Starting phenix.real_space_refine on Fri Apr 12 02:51:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8si8_40502/04_2024/8si8_40502_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8si8_40502/04_2024/8si8_40502.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8si8_40502/04_2024/8si8_40502.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8si8_40502/04_2024/8si8_40502.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8si8_40502/04_2024/8si8_40502_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8si8_40502/04_2024/8si8_40502_neut_trim_updated.pdb" } resolution = 2.99 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= 0.026 sd= 0.105 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: 8 Type Number sf(0) Gaussians Ca 1 9.91 5 P 48 5.49 5 S 240 5.16 5 Cl 8 4.86 5 C 25552 2.51 5 N 6032 2.21 5 O 6728 1.98 5 H 36144 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 197": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 261": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 750": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 843": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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 ARG 1018": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 1085": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 1198": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 197": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 261": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 750": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 843": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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 ARG 1018": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 1085": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 1198": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 197": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 261": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 750": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 843": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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 ARG 1018": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 1085": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 1198": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 197": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 261": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 750": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 843": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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 ARG 1018": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 1085": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 1198": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 74753 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 17965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1105, 17965 Classifications: {'peptide': 1105} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 1060} Chain breaks: 3 Chain: "B" Number of atoms: 17965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1105, 17965 Classifications: {'peptide': 1105} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 1060} Chain breaks: 3 Chain: "C" Number of atoms: 17965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1105, 17965 Classifications: {'peptide': 1105} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 1060} Chain breaks: 3 Chain: "D" Number of atoms: 17965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1105, 17965 Classifications: {'peptide': 1105} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 1060} Chain breaks: 3 Chain: "A" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 724 Unusual residues: {' CA': 1, '3FD': 1, 'CLR': 1, 'DU0': 1, 'POV': 13} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 790 Unusual residues: {'3FD': 1, 'CLR': 1, 'DU0': 1, 'POV': 15} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-3': 3, 'POV:plan-2': 2} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 708 Unusual residues: {'3FD': 1, 'CLR': 1, 'DU0': 2, 'POV': 12} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 671 Unusual residues: {'3FD': 1, 'CLR': 1, 'POV': 12} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 24.12, per 1000 atoms: 0.32 Number of scatterers: 74753 At special positions: 0 Unit cell: (176.79, 176.79, 155.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Ca 1 19.99 Cl 8 17.00 S 240 16.00 P 48 15.00 O 6728 8.00 N 6032 7.00 C 25552 6.00 H 36144 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 16 " - pdb=" SG CYS A 44 " distance=2.06 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 44 " distance=2.05 Simple disulfide: pdb=" SG CYS A1056 " - pdb=" SG CYS A1066 " distance=2.03 Simple disulfide: pdb=" SG CYS B 16 " - pdb=" SG CYS B 44 " distance=2.07 Simple disulfide: pdb=" SG CYS B 42 " - pdb=" SG CYS B 44 " distance=2.05 Simple disulfide: pdb=" SG CYS B1056 " - pdb=" SG CYS B1066 " distance=2.03 Simple disulfide: pdb=" SG CYS C 16 " - pdb=" SG CYS C 44 " distance=2.06 Simple disulfide: pdb=" SG CYS C 42 " - pdb=" SG CYS C 44 " distance=2.05 Simple disulfide: pdb=" SG CYS C1056 " - pdb=" SG CYS C1066 " distance=2.03 Simple disulfide: pdb=" SG CYS D 16 " - pdb=" SG CYS D 44 " distance=2.06 Simple disulfide: pdb=" SG CYS D 42 " - pdb=" SG CYS D 44 " distance=2.05 Simple disulfide: pdb=" SG CYS D1056 " - pdb=" SG CYS D1066 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 47.00 Conformation dependent library (CDL) restraints added in 5.2 seconds 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8368 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 204 helices and 12 sheets defined 52.7% alpha, 2.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.65 Creating SS restraints... Processing helix chain 'A' and resid 6 through 10 Processing helix chain 'A' and resid 32 through 39 removed outlier: 3.647A pdb=" N GLN A 37 " --> pdb=" O CYS A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 50 No H-bonds generated for 'chain 'A' and resid 48 through 50' 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 117 through 125 Processing helix chain 'A' and resid 150 through 165 removed outlier: 3.613A pdb=" N LEU A 156 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLY A 157 " --> pdb=" O LYS A 153 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS A 162 " --> pdb=" O LYS A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 191 removed outlier: 3.564A pdb=" N ASP A 186 " --> pdb=" O LYS A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 260 through 271 removed outlier: 4.278A pdb=" N GLU A 265 " --> pdb=" O ARG A 261 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU A 267 " --> pdb=" O ARG A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 305 removed outlier: 3.772A pdb=" N LEU A 298 " --> pdb=" O PRO A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 331 Processing helix chain 'A' and resid 340 through 342 No H-bonds generated for 'chain 'A' and resid 340 through 342' Processing helix chain 'A' and resid 345 through 354 removed outlier: 3.848A pdb=" N PHE A 354 " --> pdb=" O ILE A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 373 removed outlier: 3.512A pdb=" N HIS A 363 " --> pdb=" O SER A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 401 removed outlier: 3.704A pdb=" N LEU A 399 " --> pdb=" O ILE A 395 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU A 400 " --> pdb=" O LEU A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 416 removed outlier: 3.859A pdb=" N LEU A 413 " --> pdb=" O ASP A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 426 removed outlier: 3.611A pdb=" N ASN A 425 " --> pdb=" O ASP A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 448 removed outlier: 3.707A pdb=" N ASP A 445 " --> pdb=" O GLN A 441 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 461 Processing helix chain 'A' and resid 471 through 478 removed outlier: 3.832A pdb=" N TYR A 478 " --> pdb=" O LEU A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 496 Processing helix chain 'A' and resid 509 through 519 Processing helix chain 'A' and resid 527 through 529 No H-bonds generated for 'chain 'A' and resid 527 through 529' Processing helix chain 'A' and resid 531 through 538 Processing helix chain 'A' and resid 622 through 631 removed outlier: 3.574A pdb=" N LEU A 626 " --> pdb=" O LEU A 622 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE A 627 " --> pdb=" O ASN A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 643 removed outlier: 3.710A pdb=" N PHE A 640 " --> pdb=" O VAL A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 668 removed outlier: 3.640A pdb=" N TYR A 664 " --> pdb=" O ARG A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 698 removed outlier: 3.555A pdb=" N PHE A 686 " --> pdb=" O TYR A 682 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL A 691 " --> pdb=" O GLY A 687 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN A 696 " --> pdb=" O GLU A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 707 Processing helix chain 'A' and resid 731 through 734 No H-bonds generated for 'chain 'A' and resid 731 through 734' Processing helix chain 'A' and resid 741 through 748 Processing helix chain 'A' and resid 758 through 766 Processing helix chain 'A' and resid 768 through 773 removed outlier: 3.631A pdb=" N LEU A 772 " --> pdb=" O PRO A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 796 Processing helix chain 'A' and resid 841 through 849 removed outlier: 3.686A pdb=" N TYR A 846 " --> pdb=" O THR A 842 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA A 847 " --> pdb=" O ARG A 843 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N PHE A 848 " --> pdb=" O LYS A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 857 Processing helix chain 'A' and resid 860 through 875 removed outlier: 3.643A pdb=" N GLY A 865 " --> pdb=" O LEU A 861 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N MET A 868 " --> pdb=" O LEU A 864 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU A 869 " --> pdb=" O GLY A 865 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE A 872 " --> pdb=" O MET A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 905 removed outlier: 3.541A pdb=" N VAL A 904 " --> pdb=" O LYS A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 918 removed outlier: 3.817A pdb=" N LYS A 917 " --> pdb=" O SER A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 943 removed outlier: 3.580A pdb=" N PHE A 936 " --> pdb=" O ILE A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 982 removed outlier: 5.220A pdb=" N ILE A 970 " --> pdb=" O CYS A 966 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N PHE A 971 " --> pdb=" O LEU A 967 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TRP A 972 " --> pdb=" O ASN A 968 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU A 976 " --> pdb=" O TRP A 972 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LEU A 977 " --> pdb=" O TYR A 973 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ASP A 978 " --> pdb=" O VAL A 974 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE A 979 " --> pdb=" O ARG A 975 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL A 982 " --> pdb=" O ASP A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 997 removed outlier: 3.732A pdb=" N ILE A 993 " --> pdb=" O TYR A 989 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLY A 994 " --> pdb=" O VAL A 990 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS A 995 " --> pdb=" O MET A 991 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL A 997 " --> pdb=" O ILE A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1022 removed outlier: 3.681A pdb=" N VAL A1010 " --> pdb=" O ILE A1006 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU A1011 " --> pdb=" O MET A1007 " (cutoff:3.500A) Proline residue: A1017 - end of helix Processing helix chain 'A' and resid 1031 through 1034 No H-bonds generated for 'chain 'A' and resid 1031 through 1034' Processing helix chain 'A' and resid 1039 through 1042 No H-bonds generated for 'chain 'A' and resid 1039 through 1042' Processing helix chain 