Starting phenix.real_space_refine on Mon Feb 19 14:03:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8si4_40498/02_2024/8si4_40498_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8si4_40498/02_2024/8si4_40498.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8si4_40498/02_2024/8si4_40498.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8si4_40498/02_2024/8si4_40498.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8si4_40498/02_2024/8si4_40498_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8si4_40498/02_2024/8si4_40498_neut_trim_updated.pdb" } resolution = 2.46 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= 0.009 sd= 0.059 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 52 5.49 5 S 240 5.16 5 C 25688 2.51 5 N 6008 2.21 5 O 7008 1.98 5 H 36148 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 197": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 525": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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 731": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 750": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 759": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 843": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 892": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 896": "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 975": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 1085": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 1198": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 197": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 525": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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 731": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 750": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 759": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 843": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 892": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 896": "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 975": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 1085": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 1100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 1198": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 197": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 525": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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 731": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 750": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 759": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 843": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 892": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 896": "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 975": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 1085": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 1100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 1198": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 197": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 525": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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 731": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 750": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 759": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 843": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 892": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 896": "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 975": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 1085": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 1100": "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-5238/modules/chem_data/mon_lib" Total number of atoms: 75145 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 17966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1105, 17966 Classifications: {'peptide': 1105} Link IDs: {'PTRANS': 44, 'TRANS': 1060} Chain breaks: 3 Chain: "B" Number of atoms: 17966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1105, 17966 Classifications: {'peptide': 1105} Link IDs: {'PTRANS': 44, 'TRANS': 1060} Chain breaks: 3 Chain: "C" Number of atoms: 17966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1105, 17966 Classifications: {'peptide': 1105} Link IDs: {'PTRANS': 44, 'TRANS': 1060} Chain breaks: 3 Chain: "D" Number of atoms: 17966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1105, 17966 Classifications: {'peptide': 1105} Link IDs: {'PTRANS': 44, 'TRANS': 1060} Chain breaks: 3 Chain: "A" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 762 Unusual residues: {' CA': 1, 'CLR': 1, 'DU0': 2, 'POV': 13} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "B" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 798 Unusual residues: {'CLR': 1, 'DU0': 3, 'POV': 13} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "C" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 724 Unusual residues: {'CLR': 1, 'DU0': 1, 'POV': 13} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "D" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 761 Unusual residues: {'CLR': 1, 'DU0': 2, 'POV': 13} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 59 Classifications: {'water': 59} Link IDs: {None: 58} Chain: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 59 Classifications: {'water': 59} Link IDs: {None: 58} Chain: "C" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 59 Classifications: {'water': 59} Link IDs: {None: 58} Chain: "D" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 59 Classifications: {'water': 59} Link IDs: {None: 58} Time building chain proxies: 24.66, per 1000 atoms: 0.33 Number of scatterers: 75145 At special positions: 0 Unit cell: (178.45, 178.45, 157.7, 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 52 15.00 O 7008 8.00 N 6008 7.00 C 25688 6.00 H 36148 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 16 " - pdb=" SG CYS A 44 " distance=2.03 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=2.03 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=2.03 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=2.03 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: 46.83 Conformation dependent library (CDL) restraints added in 5.1 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: 204 helices and 8 sheets defined 54.9% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.76 Creating SS restraints... Processing helix chain 'A' and resid 6 through 10 Processing helix chain 'A' and resid 32 through 36 Processing helix chain 'A' and resid 48 through 51 No H-bonds generated for 'chain 'A' and resid 48 through 51' Processing helix chain 'A' and resid 57 through 60 No H-bonds generated for 'chain 'A' and resid 57 through 60' Processing helix chain 'A' and resid 72 through 75 No H-bonds generated for 'chain 'A' and resid 72 through 75' Processing helix chain 'A' and resid 117 through 124 removed outlier: 3.633A pdb=" N LEU A 121 " --> pdb=" O PRO A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 166 removed outlier: 3.950A pdb=" N GLY A 157 " --> pdb=" O LYS A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 191 removed outlier: 3.632A pdb=" N LEU A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 No H-bonds generated for 'chain 'A' and resid 213 through 216' Processing helix chain 'A' and resid 262 through 268 Processing helix chain 'A' and resid 294 through 300 removed outlier: 3.677A pdb=" N VAL A 300 " --> pdb=" O VAL A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 330 removed outlier: 3.857A pdb=" N ALA A 326 " --> pdb=" O ALA A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 353 removed outlier: 3.827A pdb=" N ILE A 347 " --> pdb=" O GLU A 343 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N SER A 348 " --> pdb=" O PRO A 344 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR A 349 " --> pdb=" O ASP A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 372 Processing helix chain 'A' and resid 391 through 399 removed outlier: 3.516A pdb=" N LEU A 399 " --> pdb=" O ILE A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 417 removed outlier: 4.085A pdb=" N LEU A 413 " --> pdb=" O ASP A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 425 Processing helix chain 'A' and resid 438 through 449 removed outlier: 3.663A pdb=" N VAL A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 460 Processing helix chain 'A' and resid 471 through 478 Processing helix chain 'A' and resid 488 through 496 Processing helix chain 'A' and resid 510 through 519 Processing helix chain 'A' and resid 531 through 539 removed outlier: 3.641A pdb=" N ASN A 538 " --> pdb=" O ARG A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 631 removed outlier: 4.163A pdb=" N LEU A 625 " --> pdb=" O LEU A 622 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A 626 " --> pdb=" O ASN A 623 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE A 627 " --> pdb=" O GLU A 624 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA A 629 " --> pdb=" O LEU A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 643 removed outlier: 3.780A pdb=" N GLN A 643 " --> pdb=" O ARG A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 669 removed outlier: 4.036A pdb=" N LYS A 667 " --> pdb=" O ALA A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 700 Processing helix chain 'A' and resid 702 through 708 Processing helix chain 'A' and resid 721 through 727 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 737 through 748 Processing helix chain 'A' and resid 758 through 766 Processing helix chain 'A' and resid 768 through 773 Processing helix chain 'A' and resid 780 through 782 No H-bonds generated for 'chain 'A' and resid 780 through 782' Processing helix chain 'A' and resid 789 through 796 removed outlier: 3.733A pdb=" N THR A 795 " --> pdb=" O ALA A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 849 removed outlier: 3.540A pdb=" N PHE A 848 " --> pdb=" O LYS A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 875 removed outlier: 3.795A pdb=" N LEU A 861 " --> pdb=" O TRP A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 905 Processing helix chain 'A' and resid 912 through 921 removed outlier: 3.549A pdb=" N LYS A 917 " --> pdb=" O SER A 913 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A 918 " --> pdb=" O GLN A 914 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TRP A 919 " --> pdb=" O LYS A 915 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER A 921 " --> pdb=" O LYS A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 943 removed outlier: 3.572A pdb=" N PHE A 936 " --> pdb=" O ILE A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 954 No H-bonds generated for 'chain 'A' and resid 952 through 954' Processing helix chain 'A' and resid 956 through 982 removed outlier: 4.765A pdb=" N ILE A 970 " --> pdb=" O CYS A 966 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N PHE A 971 " --> pdb=" O LEU A 967 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TRP A 972 " --> pdb=" O ASN A 968 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU A 