Starting phenix.real_space_refine on Sun Mar 17 10:50:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sia_40504/03_2024/8sia_40504_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sia_40504/03_2024/8sia_40504.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sia_40504/03_2024/8sia_40504.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sia_40504/03_2024/8sia_40504.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sia_40504/03_2024/8sia_40504_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sia_40504/03_2024/8sia_40504_neut_trim_updated.pdb" } resolution = 2.91 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= 0.011 sd= 0.042 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: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 P 48 5.49 5 S 240 5.16 5 C 25520 2.51 5 N 6016 2.21 5 O 6712 1.98 5 H 36144 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 197": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 525": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 618": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 634": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 639": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 699": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 729": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 750": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 843": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 892": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 942": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 962": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1018": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 1142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 1198": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 197": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 525": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 618": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 634": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 639": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 699": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 729": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 750": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 843": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 892": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 942": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 962": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1018": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 1142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 1198": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 197": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 525": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 618": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 634": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 639": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 699": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 729": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 750": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 843": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 892": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 942": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 962": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 1018": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 1142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 1198": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 197": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 525": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 618": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 634": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 639": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 699": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 729": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 750": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 843": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 892": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 942": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 962": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 1018": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 1142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 1198": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 74681 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 17965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1105, 17965 Classifications: {'peptide': 1105} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 1060} Chain breaks: 3 Chain: "B" Number of atoms: 17965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1105, 17965 Classifications: {'peptide': 1105} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 1060} Chain breaks: 3 Chain: "C" Number of atoms: 17965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1105, 17965 Classifications: {'peptide': 1105} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 1060} Chain breaks: 3 Chain: "D" Number of atoms: 17965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1105, 17965 Classifications: {'peptide': 1105} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 1060} Chain breaks: 3 Chain: "A" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 819 Unusual residues: {' CA': 1, '6RA': 1, 'DU0': 2, 'POV': 15} Classifications: {'undetermined': 19} Link IDs: {None: 18} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 711 Unusual residues: {'6RA': 1, 'CLR': 2, 'POV': 14} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-3': 3, 'POV:plan-2': 2} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 779 Unusual residues: {'6RA': 1, 'CLR': 1, 'DU0': 2, 'POV': 13} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 512 Unusual residues: {'6RA': 1, 'CLR': 1, 'POV': 10} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 1} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 24.59, per 1000 atoms: 0.33 Number of scatterers: 74681 At special positions: 0 Unit cell: (174.15, 174.15, 156.33, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 1 19.99 S 240 16.00 P 48 15.00 O 6712 8.00 N 6016 7.00 C 25520 6.00 H 36144 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 16 " - pdb=" SG CYS A 44 " distance=2.06 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 44 " distance=2.05 Simple disulfide: pdb=" SG CYS A1056 " - pdb=" SG CYS A1066 " distance=2.03 Simple disulfide: pdb=" SG CYS B 16 " - pdb=" SG CYS B 44 " distance=2.06 Simple disulfide: pdb=" SG CYS B 42 " - pdb=" SG CYS B 44 " distance=2.05 Simple disulfide: pdb=" SG CYS B1056 " - pdb=" SG CYS B1066 " distance=2.03 Simple disulfide: pdb=" SG CYS C 16 " - pdb=" SG CYS C 44 " distance=2.06 Simple disulfide: pdb=" SG CYS C 42 " - pdb=" SG CYS C 44 " distance=2.05 Simple disulfide: pdb=" SG CYS C1056 " - pdb=" SG CYS C1066 " distance=2.03 Simple disulfide: pdb=" SG CYS D 16 " - pdb=" SG CYS D 44 " distance=2.06 Simple disulfide: pdb=" SG CYS D 42 " - pdb=" SG CYS D 44 " distance=2.05 Simple disulfide: pdb=" SG CYS D1056 " - pdb=" SG CYS D1066 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 44.75 Conformation dependent library (CDL) restraints added in 5.2 seconds 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8368 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 196 helices and 8 sheets defined 51.4% alpha, 1.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.78 Creating SS restraints... Processing helix chain 'A' and resid 6 through 10 Processing helix chain 'A' and resid 33 through 39 removed outlier: 4.052A pdb=" N GLN A 38 " --> pdb=" O GLN A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 58 No H-bonds generated for 'chain 'A' and resid 55 through 58' Processing helix chain 'A' and resid 117 through 124 removed outlier: 4.095A pdb=" N LEU A 123 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU A 124 " --> pdb=" O ILE A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 165 removed outlier: 3.609A pdb=" N GLN A 154 " --> pdb=" O PRO A 150 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE A 161 " --> pdb=" O GLY A 157 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ALA A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 190 removed outlier: 3.529A pdb=" N LYS A 189 " --> pdb=" O GLY A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 267 removed outlier: 3.709A pdb=" N ARG A 264 " --> pdb=" O ARG A 261 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A 266 " --> pdb=" O ARG A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 305 removed outlier: 3.676A pdb=" N LEU A 301 " --> pdb=" O ILE A 297 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TYR A 303 " --> pdb=" O THR A 299 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU A 304 " --> pdb=" O VAL A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 327 removed outlier: 3.807A pdb=" N LEU A 324 " --> pdb=" O ARG A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 353 removed outlier: 3.520A pdb=" N THR A 353 " --> pdb=" O THR A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 373 removed outlier: 3.615A pdb=" N GLU A 370 " --> pdb=" O GLN A 366 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N CYS A 371 " --> pdb=" O THR A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 400 removed outlier: 3.605A pdb=" N LEU A 396 " --> pdb=" O ASP A 392 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU A 400 " --> pdb=" O LEU A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 417 removed outlier: 3.780A pdb=" N LEU A 413 " --> pdb=" O ASP A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 426 No H-bonds generated for 'chain 'A' and resid 423 through 426' Processing helix chain 'A' and resid 436 through 448 Processing helix chain 'A' and resid 452 through 461 Processing helix chain 'A' and resid 471 through 478 removed outlier: 3.639A pdb=" N TYR A 478 " --> pdb=" O LEU A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 496 removed outlier: 3.907A pdb=" N ARG A 494 " --> pdb=" O PHE A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 519 removed outlier: 3.788A pdb=" N TYR A 518 " --> pdb=" O LEU A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 529 No H-bonds generated for 'chain 'A' and resid 527 through 529' Processing helix chain 'A' and resid 531 through 539 removed outlier: 3.795A pdb=" N ASN A 538 " --> pdb=" O ARG A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 631 removed outlier: 4.207A pdb=" N LEU A 625 " --> pdb=" O LEU A 622 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU A 626 " --> pdb=" O ASN A 623 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE A 627 " --> pdb=" O GLU A 624 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA A 629 " --> pdb=" O LEU A 626 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N CYS A 630 " --> pdb=" O ILE A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 643 removed outlier: 3.528A pdb=" N GLN A 643 " --> pdb=" O ARG A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 668 removed outlier: 3.716A pdb=" N LEU A 653 " --> pdb=" O MET A 649 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N CYS A 656 " --> pdb=" O ALA A 652 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS A 657 " --> pdb=" O LEU A 653 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU A 665 " --> pdb=" O SER A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 686 removed outlier: 3.520A pdb=" N LYS A 680 " --> pdb=" O SER A 676 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN A 681 " --> pdb=" O GLU A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 698 removed outlier: 3.823A pdb=" N GLN A 696 " --> pdb=" O GLU A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 707 No H-bonds generated for 'chain 'A' and resid 704 through 707' Processing helix chain 'A' and resid 731 through 734 No H-bonds generated for 'chain 