Starting phenix.real_space_refine (version: dev) on Mon Feb 27 13:51:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sob_25265/02_2023/7sob_25265.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sob_25265/02_2023/7sob_25265.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sob_25265/02_2023/7sob_25265.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sob_25265/02_2023/7sob_25265.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sob_25265/02_2023/7sob_25265.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sob_25265/02_2023/7sob_25265.pdb" } resolution = 2.4 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= 0.004 sd= 0.080 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 Process input model Symmetric amino acids flipped Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 995": "NH1" <-> "NH2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 298": "OE1" <-> "OE2" Residue "D PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 995": "NH1" <-> "NH2" Residue "D PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 298": "OE1" <-> "OE2" Residue "K PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 995": "NH1" <-> "NH2" Residue "K PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 30000 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 7140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 7140 Classifications: {'peptide': 1025} Incomplete info: {'truncation_to_alanine': 250} Link IDs: {'PTRANS': 57, 'TRANS': 967} Chain breaks: 8 Unresolved non-hydrogen bonds: 923 Unresolved non-hydrogen angles: 1179 Unresolved non-hydrogen dihedrals: 765 Unresolved non-hydrogen chiralities: 68 Planarities with less than four sites: {'GLN:plan1': 18, 'HIS:plan': 2, 'TYR:plan': 16, 'ASN:plan1': 22, 'TRP:plan': 2, 'ASP:plan': 20, 'PHE:plan': 16, 'GLU:plan': 20, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 584 Chain: "B" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 560 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 282 Unresolved non-hydrogen angles: 365 Unresolved non-hydrogen dihedrals: 237 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 4, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 6, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 163 Chain: "C" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 787 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 165 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 94 Chain: "G" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 632 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'PTRANS': 3, 'TRANS': 124} Unresolved non-hydrogen bonds: 377 Unresolved non-hydrogen angles: 494 Unresolved non-hydrogen dihedrals: 327 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 8, 'ASN:plan1': 4, 'TRP:plan': 5, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 231 Chain: "I" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 501 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 93} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 256 Unresolved non-hydrogen angles: 332 Unresolved non-hydrogen dihedrals: 210 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 4, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 148 Chain: "D" Number of atoms: 7140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 7140 Classifications: {'peptide': 1025} Incomplete info: {'truncation_to_alanine': 250} Link IDs: {'PTRANS': 57, 'TRANS': 967} Chain breaks: 8 Unresolved non-hydrogen bonds: 923 Unresolved non-hydrogen angles: 1179 Unresolved non-hydrogen dihedrals: 765 Unresolved non-hydrogen chiralities: 68 Planarities with less than four sites: {'GLN:plan1': 18, 'HIS:plan': 2, 'TYR:plan': 16, 'ASN:plan1': 22, 'TRP:plan': 2, 'ASP:plan': 20, 'PHE:plan': 16, 'GLU:plan': 20, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 584 Chain: "E" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 560 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 282 Unresolved non-hydrogen angles: 365 Unresolved non-hydrogen dihedrals: 237 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 4, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 6, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 163 Chain: "F" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 787 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 165 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 94 Chain: "H" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 632 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'PTRANS': 3, 'TRANS': 124} Unresolved non-hydrogen bonds: 377 Unresolved non-hydrogen angles: 494 Unresolved non-hydrogen dihedrals: 327 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 8, 'ASN:plan1': 4, 'TRP:plan': 5, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 231 Chain: "J" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 501 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 93} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 256 Unresolved non-hydrogen angles: 332 Unresolved non-hydrogen dihedrals: 210 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 4, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 148 Chain: "K" Number of atoms: 7140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 7140 Classifications: {'peptide': 1025} Incomplete info: {'truncation_to_alanine': 250} Link IDs: {'PTRANS': 57, 'TRANS': 967} Chain breaks: 8 Unresolved non-hydrogen bonds: 923 Unresolved non-hydrogen angles: 1179 Unresolved non-hydrogen dihedrals: 765 Unresolved non-hydrogen chiralities: 68 Planarities with less than four sites: {'GLN:plan1': 18, 'HIS:plan': 2, 'TYR:plan': 16, 'ASN:plan1': 22, 'TRP:plan': 2, 'ASP:plan': 20, 'PHE:plan': 16, 'GLU:plan': 20, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 584 Chain: "L" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 560 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 282 Unresolved non-hydrogen angles: 365 Unresolved non-hydrogen dihedrals: 237 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 4, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 6, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 163 Chain: "M" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 787 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 165 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 94 Chain: "N" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 632 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'PTRANS': 3, 'TRANS': 124} Unresolved non-hydrogen bonds: 377 Unresolved non-hydrogen angles: 494 Unresolved non-hydrogen dihedrals: 327 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 8, 'ASN:plan1': 4, 'TRP:plan': 5, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 231 Chain: "O" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 501 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 93} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 256 Unresolved non-hydrogen angles: 332 Unresolved non-hydrogen dihedrals: 210 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 4, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 148 Chain: "A" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 238 Unusual residues: {'NAG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen chiralities: 17 Chain: "D" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 238 Unusual residues: {'NAG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen chiralities: 17 Chain: "K" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 238 Unusual residues: {'NAG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen chiralities: 17 Chain: "A" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 142 Classifications: {'water': 142} Link IDs: {None: 141} Chain: "D" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 142 Classifications: {'water': 142} Link IDs: {None: 141} Chain: "K" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 142 Classifications: {'water': 142} Link IDs: {None: 141} Time building chain proxies: 17.37, per 1000 atoms: 0.58 Number of scatterers: 30000 At special positions: 0 Unit cell: (157.641, 158.484, 188.832, 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 144 16.00 O 6120 8.00 N 5172 7.00 C 18564 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=57, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 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=2.08 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS K 985 " distance=2.46 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.07 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=2.01 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.05 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.16 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.12 Simple disulfide: pdb=" SG CYS A 985 " - pdb=" SG CYS D 383 " distance=2.46 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.00 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.01 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 15 " - pdb=" SG CYS D 136 " distance=2.04 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.04 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.02 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.02 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.08 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.07 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.01 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.04 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.05 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.16 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.12 Simple disulfide: pdb=" SG CYS D 985 " - pdb=" SG CYS K 383 " distance=2.46 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.02 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.00 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.01 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 89 " distance=2.03 Simple disulfide: pdb=" SG CYS K 15 " - pdb=" SG CYS K 136 " distance=2.04 Simple disulfide: pdb=" SG CYS K 131 " - pdb=" SG CYS K 166 " distance=2.04 Simple disulfide: pdb=" SG CYS K 291 " - pdb=" SG CYS K 301 " distance=2.02 Simple disulfide: pdb=" SG CYS K 336 " - pdb=" SG CYS K 361 " distance=2.02 Simple disulfide: pdb=" SG CYS K 379 " - pdb=" SG CYS K 432 " distance=2.08 Simple disulfide: pdb=" SG CYS K 391 " - pdb=" SG CYS K 525 " distance=2.07 Simple disulfide: pdb=" SG CYS K 480 " - pdb=" SG CYS K 488 " distance=2.03 Simple disulfide: pdb=" SG CYS K 538 " - pdb=" SG CYS K 590 " distance=2.01 Simple disulfide: pdb=" SG CYS K 617 " - pdb=" SG CYS K 649 " distance=2.04 Simple disulfide: pdb=" SG CYS K 662 " - pdb=" SG CYS K 671 " distance=2.05 Simple disulfide: pdb=" SG CYS K 738 " - pdb=" SG CYS K 760 " distance=2.16 Simple disulfide: pdb=" SG CYS K 743 " - pdb=" SG CYS K 749 " distance=2.12 Simple disulfide: pdb=" SG CYS K1032 " - pdb=" SG CYS K1043 " distance=2.02 Simple disulfide: pdb=" SG CYS K1082 " - pdb=" SG CYS K1126 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.00 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.01 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 89 " 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 NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 603 " " NAG A1303 " - " ASN A 657 " " NAG A1304 " - " ASN A1074 " " NAG A1305 " - " ASN A1098 " " NAG A1306 " - " ASN A1134 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A 282 " " NAG A1310 " - " ASN A 801 " " NAG A1311 " - " ASN A 717 " " NAG A1312 " - " ASN A 61 " " NAG A1313 " - " ASN A 122 " " NAG A1314 " - " ASN A 234 " " NAG A1315 " - " ASN A 17 " " NAG A1316 " - " ASN A 165 " " NAG A1317 " - " ASN A 343 " " NAG D1301 " - " ASN D 331 " " NAG D1302 " - " ASN D 603 " " NAG D1303 " - " ASN D 657 " " NAG D1304 " - " ASN D1074 " " NAG D1305 " - " ASN D1098 " " NAG D1306 " - " ASN D1134 " " NAG D1307 " - " ASN D 616 " " NAG D1308 " - " ASN D 709 " " NAG D1309 " - " ASN D 282 " " NAG D1310 " - " ASN D 801 " " NAG D1311 " - " ASN D 717 " " NAG D1312 " - " ASN D 61 " " NAG D1313 " - " ASN D 122 " " NAG D1314 " - " ASN D 234 " " NAG D1315 " - " ASN D 17 " " NAG D1316 " - " ASN D 165 " " NAG D1317 " - " ASN D 343 " " NAG K1301 " - " ASN K 331 " " NAG K1302 " - " ASN K 603 " " NAG K1303 " - " ASN K 657 " " NAG K1304 " - " ASN K1074 " " NAG K1305 " - " ASN K1098 " " NAG K1306 " - " ASN K1134 " " NAG K1307 " - " ASN K 616 " " NAG K1308 " - " ASN K 709 " " NAG K1309 " - " ASN K 282 " " NAG K1310 " - " ASN K 801 " " NAG K1311 " - " ASN K 717 " " NAG K1312 " - " ASN K 61 " " NAG K1313 " - " ASN K 122 " " NAG K1314 " - " ASN K 234 " " NAG K1315 " - " ASN K 17 " " NAG K1316 " - " ASN K 165 " " NAG K1317 " - " ASN K 343 " Time building additional restraints: 12.33 Conformation dependent library (CDL) restraints added in 5.1 seconds 8730 Ramachandran restraints generated. 4365 Oldfield, 0 Emsley, 4365 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8208 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 81 sheets defined 19.7% alpha, 40.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.18 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.652A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.418A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.657A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.510A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 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 removed outlier: 3.601A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.581A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 856 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.073A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.015A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (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: 3.532A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.374A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 removed outlier: 4.062A pdb=" N ILE B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'I' and resid 30 through 32 No H-bonds generated for 'chain 'I' and resid 30 through 32' Processing helix chain 'I' and resid 80 through 84 removed outlier: 3.835A pdb=" N PHE I 84 " --> pdb=" O PRO I 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 303 Processing helix chain 'D' and resid 338 through 343 Processing helix chain 'D' and resid 365 through 370 removed outlier: 3.652A pdb=" N ASN D 370 " --> pdb=" O SER D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 389 Processing helix chain 'D' and resid 405 through 410 removed outlier: 4.418A pdb=" N ARG D 408 " --> pdb=" O ASP D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 Processing helix chain 'D' and resid 438 through 443 removed outlier: 3.657A pdb=" N SER D 443 " --> pdb=" O ASN D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 616 through 620 removed outlier: 3.509A pdb=" N VAL D 620 " --> pdb=" O CYS D 617 " (cutoff:3.500A) Processing helix chain 'D' and resid 737 through 744 Processing helix chain 'D' and resid 746 through 754 Processing helix chain 'D' and resid 755 through 757 No H-bonds generated for 'chain 'D' and resid 755 through 757' Processing helix chain 'D' and resid 758 through 783 removed outlier: 3.601A pdb=" N ASP D 775 " --> pdb=" O ALA D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 826 removed outlier: 3.581A pdb=" N VAL D 826 " --> pdb=" O LEU D 822 " (cutoff:3.500A) Processing helix chain 'D' and resid 853 through 856 Processing helix chain 'D' and resid 866 through 885 Processing helix chain 'D' and resid 886 through 890 Processing helix chain 'D' and resid 897 through 908 Processing helix chain 'D' and resid 912 through 919 removed outlier: 4.073A