Starting phenix.real_space_refine (version: dev) on Tue May 17 03:34:10 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wpf_32685/05_2022/7wpf_32685_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wpf_32685/05_2022/7wpf_32685.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wpf_32685/05_2022/7wpf_32685.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wpf_32685/05_2022/7wpf_32685.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wpf_32685/05_2022/7wpf_32685_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wpf_32685/05_2022/7wpf_32685_neut.pdb" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 34": "NH1" <-> "NH2" Residue "A ARG 44": "NH1" <-> "NH2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 102": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A ARG 346": "NH1" <-> "NH2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A ARG 457": "NH1" <-> "NH2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "A ARG 493": "NH1" <-> "NH2" Residue "A ARG 498": "NH1" <-> "NH2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A ARG 577": "NH1" <-> "NH2" Residue "A ARG 765": "NH1" <-> "NH2" Residue "A ASP 775": "OD1" <-> "OD2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A ARG 905": "NH1" <-> "NH2" Residue "A ARG 983": "NH1" <-> "NH2" Residue "A ARG 995": "NH1" <-> "NH2" Residue "A ARG 1000": "NH1" <-> "NH2" Residue "A ARG 1014": "NH1" <-> "NH2" Residue "A ARG 1019": "NH1" <-> "NH2" Residue "A ARG 1039": "NH1" <-> "NH2" Residue "A ARG 1091": "NH1" <-> "NH2" Residue "A GLU 1111": "OE1" <-> "OE2" Residue "B ARG 34": "NH1" <-> "NH2" Residue "B ARG 44": "NH1" <-> "NH2" Residue "B ARG 102": "NH1" <-> "NH2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B ARG 273": "NH1" <-> "NH2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B ARG 454": "NH1" <-> "NH2" Residue "B ARG 457": "NH1" <-> "NH2" Residue "B ARG 466": "NH1" <-> "NH2" Residue "B ARG 493": "NH1" <-> "NH2" Residue "B ARG 498": "NH1" <-> "NH2" Residue "B ARG 567": "NH1" <-> "NH2" Residue "B ARG 577": "NH1" <-> "NH2" Residue "B ARG 765": "NH1" <-> "NH2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B ARG 905": "NH1" <-> "NH2" Residue "B ARG 983": "NH1" <-> "NH2" Residue "B ARG 995": "NH1" <-> "NH2" Residue "B ARG 1000": "NH1" <-> "NH2" Residue "B ARG 1014": "NH1" <-> "NH2" Residue "B ARG 1019": "NH1" <-> "NH2" Residue "B ARG 1039": "NH1" <-> "NH2" Residue "B ARG 1091": "NH1" <-> "NH2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 34": "NH1" <-> "NH2" Residue "C ARG 44": "NH1" <-> "NH2" Residue "C ARG 102": "NH1" <-> "NH2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C ARG 237": "NH1" <-> "NH2" Residue "C ARG 273": "NH1" <-> "NH2" Residue "C ARG 328": "NH1" <-> "NH2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ARG 403": "NH1" <-> "NH2" Residue "C ARG 408": "NH1" <-> "NH2" Residue "C ARG 457": "NH1" <-> "NH2" Residue "C ARG 466": "NH1" <-> "NH2" Residue "C ARG 493": "NH1" <-> "NH2" Residue "C ARG 498": "NH1" <-> "NH2" Residue "C ARG 509": "NH1" <-> "NH2" Residue "C ARG 567": "NH1" <-> "NH2" Residue "C ARG 577": "NH1" <-> "NH2" Residue "C ARG 765": "NH1" <-> "NH2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "C ARG 905": "NH1" <-> "NH2" Residue "C ARG 983": "NH1" <-> "NH2" Residue "C ARG 995": "NH1" <-> "NH2" Residue "C ARG 1000": "NH1" <-> "NH2" Residue "C ARG 1014": "NH1" <-> "NH2" Residue "C ARG 1019": "NH1" <-> "NH2" Residue "C ARG 1039": "NH1" <-> "NH2" Residue "C ARG 1091": "NH1" <-> "NH2" Residue "R GLU 46": "OE1" <-> "OE2" Residue "R ARG 50": "NH1" <-> "NH2" Residue "R ARG 67": "NH1" <-> "NH2" Residue "R ARG 87": "NH1" <-> "NH2" Residue "S ARG 18": "NH1" <-> "NH2" Residue "S ARG 24": "NH1" <-> "NH2" Residue "S ARG 61": "NH1" <-> "NH2" Residue "S GLU 105": "OE1" <-> "OE2" Residue "S ARG 108": "NH1" <-> "NH2" Residue "S ARG 142": "NH1" <-> "NH2" Residue "S ARG 211": "NH1" <-> "NH2" Residue "T ARG 28": "NH1" <-> "NH2" Residue "T ARG 36": "NH1" <-> "NH2" Residue "T ARG 40": "NH1" <-> "NH2" Residue "T ARG 47": "NH1" <-> "NH2" Residue "T ARG 54": "NH1" <-> "NH2" Residue "T ARG 61": "NH1" <-> "NH2" Residue "T ARG 62": "NH1" <-> "NH2" Residue "T ARG 76": "NH1" <-> "NH2" Residue "T ARG 81": "NH1" <-> "NH2" Residue "U ARG 38": "NH1" <-> "NH2" Residue "U ARG 67": "NH1" <-> "NH2" Residue "U GLU 82": "OE1" <-> "OE2" Residue "U ARG 87": "NH1" <-> "NH2" Residue "U TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 18": "NH1" <-> "NH2" Residue "V ARG 24": "NH1" <-> "NH2" Residue "V ARG 61": "NH1" <-> "NH2" Residue "V ARG 108": "NH1" <-> "NH2" Residue "V ARG 142": "NH1" <-> "NH2" Residue "V ARG 211": "NH1" <-> "NH2" Residue "W GLU 15": "OE1" <-> "OE2" Residue "W ARG 28": "NH1" <-> "NH2" Residue "W ARG 36": "NH1" <-> "NH2" Residue "W ARG 40": "NH1" <-> "NH2" Residue "W ARG 47": "NH1" <-> "NH2" Residue "W ARG 54": "NH1" <-> "NH2" Residue "W ARG 61": "NH1" <-> "NH2" Residue "W ARG 62": "NH1" <-> "NH2" Residue "W ARG 76": "NH1" <-> "NH2" Residue "W ARG 81": "NH1" <-> "NH2" Residue "X ARG 50": "NH1" <-> "NH2" Residue "X ARG 67": "NH1" <-> "NH2" Residue "X ARG 87": "NH1" <-> "NH2" Residue "Y ARG 18": "NH1" <-> "NH2" Residue "Y ARG 24": "NH1" <-> "NH2" Residue "Y ARG 61": "NH1" <-> "NH2" Residue "Y ARG 142": "NH1" <-> "NH2" Residue "Y ARG 211": "NH1" <-> "NH2" Residue "Z ARG 28": "NH1" <-> "NH2" Residue "Z ARG 36": "NH1" <-> "NH2" Residue "Z ARG 40": "NH1" <-> "NH2" Residue "Z ARG 47": "NH1" <-> "NH2" Residue "Z ARG 54": "NH1" <-> "NH2" Residue "Z ARG 61": "NH1" <-> "NH2" Residue "Z ARG 62": "NH1" <-> "NH2" Residue "Z ARG 76": "NH1" <-> "NH2" Residue "Z ARG 81": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 36202 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 7676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7676 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 94} Link IDs: {'PTRANS': 52, 'TRANS': 971} Chain breaks: 7 Unresolved non-hydrogen bonds: 355 Unresolved non-hydrogen angles: 433 Unresolved non-hydrogen dihedrals: 296 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 5, 'ASN:plan1': 5, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 188 Chain: "B" Number of atoms: 7672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1023, 7672 Classifications: {'peptide': 1023} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PTRANS': 52, 'TRANS': 970} Chain breaks: 7 Unresolved non-hydrogen bonds: 351 Unresolved non-hydrogen angles: 429 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 5, 'ASN:plan1': 5, 'ASP:plan': 10, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 191 Chain: "C" Number of atoms: 7700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 7700 Classifications: {'peptide': 1022} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 51, 'TRANS': 969, 'PCIS': 1} Chain breaks: 7 Unresolved non-hydrogen bonds: 313 Unresolved non-hydrogen angles: 385 Unresolved non-hydrogen dihedrals: 251 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 10, 'TYR:plan': 2, 'ASN:plan1': 9, 'ASP:plan': 10, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 194 Chain: "R" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1659 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 212, 'PCIS': 2} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "S" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1622 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 201, 'PCIS': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "T" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 925 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "U" Number of atoms: 1648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1648 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 212, 'PCIS': 2} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "V" Number of atoms: 1630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1630 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 201, 'PCIS': 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "W" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 925 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "X" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1656 