'A' and resid 731 through 734' Processing helix chain 'A' and resid 738 through 748 removed outlier: 3.865A pdb=" N LEU A 743 " --> pdb=" O THR A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 766 Processing helix chain 'A' and resid 768 through 773 Processing helix chain 'A' and resid 789 through 796 removed outlier: 3.773A pdb=" N GLN A 793 " --> pdb=" O GLN A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 849 removed outlier: 3.688A pdb=" N ALA A 847 " --> pdb=" O ARG A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 875 removed outlier: 3.978A pdb=" N LEU A 861 " --> pdb=" O TRP A 857 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA A 862 " --> pdb=" O PHE A 858 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY A 865 " --> pdb=" O LEU A 861 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N MET A 868 " --> pdb=" O LEU A 864 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU A 869 " --> pdb=" O GLY A 865 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR A 871 " --> pdb=" O LEU A 867 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE A 872 " --> pdb=" O MET A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 905 removed outlier: 3.544A pdb=" N ILE A 888 " --> pdb=" O VAL A 884 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL A 889 " --> pdb=" O GLN A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.575A pdb=" N LYS A 917 " --> pdb=" O SER A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 943 Processing helix chain 'A' and resid 956 through 982 removed outlier: 4.971A pdb=" N ILE A 970 " --> pdb=" O CYS A 966 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N PHE A 971 " --> pdb=" O LEU A 967 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU A 976 " --> pdb=" O TRP A 972 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU A 977 " --> pdb=" O TYR A 973 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP A 978 " --> pdb=" O VAL A 974 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL A 982 " --> pdb=" O ASP A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 990 No H-bonds generated for 'chain 'A' and resid 987 through 990' Processing helix chain 'A' and resid 992 through 995 No H-bonds generated for 'chain 'A' and resid 992 through 995' Processing helix chain 'A' and resid 1001 through 1022 removed outlier: 3.574A pdb=" N LEU A1011 " --> pdb=" O MET A1007 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A1012 " --> pdb=" O ALA A1008 " (cutoff:3.500A) Proline residue: A1017 - end of helix Processing helix chain 'A' and resid 1031 through 1034 No H-bonds generated for 'chain 'A' and resid 1031 through 1034' Processing helix chain 'A' and resid 1039 through 1045 removed outlier: 4.264A pdb=" N ILE A1044 " --> pdb=" O PRO A1040 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N PHE A1045 " --> pdb=" O TYR A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1087 removed outlier: 3.579A pdb=" N THR A1073 " --> pdb=" O THR A1070 " (cutoff:3.500A) Proline residue: A1074 - end of helix removed outlier: 3.775A pdb=" N GLN A1077 " --> pdb=" O PRO A1074 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU A1081 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE A1082 " --> pdb=" O VAL A1079 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N TYR A1085 " --> pdb=" O PHE A1082 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ILE A1086 " --> pdb=" O VAL A1083 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE A1087 " --> pdb=" O GLN A1084 " (cutoff:3.500A) Processing helix chain 'A' and resid 1089 through 1098 Processing helix chain 'A' and resid 1100 through 1122 removed outlier: 3.626A pdb=" N ASN A1108 " --> pdb=" O LYS A1104 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ILE A1109 " --> pdb=" O ALA A1105 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N TYR A1116 " --> pdb=" O LYS A1112 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N HIS A1117 " --> pdb=" O TYR A1113 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA A1121 " --> pdb=" O HIS A1117 " (cutoff:3.500A) Processing helix chain 'A' and resid 1134 through 1141 removed outlier: 3.845A pdb=" N SER A1140 " --> pdb=" O SER A1136 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1190 removed outlier: 4.262A pdb=" N ASP A1186 " --> pdb=" O PHE A1182 " (cutoff:3.500A) Processing helix chain 'A' and resid 1194 through 1229 removed outlier: 3.615A pdb=" N GLN A1210 " --> pdb=" O GLN A1206 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL A1214 " --> pdb=" O GLN A1210 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN A1219 " --> pdb=" O GLY A1215 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER A1224 " --> pdb=" O TYR A1220 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N SER A1227 " --> pdb=" O ARG A1223 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 10 Processing helix chain 'B' and resid 33 through 39 removed outlier: 4.051A pdb=" N GLN B 38 " --> pdb=" O GLN B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 58 No H-bonds generated for 'chain 'B' and resid 55 through 58' Processing helix chain 'B' and resid 117 through 124 removed outlier: 4.094A pdb=" N LEU B 123 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU B 124 " --> pdb=" O ILE B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 165 removed outlier: 3.610A pdb=" N GLN B 154 " --> pdb=" O PRO B 150 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE B 161 " --> pdb=" O GLY B 157 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ALA B 164 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 190 removed outlier: 3.528A pdb=" N LYS B 189 " --> pdb=" O GLY B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 267 removed outlier: 3.710A pdb=" N ARG B 264 " --> pdb=" O ARG B 261 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU B 266 " --> pdb=" O ARG B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 305 removed outlier: 3.676A pdb=" N LEU B 301 " --> pdb=" O ILE B 297 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TYR B 303 " --> pdb=" O THR B 299 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU B 304 " --> pdb=" O VAL B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 327 removed outlier: 3.807A pdb=" N LEU B 324 " --> pdb=" O ARG B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 353 removed outlier: 3.520A pdb=" N THR B 353 " --> pdb=" O THR B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 373 removed outlier: 3.615A pdb=" N GLU B 370 " --> pdb=" O GLN B 366 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N CYS B 371 " --> pdb=" O THR B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 400 removed outlier: 3.605A pdb=" N LEU B 396 " --> pdb=" O ASP B 392 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU B 400 " --> pdb=" O LEU B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 417 removed outlier: 3.780A pdb=" N LEU B 413 " --> pdb=" O ASP B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 426 No H-bonds generated for 'chain 'B' and resid 423 through 426' Processing helix chain 'B' and resid 436 through 448 Processing helix chain 'B' and resid 452 through 461 Processing helix chain 'B' and resid 471 through 478 removed outlier: 3.640A pdb=" N TYR B 478 " --> pdb=" O LEU B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 496 removed outlier: 3.907A pdb=" N ARG B 494 " --> pdb=" O PHE B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 519 removed outlier: 3.787A pdb=" N TYR B 518 " --> pdb=" O LEU B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 529 No H-bonds generated for 'chain 'B' and resid 527 through 529' Processing helix chain 'B' and resid 531 through 539 removed outlier: 3.795A pdb=" N ASN B 538 " --> pdb=" O ARG B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 631 removed outlier: 4.207A pdb=" N LEU B 625 " --> pdb=" O LEU B 622 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU B 626 " --> pdb=" O ASN B 623 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE B 627 " --> pdb=" O GLU B 624 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA B 629 " --> pdb=" O LEU B 626 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N CYS B 630 " --> pdb=" O ILE B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 643 removed outlier: 3.528A pdb=" N GLN B 643 " --> pdb=" O ARG B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 668 removed outlier: 3.716A pdb=" N LEU B 653 " --> pdb=" O MET B 649 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N CYS B 656 " --> pdb=" O ALA B 652 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS B 657 " --> pdb=" O LEU B 653 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU B 665 " --> pdb=" O SER B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 676 through 686 removed outlier: 3.519A pdb=" N LYS B 680 " --> pdb=" O SER B 676 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN B 681 " --> pdb=" O GLU B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 698 removed outlier: 3.823A pdb=" N GLN B 696 " --> pdb=" O GLU B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 707 No H-bonds generated for 'chain 'B' and resid 704 through 707' Processing helix chain 'B' and resid 731 through 734 No H-bonds generated for 'chain 'B' and resid 731 through 734' Processing helix chain 'B' and resid 738 through 748 removed outlier: 3.865A pdb=" N LEU B 743 " --> pdb=" O THR B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 766 Processing helix chain 'B' and resid 768 through 773 Processing helix chain 'B' and resid 789 through 796 removed outlier: 3.772A pdb=" N GLN B 793 " --> pdb=" O GLN B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 849 removed outlier: 3.688A pdb=" N ALA B 847 " --> pdb=" O ARG B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 852 through 875 removed outlier: 3.978A pdb=" N LEU B 861 " --> pdb=" O TRP B 857 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA B 862 " --> pdb=" O PHE B 858 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY B 865 " --> pdb=" O LEU B 861 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N MET B 868 " --> pdb=" O LEU B 864 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU B 869 " --> pdb=" O GLY B 865 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR B 871 " --> pdb=" O LEU B 867 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE B 872 " --> pdb=" O MET B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 905 removed outlier: 3.543A pdb=" N ILE B 888 " --> pdb=" O VAL B 884 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL B 889 " --> pdb=" O GLN B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.575A pdb=" N LYS B 917 " --> pdb=" O SER B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 943 Processing helix chain 'B' and resid 956 through 982 removed outlier: 4.971A pdb=" N ILE B 970 " --> pdb=" O CYS B 966 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N PHE B 971 " --> pdb=" O LEU B 967 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU B 976 " --> pdb=" O TRP B 972 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU B 977 " --> pdb=" O TYR B 973 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP B 978 " --> pdb=" O VAL B 974 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL B 982 " --> pdb=" O ASP B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 990 No H-bonds generated for 'chain 'B' and resid 987 through 990' Processing helix chain 'B' and resid 992 through 995 No H-bonds generated for 'chain 'B' and resid 992 through 995' Processing helix chain 'B' and resid 1001 through 1022 removed outlier: 3.575A pdb=" N LEU B1011 " --> pdb=" O MET B1007 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B1012 " --> pdb=" O ALA B1008 " (cutoff:3.500A) Proline residue: B1017 - end of helix Processing helix chain 'B' and resid 1031 through 1034 No H-bonds generated for 'chain 'B' and resid 1031 through 1034' Processing helix chain 'B' and resid 1039 through 1045 