Starting phenix.real_space_refine on Mon Oct 14 18:01:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aly_15520/10_2024/8aly_15520.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aly_15520/10_2024/8aly_15520.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aly_15520/10_2024/8aly_15520.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aly_15520/10_2024/8aly_15520.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aly_15520/10_2024/8aly_15520.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aly_15520/10_2024/8aly_15520.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.976 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 36140 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 20 6.06 5 S 240 5.16 5 C 26560 2.51 5 N 7280 2.21 5 O 7200 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 185 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 41300 Number of models: 1 Model: "" Number of chains: 40 Chain: "E" Number of atoms: 2064 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 259, 2056 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 250} Chain breaks: 4 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 44 Conformer: "B" Number of residues, atoms: 259, 2056 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 250} Chain breaks: 4 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 44 bond proxies already assigned to first conformer: 2096 Chain: "J" Number of atoms: 2064 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 259, 2056 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 250} Chain breaks: 4 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 44 Conformer: "B" Number of residues, atoms: 259, 2056 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 250} Chain breaks: 4 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 44 bond proxies already assigned to first conformer: 2096 Chain: "I" Number of atoms: 2064 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 259, 2056 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 250} Chain breaks: 4 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 44 Conformer: "B" Number of residues, atoms: 259, 2056 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 250} Chain breaks: 4 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 44 bond proxies already assigned to first conformer: 2096 Chain: "H" Number of atoms: 2064 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 259, 2056 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 250} Chain breaks: 4 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 44 Conformer: "B" Number of residues, atoms: 259, 2056 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 250} Chain breaks: 4 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 44 bond proxies already assigned to first conformer: 2096 Chain: "G" Number of atoms: 2064 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 259, 2056 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 250} Chain breaks: 4 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 44 Conformer: "B" Number of residues, atoms: 259, 2056 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 250} Chain breaks: 4 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 44 bond proxies already assigned to first conformer: 2096 Chain: "F" Number of atoms: 2064 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 259, 2056 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 250} Chain breaks: 4 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 44 Conformer: "B" Number of residues, atoms: 259, 2056 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 250} Chain breaks: 4 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 44 bond proxies already assigned to first conformer: 2096 Chain: "D" Number of atoms: 2064 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 259, 2056 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 250} Chain breaks: 4 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 44 Conformer: "B" Number of residues, atoms: 259, 2056 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 250} Chain breaks: 4 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 44 bond proxies already assigned to first conformer: 2096 Chain: "C" Number of atoms: 2064 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 259, 2056 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 250} Chain breaks: 4 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 44 Conformer: "B" Number of residues, atoms: 259, 2056 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 250} Chain breaks: 4 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 44 bond proxies already assigned to first conformer: 2096 Chain: "B" Number of atoms: 2064 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 259, 2056 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 250} Chain breaks: 4 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 44 Conformer: "B" Number of residues, atoms: 259, 2056 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 250} Chain breaks: 4 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 44 bond proxies already assigned to first conformer: 2096 Chain: "A" Number of atoms: 2064 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 259, 2056 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 250} Chain breaks: 4 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 44 Conformer: "B" Number of residues, atoms: 259, 2056 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 250} Chain breaks: 4 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 44 bond proxies already assigned to first conformer: 2096 Chain: "O" Number of atoms: 2064 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 259, 2056 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 250} Chain breaks: 4 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 44 Conformer: "B" Number of residues, atoms: 259, 2056 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 250} Chain breaks: 4 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 44 bond proxies already assigned to first conformer: 2096 Chain: "T" Number of atoms: 2064 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 259, 2056 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 250} Chain breaks: 4 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 44 Conformer: "B" Number of residues, atoms: 259, 2056 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 250} Chain breaks: 4 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 44 bond proxies already assigned to first conformer: 2096 Chain: "S" Number of atoms: 2064 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 259, 2056 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 250} Chain breaks: 4 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 44 Conformer: "B" Number of residues, atoms: 259, 2056 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 250} Chain breaks: 4 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 44 bond proxies already assigned to first conformer: 2096 Chain: "R" Number of atoms: 2064 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 259, 2056 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 250} Chain breaks: 4 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 44 Conformer: "B" Number of residues, atoms: 259, 2056 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 250} Chain breaks: 4 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 44 bond proxies already assigned to first conformer: 2096 Chain: "Q" Number of atoms: 2064 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 259, 2056 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 250} Chain breaks: 4 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 44 Conformer: "B" Number of residues, atoms: 259, 2056 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 250} Chain breaks: 4 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 44 bond proxies already assigned to first conformer: 2096 Chain: "P" Number of atoms: 2064 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 259, 2056 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 250} Chain breaks: 4 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 44 Conformer: "B" Number of residues, atoms: 259, 2056 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 250} Chain breaks: 4 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 44 bond proxies already assigned to first conformer: 2096 Chain: "N" Number of atoms: 2064 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 259, 2056 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 250} Chain breaks: 4 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 44 Conformer: "B" Number of residues, atoms: 259, 2056 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 250} Chain breaks: 4 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 44 bond proxies already assigned to first conformer: 2096 Chain: "M" Number of atoms: 2064 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 259, 2056 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 250} Chain breaks: 4 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 44 Conformer: "B" Number of residues, atoms: 259, 2056 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 250} Chain breaks: 4 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 44 bond proxies already assigned to first conformer: 2096 Chain: "L" Number of atoms: 2064 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 259, 2056 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 250} Chain breaks: 4 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 44 Conformer: "B" Number of residues, atoms: 259, 2056 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 250} Chain breaks: 4 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 44 bond proxies already assigned to first conformer: 2096 Chain: "K" Number of atoms: 2064 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 259, 2056 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 250} Chain breaks: 4 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 44 Conformer: "B" Number of residues, atoms: 259, 2056 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 250} Chain breaks: 4 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 44 bond proxies already assigned to first conformer: 2096 Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1561 SG CYS E1089 53.456 130.081 77.889 1.00 54.52 S ATOM 3571 SG CYS J1081 131.734 80.162 12.029 1.00 67.10 S ATOM 3625 SG CYS J1089 131.277 83.333 9.970 1.00 61.96 S ATOM 5689 SG CYS I1089 116.380 32.399 23.666 1.00 58.27 S ATOM 7753 SG CYS H1089 67.015 13.301 37.106 1.00 54.89 S ATOM 9817 SG CYS G1089 21.697 40.569 50.703 1.00 52.84 S ATOM 11827 SG CYS F1081 16.013 96.061 67.313 1.00 62.21 S ATOM 11881 SG CYS F1089 15.552 93.242 64.267 1.00 55.94 S ATOM 13891 SG CYS D1081 108.584 121.112 93.788 1.00 59.47 S ATOM 13945 SG CYS D1089 105.805 122.582 91.546 1.00 58.70 S ATOM 15955 SG CYS C1081 132.717 73.736 107.458 1.00 60.55 S ATOM 16009 SG CYS C1089 131.832 76.654 105.072 1.00 60.21 S ATOM 18019 SG CYS B1081 109.735 25.385 121.409 1.00 54.81 S ATOM 18073 SG CYS B1089 111.492 27.840 118.705 1.00 61.50 S ATOM 20083 SG CYS A1081 57.221 14.024 135.049 1.00 64.82 S ATOM 20137 SG CYS A1089 60.372 14.193 132.220 1.00 64.09 S ATOM 22201 SG CYS O1089 53.525 16.235 106.513 1.00 58.20 S ATOM 24211 SG CYS T1081 132.108 65.898 172.054 1.00 67.90 S ATOM 24265 SG CYS T1089 131.344 62.838 174.389 1.00 62.53 S ATOM 26329 SG CYS S1089 116.461 113.840 160.653 1.00 56.81 S ATOM 28339 SG CYS R1081 64.183 133.378 144.619 1.00 62.77 S ATOM 28393 SG CYS R1089 67.082 132.959 147.394 1.00 55.25 S ATOM 30457 SG CYS Q1089 21.639 105.565 133.833 1.00 53.22 S ATOM 32521 SG CYS P1089 15.731 52.862 120.124 1.00 56.64 S ATOM 34531 SG CYS N1081 108.537 25.179 90.651 1.00 57.88 S ATOM 34585 SG CYS N1089 105.850 23.702 92.908 1.00 60.85 S ATOM 36649 SG CYS M1089 131.935 69.441 79.458 1.00 60.54 S ATOM 38659 SG CYS L1081 109.723 120.915 63.008 1.00 54.77 S ATOM 38713 SG CYS L1089 111.471 118.420 65.785 1.00 61.14 S ATOM 40723 SG CYS K1081 57.199 132.034 49.366 1.00 66.89 S ATOM 40777 SG CYS K1089 60.304 131.973 52.317 1.00 64.54 S Time building chain proxies: 31.16, per 1000 atoms: 0.75 Number of scatterers: 41300 At special positions: 0 Unit cell: (146.28, 147.34, 184.