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 212, 'PCIS': 2} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "Y" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1622 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 201, 'PCIS': 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "Z" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 921 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 19.76, per 1000 atoms: 0.55 Number of scatterers: 36202 At special positions: 0 Unit cell: (196.936, 199.408, 228.248, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 151 16.00 O 7065 8.00 N 5977 7.00 C 23009 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 150 " - pdb=" SG CYS R 206 " distance=2.03 Simple disulfide: pdb=" SG CYS S 23 " - pdb=" SG CYS S 88 " distance=2.03 Simple disulfide: pdb=" SG CYS S 134 " - pdb=" SG CYS S 194 " distance=2.03 Simple disulfide: pdb=" SG CYS T 31 " - pdb=" SG CYS T 105 " distance=2.03 Simple disulfide: pdb=" SG CYS U 22 " - pdb=" SG CYS U 96 " distance=2.03 Simple disulfide: pdb=" SG CYS U 150 " - pdb=" SG CYS U 206 " distance=2.03 Simple disulfide: pdb=" SG CYS V 23 " - pdb=" SG CYS V 88 " distance=2.04 Simple disulfide: pdb=" SG CYS V 134 " - pdb=" SG CYS V 194 " distance=2.03 Simple disulfide: pdb=" SG CYS W 31 " - pdb=" SG CYS W 105 " distance=2.03 Simple disulfide: pdb=" SG CYS X 22 " - pdb=" SG CYS X 96 " distance=2.03 Simple disulfide: pdb=" SG CYS X 150 " - pdb=" SG CYS X 206 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 23 " - pdb=" SG CYS Y 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 134 " - pdb=" SG CYS Y 194 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 31 " - pdb=" SG CYS Z 105 " 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A1301 " - " ASN A1074 " " NAG A1302 " - " ASN A 234 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A1098 " " NAG A1305 " - " ASN A 801 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A 616 " " NAG A1309 " - " ASN A 603 " " NAG A1310 " - " ASN A 331 " " NAG A1311 " - " ASN A 165 " " NAG B1301 " - " ASN B1074 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 282 " " NAG B1305 " - " ASN B1098 " " NAG B1306 " - " ASN B 801 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 616 " " NAG B1310 " - " ASN B 603 " " NAG B1311 " - " ASN B 331 " " NAG B1312 " - " ASN B 165 " " NAG C1301 " - " ASN C 657 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C1074 " " NAG C1306 " - " ASN C1134 " " NAG C1307 " - " ASN C1098 " " NAG C1308 " - " ASN C 165 " " NAG C1309 " - " ASN C 616 " " NAG C1310 " - " ASN C 709 " " NAG C1311 " - " ASN C 801 " " NAG C1312 " - " ASN C 282 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN B 717 " Time building additional restraints: 15.88 Conformation dependent library (CDL) restraints added in 5.4 seconds 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8826 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 79 sheets defined 19.7% alpha, 32.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.07 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 345 removed outlier: 4.737A pdb=" N THR A 345 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 403 through 408 removed outlier: 4.193A pdb=" N ARG A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.763A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.791A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.564A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.675A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.687A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.506A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.222A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1129 No H-bonds generated for 'chain 'A' and resid 1127 through 1129' Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 345 Processing helix chain 'B' and resid 383 through 390 Processing helix chain 'B' and resid 403 through 408 removed outlier: 3.532A pdb=" N VAL B 407 " --> pdb=" O ARG B 403 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ARG B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 403 through 408' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.856A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.818A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.846A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.473A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.355A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.635A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 405 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 569 through 571 No H-bonds generated for 'chain 'C' and resid 569 through 571' Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.633A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.528A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.479A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.771A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.545A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.540A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.957A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 968 removed outlier: 3.941A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER C 968 " --> pdb=" O LYS C 964 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 983 removed outlier: 3.514A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.565A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1127 through 1129 No H-bonds generated for 'chain 'C' and resid 1127 through 1129' Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 3.631A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'R' and resid 28 through 32 Processing helix chain 'R' and resid 87 through 91 Processing helix chain 'R' and resid 137 through 141 Processing helix chain 'S' and resid 79 through 83 Processing helix chain 'S' and resid 121 through 127 removed outlier: 3.572A pdb=" N SER S 127 " --> pdb=" O GLU S 123 " (cutoff:3.500A) Processing helix chain 'S' and resid 150 through 153 Processing helix chain 'S' and resid 183 through 189 Processing helix chain 'T' and resid 96 through 100 Processing helix chain 'U' and resid 28 through 32 Processing helix chain 'U' and resid 87 through 91 Processing helix chain 'U' and resid 137 through 141 Processing helix chain 'U' and resid 166 through 168 No H-bonds generated for 'chain 'U' and resid 166 through 168' Processing helix chain 'V' and resid 79 through 83 removed outlier: 4.509A pdb=" N ILE V 83 " --> pdb=" O PRO V 80 " (cutoff:3.500A) Processing helix chain 'V' and resid 121 through 126 Processing helix chain 'V' and resid 150 through 153 Processing helix chain 'V' and resid 183 through 189 Processing helix chain 'W' and resid 71 through 75 removed outlier: 3.905A pdb=" N GLN W 74 " --> pdb=" O ASP W 71 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLY W 75 " --> pdb=" O SER W 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 71 through 75' Processing helix chain 'W' and resid 83 through 85 No H-bonds generated for 'chain 'W' and resid 83 through 85' Processing helix chain 'X' and resid 28 through 32 Processing helix chain 'X' and resid 87 through 91 Processing helix chain 'X' and resid 137 through 141 Processing helix chain 'X' and resid 167 through 171 Processing helix chain 'Y' and resid 79 through 83 Processing helix chain 'Y' and resid 121 through 127 removed outlier: 3.793A pdb=" N SER Y 127 " --> pdb=" O GLU Y 123 " (cutoff:3.500A) Processing helix chain 'Y' and resid 150 through 153 Processing helix chain 'Y' and resid 183 through 189 removed outlier: 3.766A pdb=" N HIS Y 189 " --> pdb=" O ASP Y 185 " (cutoff:3.500A) Processing helix chain 'Z' and resid 96 through 100 removed outlier: 3.673A pdb=" N THR Z 100 " --> pdb=" O PRO Z 97 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.613A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE A 197 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.617A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.089A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.825A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.682A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 