'A' and resid 1073 through 1084 Processing helix chain 'A' and resid 1089 through 1098 removed outlier: 3.769A pdb=" N ILE A1093 " --> pdb=" O VAL A1089 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA A1094 " --> pdb=" O ASN A1090 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN A1098 " --> pdb=" O ALA A1094 " (cutoff:3.500A) Processing helix chain 'A' and resid 1100 through 1122 removed outlier: 4.008A pdb=" N ILE A1106 " --> pdb=" O GLN A1102 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N TYR A1116 " --> pdb=" O LYS A1112 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N HIS A1117 " --> pdb=" O TYR A1113 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA A1121 " --> pdb=" O HIS A1117 " (cutoff:3.500A) Processing helix chain 'A' and resid 1133 through 1144 Processing helix chain 'A' and resid 1164 through 1190 removed outlier: 3.608A pdb=" N LYS A1168 " --> pdb=" O GLU A1164 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP A1187 " --> pdb=" O ASP A1183 " (cutoff:3.500A) Processing helix chain 'A' and resid 1193 through 1225 removed outlier: 3.783A pdb=" N VAL A1214 " --> pdb=" O GLN A1210 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG A1223 " --> pdb=" O ASN A1219 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 10 Processing helix chain 'B' and resid 32 through 39 removed outlier: 3.647A pdb=" N GLN B 37 " --> pdb=" O CYS B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 50 No H-bonds generated for 'chain 'B' and resid 48 through 50' 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 117 through 125 Processing helix chain 'B' and resid 150 through 165 removed outlier: 3.613A pdb=" N LEU B 156 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N GLY B 157 " --> pdb=" O LYS B 153 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS B 162 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 191 removed outlier: 3.564A pdb=" N ASP B 186 " --> pdb=" O LYS B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 216 Processing helix chain 'B' and resid 260 through 271 removed outlier: 4.278A pdb=" N GLU B 265 " --> pdb=" O ARG B 261 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU B 267 " --> pdb=" O ARG B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 305 removed outlier: 3.773A pdb=" N LEU B 298 " --> pdb=" O PRO B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 331 Processing helix chain 'B' and resid 340 through 342 No H-bonds generated for 'chain 'B' and resid 340 through 342' Processing helix chain 'B' and resid 345 through 354 removed outlier: 3.848A pdb=" N PHE B 354 " --> pdb=" O ILE B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 373 removed outlier: 3.512A pdb=" N HIS B 363 " --> pdb=" O SER B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 401 removed outlier: 3.704A pdb=" N LEU B 399 " --> pdb=" O ILE B 395 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU B 400 " --> pdb=" O LEU B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 416 removed outlier: 3.859A pdb=" N LEU B 413 " --> pdb=" O ASP B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 426 removed outlier: 3.611A pdb=" N ASN B 425 " --> pdb=" O ASP B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 448 removed outlier: 3.708A pdb=" N ASP B 445 " --> pdb=" O GLN B 441 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL B 448 " --> pdb=" O LEU B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 461 Processing helix chain 'B' and resid 471 through 478 removed outlier: 3.831A pdb=" N TYR B 478 " --> pdb=" O LEU B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 496 Processing helix chain 'B' and resid 509 through 519 Processing helix chain 'B' and resid 527 through 529 No H-bonds generated for 'chain 'B' and resid 527 through 529' Processing helix chain 'B' and resid 531 through 538 Processing helix chain 'B' and resid 622 through 631 removed outlier: 3.574A pdb=" N LEU B 626 " --> pdb=" O LEU B 622 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE B 627 " --> pdb=" O ASN B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 643 removed outlier: 3.711A pdb=" N PHE B 640 " --> pdb=" O VAL B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 668 removed outlier: 3.640A pdb=" N TYR B 664 " --> pdb=" O ARG B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 676 through 698 removed outlier: 3.555A pdb=" N PHE B 686 " --> pdb=" O TYR B 682 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL B 691 " --> pdb=" O GLY B 687 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN B 696 " --> pdb=" O GLU B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 707 Processing helix chain 'B' and resid 731 through 734 No H-bonds generated for 'chain 'B' and resid 731 through 734' Processing helix chain 'B' and resid 741 through 748 Processing helix chain 'B' and resid 758 through 766 Processing helix chain 'B' and resid 768 through 773 removed outlier: 3.632A pdb=" N LEU B 772 " --> pdb=" O PRO B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 796 Processing helix chain 'B' and resid 841 through 849 removed outlier: 3.685A pdb=" N TYR B 846 " --> pdb=" O THR B 842 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA B 847 " --> pdb=" O ARG B 843 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N PHE B 848 " --> pdb=" O LYS B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 852 through 857 Processing helix chain 'B' and resid 860 through 875 removed outlier: 3.642A pdb=" N GLY B 865 " --> pdb=" O LEU B 861 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N MET B 868 " --> pdb=" O LEU B 864 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU B 869 " --> pdb=" O GLY B 865 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE B 872 " --> pdb=" O MET B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 905 removed outlier: 3.540A pdb=" N VAL B 904 " --> pdb=" O LYS B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 918 removed outlier: 3.818A pdb=" N LYS B 917 " --> pdb=" O SER B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 943 removed outlier: 3.581A pdb=" N PHE B 936 " --> pdb=" O ILE B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 956 through 982 removed outlier: 5.219A pdb=" N ILE B 970 " --> pdb=" O CYS B 966 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N PHE B 971 " --> pdb=" O LEU B 967 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TRP B 972 " --> pdb=" O ASN B 968 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU B 976 " --> pdb=" O TRP B 972 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LEU B 977 " --> pdb=" O TYR B 973 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ASP B 978 " --> pdb=" O VAL B 974 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE B 979 " --> pdb=" O ARG B 975 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N VAL B 982 " --> pdb=" O ASP B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 986 through 997 removed outlier: 3.733A pdb=" N ILE B 993 " --> pdb=" O TYR B 989 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLY B 994 " --> pdb=" O VAL B 990 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS B 995 " --> pdb=" O MET B 991 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL B 997 " --> pdb=" O ILE B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1001 through 1022 removed outlier: 3.681A pdb=" N VAL B1010 " --> pdb=" O ILE B1006 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU B1011 " --> pdb=" O MET B1007 " (cutoff:3.500A) Proline residue: B1017 - end of helix Processing helix chain 'B' and resid 1031 through 1034 No H-bonds generated for 'chain 'B' and resid 1031 through 1034' Processing helix chain 'B' and resid 1039 through 1042 No H-bonds generated for 'chain 'B' and resid 1039 through 1042' Processing helix chain 'B' and resid 1073 through 1084 Processing helix chain 'B' and resid 1089 through 1098 removed outlier: 3.769A pdb=" N ILE B1093 " --> pdb=" O VAL B1089 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA B1094 " --> pdb=" O ASN B1090 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN B1098 " --> pdb=" O ALA B1094 " (cutoff:3.500A) Processing helix chain 'B' and resid 1100 through 1122 removed outlier: 4.008A pdb=" N ILE B1106 " --> pdb=" O GLN B1102 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N TYR B1116 " --> pdb=" O LYS B1112 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N HIS B1117 " --> pdb=" O TYR B1113 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA B1121 " --> pdb=" O HIS B1117 " (cutoff:3.500A) Processing helix chain 'B' and resid 1133 through 1144 Processing helix chain 'B' and resid 1164 through 1190 removed outlier: 3.609A pdb=" N LYS B1168 " --> pdb=" O GLU B1164 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP B1187 " --> pdb=" O ASP B1183 " (cutoff:3.500A) Processing helix chain 'B' and resid 1193 through 1225 removed outlier: 3.783A pdb=" N VAL B1214 " --> pdb=" O GLN B1210 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG B1223 " --> pdb=" O ASN B1219 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 10 Processing helix chain 'C' and resid 32 through 39 removed outlier: 3.647A pdb=" N GLN C 37 " --> pdb=" O CYS C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 50 No H-bonds generated for 'chain 'C' and resid 48 through 50' 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 117 through 125 Processing helix chain 'C' and resid 150 through 165 removed outlier: 3.613A pdb=" N LEU C 156 " --> pdb=" O ILE C 152 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLY C 157 " --> pdb=" O LYS C 153 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS C 162 " --> pdb=" O LYS C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 191 removed outlier: 3.563A pdb=" N ASP C 186 " --> pdb=" O LYS C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 216 Processing helix chain 'C' and resid 260 through 271 removed outlier: 4.279A pdb=" N GLU C 265 " --> pdb=" O ARG C 261 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU C 267 " --> pdb=" O ARG C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 305 removed outlier: 3.773A pdb=" N LEU C 298 " --> pdb=" O PRO C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 331 Processing helix chain 'C' and resid 340 through 342 No H-bonds generated for 'chain 'C' and resid 340 through 342' Processing helix chain 'C' and resid 345 through 354 removed outlier: 3.848A pdb=" N PHE C 354 " --> pdb=" O ILE C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 373 removed outlier: 3.512A pdb=" N HIS C 363 " --> pdb=" O SER C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 401 removed outlier: 3.703A pdb=" N LEU C 399 " --> pdb=" O ILE C 395 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU C 400 " --> pdb=" O LEU C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 416 removed outlier: 3.860A pdb=" N LEU C 413 " --> pdb=" O ASP C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 426 removed outlier: 3.612A pdb=" N ASN C 425 " --> pdb=" O ASP C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 448 removed outlier: 3.708A pdb=" N ASP C 445 " --> pdb=" O GLN C 441 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL C 448 " --> pdb=" O LEU C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 461 Processing helix chain 'C' and resid 471 through 478 removed outlier: 3.832A pdb=" N TYR C 478 " --> pdb=" O LEU C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 496 Processing helix chain 'C' and resid 509 through 519 Processing helix chain 'C' and resid 527 through 529 No H-bonds generated for 'chain 'C' and resid 527 through 529' Processing helix chain 'C' and resid 531 through 538 Processing helix chain 'C' and resid 622 through 631 removed outlier: 3.575A pdb=" N LEU C 626 " --> pdb=" O LEU C 622 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE C 627 " --> pdb=" O ASN C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 643 removed outlier: 3.711A pdb=" N PHE C 640 " --> pdb=" O VAL C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 668 removed outlier: 3.640A pdb=" N TYR C 664 " --> pdb=" O ARG C 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 676 through 698 removed outlier: 