976 " --> pdb=" O TRP A 972 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU A 977 " --> pdb=" O TYR A 973 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASP A 978 " --> pdb=" O VAL A 974 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE A 979 " --> pdb=" O ARG A 975 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL A 982 " --> pdb=" O ASP A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 999 Processing helix chain 'A' and resid 1001 through 1022 Proline residue: A1017 - end of helix Processing helix chain 'A' and resid 1030 through 1034 Processing helix chain 'A' and resid 1038 through 1045 removed outlier: 3.883A pdb=" N ILE A1044 " --> pdb=" O PRO A1040 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N PHE A1045 " --> pdb=" O TYR A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1085 Proline residue: A1074 - end of helix removed outlier: 3.840A pdb=" N LEU A1081 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE A1082 " --> pdb=" O VAL A1079 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N TYR A1085 " --> pdb=" O PHE A1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 1087 through 1121 removed outlier: 5.079A pdb=" N ASN A1108 " --> pdb=" O LYS A1104 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ILE A1109 " --> pdb=" O ALA A1105 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N TYR A1116 " --> pdb=" O LYS A1112 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N HIS A1117 " --> pdb=" O TYR A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1134 through 1146 removed outlier: 4.593A pdb=" N CYS A1144 " --> pdb=" O SER A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1191 removed outlier: 3.715A pdb=" N LYS A1169 " --> pdb=" O GLU A1165 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS A1171 " --> pdb=" O GLN A1167 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE A1182 " --> pdb=" O VAL A1178 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP A1186 " --> pdb=" O PHE A1182 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER A1191 " --> pdb=" O ASP A1187 " (cutoff:3.500A) Processing helix chain 'A' and resid 1195 through 1228 removed outlier: 3.754A pdb=" N GLU A1205 " --> pdb=" O PHE A1201 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLN A1206 " --> pdb=" O GLU A1202 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ASN A1219 " --> pdb=" O GLY A1215 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER A1224 " --> pdb=" O TYR A1220 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN A1226 " --> pdb=" O LYS A1222 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 10 Processing helix chain 'B' and resid 32 through 36 Processing helix chain 'B' and resid 48 through 51 No H-bonds generated for 'chain 'B' and resid 48 through 51' Processing helix chain 'B' and resid 57 through 60 No H-bonds generated for 'chain 'B' and resid 57 through 60' Processing helix chain 'B' and resid 72 through 75 No H-bonds generated for 'chain 'B' and resid 72 through 75' Processing helix chain 'B' and resid 117 through 124 removed outlier: 3.632A pdb=" N LEU B 121 " --> pdb=" O PRO B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 166 removed outlier: 3.949A pdb=" N GLY B 157 " --> pdb=" O LYS B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 191 removed outlier: 3.632A pdb=" N LEU B 188 " --> pdb=" O VAL B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 216 No H-bonds generated for 'chain 'B' and resid 213 through 216' Processing helix chain 'B' and resid 262 through 268 Processing helix chain 'B' and resid 294 through 300 removed outlier: 3.676A pdb=" N VAL B 300 " --> pdb=" O VAL B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 330 removed outlier: 3.857A pdb=" N ALA B 326 " --> pdb=" O ALA B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 353 removed outlier: 3.827A pdb=" N ILE B 347 " --> pdb=" O GLU B 343 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N SER B 348 " --> pdb=" O PRO B 344 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR B 349 " --> pdb=" O ASP B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 372 Processing helix chain 'B' and resid 391 through 399 removed outlier: 3.516A pdb=" N LEU B 399 " --> pdb=" O ILE B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 417 removed outlier: 4.085A pdb=" N LEU B 413 " --> pdb=" O ASP B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 425 Processing helix chain 'B' and resid 438 through 449 removed outlier: 3.663A pdb=" N VAL B 448 " --> pdb=" O LEU B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 460 Processing helix chain 'B' and resid 471 through 478 Processing helix chain 'B' and resid 488 through 496 Processing helix chain 'B' and resid 510 through 519 Processing helix chain 'B' and resid 531 through 539 removed outlier: 3.641A pdb=" N ASN B 538 " --> pdb=" O ARG B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 631 removed outlier: 4.163A pdb=" N LEU B 625 " --> pdb=" O LEU B 622 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU B 626 " --> pdb=" O ASN B 623 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE B 627 " --> pdb=" O GLU B 624 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA B 629 " --> pdb=" O LEU B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 643 removed outlier: 3.780A pdb=" N GLN B 643 " --> pdb=" O ARG B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 669 removed outlier: 4.036A pdb=" N LYS B 667 " --> pdb=" O ALA B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 700 Processing helix chain 'B' and resid 702 through 708 Processing helix chain 'B' and resid 721 through 727 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 737 through 748 Processing helix chain 'B' and resid 758 through 766 Processing helix chain 'B' and resid 768 through 773 Processing helix chain 'B' and resid 780 through 782 No H-bonds generated for 'chain 'B' and resid 780 through 782' Processing helix chain 'B' and resid 789 through 796 removed outlier: 3.732A pdb=" N THR B 795 " --> pdb=" O ALA B 791 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 849 removed outlier: 3.541A pdb=" N PHE B 848 " --> pdb=" O LYS B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 852 through 875 removed outlier: 3.795A pdb=" N LEU B 861 " --> pdb=" O TRP B 857 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 905 Processing helix chain 'B' and resid 912 through 921 removed outlier: 3.549A pdb=" N LYS B 917 " --> pdb=" O SER B 913 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B 918 " --> pdb=" O GLN B 914 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TRP B 919 " --> pdb=" O LYS B 915 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER B 921 " --> pdb=" O LYS B 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 943 removed outlier: 3.573A pdb=" N PHE B 936 " --> pdb=" O ILE B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 952 through 954 No H-bonds generated for 'chain 'B' and resid 952 through 954' Processing helix chain 'B' and resid 956 through 982 removed outlier: 4.765A pdb=" N ILE B 970 " --> pdb=" O CYS B 966 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N PHE B 971 " --> pdb=" O LEU B 967 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TRP B 972 " --> pdb=" O ASN B 968 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU B 976 " --> pdb=" O TRP B 972 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU B 977 " --> pdb=" O TYR B 973 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASP B 978 " --> pdb=" O VAL B 974 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE B 979 " --> pdb=" O ARG B 975 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL B 982 " --> pdb=" O ASP B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 999 Processing helix chain 'B' and resid 1001 through 1022 Proline residue: B1017 - end of helix Processing helix chain 'B' and resid 1030 through 1034 Processing helix chain 'B' and resid 1038 through 1045 removed outlier: 3.883A pdb=" N ILE B1044 " --> pdb=" O PRO B1040 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE B1045 " --> pdb=" O TYR B1041 " (cutoff:3.500A) Processing helix chain 'B' and resid 1070 through 1085 Proline residue: B1074 - end of helix removed outlier: 3.839A pdb=" N LEU B1081 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE B1082 " --> pdb=" O VAL B1079 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N TYR B1085 " --> pdb=" O PHE B1082 " (cutoff:3.500A) Processing helix chain 'B' and resid 1087 through 1121 removed outlier: 5.080A pdb=" N ASN B1108 " --> pdb=" O LYS B1104 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE B1109 " --> pdb=" O ALA B1105 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N TYR B1116 " --> pdb=" O LYS B1112 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N HIS B1117 " --> pdb=" O TYR B1113 " (cutoff:3.500A) Processing helix chain 'B' and resid 1134 through 1146 removed outlier: 4.593A pdb=" N CYS B1144 " --> pdb=" O SER B1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 1164 through 1191 removed outlier: 3.715A pdb=" N LYS B1169 " --> pdb=" O GLU B1165 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS B1171 " --> pdb=" O GLN B1167 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE B1182 " --> pdb=" O VAL B1178 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP B1186 " --> pdb=" O PHE B1182 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER B1191 " --> pdb=" O ASP B1187 " (cutoff:3.500A) Processing helix chain 'B' and resid 1195 through 1228 removed outlier: 3.754A pdb=" N GLU B1205 " --> pdb=" O PHE B1201 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLN B1206 " --> pdb=" O GLU B1202 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ASN B1219 " --> pdb=" O GLY B1215 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER B1224 " --> pdb=" O TYR B1220 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN B1226 " --> pdb=" O LYS B1222 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 10 Processing helix chain 'C' and resid 32 through 36 Processing helix chain 'C' and resid 48 through 51 No H-bonds generated for 'chain 'C' and resid 48 through 51' Processing helix chain 'C' and resid 57 through 60 No H-bonds generated for 'chain 'C' and resid 57 through 60' Processing helix chain 'C' and resid 72 through 75 No H-bonds generated for 'chain 'C' and resid 72 through 75' Processing helix chain 'C' and resid 117 through 124 removed outlier: 3.632A pdb=" N LEU C 121 " --> pdb=" O PRO C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 166 removed outlier: 3.949A pdb=" N GLY C 157 " --> pdb=" O LYS C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 191 removed outlier: 3.632A pdb=" N LEU C 188 " --> pdb=" O VAL C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 216 No H-bonds generated for 'chain 'C' and resid 213 through 216' Processing helix chain 'C' and resid 262 through 268 Processing helix chain 'C' and resid 294 through 300 removed outlier: 3.676A pdb=" N VAL C 300 " --> pdb=" O VAL C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 330 removed outlier: 3.856A pdb=" N ALA C 326 " --> pdb=" O ALA C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 353 removed outlier: 