3.523A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.667A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.328A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.169A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.812A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.812A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 789 removed outlier: 6.442A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1081 through 1083 removed outlier: 4.539A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.571A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.328A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.047A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.040A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 134 through 140 removed outlier: 6.703A pdb=" N GLN B 134 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N TYR B 160 " --> pdb=" O CYS B 136 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.628A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.090A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.764A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.996A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 702 through 704 removed outlier: 6.414A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.079A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.074A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.908A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.580A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.953A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.752A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.287A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.662A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.761A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 453 through 454 removed outlier: 3.948A pdb=" N TYR C 453 " --> pdb=" O ARG C 493 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG C 493 " --> pdb=" O TYR C 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.047A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.816A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1047 through 1050 removed outlier: 5.446A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.508A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.539A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'R' and resid 3 through 6 Processing sheet with id=AF1, first strand: chain 'R' and resid 10 through 12 removed outlier: 4.027A pdb=" N GLY R 49 " --> pdb=" O TRP R 36 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ARG R 38 " --> pdb=" O TRP R 47 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N TRP R 47 " --> pdb=" O ARG R 38 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR R 57 " --> pdb=" O ILE R 52 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'R' and resid 130 through 133 removed outlier: 6.054A pdb=" N TYR R 186 " --> pdb=" O ASP R 154 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N SER R 187 " --> pdb=" O ALA R 178 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ALA R 178 " --> pdb=" O SER R 187 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SER R 189 " --> pdb=" O PHE R 176 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'R' and resid 161 through 163 Processing sheet with id=AF4, first strand: chain 'S' and resid 4 through 7 removed outlier: 3.864A pdb=" N THR S 22 " --> pdb=" O SER S 7 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP S 70 " --> pdb=" O SER S 67 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'S' and resid 10 through 13 removed outlier: 3.571A pdb=" N GLN S 38 " --> pdb=" O THR S 85 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR S 87 " --> pdb=" O TYR S 36 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N TRP S 35 " --> pdb=" O LEU S 47 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU S 47 " --> pdb=" O TRP S 35 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'S' and resid 10 through 13 Processing sheet with id=AF7, first strand: chain 'S' and resid 114 through 118 Processing sheet with id=AF8, first strand: chain 'S' and resid 147 through 148 Processing sheet with id=AF9, first strand: chain 'T' and resid 14 through 17 Processing sheet with id=AG1, first strand: chain 'T' and resid 19 through 21 removed outlier: 5.307A pdb=" N TRP T 120 " --> pdb=" O ILE T 107 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE T 107 " --> pdb=" O TRP T 120 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN T 122 " --> pdb=" O CYS T 105 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA T 42 " --> pdb=" O ASP T 108 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ALA T 58 " --> pdb=" O TRP T 45 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ARG T 47 " --> pdb=" O PHE T 56 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N PHE T 56 " --> pdb=" O ARG T 47 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'U' and resid 3 through 6 removed outlier: 3.535A pdb=" N GLN U 3 " --> pdb=" O SER U 25 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER U 25 " --> pdb=" O GLN U 3 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL U 5 " --> pdb=" O LYS U 23 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR U 78 " --> pdb=" O ASP U 73 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP U 73 " --> pdb=" O THR U 78 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'U' and resid 10 through 12 removed outlier: 4.024A pdb=" N THR U 120 " --> pdb=" O GLU U 10 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LYS U 12 " --> pdb=" O THR U 120 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE U 34 " --> pdb=" O ARG U 50 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ARG U 50 " --> pdb=" O ILE U 34 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N TRP U 36 " --> pdb=" O MET U 48 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'U' and resid 130 through 133 removed outlier: 3.640A pdb=" N PHE U 132 " --> pdb=" O LEU U 151 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N TYR U 186 " --> pdb=" O ASP U 154 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'U' and resid 130 through 133 removed outlier: 3.640A pdb=" N PHE U 132 " --> pdb=" O LEU U 151 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N TYR U 186 " --> pdb=" O ASP U 154 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'U' and resid 160 through 164 Processing sheet with id=AG7, first strand: chain 'V' and resid 4 through 7 removed outlier: 3.671A pdb=" N THR V 22 " --> pdb=" O SER V 7 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N CYS V 23 " --> pdb=" O PHE V 71 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE V 71 " --> pdb=" O CYS V 23 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'V' and resid 10 through 13 removed outlier: 5.143A pdb=" N LEU V 33 " --> pdb=" O TYR V 49 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N TYR V 49 " --> pdb=" O LEU V 33 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TRP V 35 " --> pdb=" O LEU V 47 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASP V 50 " --> pdb=" O ASN V 53 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'V' and resid 10 through 13 removed outlier: 3.702A pdb=" N THR V 97 " --> pdb=" O GLN V 90 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'V' and resid 116 through 118 removed outlier: 5.194A pdb=" N TYR V 173 " --> pdb=" O ASN V 138 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'V' and resid 145 through 148 Processing sheet with id=AH3, first strand: chain 'W' and resid 14 through 17 removed outlier: 3.694A pdb=" N GLN W 14 " --> pdb=" O ALA W 32 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'W' and resid 19 through 21 removed outlier: 3.543A pdb=" N THR W 127 " --> pdb=" O GLY W 19 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'W' and resid 54 through 60 removed outlier: 7.028A pdb=" N TRP W 45 " --> pdb=" O VAL W 57 