pdb=" N LEU D 916 " --> pdb=" O THR D 912 " (cutoff:3.500A) Processing helix chain 'D' and resid 919 through 939 Processing helix chain 'D' and resid 945 through 965 removed outlier: 4.016A pdb=" N VAL D 951 " --> pdb=" O LYS D 947 " (cutoff:3.500A) Processing helix chain 'D' and resid 966 through 968 No H-bonds generated for 'chain 'D' and resid 966 through 968' Processing helix chain 'D' and resid 976 through 984 removed outlier: 3.532A pdb=" N ILE D 980 " --> pdb=" O VAL D 976 " (cutoff:3.500A) Processing helix chain 'D' and resid 985 through 1033 removed outlier: 4.374A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN D 992 " --> pdb=" O GLU D 988 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 removed outlier: 4.062A pdb=" N ILE E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'J' and resid 30 through 32 No H-bonds generated for 'chain 'J' and resid 30 through 32' Processing helix chain 'J' and resid 80 through 84 removed outlier: 3.834A pdb=" N PHE J 84 " --> pdb=" O PRO J 81 " (cutoff:3.500A) Processing helix chain 'K' and resid 294 through 303 Processing helix chain 'K' and resid 338 through 343 Processing helix chain 'K' and resid 365 through 370 removed outlier: 3.651A pdb=" N ASN K 370 " --> pdb=" O SER K 366 " (cutoff:3.500A) Processing helix chain 'K' and resid 386 through 389 Processing helix chain 'K' and resid 405 through 410 removed outlier: 4.418A pdb=" N ARG K 408 " --> pdb=" O ASP K 405 " (cutoff:3.500A) Processing helix chain 'K' and resid 416 through 422 Processing helix chain 'K' and resid 438 through 443 removed outlier: 3.657A pdb=" N SER K 443 " --> pdb=" O ASN K 439 " (cutoff:3.500A) Processing helix chain 'K' and resid 616 through 620 removed outlier: 3.509A pdb=" N VAL K 620 " --> pdb=" O CYS K 617 " (cutoff:3.500A) Processing helix chain 'K' and resid 737 through 744 Processing helix chain 'K' and resid 746 through 754 Processing helix chain 'K' and resid 755 through 757 No H-bonds generated for 'chain 'K' and resid 755 through 757' Processing helix chain 'K' and resid 758 through 783 removed outlier: 3.601A pdb=" N ASP K 775 " --> pdb=" O ALA K 771 " (cutoff:3.500A) Processing helix chain 'K' and resid 816 through 826 removed outlier: 3.581A pdb=" N VAL K 826 " --> pdb=" O LEU K 822 " (cutoff:3.500A) Processing helix chain 'K' and resid 853 through 856 Processing helix chain 'K' and resid 866 through 885 Processing helix chain 'K' and resid 886 through 890 Processing helix chain 'K' and resid 897 through 908 Processing helix chain 'K' and resid 912 through 919 removed outlier: 4.073A pdb=" N LEU K 916 " --> pdb=" O THR K 912 " (cutoff:3.500A) Processing helix chain 'K' and resid 919 through 939 Processing helix chain 'K' and resid 945 through 965 removed outlier: 4.015A pdb=" N VAL K 951 " --> pdb=" O LYS K 947 " (cutoff:3.500A) Processing helix chain 'K' and resid 966 through 968 No H-bonds generated for 'chain 'K' and resid 966 through 968' Processing helix chain 'K' and resid 976 through 984 removed outlier: 3.532A pdb=" N ILE K 980 " --> pdb=" O VAL K 976 " (cutoff:3.500A) Processing helix chain 'K' and resid 985 through 1033 removed outlier: 4.374A pdb=" N VAL K 991 " --> pdb=" O PRO K 987 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN K 992 " --> pdb=" O GLU K 988 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.062A pdb=" N ILE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 87 through 91 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'O' and resid 30 through 32 No H-bonds generated for 'chain 'O' and resid 30 through 32' Processing helix chain 'O' and resid 80 through 84 removed outlier: 3.834A pdb=" N PHE O 84 " --> pdb=" O PRO O 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.905A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.816A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.866A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.511A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 9.929A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.184A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 13.414A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 12.838A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 10.376A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 9.929A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.184A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.287A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.396A 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: 4.134A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.789A 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 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.559A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.655A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.655A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.353A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.995A pdb=" N ILE A 788 " --> pdb=" O ASN D 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.651A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 4 through 7 Processing sheet with id=AC1, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.716A pdb=" N LEU B 11 " --> pdb=" O ASP B 105 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU B 33 " --> pdb=" O SER B 49 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N SER B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.716A pdb=" N LEU B 11 " --> pdb=" O ASP B 105 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR B 97 " --> pdb=" O GLN B 90 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AC4, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.636A pdb=" N MET C 34 " --> pdb=" O PHE C 50 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N PHE C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 10 through 12 Processing sheet with id=AC6, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AC7, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.660A pdb=" N GLY G 33 " --> pdb=" O ASP G 99 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N TRP G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.975A pdb=" N ASN G 116 " --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AD1, first strand: chain 'I' and resid 54 through 55 removed outlier: 6.586A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N TYR I 50 " --> pdb=" O LEU I 34 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU I 34 " --> pdb=" O TYR I 50 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 27 through 31 removed outlier: 3.905A pdb=" N ALA D 27 " --> pdb=" O TRP D 64 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER D 60 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N ASN D 61 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N TYR D 269 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N PHE D 201 " --> pdb=" O ASP D 228 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ASP D 228 " --> pdb=" O PHE D 201 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE D 203 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N HIS D 207 " --> pdb=" O ALA D 222 " (cutoff:3.500A) removed outlier: 9.817A pdb=" N ALA D 222 " --> pdb=" O HIS D 207 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VAL D 36 " --> pdb=" O LEU D 223 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 47 through 55 removed outlier: 3.866A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 84 through 85 removed outlier: 6.511A pdb=" N ALA D 243 " --> pdb=" O ILE D 101 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE D 101 " --> pdb=" O ALA D 243 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ARG D 102 " --> pdb=" O ASN D 121 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N GLU D 132 " --> pdb=" O CYS D 166 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N CYS D 166 " --> pdb=" O GLU D 132 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLN D 134 " --> pdb=" O ASN D 164 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N ASN D 164 " --> pdb=" O GLN D 134 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N CYS D 136 " --> pdb=" O SER D 162 " (cutoff:3.500A) removed outlier: 9.929A pdb=" N SER D 162 " --> pdb=" O CYS D 136 " (cutoff:3.500A) removed outlier: 10.184A pdb=" N ASP D 138 " --> pdb=" O TYR D 160 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N TYR D 160 " --> pdb=" O ASP D 138 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 84 through 85 removed outlier: 13.414A pdb=" N PHE D 238 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 12.838A pdb=" N ASN D 137 " --> pdb=" O PHE D 238 " (cutoff:3.500A) removed outlier: 10.376A pdb=" N THR D 240 " --> pdb=" O ASN D 137 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU D 242 " --> pdb=" O PRO D 139 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N GLU D 132 " --> pdb=" O CYS D 166 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N CYS D 166 " --> pdb=" O GLU D 132 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLN D 134 " --> pdb=" O ASN D 164 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N ASN D 164 " --> pdb=" O GLN D 134 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N CYS D 136 " --> pdb=" O SER D 162 " (cutoff:3.500A) removed outlier: 9.929A pdb=" N SER D 162 " --> pdb=" O CYS D 136 " (cutoff:3.500A) removed outlier: 10.184A pdb=" N ASP D 138 " --> pdb=" O TYR D 160 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N TYR D 160 " --> pdb=" O ASP D 138 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 311 through 319 removed outlier: 5.287A pdb=" N ILE D 312 " --> pdb=" O THR D 599 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N THR D 599 " --> pdb=" O ILE D 312 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N GLN D 314 " --> pdb=" O VAL D 597 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL D 597 " --> pdb=" O GLN D 314 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER D 316 " --> pdb=" O VAL D 595 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLY D 594 " --> pdb=" O GLN D 613 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 324 through 328 removed outlier: 4.134A pdb=" N GLU D 324 " --> pdb=" O CYS D 538 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ASP D 574 " --> pdb=" O ILE D 587 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA D 575 " --> pdb=" O GLY D 566 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 354 through 358 Processing sheet with id=AD9, first strand: chain 'D' and resid 361 through 362 removed outlier: 6.789A pdb=" N CYS D 361 " --> pdb=" O CYS D 525 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AE2, first strand: chain 'D' and resid 473 through 474 Processing sheet with id=AE3, first strand: chain 'D' and resid 654 through 655 removed outlier: 6.559A pdb=" N ILE D 670 " --> pdb=" O ILE D 666 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 711 through 728 removed outlier: 6.655A pdb=" N SER D 711 " --> pdb=" O THR D1076 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR D1076 " --> pdb=" O SER D 711 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA D 713 " --> pdb=" O ASN D1074 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASN D1074 " --> pdb=" O ALA D 713 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLU D1072 " --> pdb=" O PRO D 715 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N TYR D1067 " --> pdb=" O HIS D1048 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N HIS D1048 " --> pdb=" O TYR D1067 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 711 through 728 removed outlier: 6.655A pdb=" N SER D 711 " --> pdb=" O THR D1076 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR D1076 " --> pdb=" O SER D 711 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA D 713 " --> pdb=" O ASN D1074 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASN D1074 " --> pdb=" O ALA D 713 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLU D1072 " --> pdb=" O PRO D 715 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA D1078 " --> pdb=" O PHE D1095 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N PHE D1095 " --> pdb=" O ALA D1078 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 733 through 736 removed outlier: 4.353A pdb=" N LYS D 733 " --> pdb=" O LEU D 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 788 through 790 removed outlier: 5.995A pdb=" N ILE D 788 " --> pdb=" O ASN K 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'D' and resid 1120 through 1125 removed outlier: 4.651A pdb=" N ALA D1087 " --> pdb=" O SER D1123 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AF1, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.716A pdb=" N LEU E 11 " --> pdb=" O ASP E 105 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU E 33 " --> pdb=" O SER E 49 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N SER E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.716A pdb=" N LEU E 11 " --> pdb=" O ASP E 105 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AF4, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.636A pdb=" N MET F 34 " --> pdb=" O PHE F 50 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N PHE F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 10 through 12 Processing sheet with id=AF6, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AF7, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.660A pdb=" N GLY H 33 " --> pdb=" O ASP H 99 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.975A pdb=" N ASN H 116 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AG1, first strand: chain 'J' and resid 54 through 55 removed outlier: 6.587A pdb=" N TRP J 36 " --> pdb=" O LEU J 48 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N TYR J 50 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU J 34 " --> pdb=" O TYR J 50 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 27 through 31 removed outlier: 3.906A pdb=" N ALA K 27 " --> pdb=" O TRP K 64 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER K 60 " --> pdb=" O SER K 31 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N ASN K 61 " --> pdb=" O TYR K 269 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N TYR K 269 " --> pdb=" O ASN K 61 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N PHE K 201 " --> pdb=" O ASP K 228 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ASP K 228 " --> pdb=" O PHE K 201 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE K 203 " --> pdb=" O LEU K 226 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N HIS K 207 " --> pdb=" O ALA K 222 " (cutoff:3.500A) removed outlier: 9.817A pdb=" N ALA K 222 " --> pdb=" O HIS K 207 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VAL K 36 " --> pdb=" O LEU K 223 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'K' and resid 47 through 55 removed outlier: 3.866A pdb=" N ASP K 287 " --> pdb=" O LYS K 278 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 84 through 85 removed outlier: 6.511A pdb=" N ALA K 243 " --> pdb=" O ILE K 101 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE K 101 " --> pdb=" O ALA K 243 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ARG K 102 " --> pdb=" O ASN K 121 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N GLU K 132 " --> pdb=" O CYS K 166 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N CYS K 166 " --> pdb=" O GLU K 132 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLN K 134 " --> pdb=" O ASN K 164 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N ASN K 164 " --> pdb=" O GLN K 134 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N CYS K 136 " --> pdb=" O SER K 162 " (cutoff:3.500A) removed outlier: 9.930A pdb=" N SER K 162 " --> pdb=" O CYS K 136 " (cutoff:3.500A) removed outlier: 10.184A pdb=" N ASP K 138 " --> pdb=" O TYR K 160 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N TYR K 160 " --> pdb=" O ASP K 138 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'K' and resid 84 through 85 removed outlier: 13.414A pdb=" N PHE K 238 " --> pdb=" O PHE K 135 " (cutoff:3.500A) removed outlier: 12.838A pdb=" N ASN K 137 " --> pdb=" O PHE K 238 " (cutoff:3.500A) removed outlier: 10.376A pdb=" N THR K 240 " --> pdb=" O ASN K 137 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU K 242 " --> pdb=" O PRO K 139 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N GLU K 132 " --> pdb=" O CYS K 166 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N CYS K 166 " --> pdb=" O GLU K 132 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLN K 134 " --> pdb=" O ASN K 164 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N ASN K 164 " --> pdb=" O GLN K 134 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N CYS K 136 " --> pdb=" O SER K 162 " (cutoff:3.500A) removed outlier: 9.930A pdb=" N SER K 162 " --> pdb=" O CYS K 136 " (cutoff:3.500A) removed outlier: 10.184A pdb=" N ASP K 138 " --> pdb=" O TYR K 160 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N TYR K 160 " --> pdb=" O ASP K 138 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'K' and resid 311 through 319 removed outlier: 5.288A pdb=" N ILE K 312 " --> pdb=" O THR K 599 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N THR K 599 " --> pdb=" O ILE K 312 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N GLN K 314 " --> pdb=" O VAL K 597 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL K 597 " --> pdb=" O GLN K 314 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER K 316 " --> pdb=" O VAL K 595 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLY K 594 " --> pdb=" O GLN K 613 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'K' and resid 324 through 328 removed outlier: 4.134A pdb=" N GLU K 324 " --> pdb=" O CYS K 538 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ASP K 574 " --> pdb=" O ILE K 587 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA K 575 " --> pdb=" O GLY K 566 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'K' and resid 354 through 358 Processing sheet with id=AG9, first strand: chain 'K' and resid 361 through 362 removed outlier: 6.789A pdb=" N CYS K 361 " --> pdb=" O CYS K 525 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'K' and resid 452 through 454 Processing sheet with id=AH2, first strand: chain 'K' and resid 473 through 474 Processing sheet with id=AH3, first strand: chain 'K' and resid 654 through 655 removed outlier: 6.559A pdb=" N ILE K 670 " --> pdb=" O ILE K 666 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'K' and resid 711 through 728 removed outlier: 6.655A pdb=" N SER K 711 " --> pdb=" O THR K1076 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR K1076 " --> pdb=" O SER K 711 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA K 713 " --> pdb=" O ASN K1074 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASN K1074 " --> pdb=" O ALA K 713 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLU K1072 " --> pdb=" O PRO K 715 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N TYR K1067 " --> pdb=" O HIS K1048 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N HIS K1048 " --> pdb=" O TYR K1067 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'K' and resid 711 through 728 removed outlier: 6.655A pdb=" N SER K 711 " --> pdb=" O THR K1076 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR K1076 " --> pdb=" O SER K 711 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA K 713 " --> pdb=" O ASN K1074 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASN K1074 " --> pdb=" O ALA K 713 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLU K1072 " --> pdb=" O PRO K 715 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA K1078 " --> pdb=" O PHE K1095 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N PHE K1095 " --> pdb=" O ALA K1078 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'K' and resid 733 through 736 removed outlier: 4.353A pdb=" N LYS K 733 " --> pdb=" O LEU K 861 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'K' and resid 1120 through 1125 removed outlier: 4.651A pdb=" N ALA K1087 " --> pdb=" O SER K1123 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AH9, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.716A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LEU L 33 " --> pdb=" O SER L 49 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N SER L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.716A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AI3, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.636A pdb=" N MET M 34 " --> pdb=" O PHE M 50 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N PHE M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'M' and resid 10 through 12 Processing sheet with id=AI5, first strand: chain 'N' and resid 3 through 6 Processing sheet with id=AI6, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.660A pdb=" N GLY N 33 " --> pdb=" O ASP N 99 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE N 34 " --> pdb=" O TRP N 50 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N TRP N 50 " --> pdb=" O ILE N 34 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N TRP N 36 " --> pdb=" O MET N 48 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.975A pdb=" N ASN N 116 " --> pdb=" O ARG N 98 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'O' and resid 4 through 7 Processing sheet with id=AI9, first strand: chain 'O' and resid 54 through 55 removed outlier: 6.586A pdb=" N TRP O 36 " --> pdb=" O LEU O 48 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N TYR O 50 " --> pdb=" O LEU O 34 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU O 34 " --> pdb=" O TYR O 50 " (cutoff:3.500A) 1634 hydrogen bonds defined for protein. 4191 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: 19.23 Time building geometry restraints manager: 13.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.09 - 1.24: 4880 1.24 - 1.40: 7355 1.40 - 1.55: 17587 1.55 - 1.71: 121 1.71 - 1.86: 174 Bond restraints: 30117 Sorted by residual: bond pdb=" N CYS D 985 " pdb=" CA CYS D 985 " ideal model delta sigma weight residual 1.453 1.663 -0.210 1.25e-02 6.40e+03 2.82e+02 bond pdb=" N CYS K 985 " pdb=" CA CYS K 985 " ideal model delta sigma weight residual 1.453 1.663 -0.210 1.25e-02 6.40e+03 2.81e+02 bond pdb=" N CYS A 985 " pdb=" CA CYS A 985 " ideal model delta sigma weight residual 1.453 1.662 -0.209 1.25e-02 6.40e+03 2.80e+02 bond pdb=" C CYS K1082 " pdb=" O CYS K1082 " ideal model delta sigma weight residual 1.236 1.383 -0.147 1.24e-02 6.50e+03 1.41e+02 bond pdb=" C CYS A1082 " pdb=" O CYS A1082 " ideal model delta sigma weight residual 1.236 1.383 -0.147 1.24e-02 6.50e+03 1.40e+02 ... (remaining 30112 not shown) Histogram of bond angle deviations from ideal: 95.51 - 103.18: 485 103.18 - 110.86: 11431 110.86 - 118.54: 12024 118.54 - 126.21: 17181 126.21 - 133.89: 255 Bond angle restraints: 41376 Sorted by residual: angle pdb=" C2 NAG A1301 " pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 109.64 115.02 -5.38 5.38e-01 3.45e+00 1.00e+02 angle pdb=" C2 NAG D1301 " pdb=" C1 NAG D1301 " pdb=" O5 NAG D1301 " ideal model delta sigma weight residual 109.64 115.01 -5.37 5.38e-01 3.45e+00 9.97e+01 angle pdb=" C2 NAG K1301 " pdb=" C1 NAG K1301 " pdb=" O5 NAG K1301 " ideal model delta sigma weight residual 109.64 115.00 -5.36 5.38e-01 3.45e+00 9.94e+01 angle pdb=" CA CYS A 617 " pdb=" C CYS A 617 " pdb=" N THR A 618 " ideal model delta sigma weight residual 118.08 106.48 11.60 1.30e+00 5.92e-01 7.96e+01 angle pdb=" CA CYS K 617 " pdb=" C CYS K 617 " pdb=" N THR K 618 " ideal model delta sigma weight residual 118.08 106.50 11.58 1.30e+00 5.92e-01 7.94e+01 ... (remaining 41371 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 17187 17.80 - 35.61: 371 35.61 - 53.41: 76 53.41 - 71.22: 36 71.22 - 89.02: 6 Dihedral angle restraints: 17676 sinusoidal: 4950 harmonic: 12726 Sorted by residual: dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 96 " pdb=" CB CYS C 96 " ideal model delta sinusoidal sigma weight residual 93.00 44.73 48.27 1 1.00e+01 1.00e-02 3.21e+01 dihedral pdb=" CB CYS F 22 " pdb=" SG CYS F 22 " pdb=" SG CYS F 96 " pdb=" CB CYS F 96 " ideal model delta sinusoidal sigma weight residual 93.00 44.74 48.26 1 1.00e+01 1.00e-02 3.21e+01 dihedral pdb=" CB CYS M 22 " pdb=" SG CYS M 22 " pdb=" SG CYS M 96 " pdb=" CB CYS M 96 " ideal model delta sinusoidal sigma weight residual 93.00 44.76 48.24 1 1.00e+01 1.00e-02 3.21e+01 ... (remaining 17673 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.125: 4830 0.125 - 0.250: 174 0.250 - 0.375: 78 0.375 - 0.500: 9 0.500 - 0.625: 12 Chirality restraints: 5103 Sorted by residual: chirality pdb=" CA CYS K1082 " pdb=" N CYS K1082 " pdb=" C CYS K1082 " pdb=" CB CYS K1082 " both_signs ideal model delta sigma weight residual False 2.51 1.89 0.63 2.00e-01 2.50e+01 9.77e+00 chirality pdb=" CA CYS A1082 " pdb=" N CYS A1082 " pdb=" C CYS A1082 " pdb=" CB CYS A1082 " both_signs ideal model delta sigma weight residual False 2.51 1.89 0.62 2.00e-01 2.50e+01 9.75e+00 chirality pdb=" CA CYS D1082 " pdb=" N CYS D1082 " pdb=" C CYS D1082 " pdb=" CB CYS D1082 " both_signs ideal model delta sigma weight residual False 2.51 1.89 0.62 2.00e-01 2.50e+01 9.72e+00 ... (remaining 5100 not shown) Planarity restraints: 5559 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 801 " 0.047 2.00e-02 2.50e+03 4.99e-02 3.11e+01 pdb=" CG ASN D 801 " -0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN D 801 " -0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN D 801 " -0.078 2.00e-02 2.50e+03 pdb=" C1 NAG D1310 " 0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 801 " -0.047 2.00e-02 2.50e+03 4.97e-02 3.09e+01 pdb=" CG ASN A 801 " 0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN A 801 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN A 801 " 0.078 2.00e-02 2.50e+03 pdb=" C1 NAG A1310 " -0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN K 801 " 0.047 2.00e-02 2.50e+03 4.97e-02 3.09e+01 pdb=" CG ASN K 801 " -0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN K 801 " -0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN K 801 " -0.078 2.00e-02 2.50e+03 pdb=" C1 NAG K1310 " 0.061 2.00e-02 2.50e+03 ... (remaining 5556 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 10705 2.86 - 3.37: 25462 3.37 - 3.88: 48065 3.88 - 4.39: 53294 4.39 - 4.90: 91505 Nonbonded interactions: 229031 Sorted by model distance: nonbonded pdb=" O ASN K 331 " pdb=" OD1 ASN K 331 " model vdw 2.350 3.040 nonbonded pdb=" O ASN A 331 " pdb=" OD1 ASN A 331 " model vdw 2.350 3.040 nonbonded pdb=" O ASN D 331 " pdb=" OD1 ASN D 331 " model vdw 2.350 3.040 nonbonded pdb=" O SER A 31 " pdb=" OG SER A 31 " model vdw 2.431 2.440 nonbonded pdb=" O SER D 31 " pdb=" OG SER D 31 " model vdw 2.431 2.440 ... (remaining 229026 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'L' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'M' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'N' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'O' } 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 144 5.16 5 C 18564 2.51 5 N 5172 2.21 5 O 6120 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: 11.040 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: 0.020 Extract box with map and model: 30.240 Check model and map are aligned: 0.400 Process input model: 86.070 Find NCS groups from input model: 1.980 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Set scattering table: 0.260 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:13.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 143.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 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 : 0.012 0.210 30117 Z= 0.787 Angle : 1.338 12.192 41376 Z= 0.965 Chirality : 0.077 0.625 5103 Planarity : 0.006 0.044 5508 Dihedral : 9.259 89.023 9297 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.12), residues: 4365 helix: 0.36 (0.18), residues: 672 sheet: 1.00 (0.14), residues: 1278 loop : 0.17 (0.12), residues: 2415 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8730 Ramachandran restraints generated. 4365 Oldfield, 0 Emsley, 4365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8730 Ramachandran restraints generated. 4365 Oldfield, 0 Emsley, 4365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 388 time to evaluate : 3.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 388 average time/residue: 1.4342 time to fit residues: 654.7731 Evaluate side-chains 269 residues out of total 3831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 3.184 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.4468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 369 optimal weight: 0.4980 chunk 331 optimal weight: 50.0000 chunk 184 optimal weight: 9.9990 chunk 113 optimal weight: 5.9990 chunk 223 optimal weight: 0.5980 chunk 177 optimal weight: 2.9990 chunk 343 optimal weight: 2.9990 chunk 132 optimal weight: 9.9990 chunk 208 optimal weight: 0.0970 chunk 255 optimal weight: 7.9990 chunk 397 optimal weight: 9.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 536 ASN A 787 GLN A1005 GLN A1010 GLN A1088 HIS D 532 ASN D 536 ASN D 901 GLN D 954 GLN D 992 GLN D1002 GLN D1010 GLN D1071 HIS D1088 HIS D1113 GLN K 196 ASN K 532 ASN K 751 ASN K 901 GLN K 954 GLN K1005 GLN K1010 GLN K1071 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 30117 Z= 0.280 Angle : 0.586 7.105 41376 Z= 0.326 Chirality : 0.048 0.354 5103 Planarity : 0.005 0.046 5508 Dihedral : 4.868 30.030 4896 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer Outliers : 2.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.89 % 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: 0.91 (0.12), residues: 4365 helix: 1.67 (0.20), residues: 651 sheet: 0.99 (0.13), residues: 1359 loop : 0.14 (0.12), residues: 2355 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8730 Ramachandran restraints generated. 4365 Oldfield, 0 Emsley, 4365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8730 Ramachandran restraints generated. 4365 Oldfield, 0 Emsley, 4365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 285 time to evaluate : 3.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 19 residues processed: 311 average time/residue: 1.4256 time to fit residues: 527.0864 Evaluate side-chains 286 residues out of total 3831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 267 time to evaluate : 3.480 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 11 residues processed: 9 average time/residue: 0.4312 time to fit residues: 10.9205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 221 optimal weight: 1.9990 chunk 123 optimal weight: 9.9990 chunk 331 optimal weight: 50.0000 chunk 270 optimal weight: 0.1980 chunk 109 optimal weight: 20.0000 chunk 398 optimal weight: 30.0000 chunk 430 optimal weight: 40.0000 chunk 354 optimal weight: 0.0980 chunk 395 optimal weight: 50.0000 chunk 135 optimal weight: 9.9990 chunk 319 optimal weight: 6.9990 overall best weight: 3.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 532 ASN A 751 ASN A1002 GLN A1005 GLN D 532 ASN D 536 ASN D 787 GLN ** D1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1113 GLN K 196 ASN K 239 GLN K 532 ASN K 751 ASN K 787 GLN K 954 GLN ** K 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1005 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.130 30117 Z= 0.637 Angle : 0.802 11.224 41376 Z= 0.441 Chirality : 0.059 0.384 5103 Planarity : 0.006 0.062 5508 Dihedral : 5.456 32.957 4896 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer Outliers : 2.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 1.33 % 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: 0.30 (0.12), residues: 4365 helix: 0.95 (0.20), residues: 642 sheet: 0.73 (0.13), residues: 1320 loop : -0.25 (0.12), residues: 2403 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8730 Ramachandran restraints generated. 4365 Oldfield, 0 Emsley, 4365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8730 Ramachandran restraints generated. 4365 Oldfield, 0 Emsley, 4365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 259 time to evaluate : 3.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 29 residues processed: 292 average time/residue: 1.4624 time to fit residues: 505.9292 Evaluate side-chains 275 residues out of total 3831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 246 time to evaluate : 3.299 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 29 outliers final: 18 residues processed: 12 average time/residue: 0.2754 time to fit residues: 10.8722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 393 optimal weight: 0.8980 chunk 299 optimal weight: 0.9980 chunk 206 optimal weight: 1.9990 chunk 44 optimal weight: 50.0000 chunk 190 optimal weight: 50.0000 chunk 267 optimal weight: 10.0000 chunk 399 optimal weight: 30.0000 chunk 423 optimal weight: 50.0000 chunk 208 optimal weight: 0.5980 chunk 379 optimal weight: 0.8980 chunk 114 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 751 ASN A 787 GLN A 901 GLN A1002 GLN A1005 GLN D 954 GLN D1002 GLN D1010 GLN D1113 GLN K 239 GLN K 532 ASN K 751 ASN K 954 GLN ** K 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1005 GLN K1088 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 30117 Z= 0.197 Angle : 0.528 8.934 41376 Z= 0.285 Chirality : 0.046 0.341 5103 Planarity : 0.004 0.045 5508 Dihedral : 4.619 28.640 4896 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer Outliers : 1.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.12), residues: 4365 helix: 1.79 (0.20), residues: 651 sheet: 0.78 (0.13), residues: 1356 loop : -0.10 (0.13), residues: 2358 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8730 Ramachandran restraints generated. 4365 Oldfield, 0 Emsley, 4365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8730 Ramachandran restraints generated. 4365 Oldfield, 0 Emsley, 4365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 3831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 265 time to evaluate : 3.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 26 residues processed: 293 average time/residue: 1.3950 time to fit residues: 486.3997 Evaluate side-chains 275 residues out of total 3831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 249 time to evaluate : 3.388 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 26 outliers final: 17 residues processed: 11 average time/residue: 0.4144 time to fit residues: 11.8549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 352 optimal weight: 2.9990 chunk 240 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 315 optimal weight: 0.2980 chunk 174 optimal weight: 40.0000 chunk 361 optimal weight: 0.0170 chunk 292 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 216 optimal weight: 0.8980 chunk 380 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.8422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN ** A 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN A1002 GLN A1005 GLN A1113 GLN D 314 GLN D 532 ASN D1010 GLN K 239 GLN K 314 GLN K 532 ASN K 751 ASN K1005 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 30117 Z= 0.190 Angle : 0.520 10.750 41376 Z= 0.276 Chirality : 0.046 0.315 5103 Planarity : 0.004 0.044 5508 Dihedral : 4.412 27.589 4896 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer Outliers : 1.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.12), residues: 4365 helix: 1.88 (0.20), residues: 669 sheet: 0.77 (0.13), residues: 1383 loop : -0.00 (0.13), residues: 2313 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8730 Ramachandran restraints generated. 4365 Oldfield, 0 Emsley, 4365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8730 Ramachandran restraints generated. 4365 Oldfield, 0 Emsley, 4365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 261 time to evaluate : 3.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 25 residues processed: 283 average time/residue: 1.4427 time to fit residues: 487.7774 Evaluate side-chains 267 residues out of total 3831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 242 time to evaluate : 3.258 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 18 residues processed: 9 average time/residue: 0.3165 time to fit residues: 9.5676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 142 optimal weight: 50.0000 chunk 381 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 248 optimal weight: 50.0000 chunk 104 optimal weight: 40.0000 chunk 423 optimal weight: 50.0000 chunk 351 optimal weight: 2.9990 chunk 196 optimal weight: 9.9990 chunk 35 optimal weight: 20.0000 chunk 140 optimal weight: 30.0000 chunk 222 optimal weight: 1.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN A1113 GLN ** D 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 532 ASN K 751 ASN K1005 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.129 30117 Z= 0.639 Angle : 0.797 11.137 41376 Z= 0.433 Chirality : 0.059 0.377 5103 Planarity : 0.006 0.068 5508 Dihedral : 5.308 32.562 4896 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer Outliers : 2.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 1.33 % 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: 4365 helix: 0.92 (0.20), residues: 660 sheet: 0.65 (0.13), residues: 1326 loop : -0.33 (0.12), residues: 2379 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8730 Ramachandran restraints generated. 4365 Oldfield, 0 Emsley, 4365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8730 Ramachandran restraints generated. 4365 Oldfield, 0 Emsley, 4365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 248 time to evaluate : 3.303 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: 52 outliers final: 37 residues processed: 278 average time/residue: 1.4017 time to fit residues: 465.6092 Evaluate side-chains 279 residues out of total 3831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 242 time to evaluate : 3.471 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 24 residues processed: 16 average time/residue: 0.4372 time to fit residues: 15.4577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 408 optimal weight: 20.0000 chunk 47 optimal weight: 2.9990 chunk 241 optimal weight: 0.8980 chunk 309 optimal weight: 4.9990 chunk 239 optimal weight: 0.7980 chunk 356 optimal weight: 1.9990 chunk 236 optimal weight: 0.5980 chunk 422 optimal weight: 30.0000 chunk 264 optimal weight: 20.0000 chunk 257 optimal weight: 4.9990 chunk 194 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A1002 GLN A1005 GLN D 532 ASN D1002 GLN ** D1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 196 ASN K 314 GLN K 751 ASN ** K 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1005 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 30117 Z= 0.277 Angle : 0.579 11.961 41376 Z= 0.311 Chirality : 0.048 0.355 5103 Planarity : 0.004 0.049 5508 Dihedral : 4.735 29.692 4896 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer Outliers : 2.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.12), residues: 4365 helix: 1.43 (0.20), residues: 672 sheet: 0.72 (0.13), residues: 1338 loop : -0.26 (0.13), residues: 2355 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8730 Ramachandran restraints generated. 