3.826A pdb=" N ILE C 347 " --> pdb=" O GLU C 343 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N SER C 348 " --> pdb=" O PRO C 344 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR C 349 " --> pdb=" O ASP C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 372 Processing helix chain 'C' and resid 391 through 399 removed outlier: 3.517A pdb=" N LEU C 399 " --> pdb=" O ILE C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 417 removed outlier: 4.085A pdb=" N LEU C 413 " --> pdb=" O ASP C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 425 Processing helix chain 'C' and resid 438 through 449 removed outlier: 3.664A pdb=" N VAL C 448 " --> pdb=" O LEU C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 460 Processing helix chain 'C' and resid 471 through 478 Processing helix chain 'C' and resid 488 through 496 Processing helix chain 'C' and resid 510 through 519 Processing helix chain 'C' and resid 531 through 539 removed outlier: 3.641A pdb=" N ASN C 538 " --> pdb=" O ARG C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 621 through 631 removed outlier: 4.163A pdb=" N LEU C 625 " --> pdb=" O LEU C 622 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU C 626 " --> pdb=" O ASN C 623 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE C 627 " --> pdb=" O GLU C 624 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA C 629 " --> pdb=" O LEU C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 643 removed outlier: 3.779A pdb=" N GLN C 643 " --> pdb=" O ARG C 639 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 669 removed outlier: 4.036A pdb=" N LYS C 667 " --> pdb=" O ALA C 663 " (cutoff:3.500A) Processing helix chain 'C' and resid 677 through 700 Processing helix chain 'C' and resid 702 through 708 Processing helix chain 'C' and resid 721 through 727 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 737 through 748 Processing helix chain 'C' and resid 758 through 766 Processing helix chain 'C' and resid 768 through 773 Processing helix chain 'C' and resid 780 through 782 No H-bonds generated for 'chain 'C' and resid 780 through 782' Processing helix chain 'C' and resid 789 through 796 removed outlier: 3.733A pdb=" N THR C 795 " --> pdb=" O ALA C 791 " (cutoff:3.500A) Processing helix chain 'C' and resid 841 through 849 removed outlier: 3.540A pdb=" N PHE C 848 " --> pdb=" O LYS C 844 " (cutoff:3.500A) Processing helix chain 'C' and resid 852 through 875 removed outlier: 3.795A pdb=" N LEU C 861 " --> pdb=" O TRP C 857 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 905 Processing helix chain 'C' and resid 912 through 921 removed outlier: 3.549A pdb=" N LYS C 917 " --> pdb=" O SER C 913 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL C 918 " --> pdb=" O GLN C 914 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TRP C 919 " --> pdb=" O LYS C 915 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER C 921 " --> pdb=" O LYS C 917 " (cutoff:3.500A) Processing helix chain 'C' and resid 923 through 943 removed outlier: 3.573A pdb=" N PHE C 936 " --> pdb=" O ILE C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 952 through 954 No H-bonds generated for 'chain 'C' and resid 952 through 954' Processing helix chain 'C' and resid 956 through 982 removed outlier: 4.765A pdb=" N ILE C 970 " --> pdb=" O CYS C 966 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N PHE C 971 " --> pdb=" O LEU C 967 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TRP C 972 " --> pdb=" O ASN C 968 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU C 976 " --> pdb=" O TRP C 972 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU C 977 " --> pdb=" O TYR C 973 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASP C 978 " --> pdb=" O VAL C 974 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE C 979 " --> pdb=" O ARG C 975 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL C 982 " --> pdb=" O ASP C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 987 through 999 Processing helix chain 'C' and resid 1001 through 1022 Proline residue: C1017 - end of helix Processing helix chain 'C' and resid 1030 through 1034 Processing helix chain 'C' and resid 1038 through 1045 removed outlier: 3.883A pdb=" N ILE C1044 " --> pdb=" O PRO C1040 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE C1045 " --> pdb=" O TYR C1041 " (cutoff:3.500A) Processing helix chain 'C' and resid 1070 through 1085 Proline residue: C1074 - end of helix removed outlier: 3.840A pdb=" N LEU C1081 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE C1082 " --> pdb=" O VAL C1079 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N TYR C1085 " --> pdb=" O PHE C1082 " (cutoff:3.500A) Processing helix chain 'C' and resid 1087 through 1121 removed outlier: 5.080A pdb=" N ASN C1108 " --> pdb=" O LYS C1104 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ILE C1109 " --> pdb=" O ALA C1105 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N TYR C1116 " --> pdb=" O LYS C1112 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N HIS C1117 " --> pdb=" O TYR C1113 " (cutoff:3.500A) Processing helix chain 'C' and resid 1134 through 1146 removed outlier: 4.593A pdb=" N CYS C1144 " --> pdb=" O SER C1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 1164 through 1191 removed outlier: 3.715A pdb=" N LYS C1169 " --> pdb=" O GLU C1165 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS C1171 " --> pdb=" O GLN C1167 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE C1182 " --> pdb=" O VAL C1178 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP C1186 " --> pdb=" O PHE C1182 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER C1191 " --> pdb=" O ASP C1187 " (cutoff:3.500A) Processing helix chain 'C' and resid 1195 through 1228 removed outlier: 3.754A pdb=" N GLU C1205 " --> pdb=" O PHE C1201 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLN C1206 " --> pdb=" O GLU C1202 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASN C1219 " --> pdb=" O GLY C1215 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER C1224 " --> pdb=" O TYR C1220 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN C1226 " --> pdb=" O LYS C1222 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 10 Processing helix chain 'D' and resid 32 through 36 Processing helix chain 'D' and resid 48 through 51 No H-bonds generated for 'chain 'D' and resid 48 through 51' Processing helix chain 'D' and resid 57 through 60 No H-bonds generated for 'chain 'D' and resid 57 through 60' Processing helix chain 'D' and resid 72 through 75 No H-bonds generated for 'chain 'D' and resid 72 through 75' Processing helix chain 'D' and resid 117 through 124 removed outlier: 3.632A pdb=" N LEU D 121 " --> pdb=" O PRO D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 166 removed outlier: 3.950A pdb=" N GLY D 157 " --> pdb=" O LYS D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 191 removed outlier: 3.632A pdb=" N LEU D 188 " --> pdb=" O VAL D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 216 No H-bonds generated for 'chain 'D' and resid 213 through 216' Processing helix chain 'D' and resid 262 through 268 Processing helix chain 'D' and resid 294 through 300 removed outlier: 3.676A pdb=" N VAL D 300 " --> pdb=" O VAL D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 330 removed outlier: 3.857A pdb=" N ALA D 326 " --> pdb=" O ALA D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 353 removed outlier: 3.827A pdb=" N ILE D 347 " --> pdb=" O GLU D 343 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N SER D 348 " --> pdb=" O PRO D 344 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR D 349 " --> pdb=" O ASP D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 372 Processing helix chain 'D' and resid 391 through 399 removed outlier: 3.517A pdb=" N LEU D 399 " --> pdb=" O ILE D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 417 removed outlier: 4.085A pdb=" N LEU D 413 " --> pdb=" O ASP D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 425 Processing helix chain 'D' and resid 438 through 449 removed outlier: 3.664A pdb=" N VAL D 448 " --> pdb=" O LEU D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 460 Processing helix chain 'D' and resid 471 through 478 Processing helix chain 'D' and resid 488 through 496 Processing helix chain 'D' and resid 510 through 519 Processing helix chain 'D' and resid 531 through 539 removed outlier: 3.642A pdb=" N ASN D 538 " --> pdb=" O ARG D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 621 through 631 removed outlier: 4.163A pdb=" N LEU D 625 " --> pdb=" O LEU D 622 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU D 626 " --> pdb=" O ASN D 623 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE D 627 " --> pdb=" O GLU D 624 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA D 629 " --> pdb=" O LEU D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 643 removed outlier: 3.779A pdb=" N GLN D 643 " --> pdb=" O ARG D 639 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 669 removed outlier: 4.036A pdb=" N LYS D 667 " --> pdb=" O ALA D 663 " (cutoff:3.500A) Processing helix chain 'D' and resid 677 through 700 Processing helix chain 'D' and resid 702 through 708 Processing helix chain 'D' and resid 721 through 727 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 737 through 748 Processing helix chain 'D' and resid 758 through 766 Processing helix chain 'D' and resid 768 through 773 Processing helix chain 'D' and resid 780 through 782 No H-bonds generated for 'chain 'D' and resid 780 through 782' Processing helix chain 'D' and resid 789 through 796 removed outlier: 3.733A pdb=" N THR D 795 " --> pdb=" O ALA D 791 " (cutoff:3.500A) Processing helix chain 'D' and resid 841 through 849 removed outlier: 3.540A pdb=" N PHE D 848 " --> pdb=" O LYS D 844 " (cutoff:3.500A) Processing helix chain 'D' and resid 852 through 875 removed outlier: 3.796A pdb=" N LEU D 861 " --> pdb=" O TRP D 857 " (cutoff:3.500A) Processing helix chain 'D' and resid 884 through 905 Processing helix chain 'D' and resid 912 through 921 removed outlier: 3.549A pdb=" N LYS D 917 " --> pdb=" O SER D 913 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL D 918 " --> pdb=" O GLN D 914 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TRP D 919 " --> pdb=" O LYS D 915 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER D 921 " --> pdb=" O LYS D 917 " (cutoff:3.500A) Processing helix chain 'D' and resid 923 through 943 removed outlier: 3.573A pdb=" N PHE D 936 " --> pdb=" O ILE D 932 " (cutoff:3.500A) Processing helix chain 'D' and resid 952 through 954 No H-bonds generated for 'chain 'D' and resid 952 through 954' Processing helix chain 'D' and resid 956 through 982 removed outlier: 4.765A pdb=" N ILE D 970 " --> pdb=" O CYS D 966 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N PHE D 971 " --> pdb=" O LEU D 967 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TRP D 972 " --> pdb=" O ASN D 968 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU D 976 " --> pdb=" O TRP D 972 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU D 977 " --> pdb=" O TYR D 973 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASP D 978 " --> pdb=" O VAL D 974 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE D 979 " --> pdb=" O ARG D 975 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL D 982 " --> pdb=" O ASP D 978 " (cutoff:3.500A) Processing helix chain 'D' and resid 987 through 999 Processing helix chain 'D' and resid 1001 through 1022 Proline residue: D1017 - end of helix Processing helix chain 'D' and resid 1030 through 1034 Processing helix chain 'D' and resid 1038 through 1045 removed outlier: 3.883A pdb=" N ILE D1044 " --> pdb=" O PRO D1040 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE D1045 " --> pdb=" O TYR D1041 " (cutoff:3.500A) Processing helix chain 'D' and resid 1070 through 1085 Proline residue: D1074 - end of helix removed outlier: 3.839A pdb=" N LEU D1081 " --> pdb=" O ALA D1078 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE D1082 " --> pdb=" O VAL D1079 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N TYR D1085 " --> pdb=" O PHE D1082 " (cutoff:3.500A) Processing helix chain 'D' and resid 1087 through 1121 removed outlier: 5.079A pdb=" N ASN D1108 " --> pdb=" O LYS D1104 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE D1109 " --> pdb=" O ALA D1105 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N TYR D1116 " --> pdb=" O LYS D1112 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N HIS D1117 " --> pdb=" O TYR D1113 " (cutoff:3.500A) Processing helix chain 'D' and resid 1134 through 1146 removed outlier: 4.593A pdb=" N CYS D1144 " --> pdb=" O SER D1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 1164 through 1191 removed outlier: 3.715A pdb=" N LYS D1169 " --> pdb=" O GLU D1165 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS D1171 " --> pdb=" O GLN D1167 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE D1182 " --> pdb=" O VAL D1178 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP D1186 " --> pdb=" O PHE D1182 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER D1191 " --> pdb=" O ASP D1187 " (cutoff:3.500A) Processing helix chain 'D' and resid 1195 through 1228 removed outlier: 3.754A pdb=" N GLU D1205 " --> pdb=" O PHE D1201 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLN D1206 " --> pdb=" O GLU D1202 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ASN D1219 " --> pdb=" O GLY D1215 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER D1224 " --> pdb=" O TYR D1220 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN D1226 " --> pdb=" O LYS D1222 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 107 through 111 Processing sheet with id= B, first strand: chain 'A' and resid 312 through 314 removed outlier: 8.456A pdb=" N VAL A 313 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ALA A 287 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N VAL A 136 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N LEU A 288 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N SER A 138 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N TRP A 170 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N VAL A 139 " --> pdb=" O TRP A 170 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU A 172 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N CYS A 200 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N THR A 173 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE A 202 " --> pdb=" O THR A 173 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 107 through 111 Processing sheet with id= D, first strand: chain 'B' and resid 312 through 314 removed outlier: 8.456A pdb=" N VAL B 313 " --> pdb=" O VAL B 285 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ALA B 287 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL B 136 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N LEU B 288 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N SER B 138 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N TRP B 170 " --> pdb=" O ILE B 137 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N VAL B 139 " --> pdb=" O TRP B 170 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU B 172 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N CYS B 200 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N THR B 173 " --> pdb=" O CYS B 200 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE B 202 " --> pdb=" O THR B 173 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'C' and resid 107 through 111 Processing sheet with id= F, first strand: chain 'C' and resid 312 through 314 removed outlier: 8.456A pdb=" N VAL C 313 " --> pdb=" O VAL C 285 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ALA C 287 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N VAL C 136 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N LEU C 288 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N SER C 138 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N TRP C 170 " --> pdb=" O ILE C 137 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N VAL C 139 " --> pdb=" O TRP C 170 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU C 172 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N CYS C 200 " --> pdb=" O ILE C 171 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N THR C 173 " --> pdb=" O CYS C 200 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE C 202 " --> pdb=" O THR C 173 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'D' and resid 107 through 111 Processing sheet with id= H, first strand: chain 'D' and resid 312 through 314 removed outlier: 8.456A pdb=" N VAL D 313 " --> pdb=" O VAL D 285 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ALA D 287 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N VAL D 136 " --> pdb=" O VAL D 286 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N LEU D 288 " --> pdb=" O VAL D 136 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N SER D 138 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N TRP D 170 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N VAL D 139 " --> pdb=" O TRP D 170 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU D 172 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N CYS D 200 " --> pdb=" O ILE D 171 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N THR D 173 " --> pdb=" O CYS D 200 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE D 202 " --> pdb=" O THR D 173 " (cutoff:3.500A) No H-bonds generated for sheet with id= H 1412 hydrogen bonds defined for protein. 4044 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: 24.87 Time building geometry restraints manager: 49.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.03: 36069 1.03 - 1.24: 4615 1.24 - 1.44: 11591 1.44 - 1.65: 23105 1.65 - 1.86: 392 Bond restraints: 75772 Sorted by residual: bond pdb="C217 POV A1301 " pdb="C218 POV A1301 " ideal model delta sigma weight residual 1.522 1.402 0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb="C217 POV C1304 " pdb="C218 POV C1304 " ideal model delta sigma weight residual 1.522 1.404 0.118 2.00e-02 2.50e+03 3.48e+01 bond pdb="C217 POV D1306 " pdb="C218 POV D1306 " ideal model delta sigma weight residual 1.522 1.405 0.117 2.00e-02 2.50e+03 3.40e+01 bond pdb="C217 POV B1304 " pdb="C218 POV B1304 " ideal model delta sigma weight residual 1.522 1.408 0.114 2.00e-02 2.50e+03 3.27e+01 bond pdb=" CG LEU A1081 " pdb=" CD1 LEU A1081 " ideal model delta sigma weight residual 1.521 1.368 0.153 3.30e-02 9.18e+02 2.16e+01 ... (remaining 75767 not shown) Histogram of bond angle deviations from ideal: 59.36 - 76.70: 8 76.70 - 94.03: 8 94.03 - 111.36: 79919 111.36 - 128.70: 55072 128.70 - 146.03: 425 Bond angle restraints: 135432 Sorted by residual: angle pdb=" C GLN D 305 " pdb=" N GLU D 306 " pdb=" H GLU D 306 " ideal model delta sigma weight residual 123.97 66.19 57.78 3.00e+00 1.11e-01 3.71e+02 angle pdb=" CA GLU D 306 " pdb=" N GLU D 306 " pdb=" H GLU D 306 " ideal model delta sigma weight residual 113.67 59.36 54.31 3.00e+00 1.11e-01 3.28e+02 angle pdb=" C GLU D 85 " pdb=" CA GLU D 85 " pdb=" HA GLU D 85 " ideal model delta sigma weight residual 109.00 69.05 39.95 3.00e+00 1.11e-01 1.77e+02 angle pdb=" N GLU D 85 " pdb=" CA GLU D 85 " pdb=" HA GLU D 85 " ideal model delta sigma weight residual 110.00 73.58 36.42 3.00e+00 1.11e-01 1.47e+02 angle pdb=" CG1 VAL B 237 " pdb=" CB VAL B 237 " pdb=" HB VAL B 237 " ideal model delta sigma weight residual 108.00 72.83 35.17 3.00e+00 1.11e-01 1.37e+02 ... (remaining 135427 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.91: 35740 34.91 - 69.83: 1292 69.83 - 104.74: 167 104.74 - 139.66: 51 139.66 - 174.57: 18 Dihedral angle restraints: 37268 sinusoidal: 21560 harmonic: 15708 Sorted by residual: dihedral pdb=" CA SER D 307 " pdb=" C SER D 307 " pdb=" N PRO D 308 " pdb=" CA PRO D 308 " ideal model delta harmonic sigma weight residual -180.00 -130.58 -49.42 0 5.00e+00 4.00e-02 9.77e+01 dihedral pdb=" CA SER A 307 " pdb=" C SER A 307 " pdb=" N PRO A 308 " pdb=" CA PRO A 308 " ideal model delta harmonic sigma weight residual -180.00 -130.60 -49.40 0 5.00e+00 4.00e-02 9.76e+01 dihedral pdb=" CA SER B 307 " pdb=" C SER B 307 " pdb=" N PRO B 308 " pdb=" CA PRO B 308 " ideal model delta harmonic sigma weight residual -180.00 -130.62 -49.38 0 5.00e+00 4.00e-02 9.75e+01 ... (remaining 37265 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.290: 5716 0.290 - 0.581: 0 0.581 - 0.871: 0 0.871 - 1.162: 0 1.162 - 1.452: 4 Chirality restraints: 5720 Sorted by residual: chirality pdb=" C2 POV A1309 " pdb=" C1 POV A1309 " pdb=" C3 POV A1309 " pdb=" O21 POV A1309 " both_signs ideal model delta sigma weight residual False 2.43 0.98 1.45 2.00e-01 2.50e+01 5.27e+01 chirality pdb=" C2 POV C1312 " pdb=" C1 POV C1312 " pdb=" C3 POV C1312 " pdb=" O21 POV C1312 " both_signs ideal model delta sigma weight residual False 2.43 0.98 1.45 2.00e-01 2.50e+01 5.25e+01 chirality pdb=" C2 POV D1314 " pdb=" C1 POV D1314 " pdb=" C3 POV D1314 " pdb=" O21 POV D1314 " both_signs ideal model delta sigma weight residual False 2.43 1.00 1.42 2.00e-01 2.50e+01 5.07e+01 ... (remaining 5717 not shown) Planarity restraints: 10580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN D1077 " 0.114 2.00e-02 2.50e+03 1.39e-01 2.90e+02 pdb=" CD GLN D1077 " 0.036 2.00e-02 2.50e+03 pdb=" OE1 GLN D1077 " -0.137 2.00e-02 2.50e+03 pdb=" NE2 GLN D1077 " 0.014 2.00e-02 2.50e+03 pdb="HE21 GLN D1077 " -0.216 2.00e-02 2.50e+03 pdb="HE22 GLN D1077 " 0.190 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A1077 " -0.113 2.00e-02 2.50e+03 1.38e-01 2.85e+02 pdb=" CD GLN A1077 " -0.036 2.00e-02 2.50e+03 pdb=" OE1 GLN A1077 " 0.136 2.00e-02 2.50e+03 pdb=" NE2 GLN A1077 " -0.014 2.00e-02 2.50e+03 pdb="HE21 GLN A1077 " 0.214 2.00e-02 2.50e+03 pdb="HE22 GLN A1077 " -0.188 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C1077 " 0.108 2.00e-02 2.50e+03 1.33e-01 2.66e+02 pdb=" CD GLN C1077 " 0.036 2.00e-02 2.50e+03 pdb=" OE1 GLN C1077 " -0.132 2.00e-02 2.50e+03 pdb=" NE2 GLN C1077 " 0.014 2.00e-02 2.50e+03 pdb="HE21 GLN C1077 " -0.207 2.00e-02 2.50e+03 pdb="HE22 GLN C1077 " 0.181 2.00e-02 2.50e+03 ... (remaining 10577 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.11: 1474 2.11 - 2.73: 130620 2.73 - 3.35: 214671 3.35 - 3.98: 282291 3.98 - 4.60: 444199 Nonbonded interactions: 