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N VAL W 59 " --> pdb=" O MET W 43 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N MET W 43 " --> pdb=" O VAL W 59 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'X' and resid 3 through 6 removed outlier: 3.567A pdb=" N THR X 78 " --> pdb=" O ASP X 73 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'X' and resid 10 through 12 removed outlier: 3.594A pdb=" N GLU X 10 " --> pdb=" O MET X 118 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR X 120 " --> pdb=" O GLU X 10 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS X 12 " --> pdb=" O THR X 120 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ILE X 34 " --> pdb=" O ARG X 50 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ARG X 50 " --> pdb=" O ILE X 34 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N TRP X 36 " --> pdb=" O MET X 48 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'X' and resid 130 through 133 removed outlier: 3.663A pdb=" N PHE X 132 " --> pdb=" O LEU X 151 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU X 151 " --> pdb=" O PHE X 132 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N TYR X 186 " --> pdb=" O ASP X 154 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N SER X 187 " --> pdb=" O ALA X 178 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ALA X 178 " --> pdb=" O SER X 187 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N SER X 189 " --> pdb=" O PHE X 176 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'X' and resid 161 through 164 Processing sheet with id=AI1, first strand: chain 'Y' and resid 4 through 7 removed outlier: 3.732A pdb=" N THR Y 22 " --> pdb=" O SER Y 7 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N THR Y 69 " --> pdb=" O ALA Y 25 " (cutoff:3.500A) removed outlier: 10.152A pdb=" N GLN Y 27 " --> pdb=" O SER Y 67 " (cutoff:3.500A) removed outlier: 9.637A pdb=" N SER Y 67 " --> pdb=" O GLN Y 27 " (cutoff:3.500A) removed outlier: 11.151A pdb=" N ILE Y 29 " --> pdb=" O SER Y 65 " (cutoff:3.500A) removed outlier: 10.796A pdb=" N SER Y 65 " --> pdb=" O ILE Y 29 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'Y' and resid 10 through 13 removed outlier: 3.603A pdb=" N ILE Y 48 " --> pdb=" O TRP Y 35 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLN Y 37 " --> pdb=" O LEU Y 46 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N LEU Y 46 " --> pdb=" O GLN Y 37 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'Y' and resid 10 through 13 removed outlier: 3.617A pdb=" N THR Y 97 " --> pdb=" O GLN Y 90 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'Y' and resid 114 through 118 removed outlier: 3.697A pdb=" N SER Y 176 " --> pdb=" O SER Y 162 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER Y 162 " --> pdb=" O SER Y 176 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'Y' and resid 146 through 148 Processing sheet with id=AI6, first strand: chain 'Z' and resid 14 through 17 removed outlier: 3.887A pdb=" N THR Z 78 " --> pdb=" O GLN Z 91 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'Z' and resid 19 through 21 removed outlier: 6.098A pdb=" N GLY Z 19 " --> pdb=" O THR Z 127 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N CYS Z 105 " --> pdb=" O GLY Z 121 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLY Z 123 " --> pdb=" O TYR Z 103 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N TYR Z 103 " --> pdb=" O GLY Z 123 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N GLN Z 125 " --> pdb=" O ALA Z 101 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ALA Z 101 " --> pdb=" O GLN Z 125 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ALA Z 42 " --> pdb=" O ASP Z 108 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA Z 58 " --> pdb=" O TRP Z 45 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ARG Z 47 " --> pdb=" O PHE Z 56 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N PHE Z 56 " --> pdb=" O ARG Z 47 " (cutoff:3.500A) 1471 hydrogen bonds defined for protein. 3921 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: 21.83 Time building geometry restraints manager: 17.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11599 1.34 - 1.47: 9395 1.47 - 1.59: 15840 1.59 - 1.71: 0 1.71 - 1.84: 191 Bond restraints: 37025 Sorted by residual: bond pdb=" N LYS C 195 " pdb=" CA LYS C 195 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.20e-02 6.94e+03 6.19e+00 bond pdb=" N LYS B 195 " pdb=" CA LYS B 195 " ideal model delta sigma weight residual 1.454 1.484 -0.030 1.27e-02 6.20e+03 5.59e+00 bond pdb=" N GLN T 10 " pdb=" CA GLN T 10 " ideal model delta sigma weight residual 1.458 1.499 -0.041 1.90e-02 2.77e+03 4.76e+00 bond pdb=" N GLN Z 10 " pdb=" CA GLN Z 10 " ideal model delta sigma weight residual 1.458 1.499 -0.041 1.90e-02 2.77e+03 4.70e+00 bond pdb=" C PHE A 194 " pdb=" N LYS A 195 " ideal model delta sigma weight residual 1.331 1.302 0.029 1.37e-02 5.33e+03 4.42e+00 ... (remaining 37020 not shown) Histogram of bond angle deviations from ideal: 98.96 - 107.65: 1363 107.65 - 116.33: 24281 116.33 - 125.02: 24332 125.02 - 133.70: 460 133.70 - 142.39: 52 Bond angle restraints: 50488 Sorted by residual: angle pdb=" C SER U 103 " pdb=" N SER U 104 " pdb=" CA SER U 104 " ideal model delta sigma weight residual 123.91 142.39 -18.48 1.66e+00 3.63e-01 1.24e+02 angle pdb=" N ALA Z 67 " pdb=" CA ALA Z 67 " pdb=" C ALA Z 67 " ideal model delta sigma weight residual 108.86 117.20 -8.34 1.41e+00 5.03e-01 3.50e+01 angle pdb=" OG1 THR R 126 " pdb=" CB THR R 126 " pdb=" CG2 THR R 126 " ideal model delta sigma weight residual 109.30 120.57 -11.27 2.00e+00 2.50e-01 3.17e+01 angle pdb=" OG1 THR X 28 " pdb=" CB THR X 28 " pdb=" CG2 THR X 28 " ideal model delta sigma weight residual 109.30 120.49 -11.19 2.00e+00 2.50e-01 3.13e+01 angle pdb=" OG1 THR X 126 " pdb=" CB THR X 126 " pdb=" CG2 THR X 126 " ideal model delta sigma weight residual 109.30 120.48 -11.18 2.00e+00 2.50e-01 3.12e+01 ... (remaining 50483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 20499 17.85 - 35.71: 1103 35.71 - 53.56: 158 53.56 - 71.41: 40 71.41 - 89.27: 41 Dihedral angle restraints: 21841 sinusoidal: 8099 harmonic: 13742 Sorted by residual: dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual -86.00 -163.44 77.44 1 1.00e+01 1.00e-02 7.51e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 168.48 -75.48 1 1.00e+01 1.00e-02 7.19e+01 dihedral pdb=" CB CYS C 291 " pdb=" SG CYS C 291 " pdb=" SG CYS C 301 " pdb=" CB CYS C 301 " ideal model delta sinusoidal sigma weight residual 93.00 166.37 -73.37 1 1.00e+01 1.00e-02 6.85e+01 ... (remaining 21838 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.356: 5845 0.356 - 0.712: 34 0.712 - 1.068: 0 1.068 - 1.423: 4 1.423 - 1.779: 8 Chirality restraints: 5891 Sorted by residual: chirality pdb=" CB ILE Y 117 " pdb=" CA ILE Y 117 " pdb=" CG1 ILE Y 117 " pdb=" CG2 ILE Y 117 " both_signs ideal model delta sigma weight residual False 2.64 0.87 1.78 2.00e-01 2.50e+01 7.91e+01 chirality pdb=" CG LEU T 29 " pdb=" CB LEU T 29 " pdb=" CD1 LEU T 29 " pdb=" CD2 LEU T 29 " both_signs ideal model delta sigma weight residual False -2.59 -0.90 -1.69 2.00e-01 2.50e+01 7.15e+01 chirality pdb=" CB ILE R 112 " pdb=" CA ILE R 112 " pdb=" CG1 ILE R 112 " pdb=" CG2 ILE R 112 " both_signs ideal model delta sigma weight residual False 2.64 1.01 1.64 2.00e-01 2.50e+01 6.69e+01 ... (remaining 5888 not shown) Planarity restraints: 6515 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 229 " -0.052 5.00e-02 4.00e+02 7.95e-02 1.01e+01 pdb=" N PRO C 230 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO C 230 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO C 230 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA R 40 " 0.043 5.00e-02 4.00e+02 6.50e-02 6.76e+00 pdb=" N PRO R 41 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO R 41 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO R 41 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A1068 " 0.041 5.00e-02 4.00e+02 6.27e-02 6.29e+00 pdb=" N PRO A1069 