3.554A pdb=" N PHE C 686 " --> pdb=" O TYR C 682 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL C 691 " --> pdb=" O GLY C 687 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN C 696 " --> pdb=" O GLU C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 702 through 707 Processing helix chain 'C' and resid 731 through 734 No H-bonds generated for 'chain 'C' and resid 731 through 734' Processing helix chain 'C' and resid 741 through 748 Processing helix chain 'C' and resid 758 through 766 Processing helix chain 'C' and resid 768 through 773 removed outlier: 3.631A pdb=" N LEU C 772 " --> pdb=" O PRO C 769 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 796 Processing helix chain 'C' and resid 841 through 849 removed outlier: 3.685A pdb=" N TYR C 846 " --> pdb=" O THR C 842 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA C 847 " --> pdb=" O ARG C 843 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N PHE C 848 " --> pdb=" O LYS C 844 " (cutoff:3.500A) Processing helix chain 'C' and resid 852 through 857 Processing helix chain 'C' and resid 860 through 875 removed outlier: 3.643A pdb=" N GLY C 865 " --> pdb=" O LEU C 861 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N MET C 868 " --> pdb=" O LEU C 864 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU C 869 " --> pdb=" O GLY C 865 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE C 872 " --> pdb=" O MET C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 905 removed outlier: 3.541A pdb=" N VAL C 904 " --> pdb=" O LYS C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 918 removed outlier: 3.818A pdb=" N LYS C 917 " --> pdb=" O SER C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 923 through 943 removed outlier: 3.581A pdb=" N PHE C 936 " --> pdb=" O ILE C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 956 through 982 removed outlier: 5.218A pdb=" N ILE C 970 " --> pdb=" O CYS C 966 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N PHE C 971 " --> pdb=" O LEU C 967 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TRP C 972 " --> pdb=" O ASN C 968 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU C 976 " --> pdb=" O TRP C 972 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEU C 977 " --> pdb=" O TYR C 973 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ASP C 978 " --> pdb=" O VAL C 974 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE C 979 " --> pdb=" O ARG C 975 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N VAL C 982 " --> pdb=" O ASP C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 997 removed outlier: 3.732A pdb=" N ILE C 993 " --> pdb=" O TYR C 989 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLY C 994 " --> pdb=" O VAL C 990 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS C 995 " --> pdb=" O MET C 991 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL C 997 " --> pdb=" O ILE C 993 " (cutoff:3.500A) Processing helix chain 'C' and resid 1001 through 1022 removed outlier: 3.681A pdb=" N VAL C1010 " --> pdb=" O ILE C1006 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU C1011 " --> pdb=" O MET C1007 " (cutoff:3.500A) Proline residue: C1017 - end of helix Processing helix chain 'C' and resid 1031 through 1034 No H-bonds generated for 'chain 'C' and resid 1031 through 1034' Processing helix chain 'C' and resid 1039 through 1042 No H-bonds generated for 'chain 'C' and resid 1039 through 1042' Processing helix chain 'C' and resid 1073 through 1084 Processing helix chain 'C' and resid 1089 through 1098 removed outlier: 3.769A pdb=" N ILE C1093 " --> pdb=" O VAL C1089 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA C1094 " --> pdb=" O ASN C1090 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN C1098 " --> pdb=" O ALA C1094 " (cutoff:3.500A) Processing helix chain 'C' and resid 1100 through 1122 removed outlier: 4.008A pdb=" N ILE C1106 " --> pdb=" O GLN C1102 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N TYR C1116 " --> pdb=" O LYS C1112 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N HIS C1117 " --> pdb=" O TYR C1113 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA C1121 " --> pdb=" O HIS C1117 " (cutoff:3.500A) Processing helix chain 'C' and resid 1133 through 1144 Processing helix chain 'C' and resid 1164 through 1190 removed outlier: 3.607A pdb=" N LYS C1168 " --> pdb=" O GLU C1164 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASP C1187 " --> pdb=" O ASP C1183 " (cutoff:3.500A) Processing helix chain 'C' and resid 1193 through 1225 removed outlier: 3.783A pdb=" N VAL C1214 " --> pdb=" O GLN C1210 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG C1223 " --> pdb=" O ASN C1219 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 10 Processing helix chain 'D' and resid 32 through 39 removed outlier: 3.648A pdb=" N GLN D 37 " --> pdb=" O CYS D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 50 No H-bonds generated for 'chain 'D' and resid 48 through 50' 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 117 through 125 Processing helix chain 'D' and resid 150 through 165 removed outlier: 3.614A pdb=" N LEU D 156 " --> pdb=" O ILE D 152 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N GLY D 157 " --> pdb=" O LYS D 153 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS D 162 " --> pdb=" O LYS D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 191 removed outlier: 3.563A pdb=" N ASP D 186 " --> pdb=" O LYS D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 216 Processing helix chain 'D' and resid 260 through 271 removed outlier: 4.279A pdb=" N GLU D 265 " --> pdb=" O ARG D 261 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU D 267 " --> pdb=" O ARG D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 305 removed outlier: 3.772A pdb=" N LEU D 298 " --> pdb=" O PRO D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 331 Processing helix chain 'D' and resid 340 through 342 No H-bonds generated for 'chain 'D' and resid 340 through 342' Processing helix chain 'D' and resid 345 through 354 removed outlier: 3.848A pdb=" N PHE D 354 " --> pdb=" O ILE D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 373 removed outlier: 3.512A pdb=" N HIS D 363 " --> pdb=" O SER D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 401 removed outlier: 3.703A pdb=" N LEU D 399 " --> pdb=" O ILE D 395 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU D 400 " --> pdb=" O LEU D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 416 removed outlier: 3.860A pdb=" N LEU D 413 " --> pdb=" O ASP D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 426 removed outlier: 3.611A pdb=" N ASN D 425 " --> pdb=" O ASP D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 448 removed outlier: 3.708A pdb=" N ASP D 445 " --> pdb=" O GLN D 441 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL D 448 " --> pdb=" O LEU D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 461 Processing helix chain 'D' and resid 471 through 478 removed outlier: 3.832A pdb=" N TYR D 478 " --> pdb=" O LEU D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 496 Processing helix chain 'D' and resid 509 through 519 Processing helix chain 'D' and resid 527 through 529 No H-bonds generated for 'chain 'D' and resid 527 through 529' Processing helix chain 'D' and resid 531 through 538 Processing helix chain 'D' and resid 622 through 631 removed outlier: 3.575A pdb=" N LEU D 626 " --> pdb=" O LEU D 622 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ILE D 627 " --> pdb=" O ASN D 623 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 643 removed outlier: 3.710A pdb=" N PHE D 640 " --> pdb=" O VAL D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 668 removed outlier: 3.640A pdb=" N TYR D 664 " --> pdb=" O ARG D 660 " (cutoff:3.500A) Processing helix chain 'D' and resid 676 through 698 removed outlier: 3.554A pdb=" N PHE D 686 " --> pdb=" O TYR D 682 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL D 691 " --> pdb=" O GLY D 687 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN D 696 " --> pdb=" O GLU D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 702 through 707 Processing helix chain 'D' and resid 731 through 734 No H-bonds generated for 'chain 'D' and resid 731 through 734' Processing helix chain 'D' and resid 741 through 748 Processing helix chain 'D' and resid 758 through 766 Processing helix chain 'D' and resid 768 through 773 removed outlier: 3.631A pdb=" N LEU D 772 " --> pdb=" O PRO D 769 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 796 Processing helix chain 'D' and resid 841 through 849 removed outlier: 3.685A pdb=" N TYR D 846 " --> pdb=" O THR D 842 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA D 847 " --> pdb=" O ARG D 843 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N PHE D 848 " --> pdb=" O LYS D 844 " (cutoff:3.500A) Processing helix chain 'D' and resid 852 through 857 Processing helix chain 'D' and resid 860 through 875 removed outlier: 3.642A pdb=" N GLY D 865 " --> pdb=" O LEU D 861 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N MET D 868 " --> pdb=" O LEU D 864 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU D 869 " --> pdb=" O GLY D 865 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE D 872 " --> pdb=" O MET D 868 " (cutoff:3.500A) Processing helix chain 'D' and resid 884 through 905 removed outlier: 3.541A pdb=" N VAL D 904 " --> pdb=" O LYS D 900 " (cutoff:3.500A) Processing helix chain 'D' and resid 912 through 918 removed outlier: 3.818A pdb=" N LYS D 917 " --> pdb=" O SER D 913 " (cutoff:3.500A) Processing helix chain 'D' and resid 923 through 943 removed outlier: 3.581A pdb=" N PHE D 936 " --> pdb=" O ILE D 932 " (cutoff:3.500A) Processing helix chain 'D' and resid 956 through 982 removed outlier: 5.219A pdb=" N ILE D 970 " --> pdb=" O CYS D 966 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N PHE D 971 " --> pdb=" O LEU D 967 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TRP D 972 " --> pdb=" O ASN D 968 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU D 976 " --> pdb=" O TRP D 972 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LEU D 977 " --> pdb=" O TYR D 973 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ASP D 978 " --> pdb=" O VAL D 974 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE D 979 " --> pdb=" O ARG D 975 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL D 982 " --> pdb=" O ASP D 978 " (cutoff:3.500A) Processing helix chain 'D' and resid 986 through 997 removed outlier: 3.732A pdb=" N ILE D 993 " --> pdb=" O TYR D 989 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLY D 994 " --> pdb=" O VAL D 990 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS D 995 " --> pdb=" O MET D 991 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL D 997 " --> pdb=" O ILE D 993 " (cutoff:3.500A) Processing helix chain 'D' and resid 1001 through 1022 removed outlier: 3.681A pdb=" N VAL D1010 " --> pdb=" O ILE D1006 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU D1011 " --> pdb=" O MET D1007 " (cutoff:3.500A) Proline residue: D1017 - end of helix Processing helix chain 'D' and resid 1031 through 1034 No H-bonds generated for 'chain 'D' and resid 1031 through 1034' Processing helix chain 'D' and resid 1039 through 1042 No H-bonds generated for 'chain 'D' and resid 1039 through 1042' Processing helix chain 'D' and resid 1073 through 1084 Processing helix chain 'D' and resid 1089 through 1098 removed outlier: 3.769A pdb=" N ILE D1093 " --> pdb=" O VAL D1089 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA D1094 " --> pdb=" O ASN D1090 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN D1098 " --> pdb=" O ALA D1094 " (cutoff:3.500A) Processing helix chain 'D' and resid 1100 through 1122 removed outlier: 4.008A pdb=" N ILE D1106 " --> pdb=" O GLN D1102 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N TYR D1116 " --> pdb=" O LYS D1112 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N HIS D1117 " --> pdb=" O TYR D1113 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA D1121 " --> pdb=" O HIS D1117 " (cutoff:3.500A) Processing helix chain 'D' and resid 1133 through 