removed outlier: 4.264A pdb=" N ILE B1044 " --> pdb=" O PRO B1040 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N PHE B1045 " --> pdb=" O TYR B1041 " (cutoff:3.500A) Processing helix chain 'B' and resid 1070 through 1087 removed outlier: 3.579A pdb=" N THR B1073 " --> pdb=" O THR B1070 " (cutoff:3.500A) Proline residue: B1074 - end of helix removed outlier: 3.775A pdb=" N GLN B1077 " --> pdb=" O PRO B1074 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU B1081 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE B1082 " --> pdb=" O VAL B1079 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N TYR B1085 " --> pdb=" O PHE B1082 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ILE B1086 " --> pdb=" O VAL B1083 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE B1087 " --> pdb=" O GLN B1084 " (cutoff:3.500A) Processing helix chain 'B' and resid 1089 through 1098 Processing helix chain 'B' and resid 1100 through 1122 removed outlier: 3.626A pdb=" N ASN B1108 " --> pdb=" O LYS B1104 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N ILE B1109 " --> pdb=" O ALA B1105 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N TYR B1116 " --> pdb=" O LYS B1112 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N HIS B1117 " --> pdb=" O TYR B1113 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA B1121 " --> pdb=" O HIS B1117 " (cutoff:3.500A) Processing helix chain 'B' and resid 1134 through 1141 removed outlier: 3.844A pdb=" N SER B1140 " --> pdb=" O SER B1136 " (cutoff:3.500A) Processing helix chain 'B' and resid 1165 through 1190 removed outlier: 4.261A pdb=" N ASP B1186 " --> pdb=" O PHE B1182 " (cutoff:3.500A) Processing helix chain 'B' and resid 1194 through 1229 removed outlier: 3.615A pdb=" N GLN B1210 " --> pdb=" O GLN B1206 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL B1214 " --> pdb=" O GLN B1210 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN B1219 " --> pdb=" O GLY B1215 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER B1224 " --> pdb=" O TYR B1220 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N SER B1227 " --> pdb=" O ARG B1223 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 10 Processing helix chain 'C' and resid 33 through 39 removed outlier: 4.053A pdb=" N GLN C 38 " --> pdb=" O GLN C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 58 No H-bonds generated for 'chain 'C' and resid 55 through 58' Processing helix chain 'C' and resid 117 through 124 removed outlier: 4.095A pdb=" N LEU C 123 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU C 124 " --> pdb=" O ILE C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 165 removed outlier: 3.610A pdb=" N GLN C 154 " --> pdb=" O PRO C 150 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE C 161 " --> pdb=" O GLY C 157 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ALA C 164 " --> pdb=" O LEU C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 190 removed outlier: 3.529A pdb=" N LYS C 189 " --> pdb=" O GLY C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 267 removed outlier: 3.710A pdb=" N ARG C 264 " --> pdb=" O ARG C 261 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU C 266 " --> pdb=" O ARG C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 305 removed outlier: 3.676A pdb=" N LEU C 301 " --> pdb=" O ILE C 297 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TYR C 303 " --> pdb=" O THR C 299 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU C 304 " --> pdb=" O VAL C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 327 removed outlier: 3.808A pdb=" N LEU C 324 " --> pdb=" O ARG C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 353 removed outlier: 3.520A pdb=" N THR C 353 " --> pdb=" O THR C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 373 removed outlier: 3.615A pdb=" N GLU C 370 " --> pdb=" O GLN C 366 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N CYS C 371 " --> pdb=" O THR C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 400 removed outlier: 3.605A pdb=" N LEU C 396 " --> pdb=" O ASP C 392 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU C 400 " --> pdb=" O LEU C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 417 removed outlier: 3.779A pdb=" N LEU C 413 " --> pdb=" O ASP C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 426 No H-bonds generated for 'chain 'C' and resid 423 through 426' Processing helix chain 'C' and resid 436 through 448 Processing helix chain 'C' and resid 452 through 461 Processing helix chain 'C' and resid 471 through 478 removed outlier: 3.640A pdb=" N TYR C 478 " --> pdb=" O LEU C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 496 removed outlier: 3.907A pdb=" N ARG C 494 " --> pdb=" O PHE C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 519 removed outlier: 3.788A pdb=" N TYR C 518 " --> pdb=" O LEU C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 527 through 529 No H-bonds generated for 'chain 'C' and resid 527 through 529' Processing helix chain 'C' and resid 531 through 539 removed outlier: 3.795A pdb=" N ASN C 538 " --> pdb=" O ARG C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 621 through 631 removed outlier: 4.208A pdb=" N LEU C 625 " --> pdb=" O LEU C 622 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU C 626 " --> pdb=" O ASN C 623 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE C 627 " --> pdb=" O GLU C 624 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA C 629 " --> pdb=" O LEU C 626 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N CYS C 630 " --> pdb=" O ILE C 627 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 643 removed outlier: 3.528A pdb=" N GLN C 643 " --> pdb=" O ARG C 639 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 668 removed outlier: 3.716A pdb=" N LEU C 653 " --> pdb=" O MET C 649 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N CYS C 656 " --> pdb=" O ALA C 652 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS C 657 " --> pdb=" O LEU C 653 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU C 665 " --> pdb=" O SER C 661 " (cutoff:3.500A) Processing helix chain 'C' and resid 676 through 686 removed outlier: 3.520A pdb=" N LYS C 680 " --> pdb=" O SER C 676 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN C 681 " --> pdb=" O GLU C 677 " (cutoff:3.500A) Processing helix chain 'C' and resid 689 through 698 removed outlier: 3.823A pdb=" N GLN C 696 " --> pdb=" O GLU C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 707 No H-bonds generated for 'chain 'C' and resid 704 through 707' Processing helix chain 'C' and resid 731 through 734 No H-bonds generated for 'chain 'C' and resid 731 through 734' Processing helix chain 'C' and resid 738 through 748 removed outlier: 3.865A pdb=" N LEU C 743 " --> pdb=" O THR C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 766 Processing helix chain 'C' and resid 768 through 773 Processing helix chain 'C' and resid 789 through 796 removed outlier: 3.772A pdb=" N GLN C 793 " --> pdb=" O GLN C 789 " (cutoff:3.500A) Processing helix chain 'C' and resid 842 through 849 removed outlier: 3.688A pdb=" N ALA C 847 " --> pdb=" O ARG C 843 " (cutoff:3.500A) Processing helix chain 'C' and resid 852 through 875 removed outlier: 3.979A pdb=" N LEU C 861 " --> pdb=" O TRP C 857 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA C 862 " --> pdb=" O PHE C 858 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY C 865 " --> pdb=" O LEU C 861 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N MET C 868 " --> pdb=" O LEU C 864 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU C 869 " --> pdb=" O GLY C 865 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR C 871 " --> pdb=" O LEU C 867 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE C 872 " --> pdb=" O MET C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 905 removed outlier: 3.543A pdb=" N ILE C 888 " --> pdb=" O VAL C 884 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL C 889 " --> pdb=" O GLN C 885 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.575A pdb=" N LYS C 917 " --> pdb=" O SER C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 923 through 943 Processing helix chain 'C' and resid 956 through 982 removed outlier: 4.971A pdb=" N ILE C 970 " --> pdb=" O CYS C 966 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N PHE C 971 " --> pdb=" O LEU C 967 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU C 976 " --> pdb=" O TRP C 972 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU C 977 " --> pdb=" O TYR C 973 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASP C 978 " --> pdb=" O VAL C 974 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL C 982 " --> pdb=" O ASP C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 987 through 990 No H-bonds generated for 'chain 'C' and resid 987 through 990' Processing helix chain 'C' and resid 992 through 995 No H-bonds generated for 'chain 'C' and resid 992 through 995' Processing helix chain 'C' and resid 1001 through 1022 removed outlier: 3.574A pdb=" N LEU C1011 " --> pdb=" O MET C1007 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU C1012 " --> pdb=" O ALA C1008 " (cutoff:3.500A) Proline residue: C1017 - end of helix Processing helix chain 'C' and resid 1031 through 1034 No H-bonds generated for 'chain 'C' and resid 1031 through 1034' Processing helix chain 'C' and resid 1039 through 1045 removed outlier: 4.263A pdb=" N ILE C1044 " --> pdb=" O PRO C1040 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N PHE C1045 " --> pdb=" O TYR C1041 " (cutoff:3.500A) Processing helix chain 'C' and resid 1070 through 1087 removed outlier: 3.580A pdb=" N THR C1073 " --> pdb=" O THR C1070 " (cutoff:3.500A) Proline residue: C1074 - end of helix removed outlier: 3.774A pdb=" N GLN C1077 " --> pdb=" O PRO C1074 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU C1081 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE C1082 " --> pdb=" O VAL C1079 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N TYR C1085 " --> pdb=" O PHE C1082 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ILE C1086 " --> pdb=" O VAL C1083 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE C1087 " --> pdb=" O GLN C1084 " (cutoff:3.500A) Processing helix chain 'C' and resid 1089 through 1098 Processing helix chain 'C' and resid 1100 through 1122 removed outlier: 3.626A pdb=" N ASN C1108 " --> pdb=" O LYS C1104 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ILE C1109 " --> pdb=" O ALA C1105 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N TYR C1116 " --> pdb=" O LYS C1112 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N HIS C1117 " --> pdb=" O TYR C1113 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA C1121 " --> pdb=" O HIS C1117 " (cutoff:3.500A) Processing helix chain 'C' and resid 1134 through 1141 removed outlier: 3.845A pdb=" N SER C1140 " --> pdb=" O SER C1136 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1190 removed outlier: 4.262A pdb=" N ASP C1186 " --> pdb=" O PHE C1182 " (cutoff:3.500A) Processing helix chain 'C' and resid 1194 through 1229 removed outlier: 3.614A pdb=" N GLN C1210 " --> pdb=" O GLN C1206 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL C1214 " --> pdb=" O GLN C1210 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN C1219 " --> pdb=" O GLY C1215 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER C1224 " --> pdb=" O TYR C1220 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N SER C1227 " --> pdb=" O ARG C1223 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 10 Processing helix chain 'D' and resid 33 through 39 removed outlier: 4.053A pdb=" N GLN D 38 " --> pdb=" O GLN D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 58 No H-bonds generated for 'chain 'D' and resid 55 through 58' Processing helix chain 'D' and resid 117 through 124 removed outlier: 4.095A pdb=" N LEU D 123 " --> pdb=" O ILE D 119 