_final: 0.8770 (ptm) REVERT: D 727 MET cc_start: 0.9433 (mmp) cc_final: 0.9185 (mmm) REVERT: D 857 MET cc_start: 0.9270 (pmm) cc_final: 0.9035 (pmm) REVERT: D 1158 MET cc_start: 0.9649 (mmm) cc_final: 0.9270 (mmm) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.4345 time to fit residues: 106.9252 Evaluate side-chains 127 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 4.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 455 optimal weight: 4.9990 chunk 480 optimal weight: 10.0000 chunk 438 optimal weight: 8.9990 chunk 467 optimal weight: 7.9990 chunk 281 optimal weight: 30.0000 chunk 203 optimal weight: 20.0000 chunk 366 optimal weight: 20.0000 chunk 143 optimal weight: 7.9990 chunk 422 optimal weight: 8.9990 chunk 441 optimal weight: 10.0000 chunk 465 optimal weight: 20.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 719 GLN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 719 GLN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 GLN C1066 GLN ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 342 ASN ** D 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 719 GLN ** D1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 38168 Z= 0.274 Angle : 0.597 8.090 52328 Z= 0.304 Chirality : 0.040 0.157 6224 Planarity : 0.004 0.057 6640 Dihedral : 6.203 74.220 5908 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.74 % Favored : 92.19 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % 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: -0.05 (0.12), residues: 5184 helix: 1.48 (0.10), residues: 2584 sheet: -0.84 (0.26), residues: 356 loop : -1.79 (0.13), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 944 HIS 0.006 0.001 HIS D1502 PHE 0.018 0.002 PHE D 499 TYR 0.012 0.001 TYR C 295 ARG 0.003 0.000 ARG B1357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 4.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 MET cc_start: 0.9581 (mpp) cc_final: 0.9104 (mpp) REVERT: A 675 MET cc_start: 0.9677 (mtm) cc_final: 0.8794 (ptm) REVERT: A 727 MET cc_start: 0.9420 (mmp) cc_final: 0.9191 (mmm) REVERT: A 857 MET cc_start: 0.9271 (pmm) cc_final: 0.9026 (pmm) REVERT: A 1158 MET cc_start: 0.9648 (mmm) cc_final: 0.9182 (mmm) REVERT: B 215 MET cc_start: 0.9585 (mpp) cc_final: 0.9103 (mpp) REVERT: B 675 MET cc_start: 0.9675 (mtm) cc_final: 0.8789 (ptm) REVERT: B 727 MET cc_start: 0.9421 (mmp) cc_final: 0.9196 (mmm) REVERT: B 857 MET cc_start: 0.9273 (pmm) cc_final: 0.9032 (pmm) REVERT: B 1158 MET cc_start: 0.9647 (mmm) cc_final: 0.9184 (mmm) REVERT: C 215 MET cc_start: 0.9581 (mpp) cc_final: 0.9102 (mpp) REVERT: C 675 MET cc_start: 0.9678 (mtm) cc_final: 0.8795 (ptm) REVERT: C 727 MET cc_start: 0.9431 (mmp) cc_final: 0.9202 (mmm) REVERT: C 857 MET cc_start: 0.9272 (pmm) cc_final: 0.9030 (pmm) REVERT: C 1158 MET cc_start: 0.9649 (mmm) cc_final: 0.9182 (mmm) REVERT: D 215 MET cc_start: 0.9580 (mpp) cc_final: 0.9093 (mpp) REVERT: D 675 MET cc_start: 0.9678 (mtm) cc_final: 0.8786 (ptm) REVERT: D 727 MET cc_start: 0.9421 (mmp) cc_final: 0.9194 (mmm) REVERT: D 857 MET cc_start: 0.9274 (pmm) cc_final: 0.9031 (pmm) REVERT: D 1158 MET cc_start: 0.9650 (mmm) cc_final: 0.9183 (mmm) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.4317 time to fit residues: 109.5252 Evaluate side-chains 125 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 4.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 306 optimal weight: 3.9990 chunk 493 optimal weight: 10.0000 chunk 301 optimal weight: 0.0050 chunk 234 optimal weight: 30.0000 chunk 343 optimal weight: 0.0060 chunk 518 optimal weight: 7.9990 chunk 476 optimal weight: 6.9990 chunk 412 optimal weight: 30.0000 chunk 42 optimal weight: 10.0000 chunk 318 optimal weight: 30.0000 chunk 252 optimal weight: 20.0000 overall best weight: 3.8016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 719 GLN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 719 GLN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 GLN ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 342 ASN ** D 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 719 GLN ** D1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 38168 Z= 0.169 Angle : 0.540 6.810 52328 Z= 0.268 Chirality : 0.039 0.265 6224 Planarity : 0.004 0.060 6640 Dihedral : 5.955 78.512 5908 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.17 % Favored : 93.75 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % 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: 0.20 (0.12), residues: 5184 helix: 1.71 (0.11), residues: 2588 sheet: -0.72 (0.26), residues: 356 loop : -1.70 (0.14), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 944 HIS 0.003 0.001 HIS C 283 PHE 0.012 0.001 PHE D 499 TYR 0.010 0.001 TYR A1074 ARG 0.003 0.000 ARG A1357 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 4.