4365 Oldfield, 0 Emsley, 4365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8730 Ramachandran restraints generated. 4365 Oldfield, 0 Emsley, 4365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 3831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 259 time to evaluate : 3.411 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: 47 outliers final: 28 residues processed: 292 average time/residue: 1.4297 time to fit residues: 499.9638 Evaluate side-chains 281 residues out of total 3831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 253 time to evaluate : 3.228 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 23 residues processed: 8 average time/residue: 0.3463 time to fit residues: 9.4503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 261 optimal weight: 7.9990 chunk 168 optimal weight: 0.9990 chunk 252 optimal weight: 7.9990 chunk 127 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 268 optimal weight: 0.0020 chunk 287 optimal weight: 50.0000 chunk 208 optimal weight: 0.5980 chunk 39 optimal weight: 40.0000 chunk 331 optimal weight: 50.0000 overall best weight: 1.0392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 751 ASN A1005 GLN D 532 ASN D1002 GLN D1010 GLN K 314 GLN K 751 ASN ** K 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1005 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 30117 Z= 0.220 Angle : 0.544 11.874 41376 Z= 0.289 Chirality : 0.046 0.334 5103 Planarity : 0.004 0.045 5508 Dihedral : 4.528 28.492 4896 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.13), residues: 4365 helix: 1.74 (0.20), residues: 669 sheet: 0.76 (0.14), residues: 1338 loop : -0.17 (0.13), residues: 2358 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8730 Ramachandran restraints generated. 4365 Oldfield, 0 Emsley, 4365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8730 Ramachandran restraints generated. 4365 Oldfield, 0 Emsley, 4365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 3831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 255 time to evaluate : 3.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 27 residues processed: 282 average time/residue: 1.4554 time to fit residues: 489.2898 Evaluate side-chains 275 residues out of total 3831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 248 time to evaluate : 3.418 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 22 residues processed: 8 average time/residue: 0.6208 time to fit residues: 11.6331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 384 optimal weight: 1.9990 chunk 404 optimal weight: 9.9990 chunk 368 optimal weight: 1.9990 chunk 393 optimal weight: 2.9990 chunk 236 optimal weight: 0.5980 chunk 171 optimal weight: 0.0570 chunk 308 optimal weight: 0.5980 chunk 120 optimal weight: 5.9990 chunk 355 optimal weight: 0.9990 chunk 372 optimal weight: 0.9980 chunk 392 optimal weight: 0.5980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN ** A 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN A1002 GLN A1005 GLN A1113 GLN D1002 GLN D1010 GLN K 314 GLN K 532 ASN K 607 GLN K 751 ASN ** K 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1005 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 30117 Z= 0.161 Angle : 0.512 13.338 41376 Z= 0.269 Chirality : 0.045 0.321 5103 Planarity : 0.004 0.045 5508 Dihedral : 4.288 26.203 4896 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer Outliers : 1.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.13), residues: 4365 helix: 2.33 (0.20), residues: 639 sheet: 0.76 (0.14), residues: 1365 loop : -0.10 (0.13), residues: 2361 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8730 Ramachandran restraints generated. 4365 Oldfield, 0 Emsley, 4365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8730 Ramachandran restraints generated. 4365 Oldfield, 0 Emsley, 4365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 3831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 255 time to evaluate : 3.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 20 residues processed: 280 average time/residue: 1.4856 time to fit residues: 502.7362 Evaluate side-chains 267 residues out of total 3831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 247 time to evaluate : 3.172 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 18 residues processed: 2 average time/residue: 0.2802 time to fit residues: 5.5279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 258 optimal weight: 9.9990 chunk 415 optimal weight: 0.9990 chunk 253 optimal weight: 0.8980 chunk 197 optimal weight: 6.9990 chunk 289 optimal weight: 50.0000 chunk 436 optimal weight: 40.0000 chunk 401 optimal weight: 30.0000 chunk 347 optimal weight: 0.8980 chunk 36 optimal weight: 9.9990 chunk 268 optimal weight: 2.9990 chunk 213 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 751 ASN A1005 GLN ** D 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1002 GLN D1010 GLN K 314 GLN K 532 ASN K 751 ASN K1005 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.077 30117 Z= 0.318 Angle : 0.607 13.583 41376 Z= 0.324 Chirality : 0.052 0.819 5103 Planarity : 0.005 0.051 5508 Dihedral : 4.667 29.774 4896 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer Outliers : 1.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.13), residues: 4365 helix: 1.95 (0.20), residues: 633 sheet: 0.82 (0.14), residues: 1326 loop : -0.15 (0.13), residues: 2406 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8730 Ramachandran restraints generated. 4365 Oldfield, 0 Emsley, 4365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8730 Ramachandran restraints generated. 4365 Oldfield, 0 Emsley, 4365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 3831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 245 time to evaluate : 3.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 23 residues processed: 269 average time/residue: 1.4084 time to fit residues: 452.1010 Evaluate side-chains 261 residues out of total 3831 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 238 time to evaluate : 3.211 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 20 residues processed: 3 average time/residue: 0.2738 time to fit residues: 6.0160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 276 optimal weight: 50.0000 chunk 370 optimal weight: 0.5980 chunk 106 optimal weight: 0.0170 chunk 320 optimal weight: 40.0000 chunk 51 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 348 optimal weight: 0.9990 chunk 145 optimal weight: 40.0000 chunk 357 optimal weight: 5.9990 chunk 44 optimal weight: 40.0000 chunk 64 optimal weight: 0.7980 overall best weight: 0.8822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A1002 GLN A1005 GLN D 607 GLN D1002 GLN D1010 GLN D1113 GLN K 751 ASN K1005 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.248009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.209934 restraints weight = 27039.933| |-----------------------------------------------------------------------------| r_work (start): 0.4282 rms_B_bonded: 3.57 r_work: 0.3840 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3795 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 30117 Z= 0.204 Angle : 0.543 13.389 41376 Z= 0.288 Chirality : 0.047 0.499 5103 Planarity : 0.004 0.055 5508 Dihedral : 4.478 38.498 4896 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer Outliers : 1.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.74 (0.13), residues: 4365 helix: 2.16 (0.20), residues: 636 sheet: 0.77 (0.14), residues: 1353 loop : -0.09 (0.13), residues: 2376 =============================================================================== Job complete usr+sys time: 9466.67 seconds wall clock time: 169 minutes 50.89 seconds (10190.89 seconds total)