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU D 124 " --> pdb=" O ILE D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 165 removed outlier: 3.608A pdb=" N GLN D 154 " --> pdb=" O PRO D 150 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE D 161 " --> pdb=" O GLY D 157 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ALA D 164 " --> pdb=" O LEU D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 190 removed outlier: 3.530A pdb=" N LYS D 189 " --> pdb=" O GLY D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 267 removed outlier: 3.710A pdb=" N ARG D 264 " --> pdb=" O ARG D 261 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU D 266 " --> pdb=" O ARG D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 305 removed outlier: 3.675A pdb=" N LEU D 301 " --> pdb=" O ILE D 297 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TYR D 303 " --> pdb=" O THR D 299 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU D 304 " --> pdb=" O VAL D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 327 removed outlier: 3.808A pdb=" N LEU D 324 " --> pdb=" O ARG D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 353 removed outlier: 3.519A pdb=" N THR D 353 " --> pdb=" O THR D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 373 removed outlier: 3.614A pdb=" N GLU D 370 " --> pdb=" O GLN D 366 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N CYS D 371 " --> pdb=" O THR D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 400 removed outlier: 3.605A pdb=" N LEU D 396 " --> pdb=" O ASP D 392 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU D 400 " --> pdb=" O LEU D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 417 removed outlier: 3.779A pdb=" N LEU D 413 " --> pdb=" O ASP D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 426 No H-bonds generated for 'chain 'D' and resid 423 through 426' Processing helix chain 'D' and resid 436 through 448 Processing helix chain 'D' and resid 452 through 461 Processing helix chain 'D' and resid 471 through 478 removed outlier: 3.640A pdb=" N TYR D 478 " --> pdb=" O LEU D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 496 removed outlier: 3.907A pdb=" N ARG D 494 " --> pdb=" O PHE D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 519 removed outlier: 3.787A pdb=" N TYR D 518 " --> pdb=" O LEU D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 527 through 529 No H-bonds generated for 'chain 'D' and resid 527 through 529' Processing helix chain 'D' and resid 531 through 539 removed outlier: 3.795A pdb=" N ASN D 538 " --> pdb=" O ARG D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 621 through 631 removed outlier: 4.207A pdb=" N LEU D 625 " --> pdb=" O LEU D 622 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU D 626 " --> pdb=" O ASN D 623 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE D 627 " --> pdb=" O GLU D 624 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA D 629 " --> pdb=" O LEU D 626 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N CYS D 630 " --> pdb=" O ILE D 627 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 643 removed outlier: 3.528A pdb=" N GLN D 643 " --> pdb=" O ARG D 639 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 668 removed outlier: 3.716A pdb=" N LEU D 653 " --> pdb=" O MET D 649 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N CYS D 656 " --> pdb=" O ALA D 652 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS D 657 " --> pdb=" O LEU D 653 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU D 665 " --> pdb=" O SER D 661 " (cutoff:3.500A) Processing helix chain 'D' and resid 676 through 686 removed outlier: 3.521A pdb=" N LYS D 680 " --> pdb=" O SER D 676 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN D 681 " --> pdb=" O GLU D 677 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 698 removed outlier: 3.823A pdb=" N GLN D 696 " --> pdb=" O GLU D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 704 through 707 No H-bonds generated for 'chain 'D' and resid 704 through 707' Processing helix chain 'D' and resid 731 through 734 No H-bonds generated for 'chain 'D' and resid 731 through 734' Processing helix chain 'D' and resid 738 through 748 removed outlier: 3.865A pdb=" N LEU D 743 " --> pdb=" O THR D 739 " (cutoff:3.500A) Processing helix chain 'D' and resid 758 through 766 Processing helix chain 'D' and resid 768 through 773 Processing helix chain 'D' and resid 789 through 796 removed outlier: 3.772A pdb=" N GLN D 793 " --> pdb=" O GLN D 789 " (cutoff:3.500A) Processing helix chain 'D' and resid 842 through 849 removed outlier: 3.687A pdb=" N ALA D 847 " --> pdb=" O ARG D 843 " (cutoff:3.500A) Processing helix chain 'D' and resid 852 through 875 removed outlier: 3.978A pdb=" N LEU D 861 " --> pdb=" O TRP D 857 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA D 862 " --> pdb=" O PHE D 858 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY D 865 " --> pdb=" O LEU D 861 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N MET D 868 " --> pdb=" O LEU D 864 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU D 869 " --> pdb=" O GLY D 865 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR D 871 " --> pdb=" O LEU D 867 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE D 872 " --> pdb=" O MET D 868 " (cutoff:3.500A) Processing helix chain 'D' and resid 884 through 905 removed outlier: 3.544A pdb=" N ILE D 888 " --> pdb=" O VAL D 884 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL D 889 " --> pdb=" O GLN D 885 " (cutoff:3.500A) Processing helix chain 'D' and resid 912 through 919 removed outlier: 3.574A pdb=" N LYS D 917 " --> pdb=" O SER D 913 " (cutoff:3.500A) Processing helix chain 'D' and resid 923 through 943 Processing helix chain 'D' and resid 956 through 982 removed outlier: 4.971A pdb=" N ILE D 970 " --> pdb=" O CYS D 966 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N PHE D 971 " --> pdb=" O LEU D 967 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU D 976 " --> pdb=" O TRP D 972 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU D 977 " --> pdb=" O TYR D 973 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP D 978 " --> pdb=" O VAL D 974 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL D 982 " --> pdb=" O ASP D 978 " (cutoff:3.500A) Processing helix chain 'D' and resid 987 through 990 No H-bonds generated for 'chain 'D' and resid 987 through 990' Processing helix chain 'D' and resid 992 through 995 No H-bonds generated for 'chain 'D' and resid 992 through 995' Processing helix chain 'D' and resid 1001 through 1022 removed outlier: 3.574A pdb=" N LEU D1011 " --> pdb=" O MET D1007 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU D1012 " --> pdb=" O ALA D1008 " (cutoff:3.500A) Proline residue: D1017 - end of helix Processing helix chain 'D' and resid 1031 through 1034 No H-bonds generated for 'chain 'D' and resid 1031 through 1034' Processing helix chain 'D' and resid 1039 through 1045 removed outlier: 4.263A pdb=" N ILE D1044 " --> pdb=" O PRO D1040 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N PHE D1045 " --> pdb=" O TYR D1041 " (cutoff:3.500A) Processing helix chain 'D' and resid 1070 through 1087 removed outlier: 3.579A pdb=" N THR D1073 " --> pdb=" O THR D1070 " (cutoff:3.500A) Proline residue: D1074 - end of helix removed outlier: 3.775A pdb=" N GLN D1077 " --> pdb=" O PRO D1074 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU D1081 " --> pdb=" O ALA D1078 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE D1082 " --> pdb=" O VAL D1079 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N TYR D1085 " --> pdb=" O PHE D1082 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ILE D1086 " --> pdb=" O VAL D1083 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE D1087 " --> pdb=" O GLN D1084 " (cutoff:3.500A) Processing helix chain 'D' and resid 1089 through 1098 Processing helix chain 'D' and resid 1100 through 1122 removed outlier: 3.626A pdb=" N ASN D1108 " --> pdb=" O LYS D1104 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N ILE D1109 " --> pdb=" O ALA D1105 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N TYR D1116 " --> pdb=" O LYS D1112 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N HIS D1117 " --> pdb=" O TYR D1113 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA D1121 " --> pdb=" O HIS D1117 " (cutoff:3.500A) Processing helix chain 'D' and resid 1134 through 1141 removed outlier: 3.844A pdb=" N SER D1140 " --> pdb=" O SER D1136 " (cutoff:3.500A) Processing helix chain 'D' and resid 1165 through 1190 removed outlier: 4.262A pdb=" N ASP D1186 " --> pdb=" O PHE D1182 " (cutoff:3.500A) Processing helix chain 'D' and resid 1194 through 1229 removed outlier: 3.614A pdb=" N GLN D1210 " --> pdb=" O GLN D1206 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL D1214 " --> pdb=" O GLN D1210 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN D1219 " --> pdb=" O GLY D1215 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER D1224 " --> pdb=" O TYR D1220 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N SER D1227 " --> pdb=" O ARG D1223 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 13 through 16 removed outlier: 3.562A pdb=" N GLU A 85 " --> pdb=" O GLU A 15 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 203 through 206 Processing sheet with id= C, first strand: chain 'B' and resid 13 through 16 removed outlier: 3.562A pdb=" N GLU B 85 " --> pdb=" O GLU B 15 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 203 through 206 Processing sheet with id= E, first strand: chain 'C' and resid 13 through 16 removed outlier: 3.562A pdb=" N GLU C 85 " --> pdb=" O GLU C 15 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 203 through 206 Processing sheet with id= G, first strand: chain 'D' and resid 13 through 16 removed outlier: 3.563A pdb=" N GLU D 85 " --> pdb=" O GLU D 15 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 203 through 206 1196 hydrogen bonds defined for protein. 3384 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: 24.99 Time building geometry restraints manager: 47.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 36076 1.02 - 1.23: 232 1.23 - 1.43: 15665 1.43 - 1.63: 23171 1.63 - 1.84: 392 Bond restraints: 75536 Sorted by residual: bond pdb=" C29 POV B1314 " pdb="C210 POV B1314 " ideal model delta sigma weight residual 1.333 1.529 -0.196 2.00e-02 2.50e+03 9.61e+01 bond pdb=" C29 POV D1311 " pdb="C210 POV D1311 " ideal model delta sigma weight residual 1.333 1.528 -0.195 2.00e-02 2.50e+03 9.53e+01 bond pdb=" C29 POV A1311 " pdb="C210 POV A1311 " ideal model delta sigma weight residual 1.333 1.522 -0.189 2.00e-02 2.50e+03 8.93e+01 bond pdb=" C29 POV B1317 " pdb="C210 POV B1317 " ideal model delta sigma weight residual 1.333 1.521 -0.188 2.00e-02 2.50e+03 8.81e+01 bond pdb="C217 POV D1302 " pdb="C218 POV D1302 " ideal model delta sigma weight residual 1.522 1.409 0.113 2.00e-02 2.50e+03 3.19e+01 ... (remaining 75531 not shown) Histogram of bond angle deviations from ideal: 58.90 - 74.69: 16 74.69 - 90.48: 83 90.48 - 106.27: 2579 106.27 - 122.07: 119229 122.07 - 137.86: 13185 Bond angle restraints: 135092 Sorted by residual: angle pdb=" C ASN B 72 " pdb=" N GLN B 73 " pdb=" H GLN B 73 " ideal model delta sigma weight residual 123.87 67.57 56.30 3.00e+00 1.11e-01 3.52e+02 angle pdb=" CA GLN B 73 " pdb=" N GLN B 73 " pdb=" H GLN B 73 " ideal model delta sigma weight residual 113.57 58.90 54.68 3.00e+00 1.11e-01 3.32e+02 angle pdb=" N VAL B 918 " pdb=" CA VAL B 918 " pdb=" HA VAL B 918 " ideal model delta sigma weight residual 110.00 69.84 40.16 3.00e+00 1.11e-01 1.79e+02 angle pdb=" N VAL D 918 " pdb=" CA VAL D 918 " pdb=" HA VAL D 918 " ideal model delta sigma weight residual 110.00 69.89 40.11 3.00e+00 1.11e-01 1.79e+02 angle pdb=" C GLU B 797 " pdb=" CA GLU B 797 " pdb=" HA GLU B 797 " ideal model delta sigma weight residual 109.00 69.00 40.00 3.00e+00 