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 MET cc_start: 0.9555 (mpp) cc_final: 0.9088 (mpp) REVERT: A 675 MET cc_start: 0.9705 (mtm) cc_final: 0.8897 (ptp) REVERT: A 727 MET cc_start: 0.9405 (mmp) cc_final: 0.9183 (mmm) REVERT: A 844 MET cc_start: 0.8983 (ppp) cc_final: 0.8757 (ppp) REVERT: A 857 MET cc_start: 0.9251 (pmm) cc_final: 0.8994 (pmm) REVERT: A 1158 MET cc_start: 0.9653 (mmm) cc_final: 0.9187 (mmm) REVERT: B 215 MET cc_start: 0.9554 (mpp) cc_final: 0.9084 (mpp) REVERT: B 675 MET cc_start: 0.9701 (mtm) cc_final: 0.8892 (ptp) REVERT: B 727 MET cc_start: 0.9410 (mmp) cc_final: 0.9191 (mmm) REVERT: B 844 MET cc_start: 0.8991 (ppp) cc_final: 0.8781 (ppp) REVERT: B 857 MET cc_start: 0.9253 (pmm) cc_final: 0.9001 (pmm) REVERT: B 1158 MET cc_start: 0.9651 (mmm) cc_final: 0.9191 (mmm) REVERT: C 215 MET cc_start: 0.9555 (mpp) cc_final: 0.9087 (mpp) REVERT: C 675 MET cc_start: 0.9704 (mtm) cc_final: 0.8897 (ptp) REVERT: C 727 MET cc_start: 0.9440 (mmp) cc_final: 0.9190 (mmm) REVERT: C 844 MET cc_start: 0.8977 (ppp) cc_final: 0.8747 (ppp) REVERT: C 857 MET cc_start: 0.9254 (pmm) cc_final: 0.9002 (pmm) REVERT: C 1158 MET cc_start: 0.9654 (mmm) cc_final: 0.9186 (mmm) REVERT: D 215 MET cc_start: 0.9557 (mpp) cc_final: 0.9083 (mpp) REVERT: D 675 MET cc_start: 0.9706 (mtm) cc_final: 0.8892 (ptp) REVERT: D 727 MET cc_start: 0.9409 (mmp) cc_final: 0.9187 (mmm) REVERT: D 844 MET cc_start: 0.8982 (ppp) cc_final: 0.8752 (ppp) REVERT: D 857 MET cc_start: 0.9253 (pmm) cc_final: 0.9000 (pmm) REVERT: D 1158 MET cc_start: 0.9655 (mmm) cc_final: 0.9191 (mmm) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.4218 time to fit residues: 111.4950 Evaluate side-chains 138 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 4.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 327 optimal weight: 20.0000 chunk 439 optimal weight: 30.0000 chunk 126 optimal weight: 50.0000 chunk 380 optimal weight: 50.0000 chunk 60 optimal weight: 3.9990 chunk 114 optimal weight: 20.0000 chunk 413 optimal weight: 20.0000 chunk 172 optimal weight: 2.9990 chunk 424 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 overall best weight: 5.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 719 GLN A 736 GLN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 ASN ** B 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 719 GLN B 736 GLN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 GLN C 736 GLN ** C1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 342 ASN ** D 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 719 GLN D 736 GLN ** D1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.037804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2571 r_free = 0.2571 target = 0.026528 restraints weight = 421957.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.027260 restraints weight = 270760.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.027743 restraints weight = 198171.244| |-----------------------------------------------------------------------------| r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 38168 Z= 0.218 Angle : 0.564 6.893 52328 Z= 0.281 Chirality : 0.039 0.213 6224 Planarity : 0.004 0.058 6640 Dihedral : 5.964 77.470 5908 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % 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: 0.17 (0.12), residues: 5184 helix: 1.69 (0.11), residues: 2580 sheet: -0.73 (0.26), residues: 356 loop : -1.70 (0.13), residues: 2248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 944 HIS 0.004 0.001 HIS B1068 PHE 0.018 0.001 PHE D1449 TYR 0.009 0.001 TYR C1074 ARG 0.002 0.000 ARG A1357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4935.14 seconds wall clock time: 94 minutes 44.99 seconds (5684.99 seconds total)