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO A1069 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A1069 " 0.035 5.00e-02 4.00e+02 ... (remaining 6512 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 335 2.60 - 3.17: 32217 3.17 - 3.75: 53919 3.75 - 4.32: 75744 4.32 - 4.90: 127414 Nonbonded interactions: 289629 Sorted by model distance: nonbonded pdb=" O TYR S 49 " pdb=" OH TYR S 91 " model vdw 2.025 2.440 nonbonded pdb=" O HIS U 174 " pdb=" OG SER U 190 " model vdw 2.048 2.440 nonbonded pdb=" O PRO A 85 " pdb=" OH TYR A 269 " model vdw 2.066 2.440 nonbonded pdb=" OH TYR A 351 " pdb=" OG SER X 103 " model vdw 2.087 2.440 nonbonded pdb=" O PRO C 85 " pdb=" OH TYR C 269 " model vdw 2.130 2.440 ... (remaining 289624 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 27 through 39 or (resid 40 through 41 and (name N or name \ CA or name C or name O or name CB )) or resid 42 through 45 or (resid 46 and (na \ me N or name CA or name C or name O or name CB )) or resid 47 through 51 or (res \ id 52 through 53 and (name N or name CA or name C or name O or name CB )) or res \ id 54 through 68 or resid 81 through 86 or (resid 87 and (name N or name CA or n \ ame C or name O or name CB )) or resid 88 through 96 or (resid 97 through 98 and \ (name N or name CA or name C or name O or name CB )) or resid 99 through 114 or \ (resid 115 and (name N or name CA or name C or name O or name CB )) or resid 11 \ 6 through 133 or (resid 134 and (name N or name CA or name C or name O or name C \ B )) or resid 135 through 136 or (resid 137 and (name N or name CA or name C or \ name O or name CB )) or resid 138 through 160 or (resid 161 through 164 and (nam \ e N or name CA or name C or name O or name CB )) or resid 165 through 209 or (re \ sid 210 and (name N or name CA or name C or name O or name CB )) or resid 215 th \ rough 253 or (resid 254 and (name N or name CA or name C or name O or name CB )) \ or resid 255 through 318 or (resid 319 and (name N or name CA or name C or name \ O or name CB )) or resid 320 through 355 or (resid 356 through 357 and (name N \ or name CA or name C or name O or name CB )) or resid 358 through 387 or (resid \ 388 and (name N or name CA or name C or name O or name CB )) or resid 389 throug \ h 404 or (resid 405 through 406 and (name N or name CA or name C or name O or na \ me CB )) or resid 407 through 453 or (resid 454 and (name N or name CA or name C \ or name O or name CB )) or resid 455 through 458 or (resid 459 and (name N or n \ ame CA or name C or name O or name CB )) or resid 460 through 553 or (resid 554 \ and (name N or name CA or name C or name O or name CB )) or resid 555 or (resid \ 556 through 558 and (name N or name CA or name C or name O or name CB )) or resi \ d 559 through 563 or (resid 564 and (name N or name CA or name C or name O or na \ me CB )) or resid 565 through 570 or (resid 571 through 572 and (name N or name \ CA or name C or name O or name CB )) or resid 573 through 620 or resid 641 throu \ gh 676 or (resid 690 and (name N or name CA or name C or name O or name CB )) or \ resid 691 through 747 or (resid 748 and (name N or name CA or name C or name O \ or name CB )) or resid 749 through 827 or (resid 828 and (name N or name CA or n \ ame C or name O or name CB )) or resid 855 through 984 or (resid 985 and (name N \ or name CA or name C or name O or name CB )) or resid 986 through 987 or (resid \ 988 through 989 and (name N or name CA or name C or name O or name CB )) or res \ id 990 through 993 or (resid 994 and (name N or name CA or name C or name O or n \ ame CB )) or resid 995 through 1037 or (resid 1038 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1039 through 1050 or (resid 1051 and (name \ N or name CA or name C or name O or name CB )) or resid 1052 through 1110 or (re \ sid 1111 and (name N or name CA or name C or name O or name CB )) or resid 1112 \ through 1143 or (resid 1144 through 1146 and (name N or name CA or name C or nam \ e O or name CB )) or resid 1301 through 1311)) selection = (chain 'B' and (resid 27 through 39 or (resid 40 through 41 and (name N or name \ CA or name C or name O or name CB )) or resid 42 through 45 or (resid 46 and (na \ me N or name CA or name C or name O or name CB )) or resid 47 through 51 or (res \ id 52 through 53 and (name N or name CA or name C or name O or name CB )) or res \ id 54 through 86 or (resid 87 and (name N or name CA or name C or name O or name \ CB )) or resid 88 through 96 or (resid 97 through 98 and (name N or name CA or \ name C or name O or name CB )) or resid 99 through 114 or (resid 115 and (name N \ or name CA or name C or name O or name CB )) or resid 116 through 133 or (resid \ 134 and (name N or name CA or name C or name O or name CB )) or resid 135 throu \ gh 136 or (resid 137 and (name N or name CA or name C or name O or name CB )) or \ resid 138 through 160 or (resid 161 through 164 and (name N or name CA or name \ C or name O or name CB )) or resid 165 through 209 or (resid 210 and (name N or \ name CA or name C or name O or name CB )) or resid 215 through 253 or (resid 254 \ and (name N or name CA or name C or name O or name CB )) or resid 255 through 3 \ 18 or (resid 319 and (name N or name CA or name C or name O or name CB )) or res \ id 320 through 331 or (resid 332 and (name N or name CA or name C or name O or n \ ame CB )) or resid 333 through 355 or (resid 356 through 357 and (name N or name \ CA or name C or name O or name CB )) or resid 358 through 387 or (resid 388 and \ (name N or name CA or name C or name O or name CB )) or resid 389 through 404 o \ r (resid 405 through 406 and (name N or name CA or name C or name O or name CB ) \ ) or resid 407 through 453 or (resid 454 and (name N or name CA or name C or nam \ e O or name CB )) or resid 455 through 458 or (resid 459 and (name N or name CA \ or name C or name O or name CB )) or resid 460 through 553 or (resid 554 and (na \ me N or name CA or name C or name O or name CB )) or resid 555 or (resid 556 thr \ ough 558 and (name N or name CA or name C or name O or name CB )) or resid 559 t \ hrough 563 or (resid 564 and (name N or name CA or name C or name O or name CB ) \ ) or resid 565 through 570 or (resid 571 through 572 and (name N or name CA or n \ ame C or name O or name CB )) or resid 573 through 620 or resid 641 through 676 \ or (resid 690 and (name N or name CA or name C or name O or name CB )) or resid \ 691 through 747 or (resid 748 and (name N or name CA or name C or name O or name \ CB )) or resid 749 through 827 or (resid 828 and (name N or name CA or name C o \ r name O or name CB )) or resid 855 through 984 or (resid 985 and (name N or nam \ e CA or name C or name O or name CB )) or resid 986 through 987 or (resid 988 th \ rough 989 and (name N or name CA or name C or name O or name CB )) or resid 990 \ through 1037 or (resid 1038 and (name N or name CA or name C or name O or name C \ B )) or resid 1039 through 1050 or (resid 1051 and (name N or name CA or name C \ or name O or name CB )) or resid 1052 through 1110 or (resid 1111 and (name N or \ name CA or name C or name O or name CB )) or resid 1112 through 1143 or (resid \ 1144 through 1146 and (name N or name CA or name C or name O or name CB )) or re \ sid 1301 through 1311)) selection = (chain 'C' and (resid 27 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 67 or (resid 68 and (name N or nam \ e CA or name C or name O or name CB )) or resid 81 through 107 or (resid 108 thr \ ough 113 and (name N or name CA or name C or name O or name CB )) or resid 114 t \ hrough 175 or (resid 176 through 187 and (name N or name CA or name C or name O \ or name CB )) or resid 188 through 199 or (resid 200 and (name N or name CA or n \ ame C or name O or name CB )) or resid 201 through 217 or (resid 218 and (name N \ or name CA or name C or name O or name CB )) or resid 219 through 223 or (resid \ 224 and (name N or name CA or name C or name O or name CB )) or resid 225 throu \ gh 248 or (resid 249 through 250 and (name N or name CA or name C or name O or n \ ame CB )) or resid 251 through 303 or (resid 304 and (name N or name CA or name \ C or name O or name CB )) or resid 305 through 320 or (resid 321 and (name N or \ name CA or name C or name O or name CB )) or resid 322 through 368 or (resid 369 \ and (name N or name CA or name C or name O or name CB )) or resid 370 through 4 \ 02 or (resid 403 and (name N or name CA or name C or name O or name CB )) or (re \ sid 404 through 406 and (name N or name CA or name C or name O or name CB )) or \ resid 407 or (resid 408 and (name N or name CA or name C or name O or name CB )) \ or resid 409 through 423 or (resid 424 and (name N or name CA or name C or name \ O or name CB )) or resid 425 through 427 or (resid 428 and (name N or name CA o \ r name C or name O or name CB )) or resid 429 through 438 or (resid 439 and (nam \ e N or name CA or name C or name O or name CB )) or resid 440 through 441 or (re \ sid 442 and (name N or name CA or name C or name O or name CB )) or resid 443 or \ (resid 444 through 445 and (name N or name CA or name C or name O or name CB )) \ or resid 446 through 461 or (resid 462 and (name N or name CA or name C or name \ O or name CB )) or resid 463 through 508 or (resid 509 and (name N or name CA o \ r name C or name O or name CB )) or resid 510 through 556 or (resid 557 through \ 558 and (name N or name CA or name C or name O or name CB )) or resid 559 throug \ h 568 or (resid 569 through 572 and (name N or name CA or name C or name O or na \ me CB )) or resid 573 through 662 or (resid 663 and (name N or name CA or name C \ or name O or name CB )) or resid 664 through 701 or (resid 702 and (name N or n \ ame CA or name C or name O or name CB )) or resid 703 through 739 or (resid 740 \ and (name N or name CA or name C or name O or name CB )) or resid 741 through 79 \ 4 or (resid 795 and (name N or name CA or name C or name O or name CB )) or resi \ d 796 through 807 or (resid 808 and (name N or name CA or name C or name O or na \ me CB )) or resid 809 through 818 or (resid 819 and (name N or name CA or name C \ or name O or name CB )) or resid 820 through 824 or (resid 825 and (name N or n \ ame CA or name C or name O or name CB )) or resid 826 through 917 or (resid 918 \ and (name N or name CA or name C or name O or name CB )) or resid 919 through 94 \ 6 or (resid 947 and (name N or name CA or name C or name O or name CB )) or resi \ d 948 through 963 or (resid 964 and (name N or name CA or name C or name O or na \ me CB )) or resid 965 through 993 or (resid 994 and (name N or name CA or name C \ or name O or name CB )) or resid 995 through 1072 or (resid 1073 and (name N or \ name CA or name C or name O or name CB )) or resid 1074 through 1137 or (resid \ 1138 and (name N or name CA or name C or name O or name CB )) or resid 1139 thro \ ugh 1140 or (resid 1141 through 1142 and (name N or name CA or name C or name O \ or name CB )) or resid 1143 through 1145 or (resid 1146 and (name N or name CA o \ r name C or name O or name CB )) or resid 1301 through 1311)) } ncs_group { reference = chain 'D' selection = chain 'E' } ncs_group { reference = (chain 'R' and (resid 1 through 33 or (resid 34 and (name N or name CA or name C \ or name O or name CB )) or resid 35 through 49 or (resid 50 and (name N or name \ CA or name C or name O or name CB )) or resid 51 through 72 or (resid 73 and (n \ ame N or name CA or name C or name O or name CB )) or resid 74 through 133 or (r \ esid 134 through 135 and (name N or name CA or name C or name O or name CB )) or \ resid 136 through 173 or (resid 174 and (name N or name CA or name C or name O \ or name CB )) or resid 175 through 225)) selection = (chain 'U' and (resid 1 through 37 or (resid 38 and (name N or name CA or name C \ or name O or name CB )) or resid 39 through 72 or (resid 73 and (name N or name \ CA or name C or name O or name CB )) or resid 74 through 225)) selection = (chain 'X' and (resid 1 through 33 or (resid 34 and (name N or name CA or name C \ or name O or name CB )) or resid 35 through 49 or (resid 50 and (name N or name \ CA or name C or name O or name CB )) or resid 51 through 133 or (resid 134 thro \ ugh 135 and (name N or name CA or name C or name O or name CB )) or resid 136 th \ rough 173 or (resid 174 and (name N or name CA or name C or name O or name CB )) \ or resid 175 through 225)) } ncs_group { reference = (chain 'S' and (resid 1 through 32 or (resid 33 through 34 and (name N or name C \ A or name C or name O or name CB )) or resid 35 through 104 or (resid 105 and (n \ ame N or name CA or name C or name O or name CB )) or resid 106 through 107 or ( \ resid 108 and (name N or name CA or name C or name O or name CB )) or resid 109 \ through 130 or (resid 131 and (name N or name CA or name C or name O or name CB \ )) or resid 132 through 213)) selection = (chain 'V' and (resid 1 through 48 or (resid 49 and (name N or name CA or name C \ or name O or name CB )) or resid 50 through 104 or (resid 105 and (name N or na \ me CA or name C or name O or name CB )) or resid 106 through 107 or (resid 108 a \ nd (name N or name CA or name C or name O or name CB )) or resid 109 through 130 \ or (resid 131 and (name N or name CA or name C or name O or name CB )) or resid \ 132 through 144 or (resid 145 and (name N or name CA or name C or name O or nam \ e CB )) or resid 146 through 213)) selection = (chain 'Y' and (resid 1 through 32 or (resid 33 through 34 and (name N or name C \ A or name C or name O or name CB )) or resid 35 through 48 or (resid 49 and (nam \ e N or name CA or name C or name O or name CB )) or resid 50 through 144 or (res \ id 145 and (name N or name CA or name C or name O or name CB )) or resid 146 thr \ ough 213)) } ncs_group { reference = (chain 'T' and (resid 10 through 121 or (resid 122 and (name N or name CA or nam \ e C or name O or name CB )) or resid 123 through 129)) selection = (chain 'W' and (resid 10 through 121 or (resid 122 and (name N or name CA or nam \ e C or name O or name CB )) or resid 123 through 129)) selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 151 5.16 5 C 23009 2.51 5 N 5977 2.21 5 O 7065 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 4.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 24.710 Check model and map are aligned: 0.570 Convert atoms to be neutral: 0.330 Process input model: 102.600 Find NCS groups from input model: 3.170 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:12.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 149.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6456 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 : 0.003 0.057 37025 Z= 0.169 Angle : 0.663 18.475 50488 Z= 0.381 Chirality : 0.088 1.779 5891 Planarity : 0.004 0.080 6479 Dihedral : 11.756 89.268 12853 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 4.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.12), residues: 4677 helix: 1.39 (0.21), residues: 702 sheet: 0.25 (0.13), residues: 1479 loop : -0.75 (0.13), residues: 2496 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 495 time to evaluate : 4.044 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 outliers start: 1 outliers final: 2 residues processed: 495 average time/residue: 1.1317 time to fit residues: 712.9217 Evaluate side-chains 418 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 416 time to evaluate : 4.009 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 0.4401 time to fit residues: 7.1771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 397 optimal weight: 0.9980 chunk 356 optimal weight: 1.9990 chunk 198 optimal weight: 0.2980 chunk 121 optimal weight: 2.9990 chunk 240 optimal weight: 0.9990 chunk 190 optimal weight: 0.9980 chunk 369 optimal weight: 10.0000 chunk 142 optimal weight: 40.0000 chunk 224 optimal weight: 0.9980 chunk 274 optimal weight: 0.3980 chunk 427 optimal weight: 30.