1.11e-01 1.78e+02 ... (remaining 135087 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 35499 35.99 - 71.97: 1120 71.97 - 107.96: 130 107.96 - 143.94: 43 143.94 - 179.93: 24 Dihedral angle restraints: 36816 sinusoidal: 21108 harmonic: 15708 Sorted by residual: dihedral pdb=" CB CYS C 16 " pdb=" SG CYS C 16 " pdb=" SG CYS C 44 " pdb=" CB CYS C 44 " ideal model delta sinusoidal sigma weight residual -86.00 -3.91 -82.09 1 1.00e+01 1.00e-02 8.28e+01 dihedral pdb=" CB CYS B 16 " pdb=" SG CYS B 16 " pdb=" SG CYS B 44 " pdb=" CB CYS B 44 " ideal model delta sinusoidal sigma weight residual -86.00 -3.94 -82.06 1 1.00e+01 1.00e-02 8.27e+01 dihedral pdb=" CB CYS A 16 " pdb=" SG CYS A 16 " pdb=" SG CYS A 44 " pdb=" CB CYS A 44 " ideal model delta sinusoidal sigma weight residual -86.00 -3.94 -82.06 1 1.00e+01 1.00e-02 8.27e+01 ... (remaining 36813 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.189: 5593 0.189 - 0.378: 47 0.378 - 0.567: 0 0.567 - 0.756: 1 0.756 - 0.945: 31 Chirality restraints: 5672 Sorted by residual: chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.64 -0.95 2.00e-01 2.50e+01 2.23e+01 chirality pdb=" CG LEU D 172 " pdb=" CB LEU D 172 " pdb=" CD1 LEU D 172 " pdb=" CD2 LEU D 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.64 -0.95 2.00e-01 2.50e+01 2.23e+01 chirality pdb=" CG LEU C 172 " pdb=" CB LEU C 172 " pdb=" CD1 LEU C 172 " pdb=" CD2 LEU C 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.64 -0.94 2.00e-01 2.50e+01 2.23e+01 ... (remaining 5669 not shown) Planarity restraints: 10576 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 635 " 0.156 2.00e-02 2.50e+03 1.76e-01 4.63e+02 pdb=" CD GLN A 635 " 0.004 2.00e-02 2.50e+03 pdb=" OE1 GLN A 635 " -0.153 2.00e-02 2.50e+03 pdb=" NE2 GLN A 635 " 0.004 2.00e-02 2.50e+03 pdb="HE21 GLN A 635 " -0.268 2.00e-02 2.50e+03 pdb="HE22 GLN A 635 " 0.256 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 635 " -0.153 2.00e-02 2.50e+03 1.71e-01 4.41e+02 pdb=" CD GLN C 635 " -0.005 2.00e-02 2.50e+03 pdb=" OE1 GLN C 635 " 0.150 2.00e-02 2.50e+03 pdb=" NE2 GLN C 635 " -0.004 2.00e-02 2.50e+03 pdb="HE21 GLN C 635 " 0.261 2.00e-02 2.50e+03 pdb="HE22 GLN C 635 " -0.249 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 635 " 0.151 2.00e-02 2.50e+03 1.69e-01 4.28e+02 pdb=" CD GLN B 635 " 0.005 2.00e-02 2.50e+03 pdb=" OE1 GLN B 635 " -0.148 2.00e-02 2.50e+03 pdb=" NE2 GLN B 635 " 0.003 2.00e-02 2.50e+03 pdb="HE21 GLN B 635 " -0.257 2.00e-02 2.50e+03 pdb="HE22 GLN B 635 " 0.246 2.00e-02 2.50e+03 ... (remaining 10573 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.13: 2163 2.13 - 2.75: 140181 2.75 - 3.37: 212285 3.37 - 3.98: 282213 3.98 - 4.60: 446300 Nonbonded interactions: 1083142 Sorted by model distance: nonbonded pdb=" H GLN B 73 " pdb=" HA GLN B 73 " model vdw 1.516 1.816 nonbonded pdb=" OE1 GLN C 740 " pdb="HH11 ARG C1115 " model vdw 1.548 1.850 nonbonded pdb=" OE1 GLN D 740 " pdb="HH11 ARG D1115 " model vdw 1.549 1.850 nonbonded pdb=" OE1 GLN B 740 " pdb="HH11 ARG B1115 " model vdw 1.549 1.850 nonbonded pdb=" OE1 GLN A 740 " pdb="HH11 ARG A1115 " model vdw 1.549 1.850 ... (remaining 1083137 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 1230 or resid 1302 through 1303 or resid 1307 th \ rough 1311)) selection = (chain 'B' and (resid 3 through 1230 or resid 1302 through 1303 or resid 1307 th \ rough 1308 or (resid 1309 and (name N or name C1 or name C11 or name C12 or name \ C13 or name C14 or name C15 or name C2 or name C21 or name C22 or name C23 or n \ ame C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name O11 \ or name O12 or name O13 or name O14 or name O21 or name O22 or name P or name C2 \ 10 or name C211 or name C212 or name C213 or name C214 or name C215 or name C216 \ or name C217 or name C218)) or resid 1310 or (resid 1311 and (name C22 or name \ C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 or n \ ame C210 or name C211 or name C212 or name C213 or name C214 or name C215 or nam \ e C216)))) selection = (chain 'C' and (resid 3 through 1230 or resid 1302 through 1303 or resid 1307 th \ rough 1308 or (resid 1309 and (name N or name C1 or name C11 or name C12 or name \ C13 or name C14 or name C15 or name C2 or name C21 or name C22 or name C23 or n \ ame C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name O11 \ or name O12 or name O13 or name O14 or name O21 or name O22 or name P or name C2 \ 10 or name C211 or name C212 or name C213 or name C214 or name C215 or name C216 \ or name C217 or name C218)) or resid 1310 or (resid 1311 and (name C22 or name \ C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 or n \ ame C210 or name C211 or name C212 or name C213 or name C214 or name C215 or nam \ e C216)))) selection = (chain 'D' and (resid 3 through 1230 or resid 1302 through 1303 or resid 1307 th \ rough 1311)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.700 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: 0.820 Extract box with map and model: 8.860 Check model and map are aligned: 0.940 Set scattering table: 0.530 Process input model: 182.430 Find NCS groups from input model: 3.770 Set up NCS constraints: 0.320 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: 0.020 Load rotamer database and sin/cos tables:12.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 211.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6721 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 : 0.013 0.196 39392 Z= 0.815 Angle : 1.240 15.056 52936 Z= 0.625 Chirality : 0.087 0.945 5672 Planarity : 0.007 0.106 6348 Dihedral : 19.000 179.931 16176 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.55 % Allowed : 14.49 % Favored : 84.96 % Rotamer: Outliers : 0.72 % Allowed : 3.68 % Favored : 95.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.38 % 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: -6.42 (0.08), residues: 4388 helix: -4.29 (0.05), residues: 2528 sheet: -5.37 (0.29), residues: 40 loop : -4.02 (0.11), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP C1042 HIS 0.013 0.003 HIS C 191 PHE 0.077 0.005 PHE C 858 TYR 0.037 0.004 TYR D 870 ARG 0.012 0.001 ARG D 14 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 788 time to evaluate : 4.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 942 ARG cc_start: 0.6534 (tmt-80) cc_final: 0.6302 (tmt-80) REVERT: A 1097 ASN cc_start: 0.7564 (m110) cc_final: 0.6962 (t0) REVERT: B 122 GLN cc_start: 0.3748 (pp30) cc_final: 0.3429 (tm-30) REVERT: B 942 ARG cc_start: 0.6596 (tmt-80) cc_final: 0.6303 (tmt-80) REVERT: C 122 GLN cc_start: 0.3887 (pp30) cc_final: 0.3605 (tm130) REVERT: D 122 GLN cc_start: 0.3878 (pp30) cc_final: 0.3503 (tm-30) REVERT: D 942 ARG cc_start: 0.6651 (tmt-80) cc_final: 0.6332 (tmt-80) outliers start: 28 outliers final: 4 residues processed: 804 average time/residue: 2.4910 time to fit residues: 2468.0666 Evaluate side-chains 455 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 451 time to evaluate : 4.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain D residue 527 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 371 optimal weight: 0.7980 chunk 333 optimal weight: 9.9990 chunk 185 optimal weight: 0.7980 chunk 113 optimal weight: 6.9990 chunk 224 optimal weight: 30.0000 chunk 178 optimal weight: 0.9990 chunk 344 optimal weight: 30.0000 chunk 133 optimal weight: 8.9990 chunk 209 optimal weight: 0.6980 chunk 256 optimal weight: 5.9990 chunk 399 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN A 102 HIS ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 HIS A 388 HIS A 404 ASN A 696 GLN A 948 ASN A 956 HIS A 999 ASN ** A1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 ASN ** B 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 363 HIS B 388 HIS B 404 ASN B 696 GLN B 948 ASN B 955 ASN B 956 HIS B 999 ASN ** B1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1167 GLN C 96 ASN C 102 HIS ** C 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 GLN C 363 HIS C 388 HIS C 404 ASN C 432 GLN C 684 ASN C 696 GLN C 948 ASN C 956 HIS C 999 ASN ** C1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 HIS D 96 ASN ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 331 GLN D 363 HIS D 388 HIS D 404 ASN D 696 GLN D 948 ASN D 956 HIS D 999 ASN ** D1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1167 GLN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6709 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 39392 Z= 0.227 Angle : 0.758 18.007 52936 Z= 0.383 Chirality : 0.099 1.758 5672 Planarity : 0.006 0.080 6348 Dihedral : 21.143 178.295 7500 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.36 % Allowed : 10.82 % Favored : 88.81 % Rotamer: Outliers : 1.71 % Allowed : 12.61 % Favored : 85.67 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -4.72 (0.10), residues: 4388 helix: -2.74 (0.08), residues: 2624 sheet: -5.43 (0.27), residues: 40 loop : -3.56 (0.13), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 758 HIS 0.008 0.001 HIS C1123 PHE 0.019 0.002 PHE C1118 TYR 0.017 0.002 TYR A 505 ARG 0.011 0.001 ARG C 264 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 514 time to evaluate : 4.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 MET cc_start: 0.3992 (mmt) cc_final: 0.3696 (mmm) REVERT: C 469 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7498 (tm) REVERT: C 1199 VAL cc_start: 0.8036 (t) cc_final: 0.7818 (t) REVERT: D 1097 ASN cc_start: 0.8114 (m110) cc_final: 0.7561 (t0) outliers start: 67 outliers final: 20 residues processed: 553 average time/residue: 2.3813 time to fit residues: 1641.8863 Evaluate side-chains 419 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 398 time to evaluate : 4.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 669 SER Chi-restraints excluded: chain B residue 1060 SER Chi-restraints excluded: chain C residue 460 GLU Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 669 SER Chi-restraints excluded: chain C residue 710 THR Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 929 THR Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 669 SER Chi-restraints excluded: chain D residue 741 MET Chi-restraints excluded: chain D residue 954 ASP Chi-restraints excluded: chain D residue 1060 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 222 optimal weight: 5.9990 chunk 124 optimal weight: 40.0000 chunk 332 optimal weight: 1.9990 chunk 272 optimal weight: 5.9990 chunk 110 optimal weight: 20.0000 chunk 400 optimal weight: 8.9990 chunk 432 optimal weight: 10.0000 chunk 356 optimal weight: 7.9990 chunk 396 optimal weight: 4.9990 chunk 136 optimal weight: 8.9990 chunk 321 optimal weight: 0.5980 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 GLN A 154 GLN A 538 ASN ** A1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1167 GLN B 27 HIS B 154 GLN C 538 ASN D 102 HIS D 154 GLN D 538 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 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 : 0.006 0.071 39392 Z= 0.350 Angle : 0.761 18.755 52936 Z= 0.382 Chirality : 0.101 1.791 5672 Planarity : 0.006 0.076 6348 Dihedral : 20.372 173.807 7498 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 19.11 Ramachandran Plot: Outliers : 0.30 % Allowed : 12.76 % Favored : 86.94 % Rotamer: Outliers : 2.53 % Allowed : 14.22 % Favored : 83.25 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.27 % 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: -4.10 (0.11), residues: 4388 helix: -2.22 (0.09), residues: 2596 sheet: -4.94 (0.27), residues: 88 loop : -3.26 (0.13), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 6 HIS 0.007 0.002 HIS A1123 PHE 0.029 0.003 PHE C 858 TYR 0.032 0.002 TYR C 870 ARG 0.007 0.001 ARG D 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 428 time to evaluate : 4.