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 20 29.99 S 240 16.00 O 7200 8.00 N 7280 7.00 C 26560 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.17 Conformation dependent library (CDL) restraints added in 7.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1201 " pdb="ZN ZN A1201 " - pdb=" SG CYS A1089 " pdb="ZN ZN A1201 " - pdb=" ND1 HIS A1084 " pdb="ZN ZN A1201 " - pdb=" SG CYS A1081 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1089 " pdb="ZN ZN B1201 " - pdb=" ND1 HIS B1084 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1081 " pdb=" ZN C1201 " pdb="ZN ZN C1201 " - pdb=" SG CYS C1089 " pdb="ZN ZN C1201 " - pdb=" ND1 HIS C1084 " pdb="ZN ZN C1201 " - pdb=" SG CYS C1081 " pdb=" ZN D1201 " pdb="ZN ZN D1201 " - pdb=" SG CYS D1089 " pdb="ZN ZN D1201 " - pdb=" ND1 HIS D1084 " pdb="ZN ZN D1201 " - pdb=" SG CYS D1081 " pdb=" ZN E1201 " pdb="ZN ZN E1201 " - pdb=" SG CYS E1089 " pdb="ZN ZN E1201 " - pdb=" ND1 HIS E1084 " pdb=" ZN F1201 " pdb="ZN ZN F1201 " - pdb=" ND1 HIS F1084 " pdb="ZN ZN F1201 " - pdb=" SG CYS F1089 " pdb="ZN ZN F1201 " - pdb=" SG CYS F1081 " pdb=" ZN G1201 " pdb="ZN ZN G1201 " - pdb=" SG CYS G1089 " pdb="ZN ZN G1201 " - pdb=" ND1 HIS G1084 " pdb=" ZN H1201 " pdb="ZN ZN H1201 " - pdb=" ND1 HIS H1084 " pdb="ZN ZN H1201 " - pdb=" SG CYS H1089 " pdb=" ZN I1201 " pdb="ZN ZN I1201 " - pdb=" SG CYS I1089 " pdb="ZN ZN I1201 " - pdb=" ND1 HIS I1084 " pdb=" ZN J1201 " pdb="ZN ZN J1201 " - pdb=" SG CYS J1089 " pdb="ZN ZN J1201 " - pdb=" ND1 HIS J1084 " pdb="ZN ZN J1201 " - pdb=" SG CYS J1081 " pdb=" ZN K1201 " pdb="ZN ZN K1201 " - pdb=" SG CYS K1089 " pdb="ZN ZN K1201 " - pdb=" ND1 HIS K1084 " pdb="ZN ZN K1201 " - pdb=" SG CYS K1081 " pdb=" ZN L1201 " pdb="ZN ZN L1201 " - pdb=" SG CYS L1089 " pdb="ZN ZN L1201 " - pdb=" ND1 HIS L1084 " pdb="ZN ZN L1201 " - pdb=" SG CYS L1081 " pdb=" ZN M1201 " pdb="ZN ZN M1201 " - pdb=" ND1 HIS M1084 " pdb="ZN ZN M1201 " - pdb=" SG CYS M1089 " pdb=" ZN N1201 " pdb="ZN ZN N1201 " - pdb=" SG CYS N1089 " pdb="ZN ZN N1201 " - pdb=" ND1 HIS N1084 " pdb="ZN ZN N1201 " - pdb=" SG CYS N1081 " pdb=" ZN O1201 " pdb="ZN ZN O1201 " - pdb=" SG CYS O1089 " pdb="ZN ZN O1201 " - pdb=" ND1 HIS O1084 " pdb=" ZN P1201 " pdb="ZN ZN P1201 " - pdb=" SG CYS P1089 " pdb="ZN ZN P1201 " - pdb=" ND1 HIS P1084 " pdb=" ZN Q1201 " pdb="ZN ZN Q1201 " - pdb=" SG CYS Q1089 " pdb="ZN ZN Q1201 " - pdb=" ND1 HIS Q1084 " pdb=" ZN R1201 " pdb="ZN ZN R1201 " - pdb=" ND1 HIS R1084 " pdb="ZN ZN R1201 " - pdb=" SG CYS R1089 " pdb="ZN ZN R1201 " - pdb=" SG CYS R1081 " pdb=" ZN S1201 " pdb="ZN ZN S1201 " - pdb=" SG CYS S1089 " pdb="ZN ZN S1201 " - pdb=" ND1 HIS S1084 " pdb=" ZN T1201 " pdb="ZN ZN T1201 " - pdb=" SG CYS T1089 " pdb="ZN ZN T1201 " - pdb=" ND1 HIS T1084 " pdb="ZN ZN T1201 " - pdb=" SG CYS T1081 " 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9600 Finding SS restraints... Secondary structure from input PDB file: 234 helices and 49 sheets defined 41.3% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.22 Creating SS restraints... Processing helix chain 'E' and resid 876 through 886 Processing helix chain 'E' and resid 887 through 889 No H-bonds generated for 'chain 'E' and resid 887 through 889' Processing helix chain 'E' and resid 890 through 897 Processing helix chain 'E' and resid 900 through 905 Processing helix chain 'E' and resid 908 through 915 removed outlier: 3.647A pdb=" N ILE E 915 " --> pdb=" O GLU E 911 " (cutoff:3.500A) Processing helix chain 'E' and resid 919 through 935 Processing helix chain 'E' and resid 962 through 975 Processing helix chain 'E' and resid 1002 through 1020 Processing helix chain 'E' and resid 1038 through 1043 Processing helix chain 'E' and resid 1045 through 1049 Processing helix chain 'E' and resid 1064 through 1070 removed outlier: 3.507A pdb=" N SER E1068 " --> pdb=" O ASN E1064 " (cutoff:3.500A) Processing helix chain 'E' and resid 1143 through 1145 No H-bonds generated for 'chain 'E' and resid 1143 through 1145' Processing helix chain 'J' and resid 876 through 886 Processing helix chain 'J' and resid 887 through 889 No H-bonds generated for 'chain 'J' and resid 887 through 889' Processing helix chain 'J' and resid 890 through 897 Processing helix chain 'J' and resid 900 through 905 Processing helix chain 'J' and resid 908 through 915 Processing helix chain 'J' and resid 919 through 935 Processing helix chain 'J' and resid 962 through 975 Processing helix chain 'J' and resid 1002 through 1020 Processing helix chain 'J' and resid 1038 through 1043 Processing helix chain 'J' and resid 1045 through 1049 Processing helix chain 'J' and resid 1064 through 1070 Processing helix chain 'J' and resid 1143 through 1145 No H-bonds generated for 'chain 'J' and resid 1143 through 1145' Processing helix chain 'I' and resid 876 through 886 Processing helix chain 'I' and resid 890 through 897 Processing helix chain 'I' and resid 900 through 905 Processing helix chain 'I' and resid 908 through 915 removed outlier: 3.520A pdb=" N ILE I 915 " --> pdb=" O GLU I 911 " (cutoff:3.500A) Processing helix chain 'I' and resid 919 through 935 removed outlier: 3.501A pdb=" N ARG I 923 " --> pdb=" O ALA I 919 " (cutoff:3.500A) Processing helix chain 'I' and resid 962 through 975 Processing helix chain 'I' and resid 1002 through 1020 Processing helix chain 'I' and resid 1038 through 1043 Processing helix chain 'I' and resid 1045 through 1049 Processing helix chain 'I' and resid 1064 through 1070 Processing helix chain 'I' and resid 1143 through 1145 No H-bonds generated for 'chain 'I' and resid 1143 through 1145' Processing helix chain 'H' and resid 876 through 886 Processing helix chain 'H' and resid 890 through 897 Processing helix chain 'H' and resid 900 through 905 Processing helix chain 'H' and resid 908 through 915 removed outlier: 3.507A pdb=" N ILE H 915 " --> pdb=" O GLU H 911 " (cutoff:3.500A) Processing helix chain 'H' and resid 919 through 935 Processing helix chain 'H' and resid 937 through 941 Processing helix chain 'H' and resid 962 through 975 Processing helix chain 'H' and resid 1002 through 1020 Processing helix chain 'H' and resid 1038 through 1043 Processing helix chain 'H' and resid 1045 through 1049 Processing helix chain 'H' and resid 1064 through 1070 Processing helix chain 'H' and resid 1143 through 1145 No H-bonds generated for 'chain 'H' and resid 1143 through 1145' Processing helix chain 'G' and resid 876 through 886 Processing helix chain 'G' and resid 890 through 897 Processing helix chain 'G' and resid 900 through 905 Processing helix chain 'G' and resid 908 through 915 removed outlier: 3.624A pdb=" N ILE G 915 " --> pdb=" O GLU G 911 " (cutoff:3.500A) Processing helix chain 'G' and resid 919 through 935 Processing helix chain 'G' and resid 937 through 941 Processing helix chain 'G' and resid 962 through 975 Processing helix chain 'G' and resid 1002 through 1020 Processing helix chain 'G' and resid 1035 through 1043 removed outlier: 3.534A pdb=" N ILE G1040 " --> pdb=" O VAL G1036 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N HIS G1041 " --> pdb=" O ASN G1037 " (cutoff:3.500A) Processing helix chain 'G' and resid 1045 through 1049 Processing helix chain 'G' and resid 1064 through 1070 removed outlier: 3.529A pdb=" N SER G1068 " --> pdb=" O ASN G1064 " (cutoff:3.500A) Processing helix chain 'G' and resid 1143 through 1145 No H-bonds generated for 'chain 'G' and resid 1143 through 1145' Processing helix chain 'F' and resid 876 through 886 Processing helix chain 'F' and resid 890 through 897 Processing helix chain 'F' and resid 900 through 905 Processing helix chain 'F' and resid 908 through 915 Processing helix chain 'F' and resid 919 through 935 Processing helix chain 'F' and resid 962 through 975 Processing helix chain 'F' and resid 1002 through 1020 Processing helix chain 'F' and resid 1038 through 1043 Processing helix chain 'F' and resid 1045 through 1049 Processing helix chain 'F' and resid 1064 through 1070 removed outlier: 3.631A pdb=" N SER F1068 " --> pdb=" O ASN F1064 " (cutoff:3.500A) Processing helix chain 'F' and resid 1143 through 1145 No H-bonds generated for 'chain 'F' and resid 1143 through 1145' Processing helix chain 'D' and resid 876 through 886 Processing helix chain 'D' and resid 890 through 897 Processing helix chain 'D' and resid 900 through 905 Processing helix chain 'D' and resid 908 through 915 removed outlier: 3.558A pdb=" N ILE D 915 " --> pdb=" O GLU D 911 " (cutoff:3.500A) Processing helix chain 'D' and resid 919 through 935 Processing helix chain 'D' and resid 962 through 975 Processing helix chain 'D' and resid 1002 through 1020 removed outlier: 3.529A pdb=" N TRP D1006 " --> pdb=" O ASN D1002 " (cutoff:3.500A) Processing helix chain 'D' and resid 1038 through 1043 Processing helix chain 'D' and resid 1045 through 1049 Processing helix chain 'D' and resid 1064 through 1070 Processing helix chain 'D' and resid 1143 through 1145 No H-bonds generated for 'chain 'D' and resid 1143 through 1145' Processing helix chain 'C' and resid 876 through 886 Processing helix chain 'C' and resid 890 through 897 Processing helix chain 'C' and resid 900 through 905 Processing helix chain 'C' and resid 908 through 915 Processing helix chain 'C' and