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 901 GLN A 955 ASN A 957 GLN A1135 ASN B 422 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN B 978 ASN B1134 ASN C 66 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 703 ASN ** S 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 198 HIS Y 166 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6576 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 37025 Z= 0.255 Angle : 0.637 11.773 50488 Z= 0.341 Chirality : 0.048 0.268 5891 Planarity : 0.005 0.089 6479 Dihedral : 5.288 26.458 5287 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer Outliers : 1.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.12), residues: 4677 helix: 1.29 (0.20), residues: 703 sheet: 0.29 (0.13), residues: 1510 loop : -0.82 (0.13), residues: 2464 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 450 time to evaluate : 4.013 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 outliers start: 56 outliers final: 29 residues processed: 473 average time/residue: 1.1956 time to fit residues: 728.1654 Evaluate side-chains 451 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 422 time to evaluate : 3.936 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 14 residues processed: 19 average time/residue: 0.8346 time to fit residues: 27.6302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 237 optimal weight: 0.9990 chunk 132 optimal weight: 40.0000 chunk 355 optimal weight: 0.7980 chunk 291 optimal weight: 0.9980 chunk 117 optimal weight: 0.6980 chunk 428 optimal weight: 40.0000 chunk 462 optimal weight: 6.9990 chunk 381 optimal weight: 10.0000 chunk 424 optimal weight: 6.9990 chunk 146 optimal weight: 5.9990 chunk 343 optimal weight: 6.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN A 777 ASN A 949 GLN A 957 GLN A 992 GLN B 30 ASN B 66 HIS B 196 ASN B 317 ASN B 334 ASN B 370 ASN ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN B 949 GLN B 978 ASN C 66 HIS ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN C 703 ASN C 804 GLN C1088 HIS ** S 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 39 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6709 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.098 37025 Z= 0.505 Angle : 0.701 12.031 50488 Z= 0.377 Chirality : 0.051 0.307 5891 Planarity : 0.006 0.094 6479 Dihedral : 5.654 27.132 5287 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.85 % Favored : 95.13 % Rotamer Outliers : 2.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.12), residues: 4677 helix: 0.54 (0.19), residues: 705 sheet: 0.13 (0.13), residues: 1482 loop : -0.93 (0.12), residues: 2490 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 462 time to evaluate : 4.056 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 outliers start: 102 outliers final: 51 residues processed: 512 average time/residue: 1.1117 time to fit residues: 732.5825 Evaluate side-chains 479 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 428 time to evaluate : 4.035 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 25 residues processed: 28 average time/residue: 0.5524 time to fit residues: 30.3686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 423 optimal weight: 30.0000 chunk 322 optimal weight: 10.0000 chunk 222 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 204 optimal weight: 0.5980 chunk 287 optimal weight: 0.7980 chunk 430 optimal weight: 50.0000 chunk 455 optimal weight: 7.9990 chunk 224 optimal weight: 0.5980 chunk 407 optimal weight: 6.9990 chunk 122 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN A 949 GLN A 957 GLN B 66 HIS B 196 ASN ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN B 978 ASN C 30 ASN C 188 ASN C 218 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN C 317 ASN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN ** U 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.073 37025 Z= 0.246 Angle : 0.606 13.294 50488 Z= 0.323 Chirality : 0.046 0.247 5891 Planarity : 0.005 0.094 6479 Dihedral : 5.296 27.727 5287 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer Outliers : 2.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.12), residues: 4677 helix: 0.92 (0.19), residues: 706 sheet: 0.24 (0.13), residues: 1510 loop : -0.88 (0.13), residues: 2461 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 433 time to evaluate : 4.035 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 outliers start: 90 outliers final: 46 residues processed: 489 average time/residue: 1.0898 time to fit residues: 689.9596 Evaluate side-chains 466 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 420 time to evaluate : 3.860 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 33 residues processed: 15 average time/residue: 0.5372 time to fit residues: 18.1870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 379 optimal weight: 40.0000 chunk 258 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 338 optimal weight: 5.9990 chunk 187 optimal weight: 0.8980 chunk 388 optimal weight: 20.0000 chunk 314 optimal weight: 30.0000 chunk 0 optimal weight: 1.9990 chunk 232 optimal weight: 3.9990 chunk 408 optimal weight: 10.0000 chunk 114 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN A1088 HIS B 196 ASN ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B 978 ASN C 30 ASN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN C 505 HIS ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.100 37025 Z= 0.622 Angle : 0.759 12.979 50488 Z= 0.405 Chirality : 0.054 0.360 5891 Planarity : 0.006 0.097 6479 Dihedral : 5.835 28.028 5287 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.01 % Favored : 93.95 % Rotamer Outliers : 4.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.12), residues: 4677 helix: 0.12 (0.18), residues: 704 sheet: 0.13 (0.13), residues: 1479 loop : -1.12 (0.12), residues: 2494 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 466 time to evaluate : 4.138 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 outliers start: 156 outliers final: 87 residues processed: 555 average time/residue: 1.0560 time to fit residues: 763.6594 Evaluate side-chains 516 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 429 time to evaluate : 4.038 Switching outliers to nearest non-outliers outliers start: 87 outliers final: 50 residues processed: 38 average time/residue: 0.6189 time to fit residues: 40.9018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 153 optimal weight: 0.4980 chunk 409 optimal weight: 0.0870 chunk 89 optimal weight: 0.5980 chunk 267 optimal weight: 0.5980 chunk 112 optimal weight: 0.0170 chunk 455 optimal weight: 8.9990 chunk 378 optimal weight: 50.0000 chunk 210 optimal weight: 0.8980 chunk 37 optimal weight: 30.0000 chunk 150 optimal weight: 0.9990 chunk 239 optimal weight: 4.9990 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 613 GLN A 777 ASN A 920 GLN A 957 GLN B 317 ASN ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN C 30 ASN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.190 37025 Z= 0.200 Angle : 0.615 20.303 50488 Z= 0.327 Chirality : 0.045 0.251 5891 Planarity : 0.005 0.095 6479 Dihedral : 5.195 25.325 5287 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer Outliers : 2.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.12), residues: 4677 helix: 0.92 (0.19), residues: 702 sheet: 0.31 (0.13), residues: 1507 loop : -0.95 (0.13), residues: 2468 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 445 time to evaluate : 3.946 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 outliers start: 107 outliers final: 70 residues processed: 517 average time/residue: 1.1261 time to fit residues: 759.9135 Evaluate side-chains 496 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 426 time to evaluate : 3.960 Switching outliers to nearest non-outliers outliers start: 70 outliers final: 53 residues processed: 17 average time/residue: 0.4982 time to fit residues: 20.0461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 439 optimal weight: 8.9990 chunk 51 optimal weight: 0.0980 chunk 259 optimal weight: 0.8980 chunk 332 optimal weight: 0.2980 chunk 257 optimal weight: 0.0980 chunk 383 optimal weight: 50.0000 chunk 254 optimal weight: 1.9990 chunk 453 optimal weight: 0.0020 chunk 284 optimal weight: 0.9980 chunk 276 optimal weight: 0.7980 chunk 209 optimal weight: 1.9990 overall best weight: 0.