1144 Processing helix chain 'D' and resid 1164 through 1190 removed outlier: 3.608A pdb=" N LYS D1168 " --> pdb=" O GLU D1164 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP D1187 " --> pdb=" O ASP D1183 " (cutoff:3.500A) Processing helix chain 'D' and resid 1193 through 1225 removed outlier: 3.783A pdb=" N VAL D1214 " --> pdb=" O GLN D1210 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG D1223 " --> pdb=" O ASN D1219 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 12 through 14 Processing sheet with id= B, first strand: chain 'A' and resid 136 through 138 Processing sheet with id= C, first strand: chain 'A' and resid 91 through 95 removed outlier: 5.952A pdb=" N GLY A 218 " --> pdb=" O TYR A 92 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N VAL A 94 " --> pdb=" O GLY A 218 " (cutoff:3.500A) removed outlier: 9.063A pdb=" N ASP A 220 " --> pdb=" O VAL A 94 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 12 through 14 Processing sheet with id= E, first strand: chain 'B' and resid 136 through 138 Processing sheet with id= F, first strand: chain 'B' and resid 91 through 95 removed outlier: 5.952A pdb=" N GLY B 218 " --> pdb=" O TYR B 92 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N VAL B 94 " --> pdb=" O GLY B 218 " (cutoff:3.500A) removed outlier: 9.063A pdb=" N ASP B 220 " --> pdb=" O VAL B 94 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'C' and resid 12 through 14 Processing sheet with id= H, first strand: chain 'C' and resid 136 through 138 Processing sheet with id= I, first strand: chain 'C' and resid 91 through 95 removed outlier: 5.952A pdb=" N GLY C 218 " --> pdb=" O TYR C 92 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N VAL C 94 " --> pdb=" O GLY C 218 " (cutoff:3.500A) removed outlier: 9.063A pdb=" N ASP C 220 " --> pdb=" O VAL C 94 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'D' and resid 12 through 14 Processing sheet with id= K, first strand: chain 'D' and resid 136 through 138 Processing sheet with id= L, first strand: chain 'D' and resid 91 through 95 removed outlier: 5.952A pdb=" N GLY D 218 " --> pdb=" O TYR D 92 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N VAL D 94 " --> pdb=" O GLY D 218 " (cutoff:3.500A) removed outlier: 9.062A pdb=" N ASP D 220 " --> pdb=" O VAL D 94 " (cutoff:3.500A) No H-bonds generated for sheet with id= L 1312 hydrogen bonds defined for protein. 3900 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: 27.41 Time building geometry restraints manager: 49.87 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: 36074 1.03 - 1.24: 4947 1.24 - 1.45: 11960 1.45 - 1.66: 22231 1.66 - 1.87: 400 Bond restraints: 75612 Sorted by residual: bond pdb=" C24 3FD D1306 " pdb=" C25 3FD D1306 " ideal model delta sigma weight residual 1.530 1.256 0.274 2.00e-02 2.50e+03 1.88e+02 bond pdb=" C24 3FD B1306 " pdb=" C25 3FD B1306 " ideal model delta sigma weight residual 1.530 1.259 0.271 2.00e-02 2.50e+03 1.84e+02 bond pdb=" C24 3FD C1304 " pdb=" C25 3FD C1304 " ideal model delta sigma weight residual 1.530 1.260 0.270 2.00e-02 2.50e+03 1.82e+02 bond pdb=" C24 3FD A1303 " pdb=" C25 3FD A1303 " ideal model delta sigma weight residual 1.530 1.260 0.270 2.00e-02 2.50e+03 1.82e+02 bond pdb=" C29 POV A1312 " pdb="C210 POV A1312 " ideal model delta sigma weight residual 1.333 1.511 -0.178 2.00e-02 2.50e+03 7.92e+01 ... (remaining 75607 not shown) Histogram of bond angle deviations from ideal: 73.32 - 94.55: 3 94.55 - 115.79: 95852 115.79 - 137.03: 39345 137.03 - 158.27: 0 158.27 - 179.50: 4 Bond angle restraints: 135204 Sorted by residual: angle pdb=" CB LEU B 474 " pdb=" CG LEU B 474 " pdb=" HG LEU B 474 " ideal model delta sigma weight residual 109.00 73.32 35.68 3.00e+00 1.11e-01 1.41e+02 angle pdb=" CD1 LEU B 474 " pdb=" CG LEU B 474 " pdb=" HG LEU B 474 " ideal model delta sigma weight residual 108.00 75.13 32.87 3.00e+00 1.11e-01 1.20e+02 angle pdb=" CD2 LEU B 474 " pdb=" CG LEU B 474 " pdb=" HG LEU B 474 " ideal model delta sigma weight residual 108.00 76.09 31.91 3.00e+00 1.11e-01 1.13e+02 angle pdb=" CG1 ILE A 510 " pdb=" CD1 ILE A 510 " pdb="HD13 ILE A 510 " ideal model delta sigma weight residual 109.00 124.50 -15.50 3.00e+00 1.11e-01 2.67e+01 angle pdb=" CG1 ILE D 510 " pdb=" CD1 ILE D 510 " pdb="HD13 ILE D 510 " ideal model delta sigma weight residual 109.00 124.50 -15.50 3.00e+00 1.11e-01 2.67e+01 ... (remaining 135199 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.23: 35446 35.23 - 70.45: 1189 70.45 - 105.68: 164 105.68 - 140.91: 47 140.91 - 176.13: 26 Dihedral angle restraints: 36872 sinusoidal: 21164 harmonic: 15708 Sorted by residual: dihedral pdb=" CA LEU C 338 " pdb=" C LEU C 338 " pdb=" N PRO C 339 " pdb=" CA PRO C 339 " ideal model delta harmonic sigma weight residual -180.00 -129.92 -50.08 0 5.00e+00 4.00e-02 1.00e+02 dihedral pdb=" CA LEU A 338 " pdb=" C LEU A 338 " pdb=" N PRO A 339 " pdb=" CA PRO A 339 " ideal model delta harmonic sigma weight residual -180.00 -129.93 -50.07 0 5.00e+00 4.00e-02 1.00e+02 dihedral pdb=" CA LEU B 338 " pdb=" C LEU B 338 " pdb=" N PRO B 339 " pdb=" CA PRO B 339 " ideal model delta harmonic sigma weight residual -180.00 -129.96 -50.04 0 5.00e+00 4.00e-02 1.00e+02 ... (remaining 36869 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 4563 0.077 - 0.154: 961 0.154 - 0.231: 138 0.231 - 0.308: 13 0.308 - 0.385: 9 Chirality restraints: 5684 Sorted by residual: chirality pdb=" CG LEU A 474 " pdb=" CB LEU A 474 " pdb=" CD1 LEU A 474 " pdb=" CD2 LEU A 474 " both_signs ideal model delta sigma weight residual False -2.59 -2.20 -0.39 2.00e-01 2.50e+01 3.71e+00 chirality pdb=" CG LEU D 474 " pdb=" CB LEU D 474 " pdb=" CD1 LEU D 474 " pdb=" CD2 LEU D 474 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" CG LEU C 474 " pdb=" CB LEU C 474 " pdb=" CD1 LEU C 474 " pdb=" CD2 LEU C 474 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.66e+00 ... (remaining 5681 not shown) Planarity restraints: 10580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 50 " -0.146 2.00e-02 2.50e+03 1.63e-01 3.99e+02 pdb=" CD GLN B 50 " 0.005 2.00e-02 2.50e+03 pdb=" OE1 GLN B 50 " 0.144 2.00e-02 2.50e+03 pdb=" NE2 GLN B 50 " 0.002 2.00e-02 2.50e+03 pdb="HE21 GLN B 50 " 0.240 2.00e-02 2.50e+03 pdb="HE22 GLN B 50 " -0.245 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 50 " 0.145 2.00e-02 2.50e+03 1.63e-01 3.97e+02 pdb=" CD GLN A 50 " -0.005 2.00e-02 2.50e+03 pdb=" OE1 GLN A 50 " -0.144 2.00e-02 2.50e+03 pdb=" NE2 GLN A 50 " -0.002 2.00e-02 2.50e+03 pdb="HE21 GLN A 50 " -0.239 2.00e-02 2.50e+03 pdb="HE22 GLN A 50 " 0.245 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN D 50 " 0.145 2.00e-02 2.50e+03 1.63e-01 3.97e+02 pdb=" CD GLN D 50 " -0.005 2.00e-02 2.50e+03 pdb=" OE1 GLN D 50 " -0.144 2.00e-02 2.50e+03 pdb=" NE2 GLN D 50 " -0.002 2.00e-02 2.50e+03 pdb="HE21 GLN D 50 " -0.239 2.00e-02 2.50e+03 pdb="HE22 GLN D 50 " 0.244 2.00e-02 2.50e+03 ... (remaining 10577 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.22: 6117 2.22 - 2.81: 163222 2.81 - 3.41: 200373 3.41 - 4.00: 276605 4.00 - 4.60: 431369 Nonbonded interactions: 1077686 Sorted by model distance: nonbonded pdb=" O PRO D1040 " pdb=" HH TYR D1080 " model vdw 1.623 1.850 nonbonded pdb=" O PRO B1040 " pdb=" HH TYR B1080 " model vdw 1.624 1.850 nonbonded pdb=" O PRO A1040 " pdb=" HH TYR A1080 " model vdw 1.624 1.850 nonbonded pdb=" O PRO C1040 " pdb=" HH TYR C1080 " model vdw 1.626 1.850 nonbonded pdb=" O CYS A 36 " pdb=" H VAL A 40 " model vdw 1.652 1.850 ... (remaining 1077681 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 through 1302 or resid 1308 th \ rough 1310 or (resid 1311 and (name N or name C1 or name C11 or name C12 or name \ C13 or name C14 or name C15 or name C2 or name C21 or name C22 or name C23 or n \ ame C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name O11 \ or name O12 or name O13 or name O14 or name O21 or name O22 or name P or name C2 \ 10 or name C211 or name C212 or name C213 or name C214 or name C215 or name C216 \ or name C217 or name C218)) or resid 1312 or resid 1314)) selection = (chain 'B' and (resid 3 through 1230 or resid 1301 through 1302 or resid 1308 th \ rough 1309 or (resid 1310 through 1311 and (name N or name C1 or name C11 or nam \ e C12 or name C13 or name C14 or name C15 or name C2 or name C21 or name C22 or \ name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 \ or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 or name \ P or name C210 or name C211 or name C212 or name C213 or name C214 or name C215 \ or name C216 or name C217 or name C218)) or (resid 1312 and (name C22 or name C \ 23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 or na \ me C210 or name C211 or name C212 or name C213 or name C214 or name C215 or name \ C216)) or resid 1314)) selection = (chain 'C' and (resid 3 through 1230 or resid 1301 through 1302 or resid 1308 th \ rough 1309 or (resid 1310 through 1311 and (name N or name C1 or name C11 or nam \ e C12 or name C13 or name C14 or name C15 or name C2 or name C21 or name C22 or \ name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 \ or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 or name \ P or name C210 or name C211 or name C212 or name C213 or name C214 or name C215 \ or name C216 or name C217 or name C218)) or (resid 1312 and (name C22 or name C \ 23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 or na \ me C210 or name C211 or name C212 or name C213 or name C214 or name C215 or name \ C216)) or resid 1314)) selection = (chain 'D' and (resid 3 through 1230 or resid 1301 through 1302 or resid 1308 th \ rough 1309 or (resid 1310 through 1311 and (name N or name C1 or name C11 or nam \ e C12 or name C13 or name C14 or name C15 or name C2 or name C21 or name C22 or \ name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 \ or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 or name \ P or name C210 or name C211 or name C212 or name C213 or name C214 or name C215 \ or name C216 or name C217 or name C218)) or (resid 1312 and (name C22 or name C \ 23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 or na \ me C210 or name C211 or name C212 or name C213 or name C214 or name C215 or name \ C216)) or resid 1314)) } 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: 3.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.860 Extract box with map and model: 9.180 Check model and map are aligned: 0.840 Set scattering table: 0.530 Process input model: 181.750 Find NCS groups from input model: 3.470 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 212.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 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 0.274 39468 Z= 0.889 Angle : 1.312 14.245 53048 Z= 0.689 Chirality : 0.065 0.385 5684 Planarity : 0.008 0.085 6352 Dihedral : 19.114 176.134 16232 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.73 % Allowed : 12.69 % Favored : 86.58 % Rotamer: Outliers : 0.41 % Allowed : 4.49 % Favored : 95.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.28 % 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: -5.92 (0.09), residues: 4388 helix: -3.88 (0.06), residues: 2612 sheet: -3.63 (0.44), residues: 96 loop : -3.77 (0.13), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B1111 HIS 0.016 0.002 HIS C 183 PHE 0.067 0.004 PHE A 858 TYR 0.033 0.004 TYR B 953 ARG 0.013 0.002 ARG D 320 *********************** 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 809 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 793 time to evaluate : 4.