resid 919 through 935 Processing helix chain 'C' and resid 962 through 975 Processing helix chain 'C' and resid 1002 through 1020 Processing helix chain 'C' and resid 1038 through 1043 Processing helix chain 'C' and resid 1045 through 1049 Processing helix chain 'C' and resid 1064 through 1070 Processing helix chain 'C' and resid 1143 through 1145 No H-bonds generated for 'chain 'C' and resid 1143 through 1145' Processing helix chain 'B' and resid 876 through 886 Processing helix chain 'B' and resid 887 through 889 No H-bonds generated for 'chain 'B' and resid 887 through 889' Processing helix chain 'B' and resid 890 through 897 Processing helix chain 'B' and resid 900 through 905 Processing helix chain 'B' and resid 908 through 915 Processing helix chain 'B' and resid 919 through 935 Processing helix chain 'B' and resid 937 through 941 Processing helix chain 'B' and resid 962 through 975 Processing helix chain 'B' and resid 1002 through 1020 Processing helix chain 'B' and resid 1038 through 1043 Processing helix chain 'B' and resid 1045 through 1049 Processing helix chain 'B' and resid 1064 through 1070 Processing helix chain 'B' and resid 1143 through 1145 No H-bonds generated for 'chain 'B' and resid 1143 through 1145' Processing helix chain 'A' and resid 876 through 886 Processing helix chain 'A' and resid 887 through 889 No H-bonds generated for 'chain 'A' and resid 887 through 889' Processing helix chain 'A' and resid 890 through 897 Processing helix chain 'A' and resid 900 through 905 Processing helix chain 'A' and resid 908 through 915 Processing helix chain 'A' and resid 919 through 935 Processing helix chain 'A' and resid 962 through 975 Processing helix chain 'A' and resid 1002 through 1020 Processing helix chain 'A' and resid 1038 through 1043 Processing helix chain 'A' and resid 1045 through 1049 Processing helix chain 'A' and resid 1064 through 1070 removed outlier: 3.548A pdb=" N SER A1068 " --> pdb=" O ASN A1064 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1145 No H-bonds generated for 'chain 'A' and resid 1143 through 1145' Processing helix chain 'O' and resid 876 through 886 Processing helix chain 'O' and resid 887 through 889 No H-bonds generated for 'chain 'O' and resid 887 through 889' Processing helix chain 'O' and resid 890 through 897 Processing helix chain 'O' and resid 900 through 905 Processing helix chain 'O' and resid 908 through 915 removed outlier: 3.590A pdb=" N ILE O 915 " --> pdb=" O GLU O 911 " (cutoff:3.500A) Processing helix chain 'O' and resid 919 through 935 Processing helix chain 'O' and resid 962 through 975 Processing helix chain 'O' and resid 1002 through 1020 removed outlier: 3.587A pdb=" N TRP O1006 " --> pdb=" O ASN O1002 " (cutoff:3.500A) Processing helix chain 'O' and resid 1038 through 1043 Processing helix chain 'O' and resid 1045 through 1049 Processing helix chain 'O' and resid 1064 through 1070 removed outlier: 3.508A pdb=" N SER O1068 " --> pdb=" O ASN O1064 " (cutoff:3.500A) Processing helix chain 'O' and resid 1143 through 1145 No H-bonds generated for 'chain 'O' and resid 1143 through 1145' Processing helix chain 'T' and resid 876 through 886 Processing helix chain 'T' and resid 890 through 897 Processing helix chain 'T' and resid 900 through 905 Processing helix chain 'T' and resid 908 through 915 Processing helix chain 'T' and resid 919 through 935 Processing helix chain 'T' and resid 962 through 975 Processing helix chain 'T' and resid 1002 through 1020 Processing helix chain 'T' and resid 1038 through 1043 Processing helix chain 'T' and resid 1045 through 1049 Processing helix chain 'T' and resid 1064 through 1070 Processing helix chain 'T' and resid 1143 through 1145 No H-bonds generated for 'chain 'T' and resid 1143 through 1145' Processing helix chain 'S' and resid 876 through 886 Processing helix chain 'S' and resid 890 through 897 Processing helix chain 'S' and resid 900 through 905 Processing helix chain 'S' and resid 908 through 915 removed outlier: 3.539A pdb=" N ILE S 915 " --> pdb=" O GLU S 911 " (cutoff:3.500A) Processing helix chain 'S' and resid 919 through 935 Processing helix chain 'S' and resid 937 through 941 Processing helix chain 'S' and resid 962 through 975 Processing helix chain 'S' and resid 1002 through 1020 Processing helix chain 'S' and resid 1038 through 1043 Processing helix chain 'S' and resid 1045 through 1049 Processing helix chain 'S' and resid 1064 through 1070 Processing helix chain 'S' and resid 1143 through 1145 No H-bonds generated for 'chain 'S' and resid 1143 through 1145' Processing helix chain 'R' and resid 876 through 886 Processing helix chain 'R' and resid 887 through 889 No H-bonds generated for 'chain 'R' and resid 887 through 889' Processing helix chain 'R' and resid 890 through 897 Processing helix chain 'R' and resid 900 through 905 Processing helix chain 'R' and resid 908 through 915 removed outlier: 3.551A pdb=" N ILE R 915 " --> pdb=" O GLU R 911 " (cutoff:3.500A) Processing helix chain 'R' and resid 919 through 935 Processing helix chain 'R' and resid 962 through 975 Processing helix chain 'R' and resid 1002 through 1020 Processing helix chain 'R' and resid 1038 through 1043 Processing helix chain 'R' and resid 1045 through 1049 Processing helix chain 'R' and resid 1064 through 1070 Processing helix chain 'R' and resid 1143 through 1145 No H-bonds generated for 'chain 'R' and resid 1143 through 1145' Processing helix chain 'Q' and resid 876 through 886 Processing helix chain 'Q' and resid 887 through 889 No H-bonds generated for 'chain 'Q' and resid 887 through 889' Processing helix chain 'Q' and resid 890 through 897 Processing helix chain 'Q' and resid 900 through 905 Processing helix chain 'Q' and resid 908 through 915 removed outlier: 3.680A pdb=" N ILE Q 915 " --> pdb=" O GLU Q 911 " (cutoff:3.500A) Processing helix chain 'Q' and resid 919 through 935 Processing helix chain 'Q' and resid 937 through 941 Processing helix chain 'Q' and resid 962 through 975 Processing helix chain 'Q' and resid 1002 through 1020 Processing helix chain 'Q' and resid 1038 through 1043 Processing helix chain 'Q' and resid 1045 through 1049 Processing helix chain 'Q' and resid 1064 through 1070 Processing helix chain 'Q' and resid 1143 through 1145 No H-bonds generated for 'chain 'Q' and resid 1143 through 1145' Processing helix chain 'P' and resid 876 through 886 Processing helix chain 'P' and resid 887 through 889 No H-bonds generated for 'chain 'P' and resid 887 through 889' Processing helix chain 'P' and resid 890 through 897 Processing helix chain 'P' and resid 900 through 905 Processing helix chain 'P' and resid 908 through 915 Processing helix chain 'P' and resid 919 through 935 Processing helix chain 'P' and resid 962 through 975 Processing helix chain 'P' and resid 1002 through 1020 Processing helix chain 'P' and resid 1038 through 1043 Processing helix chain 'P' and resid 1045 through 1049 Processing helix chain 'P' and resid 1064 through 1070 Processing helix chain 'P' and resid 1143 through 1145 No H-bonds generated for 'chain 'P' and resid 1143 through 1145' Processing helix chain 'N' and resid 876 through 886 Processing helix chain 'N' and resid 890 through 897 Processing helix chain 'N' and resid 900 through 905 Processing helix chain 'N' and resid 908 through 915 removed outlier: 3.656A pdb=" N ILE N 915 " --> pdb=" O GLU N 911 " (cutoff:3.500A) Processing helix chain 'N' and resid 919 through 935 Processing helix chain 'N' and resid 962 through 975 Processing helix chain 'N' and resid 1002 through 1020 Processing helix chain 'N' and resid 1038 through 1043 Processing helix chain 'N' and resid 1045 through 1049 Processing helix chain 'N' and resid 1064 through 1070 Processing helix chain 'N' and resid 1143 through 1145 No H-bonds generated for 'chain 'N' and resid 1143 through 1145' Processing helix chain 'M' and resid 876 through 886 Processing helix chain 'M' and resid 890 through 897 Processing helix chain 'M' and resid 900 through 905 Processing helix chain 'M' and resid 908 through 915 removed outlier: 3.603A pdb=" N ILE M 915 " --> pdb=" O GLU M 911 " (cutoff:3.500A) Processing helix chain 'M' and resid 919 through 935 Processing helix chain 'M' and resid 962 through 975 Processing helix chain 'M' and resid 1002 through 1020 Processing helix chain 'M' and resid 1038 through 1043 Processing helix chain 'M' and resid 1045 through 1049 Processing helix chain 'M' and resid 1064 through 1070 Processing helix chain 'M' and resid 1143 through 1145 No H-bonds generated for 'chain 'M' and resid 1143 through 1145' Processing helix chain 'L' and resid 876 through 886 Processing helix chain 'L' and resid 887 through 889 No H-bonds generated for 'chain 'L' and resid 887 through 889' Processing helix chain 'L' and resid 890 through 897 Processing helix chain 'L' and resid 900 through 905 Processing helix chain 'L' and resid 908 through 915 removed outlier: 3.545A pdb=" N ILE L 915 " --> pdb=" O GLU L 911 " (cutoff:3.500A) Processing helix chain 'L' and resid 919 through 935 Processing helix chain 'L' and resid 962 through 975 Processing helix chain 'L' and resid 1002 through 1020 Processing helix chain 'L' and resid 1038 through 1043 Processing helix chain 'L' and resid 1045 through 1049 removed outlier: 3.555A pdb=" N ALA L1049 " --> pdb=" O GLU L1046 " (cutoff:3.500A) Processing helix chain 'L' and resid 1064 through 1070 Processing helix chain 'L' and resid 1143 through 1145 No H-bonds generated for 'chain 'L' and resid 1143 through 1145' Processing helix chain 'K' and resid 876 through 886 Processing helix chain 'K' and resid 890 through 897 Processing helix chain 'K' and resid 900 through 905 Processing helix chain 'K' and resid 908 through 915 removed outlier: 3.508A pdb=" N ILE K 915 " --> pdb=" O GLU K 911 " (cutoff:3.500A) Processing helix chain 'K' and resid 919 through 935 Processing helix chain 'K' and resid 962 through 975 Processing helix chain 'K' and resid 1002 through 1020 Processing helix chain 'K' and resid 1035 through 1043 removed outlier: 3.601A pdb=" N ILE K1039 " --> pdb=" O PHE K1035 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE K1040 " --> pdb=" O VAL K1036 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N HIS K1041 " --> pdb=" O ASN K1037 " (cutoff:3.500A) Processing helix chain 'K' and resid 1045 through 1049 removed outlier: 3.560A pdb=" N ALA K1049 " --> pdb=" O GLU K1046 " (cutoff:3.500A) Processing helix chain 'K' and resid 1064 through 1070 removed outlier: 3.529A pdb=" N SER K1068 " --> pdb=" O ASN K1064 " (cutoff:3.500A) Processing helix chain 'K' and resid 1143 through 1145 No H-bonds generated for 'chain 'K' and resid 1143 through 1145' Processing sheet with id=AA1, first strand: chain 'E' and resid 954 through 