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A 957 GLN B 196 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN C 317 ASN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN ** S 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.178 37025 Z= 0.185 Angle : 0.593 21.138 50488 Z= 0.315 Chirality : 0.044 0.217 5891 Planarity : 0.005 0.106 6479 Dihedral : 4.959 28.418 5287 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer Outliers : 2.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.12), residues: 4677 helix: 1.18 (0.20), residues: 709 sheet: 0.38 (0.13), residues: 1512 loop : -0.91 (0.13), residues: 2456 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 436 time to evaluate : 4.037 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 outliers start: 101 outliers final: 66 residues processed: 509 average time/residue: 1.1324 time to fit residues: 740.4059 Evaluate side-chains 476 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 410 time to evaluate : 3.733 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 54 residues processed: 12 average time/residue: 0.5646 time to fit residues: 15.9524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 280 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 271 optimal weight: 0.9980 chunk 136 optimal weight: 50.0000 chunk 89 optimal weight: 0.5980 chunk 87 optimal weight: 0.9990 chunk 288 optimal weight: 0.9980 chunk 309 optimal weight: 10.0000 chunk 224 optimal weight: 1.9990 chunk 42 optimal weight: 0.1980 chunk 356 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A 957 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B 317 ASN ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN C 317 ASN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6656 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.354 37025 Z= 0.272 Angle : 0.630 30.006 50488 Z= 0.339 Chirality : 0.046 0.388 5891 Planarity : 0.006 0.116 6479 Dihedral : 5.002 27.877 5287 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer Outliers : 2.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.12), residues: 4677 helix: 1.08 (0.20), residues: 708 sheet: 0.37 (0.13), residues: 1518 loop : -0.92 (0.13), residues: 2451 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 408 time to evaluate : 4.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 106 outliers final: 85 residues processed: 482 average time/residue: 1.1186 time to fit residues: 695.1895 Evaluate side-chains 492 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 407 time to evaluate : 3.890 Switching outliers to nearest non-outliers outliers start: 85 outliers final: 67 residues processed: 20 average time/residue: 0.5515 time to fit residues: 22.9686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 412 optimal weight: 20.0000 chunk 434 optimal weight: 50.0000 chunk 396 optimal weight: 6.9990 chunk 423 optimal weight: 2.9990 chunk 254 optimal weight: 0.7980 chunk 184 optimal weight: 1.9990 chunk 332 optimal weight: 1.9990 chunk 129 optimal weight: 30.0000 chunk 382 optimal weight: 20.0000 chunk 400 optimal weight: 5.9990 chunk 421 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A 957 GLN A1002 GLN ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 81 ASN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN C 317 ASN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 137 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6734 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.386 37025 Z= 0.493 Angle : 0.730 35.320 50488 Z= 0.392 Chirality : 0.050 0.593 5891 Planarity : 0.006 0.118 6479 Dihedral : 5.367 28.306 5287 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer Outliers : 2.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.12), residues: 4677 helix: 0.57 (0.19), residues: 703 sheet: 0.34 (0.14), residues: 1464 loop : -1.04 (0.12), residues: 2510 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 431 time to evaluate : 4.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 101 outliers final: 73 residues processed: 504 average time/residue: 1.0849 time to fit residues: 713.2448 Evaluate side-chains 493 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 420 time to evaluate : 4.323 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 62 residues processed: 12 average time/residue: 0.5425 time to fit residues: 16.5543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 277 optimal weight: 0.8980 chunk 447 optimal weight: 10.0000 chunk 273 optimal weight: 0.7980 chunk 212 optimal weight: 0.7980 chunk 310 optimal weight: 20.0000 chunk 469 optimal weight: 20.0000 chunk 431 optimal weight: 7.9990 chunk 373 optimal weight: 0.4980 chunk 38 optimal weight: 20.0000 chunk 288 optimal weight: 0.8980 chunk 229 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN B 317 ASN ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN B 957 GLN C 81 ASN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN C 317 ASN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6678 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.582 37025 Z= 0.392 Angle : 0.722 47.413 50488 Z= 0.385 Chirality : 0.047 0.719 5891 Planarity : 0.006 0.160 6479 Dihedral : 5.145 27.649 5287 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer Outliers : 2.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.12), residues: 4677 helix: 0.86 (0.19), residues: 697 sheet: 0.40 (0.14), residues: 1458 loop : -0.98 (0.12), residues: 2522 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9354 Ramachandran restraints generated. 4677 Oldfield, 0 Emsley, 4677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 427 time to evaluate : 4.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 81 outliers final: 72 residues processed: 491 average time/residue: 1.1183 time to fit residues: 706.7018 Evaluate side-chains 494 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 422 time to evaluate : 3.708 Switching outliers to nearest non-outliers outliers start: 72 outliers final: 65 residues processed: 9 average time/residue: 0.7643 time to fit residues: 15.7770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 296 optimal weight: 0.9990 chunk 398 optimal weight: 30.0000 chunk 114 optimal weight: 4.9990 chunk 344 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 374 optimal weight: 20.0000 chunk 156 optimal weight: 1.9990 chunk 384 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN B 957 GLN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN C 317 ASN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4841 r_free = 0.4841 target = 0.244855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.181374 restraints weight = 61255.270| |-----------------------------------------------------------------------------| r_work (start): 0.4077 rms_B_bonded: 3.26 r_work: 0.4052 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.4030 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work: 0.4007 rms_B_bonded: 3.02 restraints_weight: 0.1250 r_work: 0.3983 rms_B_bonded: 3.16 restraints_weight: 0.0625 r_work: 0.3955 rms_B_bonded: 3.37 restraints_weight: 0.0312 r_work: 0.3924 rms_B_bonded: 3.65 restraints_weight: 0.0156 r_work: 0.3888 rms_B_bonded: 4.03 restraints_weight: 0.0078 r_work: 0.3846 rms_B_bonded: 4.51 restraints_weight: 0.0039 r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.566 37025 Z= 0.411 Angle : 0.770 73.900 50488 Z= 0.401 Chirality : 0.058 2.661 5891 Planarity : 0.006 0.134 6479 Dihedral : 5.257 54.761 5287 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer Outliers : 2.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.12), residues: 4677 helix: 0.89 (0.19), residues: 697 sheet: 0.40 (0.14), residues: 1458 loop : -0.99 (0.12), residues: 2522 =============================================================================== Job complete usr+sys time: 12729.81 seconds wall clock time: 227 minutes 35.84 seconds (13655.84 seconds total)