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 ARG cc_start: 0.7561 (ttt-90) cc_final: 0.6729 (ttt-90) REVERT: A 270 ILE cc_start: 0.7842 (mm) cc_final: 0.7578 (tp) REVERT: A 329 HIS cc_start: 0.6871 (t-90) cc_final: 0.6349 (t70) REVERT: A 457 LEU cc_start: 0.8633 (tp) cc_final: 0.8422 (tp) REVERT: A 681 GLN cc_start: 0.8129 (tp40) cc_final: 0.7831 (tp-100) REVERT: A 913 SER cc_start: 0.8553 (m) cc_final: 0.8342 (t) REVERT: A 1190 ASN cc_start: 0.8354 (m-40) cc_final: 0.7999 (m-40) REVERT: A 1194 GLU cc_start: 0.7925 (tp30) cc_final: 0.7609 (tp30) REVERT: B 110 ARG cc_start: 0.7534 (ttt-90) cc_final: 0.6697 (ttt-90) REVERT: B 270 ILE cc_start: 0.7860 (mm) cc_final: 0.7595 (tp) REVERT: B 329 HIS cc_start: 0.6821 (t-90) cc_final: 0.6294 (t70) REVERT: B 457 LEU cc_start: 0.8623 (tp) cc_final: 0.8414 (tp) REVERT: B 681 GLN cc_start: 0.8095 (tp40) cc_final: 0.7820 (tp-100) REVERT: B 913 SER cc_start: 0.8575 (m) cc_final: 0.8368 (t) REVERT: B 1190 ASN cc_start: 0.8366 (m-40) cc_final: 0.8000 (m-40) REVERT: B 1194 GLU cc_start: 0.7943 (tp30) cc_final: 0.7645 (tp30) REVERT: C 110 ARG cc_start: 0.7619 (ttt-90) cc_final: 0.6584 (ttt-90) REVERT: C 270 ILE cc_start: 0.7903 (mm) cc_final: 0.7661 (tp) REVERT: C 329 HIS cc_start: 0.6803 (t-90) cc_final: 0.6286 (t70) REVERT: C 457 LEU cc_start: 0.8640 (tp) cc_final: 0.8434 (tp) REVERT: C 681 GLN cc_start: 0.8103 (tp40) cc_final: 0.7815 (tp-100) REVERT: C 913 SER cc_start: 0.8580 (m) cc_final: 0.8375 (t) REVERT: C 1190 ASN cc_start: 0.8374 (m-40) cc_final: 0.8021 (m-40) REVERT: D 110 ARG cc_start: 0.7584 (ttt-90) cc_final: 0.6604 (ttt-90) REVERT: D 270 ILE cc_start: 0.7826 (mm) cc_final: 0.7536 (tp) REVERT: D 329 HIS cc_start: 0.6905 (t-90) cc_final: 0.6387 (t70) REVERT: D 457 LEU cc_start: 0.8588 (tp) cc_final: 0.8348 (tp) REVERT: D 681 GLN cc_start: 0.8111 (tp40) cc_final: 0.7794 (tp-100) REVERT: D 913 SER cc_start: 0.8531 (m) cc_final: 0.8300 (t) REVERT: D 1190 ASN cc_start: 0.8273 (m-40) cc_final: 0.7914 (m-40) REVERT: D 1194 GLU cc_start: 0.7999 (tp30) cc_final: 0.7689 (tp30) outliers start: 16 outliers final: 4 residues processed: 808 average time/residue: 2.5087 time to fit residues: 2500.5908 Evaluate side-chains 473 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 469 time to evaluate : 4.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain D residue 510 ILE 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: 4.9990 chunk 185 optimal weight: 0.6980 chunk 113 optimal weight: 9.9990 chunk 224 optimal weight: 8.9990 chunk 178 optimal weight: 3.9990 chunk 344 optimal weight: 7.9990 chunk 133 optimal weight: 8.9990 chunk 209 optimal weight: 0.7980 chunk 256 optimal weight: 5.9990 chunk 399 optimal weight: 2.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS A 271 ASN ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 HIS A 404 ASN A 635 GLN A 859 ASN ** A 956 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1098 GLN A1123 HIS B 183 HIS B 271 ASN ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 HIS B 404 ASN B 859 ASN ** B 956 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1098 GLN B1123 HIS C 183 HIS ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 HIS C 404 ASN C 859 ASN ** C 956 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1098 GLN C1123 HIS D 183 HIS ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 388 HIS D 404 ASN D 635 GLN D 859 ASN ** D 956 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1098 GLN D1123 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 39468 Z= 0.266 Angle : 0.681 11.819 53048 Z= 0.350 Chirality : 0.048 1.785 5684 Planarity : 0.006 0.061 6352 Dihedral : 21.304 177.176 7560 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.36 % Allowed : 11.67 % Favored : 87.97 % Rotamer: Outliers : 1.89 % Allowed : 11.90 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.16 (0.11), residues: 4388 helix: -2.21 (0.09), residues: 2644 sheet: -5.04 (0.28), residues: 164 loop : -3.23 (0.14), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D1111 HIS 0.013 0.002 HIS A 244 PHE 0.023 0.002 PHE A 858 TYR 0.015 0.002 TYR C 659 ARG 0.009 0.001 ARG C1198 *********************** 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 632 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 558 time to evaluate : 4.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 270 ILE cc_start: 0.7786 (mm) cc_final: 0.7524 (tp) REVERT: A 329 HIS cc_start: 0.6971 (t-90) cc_final: 0.6501 (t70) REVERT: A 461 ASN cc_start: 0.7167 (m110) cc_final: 0.6958 (m110) REVERT: A 470 THR cc_start: 0.8656 (p) cc_final: 0.8288 (t) REVERT: A 681 GLN cc_start: 0.8025 (tp40) cc_final: 0.7702 (tp-100) REVERT: A 913 SER cc_start: 0.8377 (m) cc_final: 0.8147 (t) REVERT: A 1190 ASN cc_start: 0.8286 (m-40) cc_final: 0.7982 (m-40) REVERT: A 1194 GLU cc_start: 0.7693 (tp30) cc_final: 0.7391 (tm-30) REVERT: B 270 ILE cc_start: 0.7811 (mm) cc_final: 0.7555 (tp) REVERT: B 329 HIS cc_start: 0.7032 (t-90) cc_final: 0.6463 (t70) REVERT: B 379 THR cc_start: 0.8041 (p) cc_final: 0.7841 (t) REVERT: B 461 ASN cc_start: 0.7175 (m110) cc_final: 0.6957 (m110) REVERT: B 470 THR cc_start: 0.8685 (p) cc_final: 0.8319 (t) REVERT: B 681 GLN cc_start: 0.7998 (tp40) cc_final: 0.7699 (tp-100) REVERT: B 913 SER cc_start: 0.8371 (m) cc_final: 0.8158 (t) REVERT: B 1190 ASN cc_start: 0.8283 (m-40) cc_final: 0.8003 (m-40) REVERT: B 1194 GLU cc_start: 0.7680 (tp30) cc_final: 0.7405 (tm-30) REVERT: C 270 ILE cc_start: 0.7861 (mm) cc_final: 0.7618 (tp) REVERT: C 329 HIS cc_start: 0.6993 (t-90) cc_final: 0.6437 (t70) REVERT: C 379 THR cc_start: 0.8065 (p) cc_final: 0.7860 (t) REVERT: C 461 ASN cc_start: 0.7191 (m110) cc_final: 0.6944 (m110) REVERT: C 470 THR cc_start: 0.8645 (p) cc_final: 0.8280 (t) REVERT: C 681 GLN cc_start: 0.7992 (tp40) cc_final: 0.7686 (tp-100) REVERT: C 913 SER cc_start: 0.8400 (m) cc_final: 0.8178 (t) REVERT: C 1190 ASN cc_start: 0.8308 (m-40) cc_final: 0.8009 (m-40) REVERT: C 1194 GLU cc_start: 0.7528 (mm-30) cc_final: 0.7087 (tm-30) REVERT: D 270 ILE cc_start: 0.7789 (mm) cc_final: 0.7498 (tp) REVERT: D 301 LEU cc_start: 0.8722 (tp) cc_final: 0.8329 (tp) REVERT: D 329 HIS cc_start: 0.7146 (t-90) cc_final: 0.6576 (t70) REVERT: D 379 THR cc_start: 0.8081 (p) cc_final: 0.7856 (t) REVERT: D 461 ASN cc_start: 0.7201 (m110) cc_final: 0.6982 (m110) REVERT: D 470 THR cc_start: 0.8667 (p) cc_final: 0.8278 (t) REVERT: D 681 GLN cc_start: 0.8009 (tp40) cc_final: 0.7679 (tp-100) REVERT: D 913 SER cc_start: 0.8353 (m) cc_final: 0.8105 (t) REVERT: D 1000 MET cc_start: 0.8447 (ptt) cc_final: 0.8246 (ptt) REVERT: D 1190 ASN cc_start: 0.8210 (m-40) cc_final: 0.7842 (m-40) REVERT: D 1194 GLU cc_start: 0.7734 (tp30) cc_final: 0.7384 (tm-30) outliers start: 74 outliers final: 28 residues processed: 611 average time/residue: 2.4007 time to fit residues: 1841.4895 Evaluate side-chains 420 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 392 time to evaluate : 4.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 759 TYR Chi-restraints excluded: chain A residue 999 ASN Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 759 TYR Chi-restraints excluded: chain B residue 999 ASN Chi-restraints excluded: chain B residue 1132 LEU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 759 TYR Chi-restraints excluded: chain C residue 999 ASN Chi-restraints excluded: chain C residue 1132 LEU Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 425 ASN Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 759 TYR Chi-restraints excluded: chain D residue 999 ASN Chi-restraints excluded: chain D residue 1132 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 222 optimal weight: 3.9990 chunk 124 optimal weight: 0.0010 chunk 332 optimal weight: 8.9990 chunk 272 optimal weight: 8.9990 chunk 110 optimal weight: 30.0000 chunk 400 optimal weight: 8.9990 chunk 432 optimal weight: 9.9990 chunk 356 optimal weight: 9.9990 chunk 396 optimal weight: 4.9990 chunk 136 optimal weight: 10.0000 chunk 321 optimal weight: 2.9990 overall best weight: 4.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 129 GLN ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 ASN A 635 GLN A 700 GLN A 925 ASN ** A 956 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1098 GLN A1171 HIS B 129 GLN B 140 HIS ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 ASN B 925 ASN ** B 956 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1098 GLN B1171 HIS C 50 GLN C 129 GLN ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 538 ASN C 925 ASN ** C 956 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1058 ASN C1098 GLN C1171 HIS D 129 GLN D 140 HIS ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 432 GLN D 538 ASN D 635 GLN D 925 ASN ** D 956 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1098 GLN D1171 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 39468 Z= 0.350 Angle : 0.677 10.117 53048 Z= 0.344 Chirality : 0.048 1.771 5684 Planarity : 0.005 0.069 6352 Dihedral : 20.354 172.863 7552 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.46 % Favored : 88.26 % Rotamer: Outliers : 2.12 % Allowed : 16.09 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.35 (0.12), residues: 4388 helix: -1.48 (0.09), residues: 2624 sheet: -4.80 (0.31), residues: 164 loop : -3.07 (0.14), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C1111 HIS 0.010 0.002 HIS D1137 PHE 0.024 0.002 PHE D 858 TYR 0.017 0.002 TYR C 659 ARG 0.007 0.001 ARG C 754 *********************** 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 494 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 411 time to evaluate : 4.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 681 GLN cc_start: 0.8090 (tp40) cc_final: 0.7581 (tp-100) REVERT: A 794 MET cc_start: 0.6499 (OUTLIER) cc_final: 0.6282 (mmt) REVERT: A 913 SER cc_start: 0.8392 (m) cc_final: 0.8137 (t) REVERT: A 1174 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7354 (tp30) REVERT: A 1190 ASN cc_start: 0.8363 (m-40) cc_final: 0.8133 (m-40) REVERT: A 1194 GLU cc_start: 0.7686 (tp30) cc_final: 0.7384 (tm-30) REVERT: A 1222 LYS cc_start: 0.5202 (OUTLIER) cc_final: 0.4967 (mtpp) REVERT: B 329 HIS cc_start: 0.7218 (t-90) cc_final: 0.6498 (t-90) REVERT: B 681 GLN cc_start: 0.8056 (tp40) cc_final: 0.7562 (tp-100) REVERT: B 913 SER cc_start: 0.8470 (m) cc_final: 0.8207 (t) REVERT: B 1174 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7347 (tp30) REVERT: B 1190 ASN cc_start: 0.8369 (m-40) cc_final: 0.8169 (m-40) REVERT: B 1194 GLU cc_start: 0.7686 (tp30) cc_final: 0.7411 (tm-30) REVERT: B 1207 MET cc_start: 0.8533 (mmm) cc_final: 0.8197 (mmm) REVERT: C 681 GLN cc_start: 0.8037 (tp40) cc_final: 0.7528 (tp-100) REVERT: C 913 SER cc_start: 0.8394 (m) cc_final: 0.8145 (t) REVERT: C 1174 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7329 (tp30) REVERT: C 1190 ASN cc_start: 0.8396 (m-40) cc_final: 0.8188 (m-40) REVERT: C 1194 GLU cc_start: 0.7545 (mm-30) cc_final: 0.7087 (tm-30) REVERT: C 1207 MET cc_start: 0.8112 (mtp) cc_final: 0.7844 (mmm) REVERT: D 270 ILE cc_start: 0.7796 (mm) cc_final: 0.7592 (tp) REVERT: D 681 GLN cc_start: 0.8068 (tp40) cc_final: 0.7551 (tp-100) REVERT: D 913 SER cc_start: 0.8449 (m) cc_final: 0.8145 (t) REVERT: D 1174 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7364 (tp30) REVERT: D 1190 ASN cc_start: 0.8306 (m-40) cc_final: 0.7849 (m-40) REVERT: D 1194 GLU cc_start: 0.7738 (tp30) cc_final: 0.7387 (tm-30) REVERT: D 1207 MET cc_start: 0.8537 (mmm) cc_final: 0.8334 (mmm) outliers start: 83 outliers final: 53 residues processed: 469 average time/residue: 2.0281 time to fit residues: 1224.7748 Evaluate side-chains 429 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 370 time to evaluate : 4.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 999 ASN Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1132 LEU Chi-restraints excluded: chain A residue 1171 HIS Chi-restraints excluded: chain A residue 1172 ASP Chi-restraints excluded: chain A residue 1174 GLU Chi-restraints excluded: chain A residue 1222 LYS Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 244 HIS Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 460 GLU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 632 MET Chi-restraints excluded: chain B residue 999 ASN Chi-restraints excluded: chain B residue 1109 ILE Chi-restraints excluded: chain B residue 1132 LEU Chi-restraints excluded: chain B residue 1172 ASP Chi-restraints excluded: chain B residue 1174 GLU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 244 HIS Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 632 MET Chi-restraints excluded: chain C residue 999 ASN Chi-restraints excluded: chain C residue 1109 ILE Chi-restraints excluded: chain C residue 1132 LEU Chi-restraints excluded: chain C residue 1171 HIS Chi-restraints excluded: chain C residue 1172 ASP Chi-restraints excluded: chain C residue 1174 GLU Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 244 HIS Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 425 ASN Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 632 MET Chi-restraints excluded: chain D residue 999 ASN Chi-restraints excluded: chain D residue 1109 ILE Chi-restraints excluded: chain D residue 1132 LEU Chi-restraints excluded: chain D residue 1171 HIS Chi-restraints excluded: chain D residue 1172 ASP Chi-restraints excluded: chain D residue 1174 GLU 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: 4.9990 chunk 207 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 191 optimal weight: 3.9990 chunk 268 optimal weight: 9.9990 chunk 401 optimal weight: 0.6980 chunk 425 optimal weight: 0.9990 chunk 209 optimal weight: 3.9990 chunk 380 optimal weight: 3.9990 chunk 114 optimal weight: 8.