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 942 ARG cc_start: 0.7268 (tmt-80) cc_final: 0.6831 (tmt-80) REVERT: B 202 ILE cc_start: 0.8171 (mm) cc_final: 0.7834 (tt) REVERT: B 1207 MET cc_start: 0.7700 (mtp) cc_final: 0.7474 (mtp) REVERT: C 1124 GLU cc_start: 0.6312 (OUTLIER) cc_final: 0.6068 (pm20) REVERT: D 202 ILE cc_start: 0.8167 (mm) cc_final: 0.7813 (tt) outliers start: 99 outliers final: 43 residues processed: 500 average time/residue: 2.0680 time to fit residues: 1340.4009 Evaluate side-chains 414 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 370 time to evaluate : 4.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 GLN Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 953 TYR Chi-restraints excluded: chain A residue 954 ASP Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain A residue 1058 ASN Chi-restraints excluded: chain A residue 1060 SER Chi-restraints excluded: chain B residue 244 HIS Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 669 SER Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 953 TYR Chi-restraints excluded: chain B residue 954 ASP Chi-restraints excluded: chain B residue 1060 SER Chi-restraints excluded: chain B residue 1211 ILE Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain C residue 460 GLU Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 669 SER Chi-restraints excluded: chain C residue 710 THR Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 764 SER Chi-restraints excluded: chain C residue 929 THR Chi-restraints excluded: chain C residue 1048 VAL Chi-restraints excluded: chain C residue 1124 GLU Chi-restraints excluded: chain D residue 244 HIS Chi-restraints excluded: chain D residue 460 GLU Chi-restraints excluded: chain D residue 488 MET Chi-restraints excluded: chain D residue 669 SER Chi-restraints excluded: chain D residue 741 MET Chi-restraints excluded: chain D residue 764 SER Chi-restraints excluded: chain D residue 929 THR Chi-restraints excluded: chain D residue 954 ASP Chi-restraints excluded: chain D residue 1060 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 395 optimal weight: 2.9990 chunk 300 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 191 optimal weight: 3.9990 chunk 268 optimal weight: 8.9990 chunk 401 optimal weight: 1.9990 chunk 425 optimal weight: 0.9990 chunk 209 optimal weight: 4.9990 chunk 380 optimal weight: 0.9990 chunk 114 optimal weight: 30.0000 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 GLN B 154 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 39392 Z= 0.219 Angle : 0.678 19.209 52936 Z= 0.337 Chirality : 0.100 1.772 5672 Planarity : 0.005 0.071 6348 Dihedral : 19.239 173.299 7498 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.30 % Favored : 88.42 % Rotamer: Outliers : 2.30 % Allowed : 15.09 % Favored : 82.61 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.27 % 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: -3.40 (0.11), residues: 4388 helix: -1.59 (0.09), residues: 2544 sheet: -4.80 (0.32), residues: 80 loop : -3.06 (0.13), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 747 HIS 0.006 0.001 HIS C1123 PHE 0.020 0.002 PHE B 858 TYR 0.014 0.002 TYR A1122 ARG 0.004 0.000 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 409 time to evaluate : 4.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 942 ARG cc_start: 0.7218 (tmt-80) cc_final: 0.6852 (tmt-80) REVERT: B 202 ILE cc_start: 0.8210 (mm) cc_final: 0.7896 (tt) REVERT: B 1207 MET cc_start: 0.7733 (mtp) cc_final: 0.7464 (mtp) REVERT: C 127 GLU cc_start: 0.5105 (tp30) cc_final: 0.4872 (tm-30) REVERT: C 469 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7331 (tm) REVERT: D 202 ILE cc_start: 0.8250 (mm) cc_final: 0.7872 (tt) outliers start: 90 outliers final: 44 residues processed: 468 average time/residue: 2.2089 time to fit residues: 1335.5187 Evaluate side-chains 430 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 385 time to evaluate : 4.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 953 TYR Chi-restraints excluded: chain A residue 954 ASP Chi-restraints excluded: chain A residue 1058 ASN Chi-restraints excluded: chain A residue 1132 LEU Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 244 HIS Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 669 SER Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 953 TYR Chi-restraints excluded: chain B residue 954 ASP Chi-restraints excluded: chain B residue 1048 VAL Chi-restraints excluded: chain B residue 1060 SER Chi-restraints excluded: chain B residue 1132 LEU Chi-restraints excluded: chain B residue 1211 ILE Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 460 GLU Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 669 SER Chi-restraints excluded: chain C residue 710 THR Chi-restraints excluded: chain C residue 764 SER Chi-restraints excluded: chain C residue 906 MET Chi-restraints excluded: chain C residue 1132 LEU Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 244 HIS Chi-restraints excluded: chain D residue 460 GLU Chi-restraints excluded: chain D residue 669 SER Chi-restraints excluded: chain D residue 741 MET Chi-restraints excluded: chain D residue 764 SER Chi-restraints excluded: chain D residue 929 THR Chi-restraints excluded: chain D residue 954 ASP Chi-restraints excluded: chain D residue 1048 VAL Chi-restraints excluded: chain D residue 1060 SER Chi-restraints excluded: chain D residue 1132 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 354 optimal weight: 30.0000 chunk 241 optimal weight: 0.9980 chunk 6 optimal weight: 0.3980 chunk 316 optimal weight: 2.9990 chunk 175 optimal weight: 3.9990 chunk 362 optimal weight: 30.0000 chunk 293 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 217 optimal weight: 9.9990 chunk 381 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 GLN B 538 ASN C 154 GLN D 154 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 39392 Z= 0.237 Angle : 0.669 19.496 52936 Z= 0.331 Chirality : 0.101 1.785 5672 Planarity : 0.005 0.063 6348 Dihedral : 18.465 172.596 7498 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.18 % Allowed : 12.10 % Favored : 87.72 % Rotamer: Outliers : 2.04 % Allowed : 15.81 % Favored : 82.15 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.27 % 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: -3.05 (0.12), residues: 4388 helix: -1.36 (0.10), residues: 2596 sheet: -4.62 (0.36), residues: 80 loop : -2.85 (0.14), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 747 HIS 0.005 0.001 HIS A1123 PHE 0.018 0.002 PHE C 468 TYR 0.016 0.002 TYR A 870 ARG 0.006 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 400 time to evaluate : 4.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 GLU cc_start: 0.5098 (tp30) cc_final: 0.4886 (tm-30) REVERT: B 202 ILE cc_start: 0.8246 (mm) cc_final: 0.7902 (tt) REVERT: B 794 MET cc_start: 0.4633 (mmm) cc_final: 0.4412 (mmt) REVERT: C 127 GLU cc_start: 0.5097 (tp30) cc_final: 0.4885 (tm-30) REVERT: C 469 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7325 (tm) REVERT: D 202 ILE cc_start: 0.8248 (mm) cc_final: 0.7875 (tt) REVERT: D 1092 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8311 (mt) outliers start: 80 outliers final: 43 residues processed: 461 average time/residue: 2.1508 time to fit residues: 1261.5993 Evaluate side-chains 419 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 374 time to evaluate : 4.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 953 TYR Chi-restraints excluded: chain A residue 954 ASP Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 244 HIS Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 669 SER Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 953 TYR Chi-restraints excluded: chain B residue 954 ASP Chi-restraints excluded: chain B residue 969 ILE Chi-restraints excluded: chain B residue 1048 VAL Chi-restraints excluded: chain B residue 1060 SER Chi-restraints excluded: chain B residue 1132 LEU Chi-restraints excluded: chain B residue 1211 ILE Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 460 GLU Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 669 SER Chi-restraints excluded: chain C residue 710 THR Chi-restraints excluded: chain C residue 764 SER Chi-restraints excluded: chain C residue 906 MET Chi-restraints excluded: chain C residue 929 THR Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 244 HIS Chi-restraints excluded: chain D residue 460 GLU Chi-restraints excluded: chain D residue 488 MET Chi-restraints excluded: chain D residue 669 SER Chi-restraints excluded: chain D residue 741 MET Chi-restraints excluded: chain D residue 764 SER Chi-restraints excluded: chain D residue 929 THR Chi-restraints excluded: chain D residue 954 ASP Chi-restraints excluded: chain D residue 1048 VAL Chi-restraints excluded: chain D residue 1060 SER Chi-restraints excluded: chain D residue 1092 LEU Chi-restraints excluded: chain D residue 1132 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 143 optimal weight: 20.0000 chunk 383 optimal weight: 9.9990 chunk 84 optimal weight: 4.9990 chunk 249 optimal weight: 30.0000 chunk 104 optimal weight: 6.9990 chunk 425 optimal weight: 0.4980 chunk 353 optimal weight: 9.9990 chunk 197 optimal weight: 1.9990 chunk 35 optimal weight: 30.0000 chunk 140 optimal weight: 3.9990 chunk 223 optimal weight: 30.0000 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN ** A1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.4493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 39392 Z= 0.314 Angle : 0.699 19.689 52936 Z= 0.347 Chirality : 0.102 1.789 5672 Planarity : 0.005 0.086 6348 Dihedral : 18.279 158.292 7498 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 19.66 Ramachandran Plot: Outliers : 0.18 % Allowed : 12.37 % Favored : 87.44 % Rotamer: Outliers : 2.71 % Allowed : 15.91 % Favored : 81.38 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.12), residues: 4388 helix: -1.38 (0.10), residues: 2584 sheet: -5.39 (0.32), residues: 40 loop : -2.71 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A1111 HIS 0.007 0.001 HIS B1123 PHE 0.026 0.002 PHE B 468 TYR 0.022 0.002 TYR B 870 ARG 0.011 0.001 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 388 time to evaluate : 4.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 GLU cc_start: 0.5135 (tp30) cc_final: 0.4911 (tm-30) REVERT: A 268 LYS cc_start: 0.7306 (mptt) cc_final: 0.6976 (mttp) REVERT: A 942 ARG cc_start: 0.7323 (tmt-80) cc_final: 0.7116 (tmt-80) REVERT: B 123 LEU cc_start: 0.5117 (OUTLIER) cc_final: 0.4887 (pp) REVERT: B 202 ILE cc_start: 0.8307 (mm) cc_final: 0.7945 (tt) REVERT: B 1092 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8218 (mt) REVERT: C 942 ARG cc_start: 0.7186 (ttt-90) cc_final: 0.6824 (ttt-90) REVERT: C 1092 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8243 (mt) REVERT: D 202 ILE cc_start: 0.8286 (mm) cc_final: 0.7909 (tt) REVERT: D 241 LEU cc_start: 0.7643 (mp) cc_final: 0.7344 (mt) REVERT: D 1092 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8362 (mt) outliers start: 106 outliers final: 53 residues processed: 472 average time/residue: 2.1465 time to fit residues: 1292.9655 Evaluate side-chains 438 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 381 time to evaluate : 4.