958 removed outlier: 4.900A pdb=" N ILE E 997 " --> pdb=" O LEU E 958 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N ILE E 994 " --> pdb=" O GLN E1156 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N GLN E1156 " --> pdb=" O ILE E 994 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N GLU E1150 " --> pdb=" O VAL E1000 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ALA E1147 " --> pdb=" O THR E1102 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N THR E1102 " --> pdb=" O ALA E1147 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ARG E1100 " --> pdb=" O PRO E1149 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 1059 through 1062 Processing sheet with id=AA3, first strand: chain 'J' and resid 954 through 957 removed outlier: 5.343A pdb=" N ILE J 994 " --> pdb=" O GLN J1156 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N GLN J1156 " --> pdb=" O ILE J 994 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N GLU J1150 " --> pdb=" O VAL J1000 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ALA J1147 " --> pdb=" O THR J1102 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N THR J1102 " --> pdb=" O ALA J1147 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ARG J1100 " --> pdb=" O PRO J1149 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 954 through 957 removed outlier: 5.343A pdb=" N ILE J 994 " --> pdb=" O GLN J1156 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N GLN J1156 " --> pdb=" O ILE J 994 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N GLU J1150 " --> pdb=" O VAL J1000 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ALA J1147 " --> pdb=" O THR J1102 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N THR J1102 " --> pdb=" O ALA J1147 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ARG J1100 " --> pdb=" O PRO J1149 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'J' and resid 1059 through 1062 removed outlier: 5.968A pdb=" N PHE J1107 " --> pdb=" O THR J1126 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 954 through 957 removed outlier: 5.507A pdb=" N ILE I 994 " --> pdb=" O GLN I1156 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N GLN I1156 " --> pdb=" O ILE I 994 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N GLU I1150 " --> pdb=" O VAL I1000 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ALA I1147 " --> pdb=" O THR I1102 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N THR I1102 " --> pdb=" O ALA I1147 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ARG I1100 " --> pdb=" O PRO I1149 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 1059 through 1062 Processing sheet with id=AA8, first strand: chain 'H' and resid 954 through 957 removed outlier: 5.414A pdb=" N ILE H 994 " --> pdb=" O GLN H1156 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN H1156 " --> pdb=" O ILE H 994 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLU H1150 " --> pdb=" O VAL H1000 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ALA H1147 " --> pdb=" O THR H1102 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N THR H1102 " --> pdb=" O ALA H1147 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ARG H1100 " --> pdb=" O PRO H1149 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 1059 through 1062 Processing sheet with id=AB1, first strand: chain 'G' and resid 954 through 957 removed outlier: 5.374A pdb=" N ILE G 994 " --> pdb=" O GLN G1156 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLN G1156 " --> pdb=" O ILE G 994 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N GLU G1150 " --> pdb=" O VAL G1000 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ALA G1147 " --> pdb=" O THR G1102 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N THR G1102 " --> pdb=" O ALA G1147 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ARG G1100 " --> pdb=" O PRO G1149 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 954 through 957 removed outlier: 5.374A pdb=" N ILE G 994 " --> pdb=" O GLN G1156 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLN G1156 " --> pdb=" O ILE G 994 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N GLU G1150 " --> pdb=" O VAL G1000 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ALA G1147 " --> pdb=" O THR G1102 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N THR G1102 " --> pdb=" O ALA G1147 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ARG G1100 " --> pdb=" O PRO G1149 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 1059 through 1062 Processing sheet with id=AB4, first strand: chain 'F' and resid 954 through 958 removed outlier: 4.885A pdb=" N ILE F 997 " --> pdb=" O LEU F 958 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ILE F 994 " --> pdb=" O GLN F1156 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLN F1156 " --> pdb=" O ILE F 994 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N GLU F1150 " --> pdb=" O VAL F1000 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ALA F1147 " --> pdb=" O THR F1102 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N THR F1102 " --> pdb=" O ALA F1147 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ARG F1100 " --> pdb=" O PRO F1149 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 954 through 958 removed outlier: 4.885A pdb=" N ILE F 997 " --> pdb=" O LEU F 958 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ILE F 994 " --> pdb=" O GLN F1156 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLN F1156 " --> pdb=" O ILE F 994 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N GLU F1150 " --> pdb=" O VAL F1000 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ALA F1147 " --> pdb=" O THR F1102 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N THR F1102 " --> pdb=" O ALA F1147 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ARG F1100 " --> pdb=" O PRO F1149 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 1059 through 1062 Processing sheet with id=AB7, first strand: chain 'D' and resid 954 through 958 removed outlier: 4.864A pdb=" N ILE D 997 " --> pdb=" O LEU D 958 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ILE D 994 " --> pdb=" O GLN D1156 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLN D1156 " --> pdb=" O ILE D 994 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N GLU D1150 " --> pdb=" O VAL D1000 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ALA D1147 " --> pdb=" O THR D1102 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N THR D1102 " --> pdb=" O ALA D1147 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ARG D1100 " --> pdb=" O PRO D1149 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 1059 through 1062 Processing sheet with id=AB9, first strand: chain 'C' and resid 954 through 958 removed outlier: 4.881A pdb=" N ILE C 997 " --> pdb=" O LEU C 958 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ILE C 994 " --> pdb=" O GLN C1156 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLN C1156 " --> pdb=" O ILE C 994 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N GLU C1150 " --> pdb=" O VAL C1000 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ALA C1147 " --> pdb=" O THR C1102 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N THR C1102 " --> pdb=" O ALA C1147 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ARG C1100 " --> pdb=" O PRO C1149 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 1059 through 1062 removed outlier: 5.769A pdb=" N PHE C1107 " --> pdb=" O THR C1126 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 954 through 957 removed outlier: 6.907A pdb=" N THR B1154 " --> pdb=" O LEU B 995 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ILE B 997 " --> pdb=" O LEU B1152 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU B1152 " --> pdb=" O ILE B 997 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LYS B 999 " --> pdb=" O GLU B1150 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N GLU B1150 " --> pdb=" O LYS B 999 " (cutoff:3.500A) removed outlier: 9.457A pdb=" N CYS B1001 " --> pdb=" O TYR B1148 " (cutoff:3.500A) removed outlier: 12.548A pdb=" N TYR B1148 " --> pdb=" O CYS B1001 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ALA B1147 " --> pdb=" O THR B1102 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N THR B1102 " --> pdb=" O ALA B1147 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ARG B1100 " --> pdb=" O PRO B1149 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 1059 through 1062 removed outlier: 5.789A pdb=" N PHE B1107 " --> pdb=" O THR B1126 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 954 through 958 removed outlier: 4.859A pdb=" N ILE A 997 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N THR A1154 " --> pdb=" O LEU A 995 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ILE A 997 " --> pdb=" O LEU A1152 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU A1152 " --> pdb=" O ILE A 997 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LYS A 999 " --> pdb=" O GLU A1150 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N GLU A1150 " --> pdb=" O LYS A 999 " (cutoff:3.500A) removed outlier: 9.438A pdb=" N CYS A1001 " --> pdb=" O TYR A1148 " (cutoff:3.500A) removed outlier: 12.539A pdb=" N TYR A1148 " --> pdb=" O CYS A1001 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ALA A1147 " --> pdb=" O THR A1102 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N THR A1102 " --> pdb=" O ALA A1147 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ARG A1100 " --> pdb=" O PRO A1149 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 954 through 958 removed outlier: 4.859A pdb=" N ILE A 997 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N THR A1154 " --> pdb=" O LEU A 995 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ILE A 997 " --> pdb=" O LEU A1152 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU A1152 " --> pdb=" O ILE A 997 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LYS A 999 " --> pdb=" O GLU A1150 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N GLU A1150 " --> pdb=" O LYS A 999 " (cutoff:3.500A) removed outlier: 9.438A pdb=" N CYS A1001 " --> pdb=" O TYR A1148 " (cutoff:3.500A) removed outlier: 12.539A pdb=" N TYR A1148 " --> pdb=" O CYS A1001 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ALA A1147 " --> pdb=" O THR A1102 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N THR A1102 " --> pdb=" O ALA A1147 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ARG A1100 " --> pdb=" O PRO A1149 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 1059 through 1062 Processing sheet with id=AC7, first strand: chain 'O' and resid 954 through 958 removed outlier: 4.857A pdb=" N ILE O 997 " --> pdb=" O LEU O 958 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N ILE O 994 " --> pdb=" O GLN O1156 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N GLN O1156 " --> pdb=" O ILE O 994 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N GLU O1150 " --> pdb=" O VAL O1000 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ALA O1147 " --> pdb=" O THR O1102 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N THR O1102 " --> pdb=" O ALA O1147 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ARG O1100 " --> pdb=" O PRO O1149 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'O' and resid 1059 through 1062 Processing sheet with id=AC9, first strand: chain 'T' and resid 954 through 957 removed outlier: 5.453A pdb=" N ILE T 994 " --> pdb=" O GLN T1156 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N GLN T1156 " --> pdb=" O ILE T 994 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N GLU T1150 " --> pdb=" O VAL T1000 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ALA T1147 " --> pdb=" O THR T1102 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N THR T1102 " --> pdb=" O ALA T1147 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ARG T1100 " --> pdb=" O PRO T1149 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'T' and resid 954 through 957 removed outlier: 5.453A pdb=" N ILE T 994 " --> pdb=" O GLN T1156 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N GLN T1156 " --> pdb=" O ILE T 994 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N GLU T1150 " --> pdb=" O VAL T1000 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ALA T1147 " --> pdb=" O THR T1102 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N THR T1102 " --> pdb=" O ALA T1147 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ARG T1100 " --> pdb=" O PRO T1149 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'T' and resid 1059 through 1062 Processing sheet with id=AD3, first strand: chain 'S' and resid 954 through 957 removed outlier: 5.411A pdb=" N ILE S 994 " --> pdb=" O GLN S1156 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N GLN S1156 " --> pdb=" O ILE S 994 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N GLU S1150 " --> pdb=" O VAL S1000 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ALA S1147 " --> pdb=" O THR S1102 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N THR S1102 " --> pdb=" O ALA S1147 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ARG S1100 " --> pdb=" O PRO S1149 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'S' and resid 954 through 957 removed outlier: 5.411A pdb=" N ILE S 994 " --> pdb=" O GLN S1156 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N GLN S1156 " --> pdb=" O ILE S 994 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N GLU S1150 " --> pdb=" O VAL S1000 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ALA S1147 " --> pdb=" O THR S1102 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N THR S1102 " --> pdb=" O ALA S1147 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ARG S1100 " --> pdb=" O PRO S1149 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'S' and resid 1059 through 1062 Processing sheet with id=AD6, first strand: chain 'R' and resid 954 through 957 removed outlier: 7.039A pdb=" N THR R1154 " --> pdb=" O LEU R 995 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ILE R 997 " --> pdb=" O LEU R1152 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU R1152 " --> pdb=" O ILE R 997 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N LYS R 999 " --> pdb=" O GLU R1150 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N GLU R1150 " --> pdb=" O LYS R 999 " (cutoff:3.500A) removed outlier: 9.476A pdb=" N CYS R1001 " --> pdb=" O TYR R1148 " (cutoff:3.500A) removed outlier: 12.569A pdb=" N TYR R1148 " --> pdb=" O CYS R1001 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ALA R1147 " --> pdb=" O THR R1102 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N THR R1102 " --> pdb=" O ALA R1147 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ARG R1100 " --> pdb=" O PRO R1149 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'R' and resid 1059 through 1062 Processing sheet with id=AD8, first strand: chain 'Q' and resid 954 through 957 removed outlier: 5.437A pdb=" N ILE Q 994 " --> pdb=" O GLN Q1156 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN Q1156 " --> pdb=" O ILE Q 994 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N GLU Q1150 " --> pdb=" O VAL Q1000 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ALA Q1147 " --> pdb=" O THR Q1102 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N THR Q1102 " --> pdb=" O ALA Q1147 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ARG Q1100 " --> pdb=" O PRO Q1149 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Q' and resid 954 through 957 removed outlier: 5.437A pdb=" N ILE Q 994 " --> pdb=" O GLN Q1156 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN Q1156 " --> pdb=" O ILE Q 994 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N GLU Q1150 " --> pdb=" O VAL Q1000 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ALA Q1147 " --> pdb=" O THR Q1102 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N THR Q1102 " --> pdb=" O ALA Q1147 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ARG Q1100 " --> pdb=" O PRO Q1149 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Q' and resid 1059 through 1062 Processing sheet with id=AE2, first strand: chain 'P' and resid 954 through 957 removed outlier: 5.454A pdb=" N ILE P 994 " --> pdb=" O GLN P1156 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLN P1156 " --> pdb=" O ILE P 994 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N GLU P1150 " --> pdb=" O VAL P1000 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ALA P1147 " --> pdb=" O THR P1102 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N THR P1102 " --> pdb=" O ALA P1147 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ARG P1100 " --> pdb=" O PRO P1149 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'P' and resid 954 through 957 removed outlier: 5.454A pdb=" N ILE P 994 " --> pdb=" O GLN P1156 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLN P1156 " --> pdb=" O ILE P 994 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N GLU P1150 " --> pdb=" O VAL P1000 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ALA P1147 " --> pdb=" O THR P1102 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N THR P1102 " --> pdb=" O ALA P1147 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ARG P1100 " --> pdb=" O PRO P1149 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'P' and resid 1059 through 1062 Processing sheet with id=AE5, first strand: chain 'N' and resid 954 through 958 removed outlier: 4.882A pdb=" N ILE N 997 " --> pdb=" O LEU N 958 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ILE N 994 " --> pdb=" O GLN N1156 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLN N1156 " --> pdb=" O ILE N 994 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N GLU N1150 " --> pdb=" O VAL N1000 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ALA N1147 " --> pdb=" O THR N1102 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N THR N1102 " --> pdb=" O ALA N1147 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ARG N1100 " --> pdb=" O PRO N1149 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 954 through 958 removed outlier: 4.882A pdb=" N ILE N 997 " --> pdb=" O LEU N 958 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ILE N 994 " --> pdb=" O GLN N1156 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLN N1156 " --> pdb=" O ILE N 994 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N GLU N1150 " --> pdb=" O VAL N1000 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ALA N1147 " --> pdb=" O THR N1102 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N THR N1102 " --> pdb=" O ALA N1147 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ARG N1100 " --> pdb=" O PRO N1149 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'N' and resid 1059 through 1062 Processing sheet with id=AE8, first strand: chain 'M' and resid 954 through 958 removed outlier: 4.871A pdb=" N ILE M 997 " --> pdb=" O LEU M 958 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N ILE M 994 " --> pdb=" O GLN M1156 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N GLN M1156 " --> pdb=" O ILE M 994 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N GLU M1150 " --> pdb=" O VAL M1000 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ALA M1147 " --> pdb=" O THR M1102 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N THR M1102 " --> pdb=" O ALA M1147 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ARG M1100 " --> pdb=" O PRO M1149 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 1059 through 1062 removed outlier: 5.784A pdb=" N PHE M1107 " --> pdb=" O THR M1126 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 954 through 958 removed outlier: 4.892A pdb=" N ILE L 997 " --> pdb=" O LEU L 958 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N THR L1154 " --> pdb=" O LEU L 995 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ILE L 997 " --> pdb=" O LEU L1152 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU L1152 " --> pdb=" O ILE L 997 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N LYS L 999 " --> pdb=" O GLU L1150 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N GLU L1150 " --> pdb=" O LYS L 999 " (cutoff:3.500A) removed outlier: 9.446A pdb=" N CYS L1001 " --> pdb=" O TYR L1148 " (cutoff:3.500A) removed outlier: 12.519A pdb=" N TYR L1148 " --> pdb=" O CYS L1001 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ALA L1147 " --> pdb=" O THR L1102 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N THR L1102 " --> pdb=" O ALA L1147 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ARG L1100 " --> pdb=" O PRO L1149 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 1059 through 1062 removed outlier: 6.019A pdb=" N PHE L1107 " --> pdb=" O THR L1126 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 954 through 957 removed outlier: 6.946A pdb=" N THR K1154 " --> pdb=" O LEU K 995 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ILE K 997 " --> pdb=" O LEU K1152 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU K1152 " --> pdb=" O ILE K 997 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N LYS K 999 " --> pdb=" O GLU K1150 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N GLU K1150 " --> pdb=" O LYS K 999 " (cutoff:3.500A) removed outlier: 9.469A pdb=" N CYS K1001 " --> pdb=" O TYR K1148 " (cutoff:3.500A) removed outlier: 12.556A pdb=" N TYR K1148 " --> pdb=" O CYS K1001 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N ALA K1147 " --> pdb=" O THR K1102 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N THR K1102 " --> pdb=" O ALA K1147 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ARG K1100 " --> pdb=" O PRO K1149 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 1059 through 1062 1969 hydrogen bonds defined for protein. 