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 HIS ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 956 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1084 GLN A1171 HIS ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 956 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1084 GLN B1171 HIS C 140 HIS ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 956 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1084 GLN C1171 HIS D 102 HIS D 240 ASN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 956 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1084 GLN D1171 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.4621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 39468 Z= 0.229 Angle : 0.585 10.079 53048 Z= 0.299 Chirality : 0.045 1.710 5684 Planarity : 0.004 0.048 6352 Dihedral : 18.949 178.109 7552 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.76 % Favored : 89.15 % Rotamer: Outliers : 2.37 % Allowed : 16.78 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.12), residues: 4388 helix: -1.04 (0.10), residues: 2620 sheet: -4.74 (0.31), residues: 164 loop : -2.91 (0.14), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 758 HIS 0.013 0.001 HIS A1171 PHE 0.015 0.002 PHE D 454 TYR 0.015 0.001 TYR B 664 ARG 0.005 0.001 ARG C 754 *********************** 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 468 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 375 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 259 GLU cc_start: 0.6901 (OUTLIER) cc_final: 0.6557 (pt0) REVERT: A 329 HIS cc_start: 0.7235 (t-90) cc_final: 0.6909 (t-90) REVERT: A 671 LEU cc_start: 0.5091 (OUTLIER) cc_final: 0.4849 (pp) REVERT: A 681 GLN cc_start: 0.8129 (tp40) cc_final: 0.7642 (tp-100) REVERT: A 913 SER cc_start: 0.8356 (m) cc_final: 0.8079 (t) REVERT: A 1194 GLU cc_start: 0.7659 (tp30) cc_final: 0.7393 (tm-30) REVERT: A 1195 GLU cc_start: 0.7852 (tp30) cc_final: 0.7644 (tp30) REVERT: A 1207 MET cc_start: 0.8369 (mmm) cc_final: 0.8031 (mmm) REVERT: B 259 GLU cc_start: 0.6765 (OUTLIER) cc_final: 0.6456 (pt0) REVERT: B 460 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.6847 (mp0) REVERT: B 681 GLN cc_start: 0.8095 (tp40) cc_final: 0.7635 (tp-100) REVERT: B 913 SER cc_start: 0.8479 (m) cc_final: 0.8185 (t) REVERT: B 1142 PHE cc_start: 0.6045 (OUTLIER) cc_final: 0.5813 (m-80) REVERT: B 1194 GLU cc_start: 0.7664 (tp30) cc_final: 0.7430 (tm-30) REVERT: C 259 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.6463 (pt0) REVERT: C 329 HIS cc_start: 0.7165 (t-90) cc_final: 0.6824 (t-90) REVERT: C 681 GLN cc_start: 0.8076 (tp40) cc_final: 0.7604 (tp-100) REVERT: C 913 SER cc_start: 0.8366 (m) cc_final: 0.8099 (t) REVERT: C 1142 PHE cc_start: 0.5885 (OUTLIER) cc_final: 0.5678 (m-80) REVERT: C 1190 ASN cc_start: 0.8346 (m-40) cc_final: 0.8129 (m-40) REVERT: C 1194 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7040 (tm-30) REVERT: C 1207 MET cc_start: 0.8059 (mtp) cc_final: 0.7761 (mmm) REVERT: D 259 GLU cc_start: 0.6815 (OUTLIER) cc_final: 0.6533 (pt0) REVERT: D 329 HIS cc_start: 0.7416 (t-90) cc_final: 0.7114 (t-90) REVERT: D 681 GLN cc_start: 0.8087 (tp40) cc_final: 0.7601 (tp-100) REVERT: D 913 SER cc_start: 0.8452 (m) cc_final: 0.8128 (t) REVERT: D 1142 PHE cc_start: 0.5956 (OUTLIER) cc_final: 0.5702 (m-80) REVERT: D 1165 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7385 (tm-30) REVERT: D 1178 VAL cc_start: 0.8866 (t) cc_final: 0.8555 (m) REVERT: D 1194 GLU cc_start: 0.7710 (tp30) cc_final: 0.7370 (tm-30) outliers start: 93 outliers final: 48 residues processed: 448 average time/residue: 2.0808 time to fit residues: 1193.4553 Evaluate side-chains 407 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 349 time to evaluate : 4.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 494 ARG Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 999 ASN Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1132 LEU Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 244 HIS Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 460 GLU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 494 ARG Chi-restraints excluded: chain B residue 999 ASN Chi-restraints excluded: chain B residue 1109 ILE Chi-restraints excluded: chain B residue 1132 LEU Chi-restraints excluded: chain B residue 1142 PHE Chi-restraints excluded: chain B residue 1171 HIS Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 244 HIS Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 632 MET Chi-restraints excluded: chain C residue 759 TYR Chi-restraints excluded: chain C residue 999 ASN Chi-restraints excluded: chain C residue 1109 ILE Chi-restraints excluded: chain C residue 1132 LEU Chi-restraints excluded: chain C residue 1142 PHE Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 244 HIS Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 425 ASN Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 494 ARG Chi-restraints excluded: chain D residue 632 MET Chi-restraints excluded: chain D residue 671 LEU Chi-restraints excluded: chain D residue 759 TYR Chi-restraints excluded: chain D residue 999 ASN Chi-restraints excluded: chain D residue 1109 ILE Chi-restraints excluded: chain D residue 1132 LEU Chi-restraints excluded: chain D residue 1142 PHE Chi-restraints excluded: chain D residue 1165 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 354 optimal weight: 20.0000 chunk 241 optimal weight: 30.0000 chunk 6 optimal weight: 40.0000 chunk 316 optimal weight: 0.8980 chunk 175 optimal weight: 3.9990 chunk 362 optimal weight: 20.0000 chunk 293 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 217 optimal weight: 10.0000 chunk 381 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 956 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 956 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1171 HIS ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 956 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 956 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.4877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 39468 Z= 0.248 Angle : 0.580 10.061 53048 Z= 0.295 Chirality : 0.045 1.680 5684 Planarity : 0.004 0.048 6352 Dihedral : 18.345 179.581 7552 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.87 % Favored : 89.04 % Rotamer: Outliers : 2.66 % Allowed : 17.29 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.12), residues: 4388 helix: -0.74 (0.10), residues: 2624 sheet: -4.64 (0.31), residues: 164 loop : -2.75 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 758 HIS 0.015 0.001 HIS B1171 PHE 0.017 0.002 PHE D 428 TYR 0.016 0.001 TYR D 664 ARG 0.003 0.000 ARG D 634 *********************** 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 465 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 361 time to evaluate : 4.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.6658 (pt0) REVERT: A 681 GLN cc_start: 0.8157 (tp40) cc_final: 0.7731 (tp-100) REVERT: A 913 SER cc_start: 0.8488 (m) cc_final: 0.8176 (t) REVERT: A 1109 ILE cc_start: 0.9021 (OUTLIER) cc_final: 0.8802 (mp) REVERT: A 1194 GLU cc_start: 0.7686 (tp30) cc_final: 0.7394 (tm-30) REVERT: A 1207 MET cc_start: 0.8455 (mmm) cc_final: 0.8242 (mmm) REVERT: B 259 GLU cc_start: 0.6837 (OUTLIER) cc_final: 0.6556 (pt0) REVERT: B 460 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.7058 (mp0) REVERT: B 681 GLN cc_start: 0.8117 (tp40) cc_final: 0.7718 (tp-100) REVERT: B 913 SER cc_start: 0.8536 (m) cc_final: 0.8247 (t) REVERT: B 1109 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8818 (mp) REVERT: B 1142 PHE cc_start: 0.5867 (OUTLIER) cc_final: 0.5665 (m-80) REVERT: B 1194 GLU cc_start: 0.7638 (tp30) cc_final: 0.7400 (tm-30) REVERT: C 259 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.6630 (pt0) REVERT: C 681 GLN cc_start: 0.8102 (tp40) cc_final: 0.7622 (tp-100) REVERT: C 913 SER cc_start: 0.8494 (m) cc_final: 0.8195 (t) REVERT: C 1109 ILE cc_start: 0.9057 (OUTLIER) cc_final: 0.8837 (mp) REVERT: C 1194 GLU cc_start: 0.7490 (mm-30) cc_final: 0.7034 (tm-30) REVERT: C 1207 MET cc_start: 0.8035 (mtp) cc_final: 0.7735 (mmm) REVERT: D 259 GLU cc_start: 0.6829 (OUTLIER) cc_final: 0.6579 (pt0) REVERT: D 681 GLN cc_start: 0.8113 (tp40) cc_final: 0.7628 (tp-100) REVERT: D 913 SER cc_start: 0.8537 (m) cc_final: 0.8203 (t) REVERT: D 1109 ILE cc_start: 0.9044 (OUTLIER) cc_final: 0.8832 (mp) REVERT: D 1142 PHE cc_start: 0.5792 (OUTLIER) cc_final: 0.5572 (m-80) REVERT: D 1165 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7365 (tm-30) REVERT: D 1194 GLU cc_start: 0.7695 (tp30) cc_final: 0.7372 (tm-30) outliers start: 104 outliers final: 49 residues processed: 442 average time/residue: 2.0541 time to fit residues: 1162.9073 Evaluate side-chains 414 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 353 time to evaluate : 4.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 242 HIS Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 494 ARG Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 759 TYR Chi-restraints excluded: chain A residue 999 ASN Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1132 LEU Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 460 GLU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 494 ARG Chi-restraints excluded: chain B residue 759 TYR Chi-restraints excluded: chain B residue 999 ASN Chi-restraints excluded: chain B residue 1109 ILE Chi-restraints excluded: chain B residue 1132 LEU Chi-restraints excluded: chain B residue 1142 PHE Chi-restraints excluded: chain B residue 1211 ILE Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 242 HIS Chi-restraints excluded: chain C residue 244 HIS Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain C residue 494 ARG Chi-restraints excluded: chain C residue 759 TYR Chi-restraints excluded: chain C residue 999 ASN Chi-restraints excluded: chain C residue 1109 ILE Chi-restraints excluded: chain C residue 1132 LEU Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 242 HIS Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 425 ASN Chi-restraints excluded: chain D residue 460 GLU Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 494 ARG Chi-restraints excluded: chain D residue 671 LEU Chi-restraints excluded: chain D residue 999 ASN Chi-restraints excluded: chain D residue 1109 ILE Chi-restraints excluded: chain D residue 1132 LEU Chi-restraints excluded: chain D residue 1142 PHE Chi-restraints excluded: chain D residue 1165 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 143 optimal weight: 0.6980 chunk 383 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 249 optimal weight: 0.0070 chunk 104 optimal weight: 10.0000 chunk 425 optimal weight: 2.9990 chunk 353 optimal weight: 30.0000 chunk 197 optimal weight: 2.9990 chunk 35 optimal weight: 20.0000 chunk 140 optimal weight: 1.9990 chunk 223 optimal weight: 30.0000 overall best weight: 1.7404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 956 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 956 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 956 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1171 HIS D 244 HIS ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 956 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1171 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.5117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 39468 Z= 0.182 Angle : 0.539 9.886 53048 Z= 0.275 Chirality : 0.044 1.665 5684 Planarity : 0.004 0.045 6352 Dihedral : 17.253 178.602 7552 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.76 % Favored : 89.15 % Rotamer: Outliers : 2.43 % Allowed : 17.62 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.13), residues: 4388 helix: -0.40 (0.10), residues: 2632 sheet: -4.41 (0.33), residues: 160 loop : -2.56 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 642 HIS 0.009 0.001 HIS D 140 PHE 0.016 0.001 PHE B 454 TYR 0.016 0.001 TYR D 104 ARG 0.005 0.000 ARG C 110 *********************** 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 467 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 372 time to evaluate : 4.