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 953 TYR Chi-restraints excluded: chain A residue 954 ASP Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain A residue 1058 ASN Chi-restraints excluded: chain A residue 1060 SER Chi-restraints excluded: chain A residue 1099 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 244 HIS Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 669 SER Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 775 GLU Chi-restraints excluded: chain B residue 954 ASP Chi-restraints excluded: chain B residue 969 ILE Chi-restraints excluded: chain B residue 1048 VAL Chi-restraints excluded: chain B residue 1060 SER Chi-restraints excluded: chain B residue 1092 LEU Chi-restraints excluded: chain B residue 1099 VAL Chi-restraints excluded: chain B residue 1132 LEU Chi-restraints excluded: chain B residue 1211 ILE Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain C residue 460 GLU Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 669 SER Chi-restraints excluded: chain C residue 710 THR Chi-restraints excluded: chain C residue 764 SER Chi-restraints excluded: chain C residue 906 MET Chi-restraints excluded: chain C residue 929 THR Chi-restraints excluded: chain C residue 954 ASP Chi-restraints excluded: chain C residue 1048 VAL Chi-restraints excluded: chain C residue 1092 LEU Chi-restraints excluded: chain C residue 1099 VAL Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 244 HIS Chi-restraints excluded: chain D residue 460 GLU Chi-restraints excluded: chain D residue 539 SER Chi-restraints excluded: chain D residue 669 SER Chi-restraints excluded: chain D residue 741 MET Chi-restraints excluded: chain D residue 764 SER Chi-restraints excluded: chain D residue 775 GLU Chi-restraints excluded: chain D residue 906 MET Chi-restraints excluded: chain D residue 929 THR Chi-restraints excluded: chain D residue 954 ASP Chi-restraints excluded: chain D residue 1048 VAL Chi-restraints excluded: chain D residue 1060 SER Chi-restraints excluded: chain D residue 1092 LEU Chi-restraints excluded: chain D residue 1099 VAL Chi-restraints excluded: chain D residue 1132 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 410 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 242 optimal weight: 30.0000 chunk 310 optimal weight: 0.3980 chunk 240 optimal weight: 10.0000 chunk 358 optimal weight: 7.9990 chunk 237 optimal weight: 1.9990 chunk 424 optimal weight: 0.9980 chunk 265 optimal weight: 6.9990 chunk 258 optimal weight: 20.0000 chunk 195 optimal weight: 2.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 ASN D 72 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 39392 Z= 0.215 Angle : 0.654 19.708 52936 Z= 0.323 Chirality : 0.100 1.771 5672 Planarity : 0.005 0.062 6348 Dihedral : 17.660 148.878 7498 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 18.49 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.76 % Favored : 88.06 % Rotamer: Outliers : 2.12 % Allowed : 17.24 % Favored : 80.64 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.12), residues: 4388 helix: -1.17 (0.10), residues: 2588 sheet: -5.41 (0.31), residues: 40 loop : -2.59 (0.14), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 747 HIS 0.009 0.001 HIS B1123 PHE 0.026 0.002 PHE A 894 TYR 0.014 0.001 TYR C1122 ARG 0.004 0.000 ARG A 942 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 391 time to evaluate : 4.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ARG cc_start: 0.5873 (OUTLIER) cc_final: 0.5463 (mmp80) REVERT: A 942 ARG cc_start: 0.7201 (tmt-80) cc_final: 0.6920 (ttt-90) REVERT: A 1092 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8094 (mt) REVERT: B 123 LEU cc_start: 0.5121 (OUTLIER) cc_final: 0.4861 (pp) REVERT: B 127 GLU cc_start: 0.4596 (tp30) cc_final: 0.4382 (tm-30) REVERT: B 202 ILE cc_start: 0.8300 (mm) cc_final: 0.7954 (tt) REVERT: B 241 LEU cc_start: 0.7635 (mp) cc_final: 0.7317 (mt) REVERT: B 906 MET cc_start: 0.7180 (OUTLIER) cc_final: 0.6241 (mtp) REVERT: C 127 GLU cc_start: 0.4819 (tp30) cc_final: 0.4598 (tm-30) REVERT: D 123 LEU cc_start: 0.5287 (OUTLIER) cc_final: 0.5061 (pp) REVERT: D 202 ILE cc_start: 0.8280 (mm) cc_final: 0.7913 (tt) REVERT: D 241 LEU cc_start: 0.7710 (mp) cc_final: 0.7392 (mt) REVERT: D 1092 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8329 (mt) REVERT: D 1213 GLU cc_start: 0.5455 (OUTLIER) cc_final: 0.4634 (pp20) outliers start: 83 outliers final: 49 residues processed: 456 average time/residue: 2.1569 time to fit residues: 1257.6141 Evaluate side-chains 431 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 375 time to evaluate : 4.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 953 TYR Chi-restraints excluded: chain A residue 954 ASP Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain A residue 1092 LEU Chi-restraints excluded: chain A residue 1132 LEU Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 244 HIS Chi-restraints excluded: chain B residue 669 SER Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 775 GLU Chi-restraints excluded: chain B residue 906 MET Chi-restraints excluded: chain B residue 954 ASP Chi-restraints excluded: chain B residue 969 ILE Chi-restraints excluded: chain B residue 1048 VAL Chi-restraints excluded: chain B residue 1060 SER Chi-restraints excluded: chain B residue 1132 LEU Chi-restraints excluded: chain B residue 1211 ILE Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 460 GLU Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 669 SER Chi-restraints excluded: chain C residue 710 THR Chi-restraints excluded: chain C residue 764 SER Chi-restraints excluded: chain C residue 906 MET Chi-restraints excluded: chain C residue 929 THR Chi-restraints excluded: chain C residue 954 ASP Chi-restraints excluded: chain C residue 1048 VAL Chi-restraints excluded: chain C residue 1132 LEU Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 244 HIS Chi-restraints excluded: chain D residue 460 GLU Chi-restraints excluded: chain D residue 669 SER Chi-restraints excluded: chain D residue 741 MET Chi-restraints excluded: chain D residue 764 SER Chi-restraints excluded: chain D residue 775 GLU Chi-restraints excluded: chain D residue 778 THR Chi-restraints excluded: chain D residue 906 MET Chi-restraints excluded: chain D residue 954 ASP Chi-restraints excluded: chain D residue 1060 SER Chi-restraints excluded: chain D residue 1092 LEU Chi-restraints excluded: chain D residue 1099 VAL Chi-restraints excluded: chain D residue 1132 LEU Chi-restraints excluded: chain D residue 1213 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 262 optimal weight: 9.9990 chunk 169 optimal weight: 20.0000 chunk 253 optimal weight: 40.0000 chunk 127 optimal weight: 20.0000 chunk 83 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 269 optimal weight: 6.9990 chunk 288 optimal weight: 7.9990 chunk 209 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 333 optimal weight: 0.8980 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 ASN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.4765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 39392 Z= 0.337 Angle : 0.703 19.830 52936 Z= 0.349 Chirality : 0.102 1.798 5672 Planarity : 0.005 0.066 6348 Dihedral : 17.859 151.734 7498 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 20.46 Ramachandran Plot: Outliers : 0.18 % Allowed : 12.28 % Favored : 87.53 % Rotamer: Outliers : 2.58 % Allowed : 17.34 % Favored : 80.08 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.12), residues: 4388 helix: -1.28 (0.10), residues: 2584 sheet: -4.35 (0.39), residues: 80 loop : -2.62 (0.14), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C1111 HIS 0.006 0.001 HIS A1025 PHE 0.025 0.002 PHE B 468 TYR 0.017 0.002 TYR C1122 ARG 0.004 0.000 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 386 time to evaluate : 4.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ARG cc_start: 0.6017 (OUTLIER) cc_final: 0.4891 (mmt90) REVERT: A 942 ARG cc_start: 0.7301 (tmt-80) cc_final: 0.6881 (tmt-80) REVERT: A 1092 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8127 (mt) REVERT: B 123 LEU cc_start: 0.5161 (OUTLIER) cc_final: 0.4917 (pp) REVERT: B 127 GLU cc_start: 0.4652 (tp30) cc_final: 0.4449 (tm-30) REVERT: B 202 ILE cc_start: 0.8336 (mm) cc_final: 0.7982 (tt) REVERT: B 241 LEU cc_start: 0.7677 (mp) cc_final: 0.7334 (mt) REVERT: B 465 MET cc_start: 0.6794 (mmm) cc_final: 0.6579 (mmm) REVERT: B 906 MET cc_start: 0.7227 (OUTLIER) cc_final: 0.6296 (mtp) REVERT: B 1092 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8233 (mt) REVERT: C 127 GLU cc_start: 0.4868 (tp30) cc_final: 0.4643 (tm-30) REVERT: C 197 ARG cc_start: 0.6018 (OUTLIER) cc_final: 0.4926 (mmt90) REVERT: C 1092 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8244 (mt) REVERT: D 123 LEU cc_start: 0.5295 (OUTLIER) cc_final: 0.5064 (pp) REVERT: D 202 ILE cc_start: 0.8332 (mm) cc_final: 0.7941 (tt) REVERT: D 241 LEU cc_start: 0.7744 (mp) cc_final: 0.7414 (mt) REVERT: D 1092 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8372 (mt) outliers start: 101 outliers final: 58 residues processed: 468 average time/residue: 2.1345 time to fit residues: 1281.4656 Evaluate side-chains 442 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 375 time to evaluate : 4.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 775 GLU Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain A residue 954 ASP Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain A residue 1060 SER Chi-restraints excluded: chain A residue 1092 LEU Chi-restraints excluded: chain A residue 1099 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 244 HIS Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 669 SER Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 906 MET Chi-restraints excluded: chain B residue 954 ASP Chi-restraints excluded: chain B residue 969 ILE Chi-restraints excluded: chain B residue 1048 VAL Chi-restraints excluded: chain B residue 1060 SER Chi-restraints excluded: chain B residue 1092 LEU Chi-restraints excluded: chain B residue 1099 VAL Chi-restraints excluded: chain B residue 1132 LEU Chi-restraints excluded: chain B residue 1211 ILE Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 460 GLU Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 669 SER Chi-restraints excluded: chain C residue 710 THR Chi-restraints excluded: chain C residue 764 SER Chi-restraints excluded: chain C residue 929 THR Chi-restraints excluded: chain C residue 954 ASP Chi-restraints excluded: chain C residue 1048 VAL Chi-restraints excluded: chain C residue 1092 LEU Chi-restraints excluded: chain C residue 1099 VAL Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 244 HIS Chi-restraints excluded: chain D residue 460 GLU Chi-restraints excluded: chain D residue 527 THR Chi-restraints excluded: chain D residue 539 SER Chi-restraints excluded: chain D residue 669 SER Chi-restraints excluded: chain D residue 741 MET Chi-restraints excluded: chain D residue 764 SER Chi-restraints excluded: chain D residue 778 THR Chi-restraints excluded: chain D residue 906 MET Chi-restraints excluded: chain D residue 929 THR Chi-restraints excluded: chain D residue 954 ASP Chi-restraints excluded: chain D residue 1048 VAL Chi-restraints excluded: chain D residue 1060 SER Chi-restraints excluded: chain D residue 1092 LEU Chi-restraints excluded: chain D residue 1099 VAL Chi-restraints excluded: chain D residue 1132 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 385 optimal weight: 4.9990 chunk 406 optimal weight: 0.9980 chunk 370 optimal weight: 10.0000 chunk 395 optimal weight: 0.6980 chunk 237 optimal weight: 20.0000 chunk 172 optimal weight: 7.9990 chunk 310 optimal weight: 1.9990 chunk 121 optimal weight: 20.0000 chunk 357 optimal weight: 0.9990 chunk 373 optimal weight: 5.9990 chunk 393 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN ** A1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 ASN C 461 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.4893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 39392 Z= 0.199 Angle : 0.649 19.861 52936 Z= 0.321 Chirality : 0.100 1.769 5672 Planarity : 0.005 0.061 6348 Dihedral : 17.155 149.822 7498 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 19.14 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.35 % Favored : 88.47 % Rotamer: Outliers : 1.99 % Allowed : 18.13 % Favored : 79.88 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.12), residues: 4388 helix: -1.02 (0.10), residues: 2572 sheet: -4.23 (0.40), residues: 80 loop : -2.46 (0.15), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 747 HIS 0.004 0.001 HIS B1123 PHE 0.021 0.002 PHE A 894 TYR 0.014 0.001 TYR C1122 ARG 0.005 0.000 ARG C 110 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 387 time to evaluate : 4.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 942 ARG cc_start: 0.7265 (tmt-80) cc_final: 0.6970 (ttt-90) REVERT: A 1092 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8098 (mt) REVERT: A 1213 GLU cc_start: 0.5588 (OUTLIER) cc_final: 0.4632 (pp20) REVERT: B 123 LEU cc_start: 0.5070 (OUTLIER) cc_final: 0.4831 (pp) REVERT: B 202 ILE cc_start: 0.8327 (mm) cc_final: 0.7977 (tt) REVERT: B 241 LEU cc_start: 0.7664 (mp) cc_final: 0.7337 (mt) REVERT: B 372 MET cc_start: 0.2938 (mmt) cc_final: 0.2672 (mmp) REVERT: B 906 MET cc_start: 0.7146 (OUTLIER) cc_final: 0.6235 (mtp) REVERT: B 1092 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8198 (mt) REVERT: B 1213 GLU cc_start: 0.5342 (OUTLIER) cc_final: 0.4446 (pp20) REVERT: C 127 GLU cc_start: 0.4911 (tp30) cc_final: 0.4667 (tm-30) REVERT: D 123 LEU cc_start: 0.5327 (OUTLIER) cc_final: 0.5083 (pp) REVERT: D 241 LEU cc_start: 0.7734 (mp) cc_final: 0.7419 (mt) REVERT: D 1213 GLU cc_start: 0.5477 (OUTLIER) cc_final: 0.4613 (pp20) outliers start: 78 outliers final: 46 residues processed: 447 average time/residue: 2.3428 time to fit residues: 1341.4045 Evaluate side-chains 418 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 364 time to evaluate : 4.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 775 GLU Chi-restraints excluded: chain A residue 954 ASP Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain A residue 1092 LEU Chi-restraints excluded: chain A residue 1132 LEU Chi-restraints excluded: chain A residue 1213 GLU Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 244 HIS Chi-restraints excluded: chain B residue 669 SER Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 906 MET Chi-restraints excluded: chain B residue 954 ASP Chi-restraints excluded: chain B residue 969 ILE Chi-restraints excluded: chain B residue 1048 VAL Chi-restraints excluded: chain B residue 1060 SER Chi-restraints excluded: chain B residue 1092 LEU Chi-restraints excluded: chain B residue 1132 LEU Chi-restraints excluded: chain B residue 1211 ILE Chi-restraints excluded: chain B residue 1213 GLU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain C residue 460 GLU Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 669 SER Chi-restraints excluded: chain C residue 680 LYS Chi-restraints excluded: chain C residue 710 THR Chi-restraints excluded: chain C residue 764 SER Chi-restraints excluded: chain C residue 929 THR Chi-restraints excluded: chain C residue 954 ASP Chi-restraints excluded: chain C residue 1048 VAL Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 244 HIS Chi-restraints excluded: chain D residue 460 GLU Chi-restraints excluded: chain D residue 539 SER Chi-restraints excluded: chain D residue 669 SER Chi-restraints excluded: chain D residue 741 MET Chi-restraints excluded: chain D residue 764 SER Chi-restraints excluded: chain D residue 954 ASP Chi-restraints excluded: chain D residue 1048 VAL Chi-restraints excluded: chain D residue 1060 SER Chi-restraints excluded: chain D residue 1132 LEU Chi-restraints excluded: chain D residue 1213 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 259 optimal weight: 9.9990 chunk 417 optimal weight: 3.9990 chunk 255 optimal weight: 30.0000 chunk 198 optimal weight: 2.9990 chunk 290 optimal weight: 5.9990 chunk 438 optimal weight: 7.9990 chunk 403 optimal weight: 2.9990 chunk 349 optimal weight: 20.0000 chunk 36 optimal weight: 30.0000 chunk 269 optimal weight: 0.9980 chunk 214 optimal weight: 9.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN ** A1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 ASN C1206 GLN D 461 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.4967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 39392 Z= 0.299 Angle : 0.684 19.914 52936 Z= 0.339 Chirality : 0.101 1.780 5672 Planarity : 0.005 0.063 6348 Dihedral : 17.224 150.274 7498 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 20.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 12.49 % Favored : 87.40 % Rotamer: Outliers : 1.84 % Allowed : 18.54 % Favored : 79.62 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.12), residues: 4388 helix: -1.12 (0.10), residues: 2592 sheet: -4.19 (0.41), residues: 80 loop : -2.51 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 207 HIS 0.005 0.001 HIS C 491 PHE 0.022 0.002 PHE A 894 TYR 0.016 0.002 TYR C1122 ARG 0.006 0.000 ARG B 110 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 384 time to evaluate : 5.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 ARG cc_start: 0.6159 (OUTLIER) cc_final: 0.5878 (ttm170) REVERT: A 241 LEU cc_start: 0.7686 (mp) cc_final: 0.7321 (mt) REVERT: A 942 ARG cc_start: 0.7285 (tmt-80) cc_final: 0.6778 (ttt-90) REVERT: A 1092 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8129 (mt) REVERT: A 1213 GLU cc_start: 0.5573 (OUTLIER) cc_final: 0.4601 (pp20) REVERT: B 123 LEU cc_start: 0.5149 (OUTLIER) cc_final: 0.4904 (pp) REVERT: B 202 ILE cc_start: 0.8352 (mm) cc_final: 0.7991 (tt) REVERT: B 241 LEU cc_start: 0.7696 (mp) cc_final: 0.7384 (mt) REVERT: B 372 MET cc_start: 0.2853 (mmt) cc_final: 0.2565 (mmp) REVERT: B 942 ARG cc_start: 0.7205 (tmt-80) cc_final: 0.6984 (ttt-90) REVERT: B 1092 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8231 (mt) REVERT: B 1213 GLU cc_start: 0.5383 (OUTLIER) cc_final: 0.4453 (pp20) REVERT: C 127 GLU cc_start: 0.4916 (tp30) cc_final: 0.4686 (tm-30) REVERT: D 123 LEU cc_start: 0.5359 (OUTLIER) cc_final: 0.5111 (pp) REVERT: D 202 ILE cc_start: 0.8331 (mm) cc_final: 0.7949 (tt) REVERT: D 241 LEU cc_start: 0.7742 (mp) cc_final: 0.7422 (mt) REVERT: D 1092 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8367 (mt) REVERT: D 1213 GLU cc_start: 0.5413 (OUTLIER) cc_final: 0.4573 (pp20) REVERT: D 1217 ARG cc_start: 0.6502 (tpp80) cc_final: 0.6251 (ttm-80) outliers start: 72 outliers final: 50 residues processed: 438 average time/residue: 2.1145 time to fit residues: 1181.0150 Evaluate side-chains 430 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 371 time to evaluate : 4.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 110 ARG Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 953 TYR Chi-restraints excluded: chain A residue 954 ASP Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain A residue 1092 LEU Chi-restraints excluded: chain A residue 1099 VAL Chi-restraints excluded: chain A residue 1132 LEU Chi-restraints excluded: chain A residue 1213 GLU Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 906 MET Chi-restraints excluded: chain B residue 954 ASP Chi-restraints excluded: chain B residue 969 ILE Chi-restraints excluded: chain B residue 1048 VAL Chi-restraints excluded: chain B residue 1060 SER Chi-restraints excluded: chain B residue 1092 LEU Chi-restraints excluded: chain B residue 1132 LEU Chi-restraints excluded: chain B residue 1211 ILE Chi-restraints excluded: chain B residue 1213 GLU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 460 GLU Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 669 SER Chi-restraints excluded: chain C residue 710 THR Chi-restraints excluded: chain C residue 764 SER Chi-restraints excluded: chain C residue 929 THR Chi-restraints excluded: chain C residue 954 ASP Chi-restraints excluded: chain C residue 1048 VAL Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 460 GLU Chi-restraints excluded: chain D residue 527 THR Chi-restraints excluded: chain D residue 539 SER Chi-restraints excluded: chain D residue 669 SER Chi-restraints excluded: chain D residue 741 MET Chi-restraints excluded: chain D residue 764 SER Chi-restraints excluded: chain D residue 778 THR Chi-restraints excluded: chain D residue 906 MET Chi-restraints excluded: chain D residue 954 ASP Chi-restraints excluded: chain D residue 1048 VAL Chi-restraints excluded: chain D residue 1060 SER Chi-restraints excluded: chain D residue 1092 LEU Chi-restraints excluded: chain D residue 1099 VAL Chi-restraints excluded: chain D residue 1132 LEU Chi-restraints excluded: chain D residue 1213 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 63.3316 > 50: distance: 122 - 159: 5.303 distance: 127 - 169: 4.789 distance: 138 - 186: 5.835 distance: 146 - 159: 4.884 distance: 147 - 205: 22.806 distance: 159 - 160: 4.026 distance: 159 - 164: 12.175 distance: 160 - 161: 4.590 distance: 160 - 163: 15.209 distance: 160 - 165: 7.147 distance: 161 - 162: 4.924 distance: 162 - 217: 17.255 distance: 163 - 166: 6.270 distance: 163 - 167: 5.647 distance: 163 - 168: 8.538 distance: 169 - 170: 4.616 distance: 169 - 177: 11.546 distance: 170 - 171: 3.725 distance: 170 - 173: 6.993 distance: 171 - 172: 4.979 distance: 171 - 186: 4.486 distance: 172 - 227: 3.998 distance: 173 - 174: 5.527 distance: 173 - 179: 4.785 distance: 173 - 180: 6.827 distance: 174 - 175: 8.905 distance: 174 - 181: 7.464 distance: 174 - 182: 6.452 distance: 175 - 176: 6.873 distance: 176 - 184: 3.341 distance: 186 - 187: 5.389 distance: 186 - 194: 7.682 distance: 187 - 188: 11.671 distance: 187 - 190: 8.231 distance: 188 - 189: 18.040 distance: 188 - 205: 23.080 distance: 189 - 246: 11.951 distance: 190 - 191: 5.889 distance: 190 - 196: 7.685 distance: 190 - 197: 9.402 distance: 191 - 192: 5.837 distance: 191 - 193: 8.147 distance: 191 - 198: 3.455 distance: 192 - 199: 3.840 distance: 192 - 200: 3.270 distance: 192 - 201: 3.696 distance: 193 - 202: 5.734 distance: 193 - 203: 4.185 distance: 193 - 204: 4.460 distance: 205 - 206: 18.669 distance: 205 - 213: 22.889 distance: 206 - 207: 5.825 distance: 206 - 209: 17.215 distance: 206 - 214: 21.713 distance: 207 - 208: 4.988 distance: 207 - 217: 7.785 distance: 209 - 210: 6.472 distance: 209 - 215: 4.252 distance: 209 - 216: 8.754 distance: 210 - 211: 26.118 distance: 210 - 212: 15.838 distance: 217 - 218: 5.524 distance: 217 - 222: 3.521 distance: 218 - 219: 5.626 distance: 218 - 221: 13.028 distance: 218 - 223: 5.416 distance: 219 - 220: 7.605 distance: 221 - 224: 5.594 distance: 221 - 225: 11.396 distance: 221 - 226: 7.761 distance: 228 - 229: 3.642 distance: 228 - 236: 5.326 distance: 229 - 230: 5.841 distance: 229 - 246: 6.901 distance: 231 - 232: 4.390 distance: 231 - 237: 10.442 distance: 231 - 238: 9.778 distance: 232 - 234: 3.124 distance: 233 - 240: 6.971 distance: 233 - 241: 4.979 distance: 233 - 242: 4.372 distance: 234 - 243: 7.140 distance: 234 - 244: 6.897 distance: 234 - 245: 5.852 distance: 246 - 253: 7.847 distance: 247 - 248: 8.010 distance: 247 - 250: 5.524 distance: 247 - 254: 5.761 distance: 248 - 249: 5.849 distance: 248 - 262: 7.748 distance: 250 - 251: 4.852 distance: 250 - 252: 4.745 distance: 250 - 255: 4.510 distance: 251 - 256: 5.077 distance: 251 - 257: 6.364 distance: 251 - 258: 6.975 distance: 252 - 259: 10.590 distance: 252 - 260: 8.020 distance: 252 - 261: 12.115 distance: 262 - 263: 7.910 distance: 262 - 270: 9.167 distance: 263 - 264: 11.776 distance: 263 - 266: 9.037 distance: 263 - 271: 15.216 distance: 264 - 265: 22.731 distance: 264 - 279: 24.495 distance: 266 - 267: 7.384 distance: 266 - 272: 13.612 distance: 266 - 273: 11.210 distance: 267 - 268: 3.486 distance: 267 - 274: 7.735 distance: 267 - 275: 4.346 distance: 268 - 269: 5.973 distance: 269 - 276: 7.269 distance: 269 - 277: 8.372 distance: 269 - 278: 7.516 distance: 279 - 280: 8.330 distance: 279 - 287: 20.023 distance: 280 - 281: 13.626 distance: 280 - 283: 11.073 distance: 280 - 288: 12.207 distance: 281 - 282: 12.456 distance: 281 - 291: 11.370 distance: 283 - 284: 9.459 distance: 283 - 289: 11.024 distance: 283 - 290: 9.920 distance: 284 - 285: 7.612 distance: 284 - 286: 4.543 distance: 291 - 292: 3.184 distance: 291 - 302: 8.664 distance: 292 - 295: 5.360 distance: 292 - 303: 3.041 distance: 295 - 304: 3.577 distance: 295 - 305: 3.241 distance: 296 - 297: 4.602 distance: 296 - 306: 8.382 distance: 296 - 307: 4.598 distance: 297 - 298: 3.108 distance: 298 - 310: 16.951 distance: 299 - 300: 5.707 distance: 299 - 301: 6.652 distance: 300 - 311: 5.159 distance: 301 - 313: 3.541