5449 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: 12.92 Time building geometry restraints manager: 8.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13291 1.34 - 1.45: 6821 1.45 - 1.57: 21756 1.57 - 1.69: 12 1.69 - 1.81: 400 Bond restraints: 42280 Sorted by residual: bond pdb=" CA THR K 975 " pdb=" C THR K 975 " ideal model delta sigma weight residual 1.523 1.584 -0.061 1.41e-02 5.03e+03 1.88e+01 bond pdb=" CA THR L 975 " pdb=" C THR L 975 " ideal model delta sigma weight residual 1.523 1.581 -0.059 1.41e-02 5.03e+03 1.73e+01 bond pdb=" CA THR D 975 " pdb=" C THR D 975 " ideal model delta sigma weight residual 1.523 1.579 -0.056 1.41e-02 5.03e+03 1.60e+01 bond pdb=" CA THR B 975 " pdb=" C THR B 975 " ideal model delta sigma weight residual 1.523 1.578 -0.056 1.41e-02 5.03e+03 1.56e+01 bond pdb=" CA THR M 975 " pdb=" C THR M 975 " ideal model delta sigma weight residual 1.523 1.578 -0.055 1.41e-02 5.03e+03 1.53e+01 ... (remaining 42275 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 55603 1.60 - 3.21: 1151 3.21 - 4.81: 158 4.81 - 6.41: 20 6.41 - 8.02: 8 Bond angle restraints: 56940 Sorted by residual: angle pdb=" C SER O 974 " pdb=" N THR O 975 " pdb=" CA THR O 975 " ideal model delta sigma weight residual 122.55 114.53 8.02 2.03e+00 2.43e-01 1.56e+01 angle pdb=" C SER P 974 " pdb=" N THR P 975 " pdb=" CA THR P 975 " ideal model delta sigma weight residual 122.55 114.95 7.60 2.03e+00 2.43e-01 1.40e+01 angle pdb=" C SER H 974 " pdb=" N THR H 975 " pdb=" CA THR H 975 " ideal model delta sigma weight residual 122.55 115.17 7.38 2.03e+00 2.43e-01 1.32e+01 angle pdb=" C SER F 974 " pdb=" N THR F 975 " pdb=" CA THR F 975 " ideal model delta sigma weight residual 122.31 115.26 7.05 2.00e+00 2.50e-01 1.24e+01 angle pdb=" C SER M 974 " pdb=" N THR M 975 " pdb=" CA THR M 975 " ideal model delta sigma weight residual 122.38 116.01 6.37 1.81e+00 3.05e-01 1.24e+01 ... (remaining 56935 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.10: 22130 18.10 - 36.19: 2011 36.19 - 54.29: 628 54.29 - 72.39: 82 72.39 - 90.49: 69 Dihedral angle restraints: 24920 sinusoidal: 9920 harmonic: 15000 Sorted by residual: dihedral pdb=" CA PHE J1098 " pdb=" C PHE J1098 " pdb=" N CYS J1099 " pdb=" CA CYS J1099 " ideal model delta harmonic sigma weight residual 180.00 -162.56 -17.44 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA ILE T1059 " pdb=" C ILE T1059 " pdb=" N TYR T1060 " pdb=" CA TYR T1060 " ideal model delta harmonic sigma weight residual -180.00 -162.63 -17.37 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA PHE I1098 " pdb=" C PHE I1098 " pdb=" N CYS I1099 " pdb=" CA CYS I1099 " ideal model delta harmonic sigma weight residual -180.00 -162.69 -17.31 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 24917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 3552 0.033 - 0.066: 1671 0.066 - 0.100: 583 0.100 - 0.133: 228 0.133 - 0.166: 6 Chirality restraints: 6040 Sorted by residual: chirality pdb=" CA PRO O1082 " pdb=" N PRO O1082 " pdb=" C PRO O1082 " pdb=" CB PRO O1082 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 6.88e-01 chirality pdb=" CA ILE G 997 " pdb=" N ILE G 997 " pdb=" C ILE G 997 " pdb=" CB ILE G 997 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA ILE R 997 " pdb=" N ILE R 997 " pdb=" C ILE R 997 " pdb=" CB ILE R 997 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.80e-01 ... (remaining 6037 not shown) Planarity restraints: 7260 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS O1081 " 0.061 5.00e-02 4.00e+02 9.26e-02 1.37e+01 pdb=" N PRO O1082 " -0.160 5.00e-02 4.00e+02 pdb=" CA PRO O1082 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO O1082 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS N1081 " -0.034 5.00e-02 4.00e+02 5.24e-02 4.39e+00 pdb=" N PRO N1082 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO N1082 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO N1082 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS D1081 " 0.033 5.00e-02 4.00e+02 4.98e-02 3.97e+00 pdb=" N PRO D1082 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO D1082 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D1082 " 0.027 5.00e-02 4.00e+02 ... (remaining 7257 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 513 2.67 - 3.22: 36452 3.22 - 3.78: 60603 3.78 - 4.34: 89882 4.34 - 4.90: 151882 Nonbonded interactions: 339332 Sorted by model distance: nonbonded pdb=" OE2 GLU H 964 " pdb=" OH TYR H1151 " model vdw 2.108 3.040 nonbonded pdb=" OE2 GLU G 964 " pdb=" OH TYR G1151 " model vdw 2.116 3.040 nonbonded pdb=" OH TYR M1009 " pdb=" OE2 GLU M1026 " model vdw 2.130 3.040 nonbonded pdb=" OH TYR C1009 " pdb=" OE2 GLU C1026 " model vdw 2.135 3.040 nonbonded pdb=" OE2 GLU R 964 " pdb=" OH TYR R1151 " model vdw 2.136 3.040 ... (remaining 339327 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 875 through 895 or resid 897 through 1158 or resid 1201)) selection = (chain 'B' and (resid 875 through 895 or resid 897 through 1158 or resid 1201)) selection = (chain 'C' and (resid 875 through 895 or resid 897 through 1158 or resid 1201)) selection = (chain 'D' and (resid 875 through 895 or resid 897 through 1158 or resid 1201)) selection = (chain 'E' and (resid 875 through 895 or resid 897 through 1158 or resid 1201)) selection = (chain 'F' and (resid 875 through 895 or resid 897 through 1158 or resid 1201)) selection = (chain 'G' and (resid 875 through 895 or resid 897 through 1158 or resid 1201)) selection = (chain 'H' and (resid 875 through 895 or resid 897 through 1158 or resid 1201)) selection = (chain 'I' and (resid 875 through 895 or resid 897 through 1158 or resid 1201)) selection = (chain 'J' and (resid 875 through 895 or resid 897 through 1158 or resid 1201)) selection = (chain 'K' and (resid 875 through 895 or resid 897 through 1158 or resid 1201)) selection = (chain 'L' and (resid 875 through 895 or resid 897 through 1158 or resid 1201)) selection = (chain 'M' and (resid 875 through 895 or resid 897 through 1158 or resid 1201)) selection = (chain 'N' and (resid 875 through 895 or resid 897 through 1158 or resid 1201)) selection = (chain 'O' and (resid 875 through 895 or resid 897 through 1158 or resid 1201)) selection = (chain 'P' and (resid 875 through 895 or resid 897 through 1158 or resid 1201)) selection = (chain 'Q' and (resid 875 through 895 or resid 897 through 1158 or resid 1201)) selection = (chain 'R' and (resid 875 through 895 or resid 897 through 1158 or resid 1201)) selection = (chain 'S' and (resid 875 through 895 or resid 897 through 1158 or resid 1201)) selection = (chain 'T' and (resid 875 through 895 or resid 897 through 1158 or resid 1201)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.380 Construct map_model_manager: 0.050 Extract box with map and model: 1.290 Check model and map are aligned: 0.240 Set scattering table: 0.300 Process input model: 94.070 Find NCS groups from input model: 1.900 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 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 : 0.005 0.064 42280 Z= 0.352 Angle : 0.606 8.017 56940 Z= 0.367 Chirality : 0.044 0.166 6040 Planarity : 0.004 0.093 7260 Dihedral : 16.132 90.485 15320 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.36 % Allowed : 0.51 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.11), residues: 5000 helix: -0.01 (0.12), residues: 1760 sheet: -0.87 (0.15), residues: 1180 loop : -1.91 (0.12), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP Q1032 HIS 0.007 0.001 HIS Q 909 PHE 0.023 0.002 PHE R1098 TYR 0.024 0.002 TYR F 943 ARG 0.006 0.001 ARG A1027 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 4560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 612 time to evaluate : 4.212 Fit side-chains REVERT: G 1158 MET cc_start: 0.6988 (ttp) cc_final: 0.6697 (ttm) REVERT: T 973 GLN cc_start: 0.8164 (mm-40) cc_final: 0.7959 (mm-40) REVERT: T 1156 GLN cc_start: 0.8612 (pt0) cc_final: 0.8384 (pt0) REVERT: P 1115 MET cc_start: 0.7663 (mtm) cc_final: 0.7420 (mpt) outliers start: 1 outliers final: 0 residues processed: 612 average time/residue: 1.1640 time to fit residues: 879.8551 Evaluate side-chains 543 residues out of total 4560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 543 time to evaluate : 3.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 422 optimal weight: 0.0030 chunk 378 optimal weight: 0.1980 chunk 210 optimal weight: 1.9990 chunk 129 optimal weight: 0.5980 chunk 255 optimal weight: 0.9990 chunk 202 optimal weight: 0.9980 chunk 391 optimal weight: 0.6980 chunk 151 optimal weight: 1.9990 chunk 238 optimal weight: 5.9990 chunk 291 optimal weight: 2.9990 chunk 454 optimal weight: 0.7980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E1022 ASN E1109 GLN J 966 GLN I1093 HIS I1109 GLN I1156 GLN G1022 ASN F1095 GLN F1156 GLN ** C1069 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1093 HIS A1069 ASN O1022 ASN O1109 GLN S1093 HIS S1109 GLN S1156 GLN Q1022 ASN Q1093 HIS ** P1069 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1093 HIS P1095 GLN P1156 GLN L1022 ASN L1109 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 42280 Z= 0.151 Angle : 0.484 4.957 56940 Z= 0.270 Chirality : 0.041 0.141 6040 Planarity : 0.004 0.057 7260 Dihedral : 4.246 15.816 5680 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.29 % Allowed : 6.79 % Favored : 90.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.12), residues: 5000 helix: 0.26 (0.12), residues: 1800 sheet: -0.46 (0.15), residues: 1180 loop : -1.47 (0.14), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J1032 HIS 0.017 0.001 HIS R1084 PHE 0.018 0.001 PHE J 881 TYR 0.016 0.001 TYR J 943 ARG 0.010 0.000 ARG H1094 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 4560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 564 time to evaluate : 3.665 Fit side-chains REVERT: E 1113 MET cc_start: 0.6646 (OUTLIER) cc_final: 0.6334 (tmt) REVERT: E 1115 MET cc_start: 0.7437 (OUTLIER) cc_final: 0.7082 (mtm) REVERT: J 928 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8252 (mptm) REVERT: F 975 THR cc_start: 0.7737 (p) cc_final: 0.7520 (p) REVERT: D 1113 MET cc_start: 0.6843 (OUTLIER) cc_final: 0.6508 (tmm) REVERT: A 975 THR cc_start: 0.8104 (m) cc_final: 0.7722 (m) REVERT: O 1113 MET cc_start: 0.6748 (OUTLIER) cc_final: 0.6325 (tmt) REVERT: O 1115 MET cc_start: 0.7300 (OUTLIER) cc_final: 0.7087 (mtm) REVERT: T 928 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8298 (mptm) REVERT: T 1156 GLN cc_start: 0.8556 (pt0) cc_final: 0.8290 (pt0) REVERT: Q 963 LYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7815 (ttmm) REVERT: P 1115 MET cc_start: 0.7496 (mtm) cc_final: 0.7215 (mpt) REVERT: N 1113 MET cc_start: 0.6683 (OUTLIER) cc_final: 0.6338 (tmm) REVERT: N 1115 MET cc_start: 0.7531 (mtm) cc_final: 0.7269 (mtm) outliers start: 79 outliers final: 28 residues processed: 587 average time/residue: 1.2182 time to fit residues: 878.9990 Evaluate side-chains 574 residues out of total 4560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 537 time to evaluate : 3.