1073255 Sorted by model distance: nonbonded pdb=" H GLU D 306 " pdb=" HA GLU D 306 " model vdw 1.487 1.816 nonbonded pdb=" H GLU D 85 " pdb=" HA GLU D 85 " model vdw 1.577 1.816 nonbonded pdb=" HH TYR D 923 " pdb=" O1 CLR D1309 " model vdw 1.634 1.850 nonbonded pdb=" HH TYR B 923 " pdb=" O1 CLR B1307 " model vdw 1.635 1.850 nonbonded pdb=" O GLY B 292 " pdb=" HE ARG B 320 " model vdw 1.636 1.850 ... (remaining 1073250 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 1301 or resid 1303 or (resid 1305 \ and (name N or name C1 or name C11 or name C12 or name C13 or name C14 or name C \ 15 or name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or nam \ e C26 or name C27 or name C28 or name C29 or name C3 or name C31 or name C32 or \ name C33 or name C34 or name C35 or name O11 or name O12 or name O13 or name O14 \ or name O21 or name O22 or name O31 or name O32 or name P or name C210 or name \ C211 or name C212)) or resid 1306 or resid 1308 or resid 1310 or resid 1312)) selection = (chain 'B' and (resid 3 through 1230 or resid 1301 or resid 1303 or resid 1305 t \ hrough 1306 or resid 1308 or resid 1310 or resid 1312)) selection = (chain 'C' and (resid 3 through 1230 or resid 1301 or resid 1303 or resid 1305 t \ hrough 1306 or resid 1308 or resid 1310 or resid 1312)) selection = (chain 'D' and (resid 3 through 1230 or resid 1301 or resid 1303 or (resid 1305 \ and (name N or name C1 or name C11 or name C12 or name C13 or name C14 or name C \ 15 or name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or nam \ e C26 or name C27 or name C28 or name C29 or name C3 or name C31 or name C32 or \ name C33 or name C34 or name C35 or name O11 or name O12 or name O13 or name O14 \ or name O21 or name O22 or name O31 or name O32 or name P or name C210 or name \ C211 or name C212)) or resid 1306 or resid 1308 or resid 1310 or resid 1312)) } 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: 1.020 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: 0.870 Extract box with map and model: 8.430 Check model and map are aligned: 0.820 Set scattering table: 0.520 Process input model: 179.410 Find NCS groups from input model: 3.510 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:12.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 207.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 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 : 0.014 0.153 39624 Z= 0.871 Angle : 1.269 18.359 53272 Z= 0.664 Chirality : 0.074 1.452 5720 Planarity : 0.008 0.098 6352 Dihedral : 19.133 174.574 16636 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.73 % Allowed : 11.39 % Favored : 87.88 % Rotamer: Outliers : 0.82 % Allowed : 3.78 % Favored : 95.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.26 % 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: -5.18 (0.10), residues: 4388 helix: -3.16 (0.07), residues: 2568 sheet: -5.40 (0.20), residues: 200 loop : -3.35 (0.13), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.004 TRP A1042 HIS 0.018 0.003 HIS A 242 PHE 0.071 0.004 PHE D 858 TYR 0.052 0.004 TYR C 870 ARG 0.012 0.001 ARG C 634 *********************** 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 654 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 622 time to evaluate : 4.178 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: A 506 LYS cc_start: 0.5687 (tppt) cc_final: 0.5457 (tttm) REVERT: A 674 ASP cc_start: 0.4504 (t0) cc_final: 0.2999 (p0) REVERT: A 1026 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7209 (mm-30) REVERT: A 1178 VAL cc_start: 0.8009 (t) cc_final: 0.7791 (t) REVERT: B 506 LYS cc_start: 0.6013 (tppt) cc_final: 0.5564 (tttp) REVERT: B 674 ASP cc_start: 0.4452 (t0) cc_final: 0.2659 (p0) REVERT: B 1026 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7204 (mm-30) REVERT: C 145 LYS cc_start: 0.6097 (mtmt) cc_final: 0.5885 (tptp) REVERT: C 506 LYS cc_start: 0.5847 (tppt) cc_final: 0.5524 (tttp) REVERT: C 674 ASP cc_start: 0.4422 (t0) cc_final: 0.2671 (p0) REVERT: C 1026 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7282 (mm-30) REVERT: D 506 LYS cc_start: 0.5772 (tppt) cc_final: 0.5572 (tttp) REVERT: D 674 ASP cc_start: 0.4456 (t0) cc_final: 0.2796 (p0) REVERT: D 1026 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7186 (mm-30) outliers start: 32 outliers final: 17 residues processed: 643 average time/residue: 2.8838 time to fit residues: 2227.0244 Evaluate side-chains 397 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 380 time to evaluate : 4.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 315 CYS Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 33 CYS Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 315 CYS Chi-restraints excluded: chain D residue 338 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 371 optimal weight: 3.9990 chunk 333 optimal weight: 10.0000 chunk 185 optimal weight: 0.8980 chunk 113 optimal weight: 6.9990 chunk 224 optimal weight: 40.0000 chunk 178 optimal weight: 0.9990 chunk 344 optimal weight: 10.0000 chunk 133 optimal weight: 9.9990 chunk 209 optimal weight: 0.7980 chunk 256 optimal weight: 7.9990 chunk 399 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN A 37 GLN A 96 ASN A 129 GLN A 226 GLN A 281 GLN A 337 ASN A 425 ASN A 491 HIS A 956 HIS A1084 GLN A1097 ASN A1108 ASN ** A1226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 GLN B 37 GLN B 96 ASN B 129 GLN B 226 GLN B 281 GLN B 337 ASN B 491 HIS B 956 HIS B 985 GLN B1084 GLN B1097 ASN B1108 ASN ** B1226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN C 37 GLN C 96 ASN C 129 GLN C 226 GLN C 281 GLN C 337 ASN C 425 ASN C 491 HIS C 956 HIS C1084 GLN C1097 ASN C1108 ASN ** C1210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN D 96 ASN D 129 GLN D 226 GLN D 281 GLN D 337 ASN D 425 ASN D 491 HIS D 985 GLN D1084 GLN D1097 ASN D1108 ASN ** D1226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 39624 Z= 0.251 Angle : 0.705 13.499 53272 Z= 0.374 Chirality : 0.044 1.273 5720 Planarity : 0.006 0.064 6352 Dihedral : 21.784 179.855 7984 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.84 % Favored : 90.70 % Rotamer: Outliers : 1.53 % Allowed : 9.37 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: -3.37 (0.11), residues: 4388 helix: -1.40 (0.09), residues: 2668 sheet: -4.89 (0.25), residues: 192 loop : -3.23 (0.13), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 78 HIS 0.012 0.002 HIS D 491 PHE 0.039 0.002 PHE A 858 TYR 0.021 0.002 TYR A 870 ARG 0.007 0.001 ARG A 530 *********************** 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 484 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 424 time to evaluate : 4.287 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: A 953 TYR cc_start: 0.8513 (OUTLIER) cc_final: 0.7296 (m-80) REVERT: A 1026 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7272 (mm-30) REVERT: B 369 MET cc_start: 0.5558 (tpp) cc_final: 0.5096 (tpp) REVERT: B 506 LYS cc_start: 0.5870 (tppt) cc_final: 0.5410 (tttp) REVERT: B 953 TYR cc_start: 0.8522 (OUTLIER) cc_final: 0.7345 (m-80) REVERT: B 1026 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7285 (mm-30) REVERT: C 506 LYS cc_start: 0.5742 (tppt) cc_final: 0.5361 (tttp) REVERT: C 794 MET cc_start: 0.5372 (OUTLIER) cc_final: 0.4036 (mmt) REVERT: C 953 TYR cc_start: 0.8521 (OUTLIER) cc_final: 0.7367 (m-80) REVERT: C 1026 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7320 (mm-30) REVERT: C 1088 MET cc_start: 0.8507 (mmm) cc_final: 0.8307 (mmm) REVERT: D 506 LYS cc_start: 0.5829 (tppt) cc_final: 0.5460 (tttp) REVERT: D 674 ASP cc_start: 0.4130 (t0) cc_final: 0.2559 (p0) REVERT: D 794 MET cc_start: 0.5380 (OUTLIER) cc_final: 0.3906 (mmt) REVERT: D 953 TYR cc_start: 0.8502 (OUTLIER) cc_final: 0.7292 (m-80) REVERT: D 1026 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7304 (mm-30) outliers start: 60 outliers final: 28 residues processed: 464 average time/residue: 2.5247 time to fit residues: 1442.4242 Evaluate side-chains 392 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 358 time to evaluate : 4.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 729 ARG Chi-restraints excluded: chain A residue 953 TYR Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 315 CYS Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 729 ARG Chi-restraints excluded: chain B residue 953 TYR Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 729 ARG Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain C residue 794 MET Chi-restraints excluded: chain C residue 953 TYR Chi-restraints excluded: chain D residue 33 CYS Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 315 CYS Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 729 ARG Chi-restraints excluded: chain D residue 794 MET Chi-restraints excluded: chain D residue 953 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 222 optimal weight: 0.1980 chunk 124 optimal weight: 30.0000 chunk 332 optimal weight: 30.0000 chunk 272 optimal weight: 10.0000 chunk 110 optimal weight: 20.0000 chunk 400 optimal weight: 0.8980 chunk 432 optimal weight: 4.9990 chunk 356 optimal weight: 20.0000 chunk 396 optimal weight: 5.9990 chunk 136 optimal weight: 9.9990 chunk 321 optimal weight: 2.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 ASN A 491 HIS A 789 GLN A 983 ASN A1190 ASN ** A1226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN B 491 HIS B 789 GLN B 983 ASN ** B 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1190 ASN ** B1226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 ASN C 491 HIS C 789 GLN C 983 ASN C1190 ASN ** C1226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 491 HIS D 789 GLN ** D 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1190 ASN ** D1226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 39624 Z= 0.291 Angle : 0.655 13.577 53272 Z= 0.344 Chirality : 0.045 1.374 5720 Planarity : 0.005 0.059 6352 Dihedral : 20.784 178.180 7972 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.39 % Favored : 90.25 % Rotamer: Outliers : 1.97 % Allowed : 9.98 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: -2.77 (0.12), residues: 4388 helix: -0.88 (0.09), residues: 2712 sheet: -4.55 (0.26), residues: 224 loop : -3.10 (0.14), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 78 HIS 0.011 0.002 HIS C 491 PHE 0.024 0.002 PHE D 858 TYR 0.021 0.002 TYR D 870 ARG 0.004 0.000 ARG B 942 *********************** 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 438 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 361 time to evaluate : 4.198 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: A 514 LEU cc_start: 0.7893 (mm) cc_final: 0.7637 (mp) REVERT: A 953 TYR cc_start: 0.8634 (OUTLIER) cc_final: 0.7800 (m-80) REVERT: B 506 LYS cc_start: 0.6022 (tppt) cc_final: 0.5537 (tttp) REVERT: B 514 LEU cc_start: 0.7694 (mm) cc_final: 0.7435 (mp) REVERT: B 953 TYR cc_start: 0.8616 (OUTLIER) cc_final: 0.7649 (m-80) REVERT: B 1180 MET cc_start: 0.7140 (mtm) cc_final: 0.6877 (tmt) REVERT: C 506 LYS cc_start: 0.5911 (tppt) cc_final: 0.5495 (tttp) REVERT: C 514 LEU cc_start: 0.7724 (mm) cc_final: 0.7461 (mp) REVERT: C 674 ASP cc_start: 0.4374 (t0) cc_final: 0.2743 (p0) REVERT: C 953 TYR cc_start: 0.8633 (OUTLIER) cc_final: 0.7842 (m-80) REVERT: D 506 LYS cc_start: 0.5838 (tppt) cc_final: 0.5512 (tttp) REVERT: D 514 LEU cc_start: 0.7804 (mm) cc_final: 0.7547 (mp) REVERT: D 953 TYR cc_start: 0.8635 (OUTLIER) cc_final: 0.7824 (m-80) outliers start: 77 outliers final: 39 residues processed: 399 average time/residue: 2.4390 time to fit residues: 1215.0796 Evaluate side-chains 385 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 342 time to evaluate : 4.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 729 ARG Chi-restraints excluded: chain A residue 953 TYR Chi-restraints excluded: chain A residue 1178 VAL Chi-restraints excluded: chain A residue 1179 GLU Chi-restraints excluded: chain A residue 1207 MET Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 315 CYS Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 729 ARG Chi-restraints excluded: chain B residue 953 TYR Chi-restraints excluded: chain B residue 1178 VAL Chi-restraints excluded: chain B residue 1179 GLU Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 729 ARG Chi-restraints excluded: chain C residue 953 TYR Chi-restraints excluded: chain C residue 1178 VAL Chi-restraints excluded: chain C residue 1179 GLU Chi-restraints excluded: chain D residue 33 CYS Chi-restraints excluded: chain D residue 158 LYS Chi-restraints excluded: chain D residue 315 CYS Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 729 ARG Chi-restraints excluded: chain D residue 953 TYR Chi-restraints excluded: chain D residue 1179 GLU Chi-restraints excluded: chain D residue 1207 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 395 optimal weight: 3.9990 chunk 300 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 191 optimal weight: 3.9990 chunk 268 optimal weight: 4.9990 chunk 401 optimal weight: 2.9990 chunk 425 optimal weight: 0.0770 chunk 209 optimal weight: 3.9990 chunk 380 optimal weight: 4.9990 chunk 114 optimal weight: 40.0000 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 HIS A1137 HIS ** A1226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 491 HIS ** B 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1137 HIS ** B1226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 491 HIS C 985 GLN C1137 HIS ** C1226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 425 ASN D 491 HIS D 983 ASN ** D 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1137 HIS ** D1226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 39624 Z= 0.232 Angle : 0.597 14.236 53272 Z= 0.316 Chirality : 0.044 1.437 5720 Planarity : 0.005 0.054 6352 Dihedral : 19.987 179.695 7968 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.89 % Favored : 90.84 % Rotamer: Outliers : 1.89 % Allowed : 10.52 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: -2.24 (0.12), residues: 4388 helix: -0.43 (0.10), residues: 2676 sheet: -4.33 (0.27), residues: 224 loop : -2.90 (0.14), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 78 HIS 0.011 0.002 HIS D 491 PHE 0.018 0.002 PHE D 935 TYR 0.016 0.002 TYR D1041 ARG 0.004 0.001 ARG A 699 *********************** 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 427 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 353 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: A 514 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7683 (mp) REVERT: A 518 TYR cc_start: 0.8200 (t80) cc_final: 0.7799 (t80) REVERT: A 688 GLN cc_start: 0.7341 (mm110) cc_final: 0.7141 (tp-100) REVERT: A 953 TYR cc_start: 0.8699 (OUTLIER) cc_final: 0.7932 (m-80) REVERT: B 173 THR cc_start: 0.7651 (p) cc_final: 0.7444 (p) REVERT: B 506 LYS cc_start: 0.6017 (tppt) cc_final: 0.5502 (tttp) REVERT: B 514 LEU cc_start: 0.7717 (mm) cc_final: 0.7482 (mp) REVERT: B 518 TYR cc_start: 0.8245 (t80) cc_final: 0.7877 (t80) REVERT: B 632 MET cc_start: 0.8308 (mmm) cc_final: 0.8055 (mmm) REVERT: B 688 GLN cc_start: 0.7274 (mm110) cc_final: 0.7048 (tp-100) REVERT: B 953 TYR cc_start: 0.8689 (OUTLIER) cc_final: 0.7804 (m-80) REVERT: B 1120 MET cc_start: 0.8553 (mmp) cc_final: 0.7711 (mpm) REVERT: C 506 LYS cc_start: 0.5969 (tppt) cc_final: 0.5523 (tttp) REVERT: C 514 LEU cc_start: 0.7741 (mm) cc_final: 0.7506 (mp) REVERT: C 518 TYR cc_start: 0.8264 (t80) cc_final: 0.7868 (t80) REVERT: C 632 MET cc_start: 0.8274 (mmm) cc_final: 0.8048 (mmm) REVERT: C 688 GLN cc_start: 0.7301 (mm110) cc_final: 0.7051 (tp-100) REVERT: C 953 TYR cc_start: 0.8703 (OUTLIER) cc_final: 0.7985 (m-80) REVERT: D 506 LYS cc_start: 0.5894 (tppt) cc_final: 0.5526 (tttp) REVERT: D 514 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7574 (mp) REVERT: D 518 TYR cc_start: 0.8280 (t80) cc_final: 0.7866 (t80) REVERT: D 632 MET cc_start: 0.8295 (mmm) cc_final: 0.8040 (mmm) REVERT: D 688 GLN cc_start: 0.7292 (mm110) cc_final: 0.7064 (tp-100) REVERT: D 953 TYR cc_start: 0.8706 (OUTLIER) cc_final: 0.7944 (m-80) outliers start: 74 outliers final: 45 residues processed: 393 average time/residue: 2.5188 time to fit residues: 1229.9342 Evaluate side-chains 377 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 326 time to evaluate : 4.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 240 ASN Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 729 ARG Chi-restraints excluded: chain A residue 953 TYR Chi-restraints excluded: chain A residue 1179 GLU Chi-restraints excluded: chain A residue 1207 MET Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 315 CYS Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 729 ARG Chi-restraints excluded: chain B residue 953 TYR Chi-restraints excluded: chain B residue 1179 GLU Chi-restraints excluded: chain B residue 1207 MET Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 729 ARG Chi-restraints excluded: chain C residue 953 TYR Chi-restraints excluded: chain C residue 1179 GLU Chi-restraints excluded: chain D residue 33 CYS Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 158 LYS Chi-restraints excluded: chain D residue 315 CYS Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 514 LEU Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 729 ARG Chi-restraints excluded: chain D residue 953 TYR Chi-restraints excluded: chain D residue 1179 GLU Chi-restraints excluded: chain D residue 1207 MET 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: 0.7980 chunk 6 optimal weight: 30.0000 chunk 316 optimal weight: 2.9990 chunk 175 optimal weight: 3.9990 chunk 362 optimal weight: 9.9990 chunk 293 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 217 optimal weight: 4.9990 chunk 381 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 491 HIS A 789 GLN A 850 HIS ** A1226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 491 HIS B 789 GLN ** B 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 491 HIS C 789 GLN C 850 HIS ** C1226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 491 HIS D 789 GLN D 956 HIS ** D 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 39624 Z= 0.296 Angle : 0.625 14.094 53272 Z= 0.326 Chirality : 0.045 1.424 5720 Planarity : 0.005 0.051 6352 Dihedral : 19.905 179.075 7968 Min Nonbonded Distance : 1.721 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.21 % Favored : 90.52 % Rotamer: Outliers : 2.09 % Allowed : 11.08 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.12), residues: 4388 helix: -0.27 (0.10), residues: 2640 sheet: -4.12 (0.29), residues: 224 loop : -2.67 (0.14), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 78 HIS 0.010 0.002 HIS B 183 PHE 0.023 0.002 PHE B1045 TYR 0.019 0.002 TYR B1041 ARG 0.004 0.000 ARG C 194 *********************** 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 425 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 343 time to evaluate : 4.193 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: A 514 LEU cc_start: 0.7959 (mm) cc_final: 0.7727 (mp) REVERT: A 953 TYR cc_start: 0.8780 (OUTLIER) cc_final: 0.8206 (m-80) REVERT: B 173 THR cc_start: 0.7670 (p) cc_final: 0.7461 (p) REVERT: B 506 LYS cc_start: 0.6064 (tppt) cc_final: 0.5515 (tttp) REVERT: B 514 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7524 (mp) REVERT: B 688 GLN cc_start: 0.7292 (mm110) cc_final: 0.7080 (tp-100) REVERT: B 706 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.7779 (mtt) REVERT: B 953 TYR cc_start: 0.8777 (OUTLIER) cc_final: 0.8219 (m-80) REVERT: B 1120 MET cc_start: 0.8585 (mmp) cc_final: 0.8287 (mpm) REVERT: C 372 MET cc_start: 0.4811 (OUTLIER) cc_final: 0.3810 (mpt) REVERT: C 506 LYS cc_start: 0.6057 (tppt) cc_final: 0.5552 (tttp) REVERT: C 514 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7579 (mp) REVERT: C 674 ASP cc_start: 0.4623 (t0) cc_final: 0.2981 (p0) REVERT: C 688 GLN cc_start: 0.7298 (mm110) cc_final: 0.7081 (tp-100) REVERT: C 953 TYR cc_start: 0.8772 (OUTLIER) cc_final: 0.8235 (m-80) REVERT: D 372 MET cc_start: 0.4764 (OUTLIER) cc_final: 0.3758 (mpt) REVERT: D 506 LYS cc_start: 0.6033 (tppt) cc_final: 0.5546 (tttp) REVERT: D 514 LEU cc_start: 0.7826 (mm) cc_final: 0.7595 (mp) REVERT: D 688 GLN cc_start: 0.7297 (mm110) cc_final: 0.7081 (tp-100) REVERT: D 700 GLN cc_start: 0.7265 (mm-40) cc_final: 0.7064 (mm110) REVERT: D 953 TYR cc_start: 0.8799 (OUTLIER) cc_final: 0.8239 (m-80) outliers start: 82 outliers final: 51 residues processed: 382 average time/residue: 2.4127 time to fit residues: 1147.6442 Evaluate side-chains 381 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 321 time to evaluate : 4.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 729 ARG Chi-restraints excluded: chain A residue 953 TYR Chi-restraints excluded: chain A residue 1178 VAL Chi-restraints excluded: chain A residue 1179 GLU Chi-restraints excluded: chain A residue 1207 MET Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 315 CYS Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 706 MET Chi-restraints excluded: chain B residue 953 TYR Chi-restraints excluded: chain B residue 1178 VAL Chi-restraints excluded: chain B residue 1207 MET Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 240 ASN Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 372 MET Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 729 ARG Chi-restraints excluded: chain C residue 953 TYR Chi-restraints excluded: chain C residue 1178 VAL Chi-restraints excluded: chain C residue 1179 GLU Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 158 LYS Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 953 TYR Chi-restraints excluded: chain D residue 1178 VAL Chi-restraints excluded: chain D residue 1179 GLU Chi-restraints excluded: chain D residue 1207 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 143 optimal weight: 9.9990 chunk 383 optimal weight: 10.0000 chunk 84 optimal weight: 4.9990 chunk 249 optimal weight: 9.9990 chunk 104 optimal weight: 8.9990 chunk 425 optimal weight: 0.5980 chunk 353 optimal weight: 10.0000 chunk 197 optimal weight: 2.9990 chunk 35 optimal weight: 40.0000 chunk 140 optimal weight: 10.0000 chunk 223 optimal weight: 30.0000 overall best weight: 5.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 491 HIS ** A1226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 491 HIS ** B 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 491 HIS ** C1226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 491 HIS ** D 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 39624 Z= 0.393 Angle : 0.677 14.057 53272 Z= 0.352 Chirality : 0.048 1.477 5720 Planarity : 0.006 0.064 6352 Dihedral : 20.381 179.927 7965 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.16 % Favored : 89.56 % Rotamer: Outliers : 2.09 % Allowed : 11.95 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.57 % 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: -2.16 (0.12), residues: 4388 helix: -0.45 (0.10), residues: 2648 sheet: -4.02 (0.32), residues: 200 loop : -2.75 (0.14), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 78 HIS 0.010 0.002 HIS C 644 PHE 0.026 0.003 PHE B1045 TYR 0.022 0.003 TYR C1041 ARG 0.006 0.001 ARG D 942 *********************** 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 415 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 333 time to evaluate : 4.206 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: A 514 LEU cc_start: 0.8008 (mm) cc_final: 0.7799 (mp) REVERT: A 706 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.8042 (mtt) REVERT: A 953 TYR cc_start: 0.8862 (OUTLIER) cc_final: 0.8150 (m-80) REVERT: B 173 THR cc_start: 0.7706 (p) cc_final: 0.7492 (p) REVERT: B 371 CYS cc_start: 0.2855 (OUTLIER) cc_final: 0.2413 (p) REVERT: B 506 LYS cc_start: 0.6092 (tppt) cc_final: 0.5531 (tttp) REVERT: B 688 GLN cc_start: 0.7341 (mm110) cc_final: 0.7084 (mm-40) REVERT: B 706 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.7933 (mtt) REVERT: B 729 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7225 (mpp80) REVERT: B 953 TYR cc_start: 0.8858 (OUTLIER) cc_final: 0.8154 (m-80) REVERT: B 1120 MET cc_start: 0.8612 (mmp) cc_final: 0.8284 (mpm) REVERT: C 173 THR cc_start: 0.7719 (p) cc_final: 0.7495 (p) REVERT: C 506 LYS cc_start: 0.5957 (tppt) cc_final: 0.5458 (tttp) REVERT: C 514 LEU cc_start: 0.7833 (mm) cc_final: 0.7617 (mp) REVERT: C 688 GLN cc_start: 0.7343 (mm110) cc_final: 0.7076 (mm-40) REVERT: C 700 GLN cc_start: 0.7288 (mm-40) cc_final: 0.7085 (mm110) REVERT: C 953 TYR cc_start: 0.8848 (OUTLIER) cc_final: 0.8173 (m-80) REVERT: D 158 LYS cc_start: 0.6609 (OUTLIER) cc_final: 0.6024 (ptmt) REVERT: D 506 LYS cc_start: 0.6017 (tppt) cc_final: 0.5486 (tttp) REVERT: D 514 LEU cc_start: 0.7881 (mm) cc_final: 0.7674 (mp) REVERT: D 688 GLN cc_start: 0.7346 (mm110) cc_final: 0.7088 (mm-40) REVERT: D 729 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.7281 (mpp80) REVERT: D 953 TYR cc_start: 0.8864 (OUTLIER) cc_final: 0.8160 (m-80) outliers start: 82 outliers final: 49 residues processed: 373 average time/residue: 2.4269 time to fit residues: 1128.4733 Evaluate side-chains 378 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 319 time to evaluate : 4.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 240 ASN Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 706 MET Chi-restraints excluded: chain A residue 729 ARG Chi-restraints excluded: chain A residue 953 TYR Chi-restraints excluded: chain A residue 1124 GLU Chi-restraints excluded: chain A residue 1130 PRO Chi-restraints excluded: chain A residue 1179 GLU Chi-restraints excluded: chain A residue 1207 MET Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 706 MET Chi-restraints excluded: chain B residue 729 ARG Chi-restraints excluded: chain B residue 953 TYR Chi-restraints excluded: chain B residue 1124 GLU Chi-restraints excluded: chain B residue 1130 PRO Chi-restraints excluded: chain B residue 1178 VAL Chi-restraints excluded: chain B residue 1179 GLU Chi-restraints excluded: chain B residue 1207 MET Chi-restraints excluded: chain C residue 240 ASN Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 729 ARG Chi-restraints excluded: chain C residue 953 TYR Chi-restraints excluded: chain C residue 1124 GLU Chi-restraints excluded: chain C residue 1130 PRO Chi-restraints excluded: chain C residue 1178 VAL Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 158 LYS Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 729 ARG Chi-restraints excluded: chain D residue 953 TYR Chi-restraints excluded: chain D residue 1130 PRO Chi-restraints excluded: chain D residue 1178 VAL Chi-restraints excluded: chain D residue 1179 GLU Chi-restraints excluded: chain D residue 1207 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 410 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 242 optimal weight: 10.0000 chunk 310 optimal weight: 0.7980 chunk 240 optimal weight: 20.0000 chunk 358 optimal weight: 20.0000 chunk 237 optimal weight: 20.0000 chunk 424 optimal weight: 0.6980 chunk 265 optimal weight: 9.9990 chunk 258 optimal weight: 40.0000 chunk 195 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 ASN A 491 HIS ** A1226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 491 HIS B 789 GLN ** B 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 491 HIS C 789 GLN ** C1226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 GLN D 491 HIS D 789 GLN ** D 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 39624 Z= 0.195 Angle : 0.571 14.326 53272 Z= 0.300 Chirality : 0.044 1.437 5720 Planarity : 0.005 0.047 6352 Dihedral : 19.351 178.178 7962 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.64 % Favored : 91.09 % Rotamer: Outliers : 1.69 % Allowed : 12.72 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.57 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.12), residues: 4388 helix: -0.06 (0.10), residues: 2648 sheet: -3.86 (0.33), residues: 200 loop : -2.62 (0.14), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 78 HIS 0.007 0.001 HIS A 51 PHE 0.018 0.002 PHE C 935 TYR 0.016 0.002 TYR C1041 ARG 0.003 0.000 ARG D 194 *********************** 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 406 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 340 time to evaluate : 4.317 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: A 371 CYS cc_start: 0.2513 (OUTLIER) cc_final: 0.1894 (p) REVERT: A 674 ASP cc_start: 0.4524 (t0) cc_final: 0.3139 (p0) REVERT: A 953 TYR cc_start: 0.8825 (OUTLIER) cc_final: 0.8173 (m-80) REVERT: B 173 THR cc_start: 0.7720 (p) cc_final: 0.7499 (p) REVERT: B 371 CYS cc_start: 0.2664 (OUTLIER) cc_final: 0.2159 (p) REVERT: B 506 LYS cc_start: 0.6125 (tppt) cc_final: 0.5475 (tttp) REVERT: B 674 ASP cc_start: 0.4488 (t0) cc_final: 0.2847 (p0) REVERT: B 700 GLN cc_start: 0.7298 (mm-40) cc_final: 0.7050 (mm110) REVERT: B 953 TYR cc_start: 0.8809 (OUTLIER) cc_final: 0.8171 (m-80) REVERT: C 173 THR cc_start: 0.7699 (p) cc_final: 0.7474 (p) REVERT: C 506 LYS cc_start: 0.6048 (tppt) cc_final: 0.5496 (tttp) REVERT: C 514 LEU cc_start: 0.7785 (mm) cc_final: 0.7574 (mp) REVERT: C 674 ASP cc_start: 0.4481 (t0) cc_final: 0.2903 (p0) REVERT: C 688 GLN cc_start: 0.7272 (mm110) cc_final: 0.7071 (tp-100) REVERT: C 953 TYR cc_start: 0.8794 (OUTLIER) cc_final: 0.8182 (m-80) REVERT: D 158 LYS cc_start: 0.6543 (OUTLIER) cc_final: 0.5991 (ptmt) REVERT: D 506 LYS cc_start: 0.6010 (tppt) cc_final: 0.5481 (tttp) REVERT: D 674 ASP cc_start: 0.4487 (t0) cc_final: 0.2965 (p0) REVERT: D 953 TYR cc_start: 0.8824 (OUTLIER) cc_final: 0.8181 (m-80) outliers start: 66 outliers final: 42 residues processed: 375 average time/residue: 2.4079 time to fit residues: 1125.0864 Evaluate side-chains 382 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 333 time to evaluate : 4.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 729 ARG Chi-restraints excluded: chain A residue 953 TYR Chi-restraints excluded: chain A residue 1178 VAL Chi-restraints excluded: chain A residue 1207 MET Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 315 CYS Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 729 ARG Chi-restraints excluded: chain B residue 953 TYR Chi-restraints excluded: chain B residue 1178 VAL Chi-restraints excluded: chain B residue 1207 MET Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 729 ARG Chi-restraints excluded: chain C residue 953 TYR Chi-restraints excluded: chain C residue 1178 VAL Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 158 LYS Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 729 ARG Chi-restraints excluded: chain D residue 953 TYR Chi-restraints excluded: chain D residue 1178 VAL Chi-restraints excluded: chain D residue 1179 GLU Chi-restraints excluded: chain D residue 1207 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 262 optimal weight: 20.0000 chunk 169 optimal weight: 8.9990 chunk 253 optimal weight: 0.0370 chunk 127 optimal weight: 6.9990 chunk 83 optimal weight: 8.9990 chunk 82 optimal weight: 4.9990 chunk 269 optimal weight: 5.9990 chunk 288 optimal weight: 8.9990 chunk 209 optimal weight: 0.7980 chunk 39 optimal weight: 9.9990 chunk 333 optimal weight: 10.0000 overall best weight: 3.7664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 491 HIS ** A 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 491 HIS ** B 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 491 HIS ** C 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 425 ASN D 491 HIS ** D 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 39624 Z= 0.300 Angle : 0.613 14.227 53272 Z= 0.319 Chirality : 0.046 1.466 5720 Planarity : 0.005 0.044 6352 Dihedral : 19.371 177.952 7962 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.21 % Favored : 90.52 % Rotamer: Outliers : 1.66 % Allowed : 12.90 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.12), residues: 4388 helix: -0.08 (0.10), residues: 2660 sheet: -3.72 (0.34), residues: 200 loop : -2.57 (0.15), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 78 HIS 0.015 0.002 HIS B 183 PHE 0.022 0.002 PHE B1045 TYR 0.019 0.002 TYR C1041 ARG 0.005 0.001 ARG B 194 *********************** 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 408 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 343 time to evaluate : 4.141 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: A 371 CYS cc_start: 0.2681 (OUTLIER) cc_final: 0.2059 (p) REVERT: A 674 ASP cc_start: 0.4239 (t0) cc_final: 0.2891 (p0) REVERT: A 763 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7883 (tm) REVERT: A 953 TYR cc_start: 0.8867 (OUTLIER) cc_final: 0.8135 (m-80) REVERT: B 173 THR cc_start: 0.7732 (p) cc_final: 0.7509 (p) REVERT: B 371 CYS cc_start: 0.2574 (OUTLIER) cc_final: 0.2043 (p) REVERT: B 506 LYS cc_start: 0.6128 (tppt) cc_final: 0.5492 (tttp) REVERT: B 700 GLN cc_start: 0.7306 (mm-40) cc_final: 0.7057 (mm110) REVERT: B 953 TYR cc_start: 0.8854 (OUTLIER) cc_final: 0.8136 (m-80) REVERT: C 173 THR cc_start: 0.7772 (p) cc_final: 0.7533 (p) REVERT: C 506 LYS cc_start: 0.5996 (tppt) cc_final: 0.5416 (tttp) REVERT: C 514 LEU cc_start: 0.7832 (mm) cc_final: 0.7629 (mp) REVERT: C 674 ASP cc_start: 0.4204 (t0) cc_final: 0.2669 (p0) REVERT: C 688 GLN cc_start: 0.7303 (mm110) cc_final: 0.7098 (tp40) REVERT: C 953 TYR cc_start: 0.8844 (OUTLIER) cc_final: 0.8157 (m-80) REVERT: D 158 LYS cc_start: 0.6601 (OUTLIER) cc_final: 0.6038 (ptmt) REVERT: D 506 LYS cc_start: 0.6069 (tppt) cc_final: 0.5433 (tttp) REVERT: D 674 ASP cc_start: 0.4197 (t0) cc_final: 0.2710 (p0) REVERT: D 729 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7231 (mpp80) REVERT: D 953 TYR cc_start: 0.8867 (OUTLIER) cc_final: 0.8147 (m-80) outliers start: 65 outliers final: 40 residues processed: 384 average time/residue: 2.4783 time to fit residues: 1184.1539 Evaluate side-chains 380 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 331 time to evaluate : 4.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 953 TYR Chi-restraints excluded: chain A residue 1207 MET Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 315 CYS Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 729 ARG Chi-restraints excluded: chain B residue 953 TYR Chi-restraints excluded: chain B residue 1178 VAL Chi-restraints excluded: chain B residue 1207 MET Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 729 ARG Chi-restraints excluded: chain C residue 953 TYR Chi-restraints excluded: chain C residue 1178 VAL Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 158 LYS Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 729 ARG Chi-restraints excluded: chain D residue 953 TYR Chi-restraints excluded: chain D residue 1178 VAL Chi-restraints excluded: chain D residue 1207 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 385 optimal weight: 5.9990 chunk 406 optimal weight: 2.9990 chunk 370 optimal weight: 20.0000 chunk 395 optimal weight: 3.9990 chunk 237 optimal weight: 10.0000 chunk 172 optimal weight: 6.9990 chunk 310 optimal weight: 0.3980 chunk 121 optimal weight: 9.9990 chunk 357 optimal weight: 20.0000 chunk 373 optimal weight: 10.0000 chunk 393 optimal weight: 4.9990 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 491 HIS ** A 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 479 ASN B 491 HIS B 789 GLN ** B 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 491 HIS ** C 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 425 ASN D 491 HIS ** D 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.4354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 39624 Z= 0.278 Angle : 0.600 14.246 53272 Z= 0.313 Chirality : 0.045 1.437 5720 Planarity : 0.005 0.046 6352 Dihedral : 19.151 177.358 7962 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.07 % Favored : 90.66 % Rotamer: Outliers : 1.81 % Allowed : 13.02 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.12), residues: 4388 helix: -0.02 (0.10), residues: 2660 sheet: -3.64 (0.34), residues: 200 loop : -2.52 (0.15), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 78 HIS 0.010 0.002 HIS B 183 PHE 0.019 0.002 PHE B1045 TYR 0.019 0.002 TYR D1041 ARG 0.005 0.001 ARG B 754 *********************** 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 415 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 344 time to evaluate : 5.660 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: A 371 CYS cc_start: 0.2681 (OUTLIER) cc_final: 0.2059 (p) REVERT: A 674 ASP cc_start: 0.4584 (t0) cc_final: 0.3171 (p0) REVERT: A 763 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7884 (tm) REVERT: A 953 TYR cc_start: 0.8868 (OUTLIER) cc_final: 0.8122 (m-80) REVERT: B 173 THR cc_start: 0.7742 (p) cc_final: 0.7522 (p) REVERT: B 371 CYS cc_start: 0.2744 (OUTLIER) cc_final: 0.2225 (p) REVERT: B 506 LYS cc_start: 0.6139 (tppt) cc_final: 0.5471 (tttp) REVERT: B 674 ASP cc_start: 0.4545 (t0) cc_final: 0.2877 (p0) REVERT: B 700 GLN cc_start: 0.7266 (mm-40) cc_final: 0.7015 (mm110) REVERT: B 729 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7586 (tpp80) REVERT: B 953 TYR cc_start: 0.8867 (OUTLIER) cc_final: 0.8127 (m-80) REVERT: C 173 THR cc_start: 0.7770 (p) cc_final: 0.7545 (p) REVERT: C 424 LYS cc_start: 0.7342 (OUTLIER) cc_final: 0.7016 (ptpt) REVERT: C 506 LYS cc_start: 0.6102 (tppt) cc_final: 0.5419 (tttp) REVERT: C 674 ASP cc_start: 0.4537 (t0) cc_final: 0.2971 (p0) REVERT: C 953 TYR cc_start: 0.8858 (OUTLIER) cc_final: 0.8150 (m-80) REVERT: D 158 LYS cc_start: 0.6607 (OUTLIER) cc_final: 0.6041 (ptmt) REVERT: D 506 LYS cc_start: 0.6081 (tppt) cc_final: 0.5406 (tttp) REVERT: D 674 ASP cc_start: 0.4575 (t0) cc_final: 0.3021 (p0) REVERT: D 729 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.7616 (tpp80) REVERT: D 953 TYR cc_start: 0.8872 (OUTLIER) cc_final: 0.8139 (m-80) outliers start: 71 outliers final: 41 residues processed: 393 average time/residue: 2.5129 time to fit residues: 1241.3822 Evaluate side-chains 383 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 331 time to evaluate : 4.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 953 TYR Chi-restraints excluded: chain A residue 1124 GLU Chi-restraints excluded: chain A residue 1178 VAL Chi-restraints excluded: chain A residue 1207 MET Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 315 CYS Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 729 ARG Chi-restraints excluded: chain B residue 953 TYR Chi-restraints excluded: chain B residue 1124 GLU Chi-restraints excluded: chain B residue 1178 VAL Chi-restraints excluded: chain B residue 1207 MET Chi-restraints excluded: chain C residue 240 ASN Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 953 TYR Chi-restraints excluded: chain C residue 1124 GLU Chi-restraints excluded: chain C residue 1178 VAL Chi-restraints excluded: chain D residue 158 LYS Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 729 ARG Chi-restraints excluded: chain D residue 953 TYR Chi-restraints excluded: chain D residue 1178 VAL Chi-restraints excluded: chain D residue 1207 MET 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: 8.9990 chunk 198 optimal weight: 2.9990 chunk 290 optimal weight: 8.9990 chunk 438 optimal weight: 20.0000 chunk 403 optimal weight: 3.9990 chunk 349 optimal weight: 6.9990 chunk 36 optimal weight: 30.0000 chunk 269 optimal weight: 2.9990 chunk 214 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 491 HIS ** A 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 491 HIS B 789 GLN ** B 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 491 HIS C 688 GLN ** C 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 425 ASN D 491 HIS ** D 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.4454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 39624 Z= 0.321 Angle : 0.625 14.153 53272 Z= 0.324 Chirality : 0.046 1.460 5720 Planarity : 0.005 0.042 6352 Dihedral : 19.219 179.360 7962 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.37 % Favored : 90.41 % Rotamer: Outliers : 1.61 % Allowed : 13.43 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.12), residues: 4388 helix: -0.05 (0.10), residues: 2660 sheet: -3.48 (0.35), residues: 200 loop : -2.51 (0.15), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 78 HIS 0.009 0.002 HIS A1171 PHE 0.022 0.002 PHE B1045 TYR 0.021 0.002 TYR A1041 ARG 0.004 0.001 ARG B 942 ********************** 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 404 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 341 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: A 368 MET cc_start: 0.5001 (ttm) cc_final: 0.4780 (ttt) REVERT: A 371 CYS cc_start: 0.2669 (OUTLIER) cc_final: 0.2037 (p) REVERT: A 674 ASP cc_start: 0.4281 (t0) cc_final: 0.2934 (p0) REVERT: A 763 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7926 (tm) REVERT: A 953 TYR cc_start: 0.8884 (OUTLIER) cc_final: 0.8026 (m-80) REVERT: B 173 THR cc_start: 0.7743 (p) cc_final: 0.7514 (p) REVERT: B 371 CYS cc_start: 0.2864 (OUTLIER) cc_final: 0.2348 (p) REVERT: B 506 LYS cc_start: 0.6255 (tppt) cc_final: 0.5502 (tttp) REVERT: B 700 GLN cc_start: 0.7266 (mm-40) cc_final: 0.7018 (mm110) REVERT: B 729 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.7598 (tpp80) REVERT: B 953 TYR cc_start: 0.8883 (OUTLIER) cc_final: 0.8035 (m-80) REVERT: C 173 THR cc_start: 0.7786 (p) cc_final: 0.7548 (p) REVERT: C 506 LYS cc_start: 0.6094 (tppt) cc_final: 0.5420 (tttp) REVERT: C 674 ASP cc_start: 0.4176 (t0) cc_final: 0.2688 (p0) REVERT: C 953 TYR cc_start: 0.8874 (OUTLIER) cc_final: 0.8062 (m-80) REVERT: D 158 LYS cc_start: 0.6600 (OUTLIER) cc_final: 0.6016 (ptmt) REVERT: D 424 LYS cc_start: 0.7328 (OUTLIER) cc_final: 0.6984 (ptpt) REVERT: D 506 LYS cc_start: 0.6082 (tppt) cc_final: 0.5469 (tttp) REVERT: D 674 ASP cc_start: 0.4217 (t0) cc_final: 0.2737 (p0) REVERT: D 729 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7638 (tpp80) REVERT: D 953 TYR cc_start: 0.8889 (OUTLIER) cc_final: 0.8046 (m-80) outliers start: 63 outliers final: 38 residues processed: 382 average time/residue: 2.4146 time to fit residues: 1146.2447 Evaluate side-chains 381 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 332 time to evaluate : 4.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 953 TYR Chi-restraints excluded: chain A residue 1124 GLU Chi-restraints excluded: chain A residue 1178 VAL Chi-restraints excluded: chain A residue 1207 MET Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 315 CYS Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 729 ARG Chi-restraints excluded: chain B residue 953 TYR Chi-restraints excluded: chain B residue 1124 GLU Chi-restraints excluded: chain B residue 1178 VAL Chi-restraints excluded: chain B residue 1207 MET Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 953 TYR Chi-restraints excluded: chain C residue 1124 GLU Chi-restraints excluded: chain D residue 158 LYS Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 424 LYS Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 729 ARG Chi-restraints excluded: chain D residue 953 TYR Chi-restraints excluded: chain D residue 1178 VAL Chi-restraints excluded: chain D residue 1207 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 277 optimal weight: 5.9990 chunk 371 optimal weight: 9.9990 chunk 106 optimal weight: 20.0000 chunk 321 optimal weight: 0.0670 chunk 51 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 349 optimal weight: 8.9990 chunk 146 optimal weight: 40.0000 chunk 359 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 overall best weight: 4.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 491 HIS ** A 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 789 GLN B 491 HIS ** B 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 479 ASN C 491 HIS ** C 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 491 HIS ** D 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.239766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.185361 restraints weight = 112016.306| |-----------------------------------------------------------------------------| r_work (start): 0.4106 rms_B_bonded: 1.49 r_work: 0.3890 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3811 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.4537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 39624 Z= 0.312 Angle : 0.618 14.204 53272 Z= 0.322 Chirality : 0.046 1.433 5720 Planarity : 0.005 0.043 6352 Dihedral : 19.165 178.290 7962 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.23 % Favored : 90.52 % Rotamer: Outliers : 1.61 % Allowed : 13.64 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.12), residues: 4388 helix: -0.02 (0.10), residues: 2656 sheet: -3.48 (0.35), residues: 200 loop : -2.51 (0.15), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 78 HIS 0.014 0.002 HIS D 183 PHE 0.021 0.002 PHE A1045 TYR 0.021 0.002 TYR C1041 ARG 0.005 0.001 ARG B 754 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20201.65 seconds wall clock time: 349 minutes 10.65 seconds (20950.65 seconds total)