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.6724 (pt0) REVERT: A 681 GLN cc_start: 0.8171 (tp40) cc_final: 0.7703 (tp-100) REVERT: A 913 SER cc_start: 0.8417 (m) cc_final: 0.8118 (t) REVERT: A 1207 MET cc_start: 0.8489 (mmm) cc_final: 0.8214 (mmm) REVERT: B 259 GLU cc_start: 0.6924 (OUTLIER) cc_final: 0.5489 (mm-30) REVERT: B 671 LEU cc_start: 0.5186 (OUTLIER) cc_final: 0.4821 (mt) REVERT: B 681 GLN cc_start: 0.8139 (tp40) cc_final: 0.7696 (tp-100) REVERT: B 913 SER cc_start: 0.8498 (m) cc_final: 0.8208 (t) REVERT: B 1194 GLU cc_start: 0.7653 (tp30) cc_final: 0.7419 (tm-30) REVERT: C 259 GLU cc_start: 0.7006 (OUTLIER) cc_final: 0.6671 (pt0) REVERT: C 671 LEU cc_start: 0.5240 (OUTLIER) cc_final: 0.4811 (mt) REVERT: C 681 GLN cc_start: 0.8098 (tp40) cc_final: 0.7638 (tp-100) REVERT: C 913 SER cc_start: 0.8420 (m) cc_final: 0.8127 (t) REVERT: C 1194 GLU cc_start: 0.7466 (mm-30) cc_final: 0.6997 (tm-30) REVERT: C 1207 MET cc_start: 0.8013 (mtp) cc_final: 0.7705 (mmm) REVERT: D 259 GLU cc_start: 0.6901 (OUTLIER) cc_final: 0.5372 (mm-30) REVERT: D 681 GLN cc_start: 0.8141 (tp40) cc_final: 0.7728 (tp-100) REVERT: D 913 SER cc_start: 0.8501 (m) cc_final: 0.8162 (t) REVERT: D 1142 PHE cc_start: 0.5775 (OUTLIER) cc_final: 0.5572 (m-80) REVERT: D 1165 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7349 (tm-30) outliers start: 95 outliers final: 46 residues processed: 448 average time/residue: 2.2018 time to fit residues: 1243.5703 Evaluate side-chains 408 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 354 time to evaluate : 4.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 242 HIS Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 494 ARG Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 759 TYR Chi-restraints excluded: chain A residue 999 ASN Chi-restraints excluded: chain A residue 1132 LEU Chi-restraints excluded: chain A residue 1171 HIS Chi-restraints excluded: chain A residue 1211 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 460 GLU Chi-restraints excluded: chain B residue 494 ARG Chi-restraints excluded: chain B residue 632 MET Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 759 TYR Chi-restraints excluded: chain B residue 999 ASN Chi-restraints excluded: chain B residue 1211 ILE Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 242 HIS Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain C residue 494 ARG Chi-restraints excluded: chain C residue 671 LEU Chi-restraints excluded: chain C residue 999 ASN Chi-restraints excluded: chain C residue 1132 LEU Chi-restraints excluded: chain C residue 1171 HIS Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 242 HIS Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 425 ASN Chi-restraints excluded: chain D residue 494 ARG Chi-restraints excluded: chain D residue 671 LEU Chi-restraints excluded: chain D residue 759 TYR Chi-restraints excluded: chain D residue 999 ASN Chi-restraints excluded: chain D residue 1142 PHE Chi-restraints excluded: chain D residue 1165 GLU Chi-restraints excluded: chain D residue 1171 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 410 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 242 optimal weight: 20.0000 chunk 310 optimal weight: 2.9990 chunk 240 optimal weight: 9.9990 chunk 358 optimal weight: 10.0000 chunk 237 optimal weight: 8.9990 chunk 424 optimal weight: 4.9990 chunk 265 optimal weight: 2.9990 chunk 258 optimal weight: 30.0000 chunk 195 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 956 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 956 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 956 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1171 HIS ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 956 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1171 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.5287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 39468 Z= 0.296 Angle : 0.596 10.189 53048 Z= 0.303 Chirality : 0.046 1.670 5684 Planarity : 0.005 0.113 6352 Dihedral : 17.435 177.914 7552 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.28 % Favored : 88.63 % Rotamer: Outliers : 2.30 % Allowed : 18.23 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.13), residues: 4388 helix: -0.40 (0.10), residues: 2628 sheet: -4.36 (0.33), residues: 160 loop : -2.51 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 758 HIS 0.017 0.001 HIS D1171 PHE 0.036 0.002 PHE B 365 TYR 0.018 0.002 TYR B 664 ARG 0.013 0.001 ARG B 264 *********************** 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 443 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 353 time to evaluate : 4.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6840 (pt0) REVERT: A 913 SER cc_start: 0.8436 (m) cc_final: 0.8117 (t) REVERT: A 1142 PHE cc_start: 0.6289 (m-80) cc_final: 0.5905 (m-80) REVERT: A 1190 ASN cc_start: 0.7893 (m-40) cc_final: 0.7590 (m-40) REVERT: A 1207 MET cc_start: 0.8535 (mmm) cc_final: 0.8253 (mmm) REVERT: A 1222 LYS cc_start: 0.5212 (OUTLIER) cc_final: 0.4926 (mtpp) REVERT: B 913 SER cc_start: 0.8540 (m) cc_final: 0.8209 (t) REVERT: B 1194 GLU cc_start: 0.7679 (tp30) cc_final: 0.7419 (tm-30) REVERT: C 259 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6753 (pt0) REVERT: C 913 SER cc_start: 0.8436 (m) cc_final: 0.8135 (t) REVERT: C 1194 GLU cc_start: 0.7497 (mm-30) cc_final: 0.7054 (tm-30) REVERT: C 1207 MET cc_start: 0.8093 (mtp) cc_final: 0.7789 (mmm) REVERT: D 913 SER cc_start: 0.8544 (m) cc_final: 0.8180 (t) REVERT: D 1165 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7398 (tm-30) outliers start: 90 outliers final: 54 residues processed: 427 average time/residue: 2.1052 time to fit residues: 1157.4740 Evaluate side-chains 403 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 345 time to evaluate : 4.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 242 HIS Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain A residue 494 ARG Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 759 TYR Chi-restraints excluded: chain A residue 999 ASN Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1211 ILE Chi-restraints excluded: chain A residue 1222 LYS Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 460 GLU Chi-restraints excluded: chain B residue 494 ARG Chi-restraints excluded: chain B residue 632 MET Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 759 TYR Chi-restraints excluded: chain B residue 999 ASN Chi-restraints excluded: chain B residue 1053 ILE Chi-restraints excluded: chain B residue 1211 ILE Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 242 HIS Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain C residue 494 ARG Chi-restraints excluded: chain C residue 671 LEU Chi-restraints excluded: chain C residue 759 TYR Chi-restraints excluded: chain C residue 999 ASN Chi-restraints excluded: chain C residue 1053 ILE Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 242 HIS Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 425 ASN Chi-restraints excluded: chain D residue 460 GLU Chi-restraints excluded: chain D residue 494 ARG Chi-restraints excluded: chain D residue 671 LEU Chi-restraints excluded: chain D residue 759 TYR Chi-restraints excluded: chain D residue 999 ASN Chi-restraints excluded: chain D residue 1053 ILE Chi-restraints excluded: chain D residue 1165 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 262 optimal weight: 9.9990 chunk 169 optimal weight: 10.0000 chunk 253 optimal weight: 2.9990 chunk 127 optimal weight: 20.0000 chunk 83 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 chunk 269 optimal weight: 6.9990 chunk 288 optimal weight: 3.9990 chunk 209 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 333 optimal weight: 40.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 956 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 HIS ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 956 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 HIS C 240 ASN ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 956 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 700 GLN ** D 956 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.5499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 39468 Z= 0.380 Angle : 0.645 10.657 53048 Z= 0.328 Chirality : 0.048 1.679 5684 Planarity : 0.005 0.064 6352 Dihedral : 17.749 171.610 7552 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.85 % Favored : 88.06 % Rotamer: Outliers : 2.30 % Allowed : 18.39 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.12), residues: 4388 helix: -0.52 (0.10), residues: 2620 sheet: -4.44 (0.32), residues: 160 loop : -2.56 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 758 HIS 0.007 0.001 HIS D 83 PHE 0.020 0.002 PHE B 365 TYR 0.020 0.002 TYR D 664 ARG 0.007 0.001 ARG B 264 *********************** 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 430 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 340 time to evaluate : 4.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6847 (pt0) REVERT: A 632 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.7973 (mtm) REVERT: A 913 SER cc_start: 0.8464 (m) cc_final: 0.8143 (t) REVERT: A 1142 PHE cc_start: 0.6151 (OUTLIER) cc_final: 0.5885 (m-80) REVERT: B 460 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.6483 (mp0) REVERT: B 632 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.7934 (mtm) REVERT: B 913 SER cc_start: 0.8549 (m) cc_final: 0.8210 (t) REVERT: B 1142 PHE cc_start: 0.6205 (OUTLIER) cc_final: 0.5897 (m-80) REVERT: B 1194 GLU cc_start: 0.7691 (tp30) cc_final: 0.7432 (tm-30) REVERT: C 259 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6908 (pt0) REVERT: C 632 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.7959 (mtm) REVERT: C 913 SER cc_start: 0.8449 (m) cc_final: 0.8146 (t) REVERT: C 1194 GLU cc_start: 0.7573 (mm-30) cc_final: 0.7074 (tm-30) REVERT: C 1207 MET cc_start: 0.8158 (mtp) cc_final: 0.7892 (mmm) REVERT: D 84 THR cc_start: 0.5052 (OUTLIER) cc_final: 0.4840 (m) REVERT: D 632 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.7976 (mtm) REVERT: D 913 SER cc_start: 0.8528 (m) cc_final: 0.8173 (t) REVERT: D 1165 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7483 (tm-30) outliers start: 90 outliers final: 49 residues processed: 416 average time/residue: 2.1087 time to fit residues: 1135.6927 Evaluate side-chains 396 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 336 time to evaluate : 4.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 242 HIS Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain A residue 494 ARG Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 999 ASN Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1142 PHE Chi-restraints excluded: chain A residue 1211 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 460 GLU Chi-restraints excluded: chain B residue 494 ARG Chi-restraints excluded: chain B residue 632 MET Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 999 ASN Chi-restraints excluded: chain B residue 1053 ILE Chi-restraints excluded: chain B residue 1142 PHE Chi-restraints excluded: chain B residue 1211 ILE Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 242 HIS Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain C residue 494 ARG Chi-restraints excluded: chain C residue 632 MET Chi-restraints excluded: chain C residue 671 LEU Chi-restraints excluded: chain C residue 759 TYR Chi-restraints excluded: chain C residue 999 ASN Chi-restraints excluded: chain C residue 1053 ILE Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 242 HIS Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 425 ASN Chi-restraints excluded: chain D residue 460 GLU Chi-restraints excluded: chain D residue 494 ARG Chi-restraints excluded: chain D residue 632 MET Chi-restraints excluded: chain D residue 671 LEU Chi-restraints excluded: chain D residue 759 TYR Chi-restraints excluded: chain D residue 999 ASN Chi-restraints excluded: chain D residue 1053 ILE Chi-restraints excluded: chain D residue 1165 GLU 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: 10.0000 chunk 395 optimal weight: 3.9990 chunk 237 optimal weight: 20.0000 chunk 172 optimal weight: 5.9990 chunk 310 optimal weight: 0.6980 chunk 121 optimal weight: 4.9990 chunk 357 optimal weight: 8.9990 chunk 373 optimal weight: 0.8980 chunk 393 optimal weight: 2.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 956 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1171 HIS ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 956 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1171 HIS ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 956 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 956 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.5598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 39468 Z= 0.214 Angle : 0.561 9.795 53048 Z= 0.286 Chirality : 0.044 1.661 5684 Planarity : 0.004 0.063 6352 Dihedral : 16.606 164.548 7552 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.60 % Favored : 89.31 % Rotamer: Outliers : 1.76 % Allowed : 19.10 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.13), residues: 4388 helix: -0.27 (0.10), residues: 2620 sheet: -4.23 (0.33), residues: 160 loop : -2.48 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 758 HIS 0.007 0.001 HIS C 83 PHE 0.019 0.001 PHE B 454 TYR 0.017 0.001 TYR C 664 ARG 0.006 0.000 ARG C 750 *********************** 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 419 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 350 time to evaluate : 4.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 THR cc_start: 0.4992 (OUTLIER) cc_final: 0.4740 (m) REVERT: A 149 HIS cc_start: 0.7002 (t-90) cc_final: 0.6199 (m90) REVERT: A 259 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6953 (pt0) REVERT: A 913 SER cc_start: 0.8377 (m) cc_final: 0.8086 (t) REVERT: A 1207 MET cc_start: 0.8511 (mmm) cc_final: 0.8191 (mmm) REVERT: B 84 THR cc_start: 0.4942 (OUTLIER) cc_final: 0.4672 (m) REVERT: B 149 HIS cc_start: 0.7001 (t-90) cc_final: 0.6192 (m90) REVERT: B 913 SER cc_start: 0.8518 (m) cc_final: 0.8169 (t) REVERT: B 996 MET cc_start: 0.8086 (mmt) cc_final: 0.7587 (mmt) REVERT: B 1142 PHE cc_start: 0.6180 (m-80) cc_final: 0.5851 (m-80) REVERT: B 1178 VAL cc_start: 0.8903 (t) cc_final: 0.8573 (m) REVERT: B 1194 GLU cc_start: 0.7662 (tp30) cc_final: 0.7406 (tm-30) REVERT: C 84 THR cc_start: 0.4918 (OUTLIER) cc_final: 0.4639 (m) REVERT: C 259 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6859 (pt0) REVERT: C 488 MET cc_start: 0.8536 (ttm) cc_final: 0.8288 (ttt) REVERT: C 913 SER cc_start: 0.8377 (m) cc_final: 0.8085 (t) REVERT: C 1194 GLU cc_start: 0.7523 (mm-30) cc_final: 0.7030 (tm-30) REVERT: C 1207 MET cc_start: 0.8123 (mtp) cc_final: 0.7823 (mmm) REVERT: D 84 THR cc_start: 0.5061 (OUTLIER) cc_final: 0.4839 (m) REVERT: D 149 HIS cc_start: 0.6986 (t-90) cc_final: 0.6194 (m90) REVERT: D 913 SER cc_start: 0.8514 (m) cc_final: 0.8137 (t) REVERT: D 1165 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7428 (tm-30) REVERT: D 1178 VAL cc_start: 0.8884 (t) cc_final: 0.8529 (m) outliers start: 69 outliers final: 47 residues processed: 407 average time/residue: 2.0626 time to fit residues: 1078.3404 Evaluate side-chains 387 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 333 time to evaluate : 4.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 242 HIS Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 494 ARG Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 759 TYR Chi-restraints excluded: chain A residue 999 ASN Chi-restraints excluded: chain A residue 1171 HIS Chi-restraints excluded: chain A residue 1211 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 460 GLU Chi-restraints excluded: chain B residue 494 ARG Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 759 TYR Chi-restraints excluded: chain B residue 999 ASN Chi-restraints excluded: chain B residue 1060 SER Chi-restraints excluded: chain B residue 1171 HIS Chi-restraints excluded: chain B residue 1211 ILE Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 242 HIS Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain C residue 494 ARG Chi-restraints excluded: chain C residue 671 LEU Chi-restraints excluded: chain C residue 759 TYR Chi-restraints excluded: chain C residue 999 ASN Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 242 HIS Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 425 ASN Chi-restraints excluded: chain D residue 494 ARG Chi-restraints excluded: chain D residue 671 LEU Chi-restraints excluded: chain D residue 722 LEU Chi-restraints excluded: chain D residue 759 TYR Chi-restraints excluded: chain D residue 999 ASN Chi-restraints excluded: chain D residue 1060 SER Chi-restraints excluded: chain D residue 1165 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 259 optimal weight: 6.9990 chunk 417 optimal weight: 2.9990 chunk 255 optimal weight: 7.9990 chunk 198 optimal weight: 2.9990 chunk 290 optimal weight: 7.9990 chunk 438 optimal weight: 10.0000 chunk 403 optimal weight: 3.9990 chunk 349 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 269 optimal weight: 9.9990 chunk 214 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 956 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1171 HIS ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 956 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 956 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 956 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.5661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 39468 Z= 0.366 Angle : 0.634 12.097 53048 Z= 0.321 Chirality : 0.047 1.666 5684 Planarity : 0.005 0.058 6352 Dihedral : 17.061 160.536 7552 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.53 % Favored : 88.38 % Rotamer: Outliers : 1.74 % Allowed : 19.41 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.13), residues: 4388 helix: -0.42 (0.10), residues: 2620 sheet: -4.35 (0.34), residues: 156 loop : -2.49 (0.15), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 758 HIS 0.007 0.001 HIS B 140 PHE 0.028 0.002 PHE B 365 TYR 0.019 0.002 TYR B 664 ARG 0.006 0.001 ARG C 110 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8776 Ramachandran restraints generated. 4388 Oldfield, 0 Emsley, 4388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 328 time to evaluate : 4.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 THR cc_start: 0.5017 (OUTLIER) cc_final: 0.4767 (m) REVERT: A 149 HIS cc_start: 0.7003 (t-90) cc_final: 0.6179 (m90) REVERT: A 259 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6990 (pt0) REVERT: A 753 MET cc_start: 0.8968 (mmt) cc_final: 0.8393 (mmt) REVERT: A 913 SER cc_start: 0.8417 (m) cc_final: 0.8123 (t) REVERT: A 1142 PHE cc_start: 0.6049 (m-80) cc_final: 0.5746 (m-80) REVERT: A 1207 MET cc_start: 0.8556 (mmm) cc_final: 0.8284 (mmm) REVERT: B 84 THR cc_start: 0.4979 (OUTLIER) cc_final: 0.4719 (m) REVERT: B 149 HIS cc_start: 0.7001 (t-90) cc_final: 0.6168 (m90) REVERT: B 913 SER cc_start: 0.8522 (m) cc_final: 0.8170 (t) REVERT: B 1142 PHE cc_start: 0.6161 (m-80) cc_final: 0.5911 (m-80) REVERT: B 1178 VAL cc_start: 0.8912 (t) cc_final: 0.8581 (m) REVERT: B 1194 GLU cc_start: 0.7657 (tp30) cc_final: 0.7404 (tm-30) REVERT: C 84 THR cc_start: 0.4961 (OUTLIER) cc_final: 0.4689 (m) REVERT: C 149 HIS cc_start: 0.7054 (t-90) cc_final: 0.6237 (m90) REVERT: C 259 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6906 (pt0) REVERT: C 488 MET cc_start: 0.8565 (ttm) cc_final: 0.8324 (ttt) REVERT: C 913 SER cc_start: 0.8430 (m) cc_final: 0.8122 (t) REVERT: C 1194 GLU cc_start: 0.7566 (mm-30) cc_final: 0.7058 (tm-30) REVERT: C 1207 MET cc_start: 0.8166 (mtp) cc_final: 0.7890 (mmm) REVERT: D 84 THR cc_start: 0.5065 (OUTLIER) cc_final: 0.4853 (m) REVERT: D 149 HIS cc_start: 0.6985 (t-90) cc_final: 0.6175 (m90) REVERT: D 913 SER cc_start: 0.8525 (m) cc_final: 0.8160 (t) REVERT: D 1165 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7473 (tm-30) outliers start: 68 outliers final: 48 residues processed: 385 average time/residue: 2.0990 time to fit residues: 1036.2316 Evaluate side-chains 381 residues out of total 3916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 326 time to evaluate : 4.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 242 HIS Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 259 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 494 ARG Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 999 ASN Chi-restraints excluded: chain A residue 1060 SER Chi-restraints excluded: chain A residue 1171 HIS Chi-restraints excluded: chain A residue 1211 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 460 GLU Chi-restraints excluded: chain B residue 494 ARG Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 999 ASN Chi-restraints excluded: chain B residue 1060 SER Chi-restraints excluded: chain B residue 1180 MET Chi-restraints excluded: chain B residue 1211 ILE Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 242 HIS Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 259 GLU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain C residue 494 ARG Chi-restraints excluded: chain C residue 671 LEU Chi-restraints excluded: chain C residue 759 TYR Chi-restraints excluded: chain C residue 953 TYR Chi-restraints excluded: chain C residue 999 ASN Chi-restraints excluded: chain C residue 1060 SER Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 242 HIS Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 425 ASN Chi-restraints excluded: chain D residue 494 ARG Chi-restraints excluded: chain D residue 671 LEU Chi-restraints excluded: chain D residue 722 LEU Chi-restraints excluded: chain D residue 759 TYR Chi-restraints excluded: chain D residue 999 ASN Chi-restraints excluded: chain D residue 1060 SER Chi-restraints excluded: chain D residue 1165 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 277 optimal weight: 3.9990 chunk 371 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 chunk 321 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 349 optimal weight: 5.9990 chunk 146 optimal weight: 30.0000 chunk 359 optimal weight: 8.9990 chunk 44 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 956 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1171 HIS ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 956 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 956 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 956 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.183329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.117183 restraints weight = 146701.991| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.91 r_work: 0.3251 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.5713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 39468 Z= 0.267 Angle : 0.588 11.320 53048 Z= 0.299 Chirality : 0.045 1.662 5684 Planarity : 0.004 0.054 6352 Dihedral : 16.655 151.096 7552 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.19 % Favored : 88.72 % Rotamer: Outliers : 1.58 % Allowed : 19.61 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.13), residues: 4388 helix: -0.30 (0.10), residues: 2620 sheet: -4.28 (0.34), residues: 156 loop : -2.45 (0.15), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 758 HIS 0.007 0.001 HIS B 140 PHE 0.025 0.002 PHE B 365 TYR 0.018 0.002 TYR B 664 ARG 0.006 0.001 ARG C 110 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21581.12 seconds wall clock time: 371 minutes 12.55 seconds (22272.55 seconds total)