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1108 LEU Chi-restraints excluded: chain E residue 1113 MET Chi-restraints excluded: chain E residue 1115 MET Chi-restraints excluded: chain J residue 928 LYS Chi-restraints excluded: chain I residue 902 ASP Chi-restraints excluded: chain H residue 902 ASP Chi-restraints excluded: chain H residue 1035 PHE Chi-restraints excluded: chain G residue 902 ASP Chi-restraints excluded: chain G residue 943 TYR Chi-restraints excluded: chain G residue 1035 PHE Chi-restraints excluded: chain F residue 1115 MET Chi-restraints excluded: chain D residue 902 ASP Chi-restraints excluded: chain D residue 1113 MET Chi-restraints excluded: chain C residue 943 TYR Chi-restraints excluded: chain C residue 1069 ASN Chi-restraints excluded: chain B residue 902 ASP Chi-restraints excluded: chain B residue 1035 PHE Chi-restraints excluded: chain A residue 1035 PHE Chi-restraints excluded: chain A residue 1069 ASN Chi-restraints excluded: chain O residue 1108 LEU Chi-restraints excluded: chain O residue 1113 MET Chi-restraints excluded: chain O residue 1115 MET Chi-restraints excluded: chain T residue 928 LYS Chi-restraints excluded: chain S residue 892 ASP Chi-restraints excluded: chain S residue 902 ASP Chi-restraints excluded: chain R residue 902 ASP Chi-restraints excluded: chain R residue 1035 PHE Chi-restraints excluded: chain Q residue 902 ASP Chi-restraints excluded: chain Q residue 963 LYS Chi-restraints excluded: chain Q residue 1035 PHE Chi-restraints excluded: chain N residue 902 ASP Chi-restraints excluded: chain N residue 1113 MET Chi-restraints excluded: chain L residue 902 ASP Chi-restraints excluded: chain L residue 1035 PHE Chi-restraints excluded: chain K residue 1022 ASN Chi-restraints excluded: chain K residue 1069 ASN Chi-restraints excluded: chain K residue 1105 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 252 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 chunk 377 optimal weight: 2.9990 chunk 309 optimal weight: 4.9990 chunk 125 optimal weight: 0.7980 chunk 454 optimal weight: 0.5980 chunk 491 optimal weight: 0.5980 chunk 405 optimal weight: 1.9990 chunk 451 optimal weight: 0.0870 chunk 155 optimal weight: 1.9990 chunk 364 optimal weight: 0.0030 overall best weight: 0.4168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 966 GLN J 993 ASN J1156 GLN I1093 HIS I1109 GLN G1022 ASN G1156 GLN F1095 GLN F1156 GLN ** C1069 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 993 ASN A1070 GLN S1093 HIS S1109 GLN S1156 GLN ** P1069 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1095 GLN ** P1109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M1109 GLN L1022 ASN L1109 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 42280 Z= 0.136 Angle : 0.435 4.614 56940 Z= 0.242 Chirality : 0.040 0.133 6040 Planarity : 0.003 0.045 7260 Dihedral : 4.018 15.505 5680 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.15 % Allowed : 8.26 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.12), residues: 5000 helix: 0.49 (0.12), residues: 1820 sheet: -0.14 (0.16), residues: 1100 loop : -1.37 (0.14), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R1032 HIS 0.005 0.001 HIS A 909 PHE 0.017 0.001 PHE J 881 TYR 0.015 0.001 TYR F1050 ARG 0.003 0.000 ARG K1027 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 4560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 572 time to evaluate : 3.651 Fit side-chains REVERT: E 943 TYR cc_start: 0.5564 (OUTLIER) cc_final: 0.5046 (p90) REVERT: G 1115 MET cc_start: 0.7324 (mtm) cc_final: 0.7106 (mtt) REVERT: F 975 THR cc_start: 0.7766 (p) cc_final: 0.7552 (p) REVERT: D 1113 MET cc_start: 0.6781 (OUTLIER) cc_final: 0.6468 (tmm) REVERT: A 975 THR cc_start: 0.7833 (m) cc_final: 0.7469 (m) REVERT: O 1113 MET cc_start: 0.6734 (OUTLIER) cc_final: 0.6297 (tmt) REVERT: T 1156 GLN cc_start: 0.8542 (pt0) cc_final: 0.8252 (pt0) REVERT: R 943 TYR cc_start: 0.5163 (OUTLIER) cc_final: 0.4828 (p90) REVERT: Q 1093 HIS cc_start: 0.8006 (m90) cc_final: 0.7776 (m170) outliers start: 69 outliers final: 34 residues processed: 592 average time/residue: 1.1423 time to fit residues: 834.5982 Evaluate side-chains 580 residues out of total 4560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 542 time to evaluate : 3.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 943 TYR Chi-restraints excluded: chain I residue 892 ASP Chi-restraints excluded: chain I residue 902 ASP Chi-restraints excluded: chain I residue 1158 MET Chi-restraints excluded: chain H residue 902 ASP Chi-restraints excluded: chain H residue 1035 PHE Chi-restraints excluded: chain G residue 902 ASP Chi-restraints excluded: chain G residue 943 TYR Chi-restraints excluded: chain G residue 1035 PHE Chi-restraints excluded: chain F residue 1115 MET Chi-restraints excluded: chain D residue 902 ASP Chi-restraints excluded: chain D residue 1113 MET Chi-restraints excluded: chain C residue 902 ASP Chi-restraints excluded: chain C residue 943 TYR Chi-restraints excluded: chain C residue 1069 ASN Chi-restraints excluded: chain B residue 902 ASP Chi-restraints excluded: chain B residue 1035 PHE Chi-restraints excluded: chain A residue 1035 PHE Chi-restraints excluded: chain A residue 1069 ASN Chi-restraints excluded: chain O residue 1113 MET Chi-restraints excluded: chain T residue 1035 PHE Chi-restraints excluded: chain T residue 1093 HIS Chi-restraints excluded: chain S residue 892 ASP Chi-restraints excluded: chain S residue 902 ASP Chi-restraints excluded: chain R residue 902 ASP Chi-restraints excluded: chain R residue 943 TYR Chi-restraints excluded: chain R residue 1035 PHE Chi-restraints excluded: chain Q residue 902 ASP Chi-restraints excluded: chain Q residue 943 TYR Chi-restraints excluded: chain Q residue 1035 PHE Chi-restraints excluded: chain N residue 902 ASP Chi-restraints excluded: chain M residue 902 ASP Chi-restraints excluded: chain M residue 943 TYR Chi-restraints excluded: chain L residue 902 ASP Chi-restraints excluded: chain L residue 1035 PHE Chi-restraints excluded: chain K residue 1035 PHE Chi-restraints excluded: chain K residue 1069 ASN Chi-restraints excluded: chain K residue 1105 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 449 optimal weight: 4.9990 chunk 341 optimal weight: 0.5980 chunk 236 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 217 optimal weight: 3.9990 chunk 305 optimal weight: 0.7980 chunk 456 optimal weight: 0.0010 chunk 483 optimal weight: 0.7980 chunk 238 optimal weight: 5.9990 chunk 432 optimal weight: 0.2980 chunk 130 optimal weight: 1.9990 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E1109 GLN J 966 GLN I1093 HIS I1109 GLN I1156 GLN G1022 ASN F1095 GLN F1156 GLN ** C1069 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1069 ASN O1109 GLN S1109 GLN S1156 GLN R1022 ASN ** P1069 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1095 GLN ** P1109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1146 GLN M1109 GLN L1022 ASN K1109 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 42280 Z= 0.136 Angle : 0.426 10.936 56940 Z= 0.235 Chirality : 0.040 0.135 6040 Planarity : 0.003 0.053 7260 Dihedral : 3.909 15.010 5680 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.22 % Allowed : 9.20 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.12), residues: 5000 helix: 0.64 (0.13), residues: 1820 sheet: -0.00 (0.16), residues: 1100 loop : -1.34 (0.14), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R1032 HIS 0.011 0.001 HIS T1093 PHE 0.016 0.001 PHE J 881 TYR 0.013 0.001 TYR F1050 ARG 0.011 0.000 ARG N1094 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 4560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 560 time to evaluate : 3.706 Fit side-chains revert: symmetry clash REVERT: J 963 LYS cc_start: 0.8368 (tttt) cc_final: 0.8114 (ttpp) REVERT: F 1028 MET cc_start: 0.8695 (mtp) cc_final: 0.8488 (mmm) REVERT: D 1113 MET cc_start: 0.6736 (OUTLIER) cc_final: 0.6404 (tmm) REVERT: O 1113 MET cc_start: 0.6558 (OUTLIER) cc_final: 0.6288 (tmt) REVERT: T 1156 GLN cc_start: 0.8552 (pt0) cc_final: 0.8286 (pt0) REVERT: R 943 TYR cc_start: 0.5123 (OUTLIER) cc_final: 0.4788 (p90) REVERT: Q 957 ASP cc_start: 0.7707 (OUTLIER) cc_final: 0.7485 (m-30) REVERT: P 1115 MET cc_start: 0.7589 (mtm) cc_final: 0.7350 (mpt) REVERT: N 1113 MET cc_start: 0.6673 (OUTLIER) cc_final: 0.6408 (tmm) outliers start: 73 outliers final: 42 residues processed: 582 average time/residue: 1.1526 time to fit residues: 826.5529 Evaluate side-chains 587 residues out of total 4560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 540 time to evaluate : 3.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 892 ASP Chi-restraints excluded: chain I residue 1158 MET Chi-restraints excluded: chain H residue 902 ASP Chi-restraints excluded: chain H residue 1035 PHE Chi-restraints excluded: chain G residue 902 ASP Chi-restraints excluded: chain G residue 943 TYR Chi-restraints excluded: chain G residue 1035 PHE Chi-restraints excluded: chain G residue 1036 VAL Chi-restraints excluded: chain G residue 1093 HIS Chi-restraints excluded: chain F residue 943 TYR Chi-restraints excluded: chain F residue 1108 LEU Chi-restraints excluded: chain F residue 1115 MET Chi-restraints excluded: chain D residue 902 ASP Chi-restraints excluded: chain D residue 975 THR Chi-restraints excluded: chain D residue 1113 MET Chi-restraints excluded: chain C residue 902 ASP Chi-restraints excluded: chain C residue 943 TYR Chi-restraints excluded: chain C residue 1069 ASN Chi-restraints excluded: chain B residue 902 ASP Chi-restraints excluded: chain B residue 1035 PHE Chi-restraints excluded: chain A residue 1035 PHE Chi-restraints excluded: chain A residue 1108 LEU Chi-restraints excluded: chain O residue 1113 MET Chi-restraints excluded: chain T residue 1028 MET Chi-restraints excluded: chain T residue 1035 PHE Chi-restraints excluded: chain S residue 892 ASP Chi-restraints excluded: chain S residue 902 ASP Chi-restraints excluded: chain R residue 902 ASP Chi-restraints excluded: chain R residue 943 TYR Chi-restraints excluded: chain R residue 1035 PHE Chi-restraints excluded: chain Q residue 943 TYR Chi-restraints excluded: chain Q residue 957 ASP Chi-restraints excluded: chain Q residue 1035 PHE Chi-restraints excluded: chain P residue 1035 PHE Chi-restraints excluded: chain P residue 1051 ILE Chi-restraints excluded: chain P residue 1108 LEU Chi-restraints excluded: chain N residue 902 ASP Chi-restraints excluded: chain N residue 975 THR Chi-restraints excluded: chain N residue 1113 MET Chi-restraints excluded: chain M residue 902 ASP Chi-restraints excluded: chain M residue 943 TYR Chi-restraints excluded: chain M residue 975 THR Chi-restraints excluded: chain L residue 902 ASP Chi-restraints excluded: chain L residue 1035 PHE Chi-restraints excluded: chain K residue 1035 PHE Chi-restraints excluded: chain K residue 1069 ASN Chi-restraints excluded: chain K residue 1109 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 402 optimal weight: 0.7980 chunk 274 optimal weight: 0.1980 chunk 7 optimal weight: 0.5980 chunk 359 optimal weight: 4.9990 chunk 199 optimal weight: 3.9990 chunk 412 optimal weight: 2.9990 chunk 334 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 246 optimal weight: 0.0980 chunk 433 optimal weight: 0.9990 chunk 121 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 966 GLN J 993 ASN J1093 HIS J1109 GLN J1156 GLN I1093 HIS I1109 GLN G1022 ASN G1156 GLN F1095 GLN ** F1109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1156 GLN ** C1069 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1070 GLN A1069 ASN A1093 HIS S1109 GLN S1156 GLN Q1093 HIS ** P1069 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1095 GLN ** P1109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1146 GLN M1109 GLN L1109 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 42280 Z= 0.136 Angle : 0.417 5.232 56940 Z= 0.231 Chirality : 0.040 0.134 6040 Planarity : 0.003 0.044 7260 Dihedral : 3.852 14.625 5680 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.13 % Allowed : 10.46 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.12), residues: 5000 helix: 0.75 (0.13), residues: 1820 sheet: 0.09 (0.16), residues: 1100 loop : -1.32 (0.15), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP S1032 HIS 0.013 0.001 HIS G1093 PHE 0.015 0.001 PHE J 881 TYR 0.033 0.001 TYR P1050 ARG 0.005 0.000 ARG N1094 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 4560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 552 time to evaluate : 3.666 Fit side-chains revert: symmetry clash REVERT: E 1113 MET cc_start: 0.6410 (OUTLIER) cc_final: 0.6113 (tmt) REVERT: J 963 LYS cc_start: 0.8367 (tttt) cc_final: 0.8116 (ttpp) REVERT: D 1113 MET cc_start: 0.6730 (OUTLIER) cc_final: 0.6355 (tmm) REVERT: O 1113 MET cc_start: 0.6533 (OUTLIER) cc_final: 0.6267 (tmt) REVERT: T 1156 GLN cc_start: 0.8563 (pt0) cc_final: 0.8336 (pt0) REVERT: Q 957 ASP cc_start: 0.7701 (OUTLIER) cc_final: 0.7483 (m-30) REVERT: N 1113 MET cc_start: 0.6675 (OUTLIER) cc_final: 0.6413 (tmm) outliers start: 69 outliers final: 42 residues processed: 576 average time/residue: 1.1391 time to fit residues: 810.5822 Evaluate side-chains 589 residues out of total 4560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 542 time to evaluate : 4.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1113 MET Chi-restraints excluded: chain J residue 1028 MET Chi-restraints excluded: chain J residue 1035 PHE Chi-restraints excluded: chain I residue 892 ASP Chi-restraints excluded: chain I residue 1158 MET Chi-restraints excluded: chain H residue 902 ASP Chi-restraints excluded: chain H residue 1035 PHE Chi-restraints excluded: chain G residue 902 ASP Chi-restraints excluded: chain G residue 1035 PHE Chi-restraints excluded: chain G residue 1036 VAL Chi-restraints excluded: chain F residue 1108 LEU Chi-restraints excluded: chain F residue 1115 MET Chi-restraints excluded: chain D residue 902 ASP Chi-restraints excluded: chain D residue 975 THR Chi-restraints excluded: chain D residue 1113 MET Chi-restraints excluded: chain C residue 902 ASP Chi-restraints excluded: chain C residue 1069 ASN Chi-restraints excluded: chain B residue 902 ASP Chi-restraints excluded: chain B residue 1035 PHE Chi-restraints excluded: chain A residue 1035 PHE Chi-restraints excluded: chain A residue 1108 LEU Chi-restraints excluded: chain O residue 1035 PHE Chi-restraints excluded: chain O residue 1113 MET Chi-restraints excluded: chain T residue 1028 MET Chi-restraints excluded: chain T residue 1035 PHE Chi-restraints excluded: chain S residue 892 ASP Chi-restraints excluded: chain S residue 902 ASP Chi-restraints excluded: chain R residue 902 ASP Chi-restraints excluded: chain Q residue 902 ASP Chi-restraints excluded: chain Q residue 943 TYR Chi-restraints excluded: chain Q residue 957 ASP Chi-restraints excluded: chain Q residue 1035 PHE Chi-restraints excluded: chain Q residue 1093 HIS Chi-restraints excluded: chain P residue 1035 PHE Chi-restraints excluded: chain P residue 1108 LEU Chi-restraints excluded: chain N residue 902 ASP Chi-restraints excluded: chain N residue 975 THR Chi-restraints excluded: chain N residue 1113 MET Chi-restraints excluded: chain M residue 902 ASP Chi-restraints excluded: chain M residue 943 TYR Chi-restraints excluded: chain M residue 975 THR Chi-restraints excluded: chain L residue 892 ASP Chi-restraints excluded: chain L residue 902 ASP Chi-restraints excluded: chain L residue 1035 PHE Chi-restraints excluded: chain K residue 1035 PHE Chi-restraints excluded: chain K residue 1069 ASN Chi-restraints excluded: chain K residue 1108 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 162 optimal weight: 2.9990 chunk 435 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 283 optimal weight: 0.0870 chunk 119 optimal weight: 7.9990 chunk 483 optimal weight: 0.6980 chunk 401 optimal weight: 0.9980 chunk 223 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 160 optimal weight: 3.9990 chunk 253 optimal weight: 1.9990 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 966 GLN J 993 ASN J1093 HIS I1093 HIS I1156 GLN G 993 ASN G1022 ASN G1156 GLN F1095 GLN F1156 GLN A1069 ASN S1109 GLN S1156 GLN R1093 HIS Q1156 GLN P1095 GLN ** P1109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1146 GLN M1109 GLN L1109 GLN K1109 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 42280 Z= 0.234 Angle : 0.451 6.289 56940 Z= 0.248 Chirality : 0.042 0.147 6040 Planarity : 0.003 0.044 7260 Dihedral : 3.946 15.138 5680 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.29 % Allowed : 10.82 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.12), residues: 5000 helix: 0.66 (0.13), residues: 1820 sheet: 0.13 (0.16), residues: 1100 loop : -1.34 (0.14), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E1032 HIS 0.027 0.001 HIS Q1093 PHE 0.016 0.001 PHE R1098 TYR 0.010 0.001 TYR G1142 ARG 0.005 0.000 ARG Q1094 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10000 Ramachandran restraints generated. 5000 Oldfield, 0 Emsley, 5000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 4560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 543 time to evaluate : 3.738 Fit side-chains revert: symmetry clash REVERT: E 1113 MET cc_start: 0.6400 (OUTLIER) cc_final: 0.6110 (tmt) REVERT: F 1028 MET cc_start: 0.8731 (mtp) cc_final: 0.8529 (mmm) REVERT: O 1113 MET cc_start: 0.6599 (OUTLIER) cc_final: 0.6316 (tmt) REVERT: T 1156 GLN cc_start: 0.8601 (pt0) cc_final: 0.8377 (pt0) REVERT: Q 957 ASP cc_start: 0.7728 (OUTLIER) cc_final: 0.7505 (m-30) REVERT: N 1113 MET cc_start: 0.6741 (OUTLIER) cc_final: 0.6459 (tmm) outliers start: 75 outliers final: 49 residues processed: 570 average time/residue: 1.1559 time to fit residues: 812.4878 Evaluate side-chains 585 residues out of total 4560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 532 time to evaluate : 3.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1113 MET Chi-restraints excluded: chain J residue 892 ASP Chi-restraints excluded: chain J residue 1028 MET Chi-restraints excluded: chain J residue 1035 PHE Chi-restraints excluded: chain J residue 1093 HIS Chi-restraints excluded: chain I residue 892 ASP Chi-restraints excluded: chain I residue 902 ASP Chi-restraints excluded: chain I residue 1108 LEU Chi-restraints excluded: chain I residue 1158 MET Chi-restraints excluded: chain H residue 902 ASP Chi-restraints excluded: chain H residue 1035 PHE Chi-restraints excluded: chain G residue 902 ASP Chi-restraints excluded: chain G residue 943 TYR Chi-restraints excluded: chain G residue 1035 PHE Chi-restraints excluded: chain G residue 1036 VAL Chi-restraints excluded: chain F residue 943 TYR Chi-restraints excluded: chain F residue 1083 VAL Chi-restraints excluded: chain F residue 1108 LEU Chi-restraints excluded: chain F residue 1115 MET Chi-restraints excluded: chain D residue 902 ASP Chi-restraints excluded: chain D residue 975 THR Chi-restraints excluded: chain C residue 902 ASP Chi-restraints excluded: chain C residue 1069 ASN Chi-restraints excluded: chain B residue 902 ASP Chi-restraints excluded: chain B residue 1035 PHE Chi-restraints excluded: chain A residue 1035 PHE Chi-restraints excluded: chain A residue 1108 LEU Chi-restraints excluded: chain O residue 1035 PHE Chi-restraints excluded: chain O residue 1113 MET Chi-restraints excluded: chain T residue 1028 MET Chi-restraints excluded: chain T residue 1035 PHE Chi-restraints excluded: chain T residue 1093 HIS Chi-restraints excluded: chain S residue 892 ASP Chi-restraints excluded: chain S residue 902 ASP Chi-restraints excluded: chain R residue 902 ASP Chi-restraints excluded: chain R residue 1035 PHE Chi-restraints excluded: chain Q residue 902 ASP Chi-restraints excluded: chain Q residue 943 TYR Chi-restraints excluded: chain Q residue 957 ASP Chi-restraints excluded: chain Q residue 1035 PHE Chi-restraints excluded: chain P residue 1035 PHE Chi-restraints excluded: chain P residue 1051 ILE Chi-restraints excluded: chain P residue 1108 LEU Chi-restraints excluded: chain N residue 902 ASP Chi-restraints excluded: chain N residue 975 THR Chi-restraints excluded: chain N residue 1113 MET Chi-restraints excluded: chain M residue 902 ASP Chi-restraints excluded: chain M residue 943 TYR Chi-restraints excluded: chain M residue 975 THR Chi-restraints excluded: chain L residue 902 ASP Chi-restraints excluded: chain L residue 1035 PHE Chi-restraints excluded: chain K residue 1035 PHE Chi-restraints excluded: chain K residue 1069 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 466 optimal weight: 0.7980 chunk 54 optimal weight: 0.4980 chunk 275 optimal weight: 3.9990 chunk 353 optimal weight: 0.0060 chunk 273 optimal weight: 6.9990 chunk 407 optimal weight: 1.9990 chunk 270 optimal weight: 0.6980 chunk 481 optimal weight: 0.0770 chunk 301 optimal weight: 0.8980 chunk 293 optimal weight: 0.9990 chunk 222 optimal weight: 3.9990 overall best weight: 0.4154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: