Starting phenix.real_space_refine (version: dev) on Wed Dec 21 22:02:53 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fgg_31580/12_2022/7fgg_31580_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fgg_31580/12_2022/7fgg_31580.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fgg_31580/12_2022/7fgg_31580_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fgg_31580/12_2022/7fgg_31580_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fgg_31580/12_2022/7fgg_31580_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fgg_31580/12_2022/7fgg_31580.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fgg_31580/12_2022/7fgg_31580.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fgg_31580/12_2022/7fgg_31580_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fgg_31580/12_2022/7fgg_31580_updated.pdb" } resolution = 2.19 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 26": "OE1" <-> "OE2" Residue "A ARG 76": "NH1" <-> "NH2" Residue "A ARG 85": "NH1" <-> "NH2" Residue "A ARG 222": "NH1" <-> "NH2" Residue "A ARG 238": "NH1" <-> "NH2" Residue "A GLU 250": "OE1" <-> "OE2" Residue "A ARG 275": "NH1" <-> "NH2" Residue "A ASP 277": "OD1" <-> "OD2" Residue "A ARG 289": "NH1" <-> "NH2" Residue "A ARG 289": "NH1" <-> "NH2" Residue "A TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 322": "OD1" <-> "OD2" Residue "A ARG 365": "NH1" <-> "NH2" Residue "A ARG 399": "NH1" <-> "NH2" Residue "A GLU 446": "OE1" <-> "OE2" Residue "A ARG 467": "NH1" <-> "NH2" Residue "B GLU 26": "OE1" <-> "OE2" Residue "B ARG 76": "NH1" <-> "NH2" Residue "B ARG 85": "NH1" <-> "NH2" Residue "B ARG 222": "NH1" <-> "NH2" Residue "B ARG 238": "NH1" <-> "NH2" Residue "B GLU 250": "OE1" <-> "OE2" Residue "B ARG 275": "NH1" <-> "NH2" Residue "B ASP 277": "OD1" <-> "OD2" Residue "B ARG 289": "NH1" <-> "NH2" Residue "B ARG 289": "NH1" <-> "NH2" Residue "B TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 322": "OD1" <-> "OD2" Residue "B ARG 365": "NH1" <-> "NH2" Residue "B ARG 399": "NH1" <-> "NH2" Residue "B GLU 446": "OE1" <-> "OE2" Residue "B ARG 467": "NH1" <-> "NH2" Residue "C GLU 26": "OE1" <-> "OE2" Residue "C ARG 76": "NH1" <-> "NH2" Residue "C ARG 85": "NH1" <-> "NH2" Residue "C ARG 222": "NH1" <-> "NH2" Residue "C ARG 238": "NH1" <-> "NH2" Residue "C GLU 250": "OE1" <-> "OE2" Residue "C ARG 275": "NH1" <-> "NH2" Residue "C ASP 277": "OD1" <-> "OD2" Residue "C ARG 289": "NH1" <-> "NH2" Residue "C ARG 289": "NH1" <-> "NH2" Residue "C TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 322": "OD1" <-> "OD2" Residue "C ARG 365": "NH1" <-> "NH2" Residue "C ARG 399": "NH1" <-> "NH2" Residue "C GLU 446": "OE1" <-> "OE2" Residue "C ARG 467": "NH1" <-> "NH2" Residue "D GLU 26": "OE1" <-> "OE2" Residue "D ARG 76": "NH1" <-> "NH2" Residue "D ARG 85": "NH1" <-> "NH2" Residue "D ARG 222": "NH1" <-> "NH2" Residue "D ARG 238": "NH1" <-> "NH2" Residue "D GLU 250": "OE1" <-> "OE2" Residue "D ARG 275": "NH1" <-> "NH2" Residue "D ASP 277": "OD1" <-> "OD2" Residue "D ARG 289": "NH1" <-> "NH2" Residue "D ARG 289": "NH1" <-> "NH2" Residue "D TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 322": "OD1" <-> "OD2" Residue "D ARG 365": "NH1" <-> "NH2" Residue "D ARG 399": "NH1" <-> "NH2" Residue "D GLU 446": "OE1" <-> "OE2" Residue "D ARG 467": "NH1" <-> "NH2" Residue "E GLU 26": "OE1" <-> "OE2" Residue "E ARG 76": "NH1" <-> "NH2" Residue "E ARG 85": "NH1" <-> "NH2" Residue "E ARG 222": "NH1" <-> "NH2" Residue "E ARG 238": "NH1" <-> "NH2" Residue "E GLU 250": "OE1" <-> "OE2" Residue "E ARG 275": "NH1" <-> "NH2" Residue "E ASP 277": "OD1" <-> "OD2" Residue "E ARG 289": "NH1" <-> "NH2" Residue "E ARG 289": "NH1" <-> "NH2" Residue "E TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 322": "OD1" <-> "OD2" Residue "E ARG 365": "NH1" <-> "NH2" Residue "E ARG 399": "NH1" <-> "NH2" Residue "E GLU 446": "OE1" <-> "OE2" Residue "E ARG 467": "NH1" <-> "NH2" Residue "F GLU 26": "OE1" <-> "OE2" Residue "F ARG 76": "NH1" <-> "NH2" Residue "F ARG 85": "NH1" <-> "NH2" Residue "F ARG 222": "NH1" <-> "NH2" Residue "F ARG 238": "NH1" <-> "NH2" Residue "F GLU 250": "OE1" <-> "OE2" Residue "F ARG 275": "NH1" <-> "NH2" Residue "F ASP 277": "OD1" <-> "OD2" Residue "F ARG 289": "NH1" <-> "NH2" Residue "F ARG 289": "NH1" <-> "NH2" Residue "F TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 322": "OD1" <-> "OD2" Residue "F ARG 365": "NH1" <-> "NH2" Residue "F ARG 399": "NH1" <-> "NH2" Residue "F GLU 446": "OE1" <-> "OE2" Residue "F ARG 467": "NH1" <-> "NH2" Residue "G GLU 26": "OE1" <-> "OE2" Residue "G ARG 76": "NH1" <-> "NH2" Residue "G ARG 85": "NH1" <-> "NH2" Residue "G ARG 222": "NH1" <-> "NH2" Residue "G ARG 238": "NH1" <-> "NH2" Residue "G GLU 250": "OE1" <-> "OE2" Residue "G ARG 275": "NH1" <-> "NH2" Residue "G ASP 277": "OD1" <-> "OD2" Residue "G ARG 289": "NH1" <-> "NH2" Residue "G ARG 289": "NH1" <-> "NH2" Residue "G TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 322": "OD1" <-> "OD2" Residue "G ARG 365": "NH1" <-> "NH2" Residue "G ARG 399": "NH1" <-> "NH2" Residue "G GLU 446": "OE1" <-> "OE2" Residue "G ARG 467": "NH1" <-> "NH2" Residue "H GLU 26": "OE1" <-> "OE2" Residue "H ARG 76": "NH1" <-> "NH2" Residue "H ARG 85": "NH1" <-> "NH2" Residue "H ARG 222": "NH1" <-> "NH2" Residue "H ARG 238": "NH1" <-> "NH2" Residue "H GLU 250": "OE1" <-> "OE2" Residue "H ARG 275": "NH1" <-> "NH2" Residue "H ASP 277": "OD1" <-> "OD2" Residue "H ARG 289": "NH1" <-> "NH2" Residue "H ARG 289": "NH1" <-> "NH2" Residue "H TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 322": "OD1" <-> "OD2" Residue "H ARG 365": "NH1" <-> "NH2" Residue "H ARG 399": "NH1" <-> "NH2" Residue "H GLU 446": "OE1" <-> "OE2" Residue "H ARG 467": "NH1" <-> "NH2" Residue "I GLU 26": "OE1" <-> "OE2" Residue "I ARG 76": "NH1" <-> "NH2" Residue "I ARG 85": "NH1" <-> "NH2" Residue "I ARG 222": "NH1" <-> "NH2" Residue "I ARG 238": "NH1" <-> "NH2" Residue "I GLU 250": "OE1" <-> "OE2" Residue "I ARG 275": "NH1" <-> "NH2" Residue "I ASP 277": "OD1" <-> "OD2" Residue "I ARG 289": "NH1" <-> "NH2" Residue "I ARG 289": "NH1" <-> "NH2" Residue "I TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 322": "OD1" <-> "OD2" Residue "I ARG 365": "NH1" <-> "NH2" Residue "I ARG 399": "NH1" <-> "NH2" Residue "I GLU 446": "OE1" <-> "OE2" Residue "I ARG 467": "NH1" <-> "NH2" Residue "J GLU 26": "OE1" <-> "OE2" Residue "J ARG 76": "NH1" <-> "NH2" Residue "J ARG 85": "NH1" <-> "NH2" Residue "J ARG 222": "NH1" <-> "NH2" Residue "J ARG 238": "NH1" <-> "NH2" Residue "J GLU 250": "OE1" <-> "OE2" Residue "J ARG 275": "NH1" <-> "NH2" Residue "J ASP 277": "OD1" <-> "OD2" Residue "J ARG 289": "NH1" <-> "NH2" Residue "J ARG 289": "NH1" <-> "NH2" Residue "J TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 322": "OD1" <-> "OD2" Residue "J ARG 365": "NH1" <-> "NH2" Residue "J ARG 399": "NH1" <-> "NH2" Residue "J GLU 446": "OE1" <-> "OE2" Residue "J ARG 467": "NH1" <-> "NH2" Residue "K GLU 26": "OE1" <-> "OE2" Residue "K ARG 76": "NH1" <-> "NH2" Residue "K ARG 85": "NH1" <-> "NH2" Residue "K ARG 222": "NH1" <-> "NH2" Residue "K ARG 238": "NH1" <-> "NH2" Residue "K GLU 250": "OE1" <-> "OE2" Residue "K ARG 275": "NH1" <-> "NH2" Residue "K ASP 277": "OD1" <-> "OD2" Residue "K ARG 289": "NH1" <-> "NH2" Residue "K ARG 289": "NH1" <-> "NH2" Residue "K TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 322": "OD1" <-> "OD2" Residue "K ARG 365": "NH1" <-> "NH2" Residue "K ARG 399": "NH1" <-> "NH2" Residue "K GLU 446": "OE1" <-> "OE2" Residue "K ARG 467": "NH1" <-> "NH2" Residue "L GLU 26": "OE1" <-> "OE2" Residue "L ARG 76": "NH1" <-> "NH2" Residue "L ARG 85": "NH1" <-> "NH2" Residue "L ARG 222": "NH1" <-> "NH2" Residue "L ARG 238": "NH1" <-> "NH2" Residue "L GLU 250": "OE1" <-> "OE2" Residue "L ARG 275": "NH1" <-> "NH2" Residue "L ASP 277": "OD1" <-> "OD2" Residue "L ARG 289": "NH1" <-> "NH2" Residue "L ARG 289": "NH1" <-> "NH2" Residue "L TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 322": "OD1" <-> "OD2" Residue "L ARG 365": "NH1" <-> "NH2" Residue "L ARG 399": "NH1" <-> "NH2" Residue "L GLU 446": "OE1" <-> "OE2" Residue "L ARG 467": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 45132 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 3553 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 451, 3536 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 451, 3536 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 3593 Chain: "B" Number of atoms: 3553 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 451, 3536 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 451, 3536 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 3593 Chain: "C" Number of atoms: 3553 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 451, 3536 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 451, 3536 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 3593 Chain: "D" Number of atoms: 3553 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 451, 3536 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 451, 3536 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 3593 Chain: "E" Number of atoms: 3553 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 451, 3536 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 451, 3536 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 3593 Chain: "F" Number of atoms: 3553 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 451, 3536 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 451, 3536 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 3593 Chain: "G" Number of atoms: 3553 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 451, 3536 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 451, 3536 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 3593 Chain: "H" Number of atoms: 3553 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 451, 3536 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 451, 3536 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 3593 Chain: "I" Number of atoms: 3553 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 451, 3536 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 451, 3536 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 3593 Chain: "J" Number of atoms: 3553 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 451, 3536 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 451, 3536 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 3593 Chain: "K" Number of atoms: 3553 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 451, 3536 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 451, 3536 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 3593 Chain: "L" Number of atoms: 3553 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 451, 3536 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 451, 3536 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 3593 Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 61 Unusual residues: {' MG': 1, ' ZN': 1, 'MGP': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 61 Unusual residues: {' MG': 1, ' ZN': 1, 'MGP': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 61 Unusual residues: {' MG': 1, ' ZN': 1, 'MGP': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain: "D" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 61 Unusual residues: {' MG': 1, ' ZN': 1, 'MGP': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 61 Unusual residues: {' MG': 1, ' ZN': 1, 'MGP': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 61 Unusual residues: {' MG': 1, ' ZN': 1, 'MGP': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 61 Unusual residues: {' MG': 1, ' ZN': 1, 'MGP': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 61 Unusual residues: {' MG': 1, ' ZN': 1, 'MGP': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 61 Unusual residues: {' MG': 1, ' ZN': 1, 'MGP': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 61 Unusual residues: {' MG': 1, ' ZN': 1, 'MGP': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain: "K" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 61 Unusual residues: {' MG': 1, ' ZN': 1, 'MGP': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain: "L" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 61 Unusual residues: {' MG': 1, ' ZN': 1, 'MGP': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain: "A" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 147 Classifications: {'water': 147} Link IDs: {None: 146} Chain: "B" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 147 Classifications: {'water': 147} Link IDs: {None: 146} Chain: "C" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 147 Classifications: {'water': 147} Link IDs: {None: 146} Chain: "D" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 147 Classifications: {'water': 147} Link IDs: {None: 146} Chain: "E" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 147 Classifications: {'water': 147} Link IDs: {None: 146} Chain: "F" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 147 Classifications: {'water': 147} Link IDs: {None: 146} Chain: "G" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 147 Classifications: {'water': 147} Link IDs: {None: 146} Chain: "H" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 147 Classifications: {'water': 147} Link IDs: {None: 146} Chain: "I" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 147 Classifications: {'water': 147} Link IDs: {None: 146} Chain: "J" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 147 Classifications: {'water': 147} Link IDs: {None: 146} Chain: "K" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 147 Classifications: {'water': 147} Link IDs: {None: 146} Chain: "L" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 147 Classifications: {'water': 147} Link IDs: {None: 146} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1024 SG CYS A 134 160.681 36.869 62.044 1.00 0.00 S ATOM 1076 SG CYS A 141 157.732 34.016 61.465 1.00 0.00 S ATOM 4577 SG CYS B 134 185.913 74.618 62.070 1.00 0.00 S ATOM 4629 SG CYS B 141 184.786 70.674 61.489 1.00 0.00 S ATOM 8130 SG CYS C 134 188.902 119.933 62.108 1.00 0.00 S ATOM 8182 SG CYS C 141 189.899 115.952 61.526 1.00 0.00 S ATOM 11683 SG CYS D 134 168.830 160.657 62.148 1.00 0.00 S ATOM 11735 SG CYS D 141 171.684 157.709 61.566 1.00 0.00 S ATOM 15236 SG CYS E 134 131.075 185.898 62.179 1.00 0.00 S ATOM 15288 SG CYS E 141 135.020 184.772 61.599 1.00 0.00 S ATOM 18789 SG CYS F 134 85.772 188.887 62.193 1.00 0.00 S ATOM 18841 SG CYS F 141 89.752 189.884 61.615 1.00 0.00 S ATOM 22342 SG CYS G 134 45.042 168.806 62.187 1.00 0.00 S ATOM 22394 SG CYS G 141 47.990 171.660 61.611 1.00 0.00 S ATOM 25895 SG CYS H 134 19.795 131.060 62.161 1.00 0.00 S ATOM 25947 SG CYS H 141 20.922 135.005 61.586 1.00 0.00 S ATOM 29448 SG CYS I 134 16.816 85.757 62.123 1.00 0.00 S ATOM 29500 SG CYS I 141 15.820 89.737 61.549 1.00 0.00 S ATOM 33001 SG CYS J 134 36.892 45.018 62.084 1.00 0.00 S ATOM 33053 SG CYS J 141 34.038 47.967 61.509 1.00 0.00 S ATOM 36554 SG CYS K 134 74.633 19.779 62.052 1.00 0.00 S ATOM 36606 SG CYS K 141 70.687 20.906 61.476 1.00 0.00 S ATOM 40107 SG CYS L 134 119.947 16.801 62.038 1.00 0.00 S ATOM 40159 SG CYS L 141 115.966 15.805 61.460 1.00 0.00 S Residues with excluded nonbonded symmetry interactions: 24 residue: pdb=" N ACYS A 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS A 236 " occ=0.50 residue: pdb=" N AARG A 289 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 289 " occ=0.50 residue: pdb=" N ACYS B 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS B 236 " occ=0.50 residue: pdb=" N AARG B 289 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG B 289 " occ=0.50 residue: pdb=" N ACYS C 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS C 236 " occ=0.50 residue: pdb=" N AARG C 289 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 289 " occ=0.50 residue: pdb=" N ACYS D 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS D 236 " occ=0.50 residue: pdb=" N AARG D 289 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG D 289 " occ=0.50 residue: pdb=" N ACYS E 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS E 236 " occ=0.50 residue: pdb=" N AARG E 289 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG E 289 " occ=0.50 residue: pdb=" N ACYS F 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS F 236 " occ=0.50 residue: pdb=" N AARG F 289 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG F 289 " occ=0.50 ... (remaining 12 not shown) Time building chain proxies: 44.71, per 1000 atoms: 0.99 Number of scatterers: 45132 At special positions: 0 Unit cell: (206.55, 206.55, 90.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 12 29.99 S 348 16.00 P 36 15.00 Mg 12 11.99 O 9912 8.00 N 7584 7.00 C 27228 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 19.63 Conformation dependent library (CDL) restraints added in 12.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" NE2 HIS A 79 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 141 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 134 " pdb=" ZN B1001 " pdb="ZN ZN B1001 " - pdb=" NE2 HIS B 79 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 141 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 134 " pdb=" ZN C1001 " pdb="ZN ZN C1001 " - pdb=" NE2 HIS C 79 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 141 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 134 " pdb=" ZN D1001 " pdb="ZN ZN D1001 " - pdb=" NE2 HIS D 79 " pdb="ZN ZN D1001 " - pdb=" SG CYS D 141 " pdb="ZN ZN D1001 " - pdb=" SG CYS D 134 " pdb=" ZN E1001 " pdb="ZN ZN E1001 " - pdb=" NE2 HIS E 79 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 141 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 134 " pdb=" ZN F1001 " pdb="ZN ZN F1001 " - pdb=" NE2 HIS F 79 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 141 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 134 " pdb=" ZN G1001 " pdb="ZN ZN G1001 " - pdb=" NE2 HIS G 79 " pdb="ZN ZN G1001 " - pdb=" SG CYS G 141 " pdb="ZN ZN G1001 " - pdb=" SG CYS G 134 " pdb=" ZN H1001 " pdb="ZN ZN H1001 " - pdb=" NE2 HIS H 79 " pdb="ZN ZN H1001 " - pdb=" SG CYS H 141 " pdb="ZN ZN H1001 " - pdb=" SG CYS H 134 " pdb=" ZN I1001 " pdb="ZN ZN I1001 " - pdb=" NE2 HIS I 79 " pdb="ZN ZN I1001 " - pdb=" SG CYS I 141 " pdb="ZN ZN I1001 " - pdb=" SG CYS I 134 " pdb=" ZN J1001 " pdb="ZN ZN J1001 " - pdb=" NE2 HIS J 79 " pdb="ZN ZN J1001 " - pdb=" SG CYS J 141 " pdb="ZN ZN J1001 " - pdb=" SG CYS J 134 " pdb=" ZN K1001 " pdb="ZN ZN K1001 " - pdb=" NE2 HIS K 79 " pdb="ZN ZN K1001 " - pdb=" SG CYS K 141 " pdb="ZN ZN K1001 " - pdb=" SG CYS K 134 " pdb=" ZN L1001 " pdb="ZN ZN L1001 " - pdb=" NE2 HIS L 79 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 141 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 134 " 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10344 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 180 helices and 60 sheets defined 31.0% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.09 Creating SS restraints... Processing helix chain 'A' and resid 14 through 21 Processing helix chain 'A' and resid 38 through 54 Processing helix chain 'A' and resid 68 through 71 Processing helix chain 'A' and resid 89 through 102 Processing helix chain 'A' and resid 112 through 124 Processing helix chain 'A' and resid 158 through 168 removed outlier: 4.135A pdb=" N LYS A 168 " --> pdb=" O HIS A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 184 No H-bonds generated for 'chain 'A' and resid 181 through 184' Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 252 through 258 removed outlier: 3.829A pdb=" N TRP A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 342 Processing helix chain 'A' and resid 345 through 347 No H-bonds generated for 'chain 'A' and resid 345 through 347' Processing helix chain 'A' and resid 352 through 363 Processing helix chain 'A' and resid 381 through 403 Proline residue: A 385 - end of helix removed outlier: 3.544A pdb=" N GLN A 389 " --> pdb=" O VAL A 386 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE A 391 " --> pdb=" O ALA A 388 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA A 395 " --> pdb=" O SER A 392 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS A 400 " --> pdb=" O GLU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 472 Processing helix chain 'B' and resid 14 through 21 Processing helix chain 'B' and resid 38 through 54 Processing helix chain 'B' and resid 68 through 71 Processing helix chain 'B' and resid 89 through 102 Processing helix chain 'B' and resid 112 through 124 Processing helix chain 'B' and resid 158 through 168 removed outlier: 4.134A pdb=" N LYS B 168 " --> pdb=" O HIS B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 184 No H-bonds generated for 'chain 'B' and resid 181 through 184' Processing helix chain 'B' and resid 193 through 195 No H-bonds generated for 'chain 'B' and resid 193 through 195' Processing helix chain 'B' and resid 202 through 204 No H-bonds generated for 'chain 'B' and resid 202 through 204' Processing helix chain 'B' and resid 252 through 258 removed outlier: 3.830A pdb=" N TRP B 258 " --> pdb=" O LEU B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 342 Processing helix chain 'B' and resid 345 through 347 No H-bonds generated for 'chain 'B' and resid 345 through 347' Processing helix chain 'B' and resid 352 through 363 Processing helix chain 'B' and resid 381 through 403 Proline residue: B 385 - end of helix removed outlier: 3.543A pdb=" N GLN B 389 " --> pdb=" O VAL B 386 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE B 391 " --> pdb=" O ALA B 388 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA B 395 " --> pdb=" O SER B 392 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS B 400 " --> pdb=" O GLU B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 472 Processing helix chain 'C' and resid 14 through 21 Processing helix chain 'C' and resid 38 through 54 Processing helix chain 'C' and resid 68 through 71 Processing helix chain 'C' and resid 89 through 102 Processing helix chain 'C' and resid 112 through 124 Processing helix chain 'C' and resid 158 through 168 removed outlier: 4.134A pdb=" N LYS C 168 " --> pdb=" O HIS C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 184 No H-bonds generated for 'chain 'C' and resid 181 through 184' Processing helix chain 'C' and resid 193 through 195 No H-bonds generated for 'chain 'C' and resid 193 through 195' Processing helix chain 'C' and resid 202 through 204 No H-bonds generated for 'chain 'C' and resid 202 through 204' Processing helix chain 'C' and resid 252 through 258 removed outlier: 3.830A pdb=" N TRP C 258 " --> pdb=" O LEU C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 342 Processing helix chain 'C' and resid 345 through 347 No H-bonds generated for 'chain 'C' and resid 345 through 347' Processing helix chain 'C' and resid 352 through 363 Processing helix chain 'C' and resid 381 through 403 Proline residue: C 385 - end of helix removed outlier: 3.544A pdb=" N GLN C 389 " --> pdb=" O VAL C 386 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE C 391 " --> pdb=" O ALA C 388 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA C 395 " --> pdb=" O SER C 392 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS C 400 " --> pdb=" O GLU C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 472 Processing helix chain 'D' and resid 14 through 21 Processing helix chain 'D' and resid 38 through 54 Processing helix chain 'D' and resid 68 through 71 Processing helix chain 'D' and resid 89 through 102 Processing helix chain 'D' and resid 112 through 124 Processing helix chain 'D' and resid 158 through 168 removed outlier: 4.134A pdb=" N LYS D 168 " --> pdb=" O HIS D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 184 No H-bonds generated for 'chain 'D' and resid 181 through 184' Processing helix chain 'D' and resid 193 through 195 No H-bonds generated for 'chain 'D' and resid 193 through 195' Processing helix chain 'D' and resid 202 through 204 No H-bonds generated for 'chain 'D' and resid 202 through 204' Processing helix chain 'D' and resid 252 through 258 removed outlier: 3.829A pdb=" N TRP D 258 " --> pdb=" O LEU D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 342 Processing helix chain 'D' and resid 345 through 347 No H-bonds generated for 'chain 'D' and resid 345 through 347' Processing helix chain 'D' and resid 352 through 363 Processing helix chain 'D' and resid 381 through 403 Proline residue: D 385 - end of helix removed outlier: 3.543A pdb=" N GLN D 389 " --> pdb=" O VAL D 386 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE D 391 " --> pdb=" O ALA D 388 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA D 395 " --> pdb=" O SER D 392 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS D 400 " --> pdb=" O GLU D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 472 Processing helix chain 'E' and resid 14 through 21 Processing helix chain 'E' and resid 38 through 54 Processing helix chain 'E' and resid 68 through 71 Processing helix chain 'E' and resid 89 through 102 Processing helix chain 'E' and resid 112 through 124 Processing helix chain 'E' and resid 158 through 168 removed outlier: 4.134A pdb=" N LYS E 168 " --> pdb=" O HIS E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 184 No H-bonds generated for 'chain 'E' and resid 181 through 184' Processing helix chain 'E' and resid 193 through 195 No H-bonds generated for 'chain 'E' and resid 193 through 195' Processing helix chain 'E' and resid 202 through 204 No H-bonds generated for 'chain 'E' and resid 202 through 204' Processing helix chain 'E' and resid 252 through 258 removed outlier: 3.829A pdb=" N TRP E 258 " --> pdb=" O LEU E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 342 Processing helix chain 'E' and resid 345 through 347 No H-bonds generated for 'chain 'E' and resid 345 through 347' Processing helix chain 'E' and resid 352 through 363 Processing helix chain 'E' and resid 381 through 403 Proline residue: E 385 - end of helix removed outlier: 3.543A pdb=" N GLN E 389 " --> pdb=" O VAL E 386 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE E 391 " --> pdb=" O ALA E 388 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA E 395 " --> pdb=" O SER E 392 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS E 400 " --> pdb=" O GLU E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 472 Processing helix chain 'F' and resid 14 through 21 Processing helix chain 'F' and resid 38 through 54 Processing helix chain 'F' and resid 68 through 71 Processing helix chain 'F' and resid 89 through 102 Processing helix chain 'F' and resid 112 through 124 Processing helix chain 'F' and resid 158 through 168 removed outlier: 4.135A pdb=" N LYS F 168 " --> pdb=" O HIS F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 184 No H-bonds generated for 'chain 'F' and resid 181 through 184' Processing helix chain 'F' and resid 193 through 195 No H-bonds generated for 'chain 'F' and resid 193 through 195' Processing helix chain 'F' and resid 202 through 204 No H-bonds generated for 'chain 'F' and resid 202 through 204' Processing helix chain 'F' and resid 252 through 258 removed outlier: 3.829A pdb=" N TRP F 258 " --> pdb=" O LEU F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 342 Processing helix chain 'F' and resid 345 through 347 No H-bonds generated for 'chain 'F' and resid 345 through 347' Processing helix chain 'F' and resid 352 through 363 Processing helix chain 'F' and resid 381 through 403 Proline residue: F 385 - end of helix removed outlier: 3.544A pdb=" N GLN F 389 " --> pdb=" O VAL F 386 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE F 391 " --> pdb=" O ALA F 388 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA F 395 " --> pdb=" O SER F 392 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS F 400 " --> pdb=" O GLU F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 462 through 472 Processing helix chain 'G' and resid 14 through 21 Processing helix chain 'G' and resid 38 through 54 Processing helix chain 'G' and resid 68 through 71 Processing helix chain 'G' and resid 89 through 102 Processing helix chain 'G' and resid 112 through 124 Processing helix chain 'G' and resid 158 through 168 removed outlier: 4.135A pdb=" N LYS G 168 " --> pdb=" O HIS G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 184 No H-bonds generated for 'chain 'G' and resid 181 through 184' Processing helix chain 'G' and resid 193 through 195 No H-bonds generated for 'chain 'G' and resid 193 through 195' Processing helix chain 'G' and resid 202 through 204 No H-bonds generated for 'chain 'G' and resid 202 through 204' Processing helix chain 'G' and resid 252 through 258 removed outlier: 3.829A pdb=" N TRP G 258 " --> pdb=" O LEU G 254 " (cutoff:3.500A) Processing helix chain 'G' and resid 336 through 342 Processing helix chain 'G' and resid 345 through 347 No H-bonds generated for 'chain 'G' and resid 345 through 347' Processing helix chain 'G' and resid 352 through 363 Processing helix chain 'G' and resid 381 through 403 Proline residue: G 385 - end of helix removed outlier: 3.543A pdb=" N GLN G 389 " --> pdb=" O VAL G 386 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE G 391 " --> pdb=" O ALA G 388 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA G 395 " --> pdb=" O SER G 392 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS G 400 " --> pdb=" O GLU G 397 " (cutoff:3.500A) Processing helix chain 'G' and resid 462 through 472 Processing helix chain 'H' and resid 14 through 21 Processing helix chain 'H' and resid 38 through 54 Processing helix chain 'H' and resid 68 through 71 Processing helix chain 'H' and resid 89 through 102 Processing helix chain 'H' and resid 112 through 124 Processing helix chain 'H' and resid 158 through 168 removed outlier: 4.134A pdb=" N LYS H 168 " --> pdb=" O HIS H 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 184 No H-bonds generated for 'chain 'H' and resid 181 through 184' Processing helix chain 'H' and resid 193 through 195 No H-bonds generated for 'chain 'H' and resid 193 through 195' Processing helix chain 'H' and resid 202 through 204 No H-bonds generated for 'chain 'H' and resid 202 through 204' Processing helix chain 'H' and resid 252 through 258 removed outlier: 3.830A pdb=" N TRP H 258 " --> pdb=" O LEU H 254 " (cutoff:3.500A) Processing helix chain 'H' and resid 336 through 342 Processing helix chain 'H' and resid 345 through 347 No H-bonds generated for 'chain 'H' and resid 345 through 347' Processing helix chain 'H' and resid 352 through 363 Processing helix chain 'H' and resid 381 through 403 Proline residue: H 385 - end of helix removed outlier: 3.543A pdb=" N GLN H 389 " --> pdb=" O VAL H 386 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE H 391 " --> pdb=" O ALA H 388 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA H 395 " --> pdb=" O SER H 392 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS H 400 " --> pdb=" O GLU H 397 " (cutoff:3.500A) Processing helix chain 'H' and resid 462 through 472 Processing helix chain 'I' and resid 14 through 21 Processing helix chain 'I' and resid 38 through 54 Processing helix chain 'I' and resid 68 through 71 Processing helix chain 'I' and resid 89 through 102 Processing helix chain 'I' and resid 112 through 124 Processing helix chain 'I' and resid 158 through 168 removed outlier: 4.135A pdb=" N LYS I 168 " --> pdb=" O HIS I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 184 No H-bonds generated for 'chain 'I' and resid 181 through 184' Processing helix chain 'I' and resid 193 through 195 No H-bonds generated for 'chain 'I' and resid 193 through 195' Processing helix chain 'I' and resid 202 through 204 No H-bonds generated for 'chain 'I' and resid 202 through 204' Processing helix chain 'I' and resid 252 through 258 removed outlier: 3.830A pdb=" N TRP I 258 " --> pdb=" O LEU I 254 " (cutoff:3.500A) Processing helix chain 'I' and resid 336 through 342 Processing helix chain 'I' and resid 345 through 347 No H-bonds generated for 'chain 'I' and resid 345 through 347' Processing helix chain 'I' and resid 352 through 363 Processing helix chain 'I' and resid 381 through 403 Proline residue: I 385 - end of helix removed outlier: 3.545A pdb=" N GLN I 389 " --> pdb=" O VAL I 386 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE I 391 " --> pdb=" O ALA I 388 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA I 395 " --> pdb=" O SER I 392 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS I 400 " --> pdb=" O GLU I 397 " (cutoff:3.500A) Processing helix chain 'I' and resid 462 through 472 Processing helix chain 'J' and resid 14 through 21 Processing helix chain 'J' and resid 38 through 54 Processing helix chain 'J' and resid 68 through 71 Processing helix chain 'J' and resid 89 through 102 Processing helix chain 'J' and resid 112 through 124 Processing helix chain 'J' and resid 158 through 168 removed outlier: 4.134A pdb=" N LYS J 168 " --> pdb=" O HIS J 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 181 through 184 No H-bonds generated for 'chain 'J' and resid 181 through 184' Processing helix chain 'J' and resid 193 through 195 No H-bonds generated for 'chain 'J' and resid 193 through 195' Processing helix chain 'J' and resid 202 through 204 No H-bonds generated for 'chain 'J' and resid 202 through 204' Processing helix chain 'J' and resid 252 through 258 removed outlier: 3.829A pdb=" N TRP J 258 " --> pdb=" O LEU J 254 " (cutoff:3.500A) Processing helix chain 'J' and resid 336 through 342 Processing helix chain 'J' and resid 345 through 347 No H-bonds generated for 'chain 'J' and resid 345 through 347' Processing helix chain 'J' and resid 352 through 363 Processing helix chain 'J' and resid 381 through 403 Proline residue: J 385 - end of helix removed outlier: 3.544A pdb=" N GLN J 389 " --> pdb=" O VAL J 386 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE J 391 " --> pdb=" O ALA J 388 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA J 395 " --> pdb=" O SER J 392 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS J 400 " --> pdb=" O GLU J 397 " (cutoff:3.500A) Processing helix chain 'J' and resid 462 through 472 Processing helix chain 'K' and resid 14 through 21 Processing helix chain 'K' and resid 38 through 54 Processing helix chain 'K' and resid 68 through 71 Processing helix chain 'K' and resid 89 through 102 Processing helix chain 'K' and resid 112 through 124 Processing helix chain 'K' and resid 158 through 168 removed outlier: 4.135A pdb=" N LYS K 168 " --> pdb=" O HIS K 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 181 through 184 No H-bonds generated for 'chain 'K' and resid 181 through 184' Processing helix chain 'K' and resid 193 through 195 No H-bonds generated for 'chain 'K' and resid 193 through 195' Processing helix chain 'K' and resid 202 through 204 No H-bonds generated for 'chain 'K' and resid 202 through 204' Processing helix chain 'K' and resid 252 through 258 removed outlier: 3.830A pdb=" N TRP K 258 " --> pdb=" O LEU K 254 " (cutoff:3.500A) Processing helix chain 'K' and resid 336 through 342 Processing helix chain 'K' and resid 345 through 347 No H-bonds generated for 'chain 'K' and resid 345 through 347' Processing helix chain 'K' and resid 352 through 363 Processing helix chain 'K' and resid 381 through 403 Proline residue: K 385 - end of helix removed outlier: 3.544A pdb=" N GLN K 389 " --> pdb=" O VAL K 386 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE K 391 " --> pdb=" O ALA K 388 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA K 395 " --> pdb=" O SER K 392 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS K 400 " --> pdb=" O GLU K 397 " (cutoff:3.500A) Processing helix chain 'K' and resid 462 through 472 Processing helix chain 'L' and resid 14 through 21 Processing helix chain 'L' and resid 38 through 54 Processing helix chain 'L' and resid 68 through 71 Processing helix chain 'L' and resid 89 through 102 Processing helix chain 'L' and resid 112 through 124 Processing helix chain 'L' and resid 158 through 168 removed outlier: 4.135A pdb=" N LYS L 168 " --> pdb=" O HIS L 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 181 through 184 No H-bonds generated for 'chain 'L' and resid 181 through 184' Processing helix chain 'L' and resid 193 through 195 No H-bonds generated for 'chain 'L' and resid 193 through 195' Processing helix chain 'L' and resid 202 through 204 No H-bonds generated for 'chain 'L' and resid 202 through 204' Processing helix chain 'L' and resid 252 through 258 removed outlier: 3.828A pdb=" N TRP L 258 " --> pdb=" O LEU L 254 " (cutoff:3.500A) Processing helix chain 'L' and resid 336 through 342 Processing helix chain 'L' and resid 345 through 347 No H-bonds generated for 'chain 'L' and resid 345 through 347' Processing helix chain 'L' and resid 352 through 363 Processing helix chain 'L' and resid 381 through 403 Proline residue: L 385 - end of helix removed outlier: 3.544A pdb=" N GLN L 389 " --> pdb=" O VAL L 386 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE L 391 " --> pdb=" O ALA L 388 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA L 395 " --> pdb=" O SER L 392 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS L 400 " --> pdb=" O GLU L 397 " (cutoff:3.500A) Processing helix chain 'L' and resid 462 through 472 Processing sheet with id= A, first strand: chain 'A' and resid 3 through 6 removed outlier: 6.280A pdb=" N GLU A 26 " --> pdb=" O VAL A 4 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N VAL A 6 " --> pdb=" O GLU A 26 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLU A 28 " --> pdb=" O VAL A 6 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 77 through 81 removed outlier: 6.865A pdb=" N VAL A 147 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ILE A 64 " --> pdb=" O VAL A 147 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE A 149 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU A 172 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N TYR A 150 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TYR A 174 " --> pdb=" O TYR A 150 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 280 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N AARG A 289 " --> pdb=" O THR A 278 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N THR A 278 " --> pdb=" O AARG A 289 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N THR A 291 " --> pdb=" O CYS A 276 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N CYS A 276 " --> pdb=" O THR A 291 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N SER A 293 " --> pdb=" O CYS A 274 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N CYS A 274 " --> pdb=" O SER A 293 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 189 through 192 removed outlier: 3.638A pdb=" N THR A 197 " --> pdb=" O TYR A 192 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 303 through 307 Processing sheet with id= E, first strand: chain 'A' and resid 324 through 334 Processing sheet with id= F, first strand: chain 'B' and resid 3 through 6 removed outlier: 6.281A pdb=" N GLU B 26 " --> pdb=" O VAL B 4 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N VAL B 6 " --> pdb=" O GLU B 26 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLU B 28 " --> pdb=" O VAL B 6 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 77 through 81 removed outlier: 6.865A pdb=" N VAL B 147 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ILE B 64 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE B 149 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU B 172 " --> pdb=" O ALA B 148 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N TYR B 150 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TYR B 174 " --> pdb=" O TYR B 150 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL B 280 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N AARG B 289 " --> pdb=" O THR B 278 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N THR B 278 " --> pdb=" O AARG B 289 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N THR B 291 " --> pdb=" O CYS B 276 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N CYS B 276 " --> pdb=" O THR B 291 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N SER B 293 " --> pdb=" O CYS B 274 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N CYS B 274 " --> pdb=" O SER B 293 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.639A pdb=" N THR B 197 " --> pdb=" O TYR B 192 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 303 through 307 Processing sheet with id= J, first strand: chain 'B' and resid 324 through 334 Processing sheet with id= K, first strand: chain 'C' and resid 3 through 6 removed outlier: 6.280A pdb=" N GLU C 26 " --> pdb=" O VAL C 4 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N VAL C 6 " --> pdb=" O GLU C 26 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLU C 28 " --> pdb=" O VAL C 6 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'C' and resid 77 through 81 removed outlier: 6.866A pdb=" N VAL C 147 " --> pdb=" O LEU C 62 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ILE C 64 " --> pdb=" O VAL C 147 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE C 149 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU C 172 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N TYR C 150 " --> pdb=" O LEU C 172 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TYR C 174 " --> pdb=" O TYR C 150 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL C 280 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N AARG C 289 " --> pdb=" O THR C 278 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N THR C 278 " --> pdb=" O AARG C 289 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N THR C 291 " --> pdb=" O CYS C 276 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N CYS C 276 " --> pdb=" O THR C 291 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N SER C 293 " --> pdb=" O CYS C 274 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N CYS C 274 " --> pdb=" O SER C 293 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 189 through 192 removed outlier: 3.638A pdb=" N THR C 197 " --> pdb=" O TYR C 192 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 303 through 307 Processing sheet with id= O, first strand: chain 'C' and resid 324 through 334 Processing sheet with id= P, first strand: chain 'D' and resid 3 through 6 removed outlier: 6.281A pdb=" N GLU D 26 " --> pdb=" O VAL D 4 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N VAL D 6 " --> pdb=" O GLU D 26 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLU D 28 " --> pdb=" O VAL D 6 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'D' and resid 77 through 81 removed outlier: 6.865A pdb=" N VAL D 147 " --> pdb=" O LEU D 62 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ILE D 64 " --> pdb=" O VAL D 147 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE D 149 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU D 172 " --> pdb=" O ALA D 148 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N TYR D 150 " --> pdb=" O LEU D 172 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TYR D 174 " --> pdb=" O TYR D 150 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL D 280 " --> pdb=" O VAL D 287 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N AARG D 289 " --> pdb=" O THR D 278 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N THR D 278 " --> pdb=" O AARG D 289 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N THR D 291 " --> pdb=" O CYS D 276 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N CYS D 276 " --> pdb=" O THR D 291 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N SER D 293 " --> pdb=" O CYS D 274 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N CYS D 274 " --> pdb=" O SER D 293 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 189 through 192 removed outlier: 3.639A pdb=" N THR D 197 " --> pdb=" O TYR D 192 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 303 through 307 Processing sheet with id= T, first strand: chain 'D' and resid 324 through 334 Processing sheet with id= U, first strand: chain 'E' and resid 3 through 6 removed outlier: 6.280A pdb=" N GLU E 26 " --> pdb=" O VAL E 4 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N VAL E 6 " --> pdb=" O GLU E 26 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLU E 28 " --> pdb=" O VAL E 6 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'E' and resid 77 through 81 removed outlier: 6.866A pdb=" N VAL E 147 " --> pdb=" O LEU E 62 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ILE E 64 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE E 149 " --> pdb=" O ILE E 64 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU E 172 " --> pdb=" O ALA E 148 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N TYR E 150 " --> pdb=" O LEU E 172 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TYR E 174 " --> pdb=" O TYR E 150 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL E 280 " --> pdb=" O VAL E 287 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N AARG E 289 " --> pdb=" O THR E 278 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N THR E 278 " --> pdb=" O AARG E 289 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N THR E 291 " --> pdb=" O CYS E 276 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N CYS E 276 " --> pdb=" O THR E 291 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N SER E 293 " --> pdb=" O CYS E 274 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N CYS E 274 " --> pdb=" O SER E 293 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 189 through 192 removed outlier: 3.638A pdb=" N THR E 197 " --> pdb=" O TYR E 192 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 303 through 307 Processing sheet with id= Y, first strand: chain 'E' and resid 324 through 334 Processing sheet with id= Z, first strand: chain 'F' and resid 3 through 6 removed outlier: 6.280A pdb=" N GLU F 26 " --> pdb=" O VAL F 4 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N VAL F 6 " --> pdb=" O GLU F 26 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLU F 28 " --> pdb=" O VAL F 6 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'F' and resid 77 through 81 removed outlier: 6.866A pdb=" N VAL F 147 " --> pdb=" O LEU F 62 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ILE F 64 " --> pdb=" O VAL F 147 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE F 149 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU F 172 " --> pdb=" O ALA F 148 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N TYR F 150 " --> pdb=" O LEU F 172 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TYR F 174 " --> pdb=" O TYR F 150 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL F 280 " --> pdb=" O VAL F 287 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N AARG F 289 " --> pdb=" O THR F 278 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N THR F 278 " --> pdb=" O AARG F 289 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N THR F 291 " --> pdb=" O CYS F 276 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N CYS F 276 " --> pdb=" O THR F 291 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N SER F 293 " --> pdb=" O CYS F 274 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N CYS F 274 " --> pdb=" O SER F 293 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 189 through 192 removed outlier: 3.638A pdb=" N THR F 197 " --> pdb=" O TYR F 192 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 303 through 307 Processing sheet with id= AD, first strand: chain 'F' and resid 324 through 334 Processing sheet with id= AE, first strand: chain 'G' and resid 3 through 6 removed outlier: 6.280A pdb=" N GLU G 26 " --> pdb=" O VAL G 4 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N VAL G 6 " --> pdb=" O GLU G 26 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLU G 28 " --> pdb=" O VAL G 6 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'G' and resid 77 through 81 removed outlier: 6.866A pdb=" N VAL G 147 " --> pdb=" O LEU G 62 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ILE G 64 " --> pdb=" O VAL G 147 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE G 149 " --> pdb=" O ILE G 64 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU G 172 " --> pdb=" O ALA G 148 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N TYR G 150 " --> pdb=" O LEU G 172 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TYR G 174 " --> pdb=" O TYR G 150 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL G 280 " --> pdb=" O VAL G 287 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N AARG G 289 " --> pdb=" O THR G 278 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N THR G 278 " --> pdb=" O AARG G 289 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N THR G 291 " --> pdb=" O CYS G 276 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N CYS G 276 " --> pdb=" O THR G 291 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N SER G 293 " --> pdb=" O CYS G 274 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N CYS G 274 " --> pdb=" O SER G 293 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'G' and resid 189 through 192 removed outlier: 3.638A pdb=" N THR G 197 " --> pdb=" O TYR G 192 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'G' and resid 303 through 307 Processing sheet with id= AI, first strand: chain 'G' and resid 324 through 334 Processing sheet with id= AJ, first strand: chain 'H' and resid 3 through 6 removed outlier: 6.280A pdb=" N GLU H 26 " --> pdb=" O VAL H 4 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N VAL H 6 " --> pdb=" O GLU H 26 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLU H 28 " --> pdb=" O VAL H 6 " (cutoff:3.500A) No H-bonds generated for sheet with id= AJ Processing sheet with id= AK, first strand: chain 'H' and resid 77 through 81 removed outlier: 6.866A pdb=" N VAL H 147 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ILE H 64 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE H 149 " --> pdb=" O ILE H 64 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU H 172 " --> pdb=" O ALA H 148 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N TYR H 150 " --> pdb=" O LEU H 172 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TYR H 174 " --> pdb=" O TYR H 150 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL H 280 " --> pdb=" O VAL H 287 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N AARG H 289 " --> pdb=" O THR H 278 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N THR H 278 " --> pdb=" O AARG H 289 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N THR H 291 " --> pdb=" O CYS H 276 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N CYS H 276 " --> pdb=" O THR H 291 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N SER H 293 " --> pdb=" O CYS H 274 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N CYS H 274 " --> pdb=" O SER H 293 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'H' and resid 189 through 192 removed outlier: 3.638A pdb=" N THR H 197 " --> pdb=" O TYR H 192 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'H' and resid 303 through 307 Processing sheet with id= AN, first strand: chain 'H' and resid 324 through 334 Processing sheet with id= AO, first strand: chain 'I' and resid 3 through 6 removed outlier: 6.281A pdb=" N GLU I 26 " --> pdb=" O VAL I 4 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N VAL I 6 " --> pdb=" O GLU I 26 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLU I 28 " --> pdb=" O VAL I 6 " (cutoff:3.500A) No H-bonds generated for sheet with id= AO Processing sheet with id= AP, first strand: chain 'I' and resid 77 through 81 removed outlier: 6.867A pdb=" N VAL I 147 " --> pdb=" O LEU I 62 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ILE I 64 " --> pdb=" O VAL I 147 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE I 149 " --> pdb=" O ILE I 64 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU I 172 " --> pdb=" O ALA I 148 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N TYR I 150 " --> pdb=" O LEU I 172 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N TYR I 174 " --> pdb=" O TYR I 150 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL I 280 " --> pdb=" O VAL I 287 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N AARG I 289 " --> pdb=" O THR I 278 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N THR I 278 " --> pdb=" O AARG I 289 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N THR I 291 " --> pdb=" O CYS I 276 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N CYS I 276 " --> pdb=" O THR I 291 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N SER I 293 " --> pdb=" O CYS I 274 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N CYS I 274 " --> pdb=" O SER I 293 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'I' and resid 189 through 192 removed outlier: 3.638A pdb=" N THR I 197 " --> pdb=" O TYR I 192 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'I' and resid 303 through 307 Processing sheet with id= AS, first strand: chain 'I' and resid 324 through 334 Processing sheet with id= AT, first strand: chain 'J' and resid 3 through 6 removed outlier: 6.281A pdb=" N GLU J 26 " --> pdb=" O VAL J 4 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N VAL J 6 " --> pdb=" O GLU J 26 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLU J 28 " --> pdb=" O VAL J 6 " (cutoff:3.500A) No H-bonds generated for sheet with id= AT Processing sheet with id= AU, first strand: chain 'J' and resid 77 through 81 removed outlier: 6.866A pdb=" N VAL J 147 " --> pdb=" O LEU J 62 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ILE J 64 " --> pdb=" O VAL J 147 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE J 149 " --> pdb=" O ILE J 64 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU J 172 " --> pdb=" O ALA J 148 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N TYR J 150 " --> pdb=" O LEU J 172 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TYR J 174 " --> pdb=" O TYR J 150 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL J 280 " --> pdb=" O VAL J 287 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N AARG J 289 " --> pdb=" O THR J 278 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N THR J 278 " --> pdb=" O AARG J 289 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N THR J 291 " --> pdb=" O CYS J 276 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N CYS J 276 " --> pdb=" O THR J 291 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N SER J 293 " --> pdb=" O CYS J 274 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N CYS J 274 " --> pdb=" O SER J 293 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'J' and resid 189 through 192 removed outlier: 3.638A pdb=" N THR J 197 " --> pdb=" O TYR J 192 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'J' and resid 303 through 307 Processing sheet with id= AX, first strand: chain 'J' and resid 324 through 334 Processing sheet with id= AY, first strand: chain 'K' and resid 3 through 6 removed outlier: 6.281A pdb=" N GLU K 26 " --> pdb=" O VAL K 4 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N VAL K 6 " --> pdb=" O GLU K 26 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLU K 28 " --> pdb=" O VAL K 6 " (cutoff:3.500A) No H-bonds generated for sheet with id= AY Processing sheet with id= AZ, first strand: chain 'K' and resid 77 through 81 removed outlier: 6.866A pdb=" N VAL K 147 " --> pdb=" O LEU K 62 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ILE K 64 " --> pdb=" O VAL K 147 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE K 149 " --> pdb=" O ILE K 64 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU K 172 " --> pdb=" O ALA K 148 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N TYR K 150 " --> pdb=" O LEU K 172 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N TYR K 174 " --> pdb=" O TYR K 150 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL K 280 " --> pdb=" O VAL K 287 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N AARG K 289 " --> pdb=" O THR K 278 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N THR K 278 " --> pdb=" O AARG K 289 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N THR K 291 " --> pdb=" O CYS K 276 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N CYS K 276 " --> pdb=" O THR K 291 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N SER K 293 " --> pdb=" O CYS K 274 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N CYS K 274 " --> pdb=" O SER K 293 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'K' and resid 189 through 192 removed outlier: 3.638A pdb=" N THR K 197 " --> pdb=" O TYR K 192 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'K' and resid 303 through 307 Processing sheet with id= BC, first strand: chain 'K' and resid 324 through 334 Processing sheet with id= BD, first strand: chain 'L' and resid 3 through 6 removed outlier: 6.280A pdb=" N GLU L 26 " --> pdb=" O VAL L 4 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N VAL L 6 " --> pdb=" O GLU L 26 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLU L 28 " --> pdb=" O VAL L 6 " (cutoff:3.500A) No H-bonds generated for sheet with id= BD Processing sheet with id= BE, first strand: chain 'L' and resid 77 through 81 removed outlier: 6.866A pdb=" N VAL L 147 " --> pdb=" O LEU L 62 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ILE L 64 " --> pdb=" O VAL L 147 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE L 149 " --> pdb=" O ILE L 64 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU L 172 " --> pdb=" O ALA L 148 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N TYR L 150 " --> pdb=" O LEU L 172 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N TYR L 174 " --> pdb=" O TYR L 150 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL L 280 " --> pdb=" O VAL L 287 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N AARG L 289 " --> pdb=" O THR L 278 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N THR L 278 " --> pdb=" O AARG L 289 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N THR L 291 " --> pdb=" O CYS L 276 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N CYS L 276 " --> pdb=" O THR L 291 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N SER L 293 " --> pdb=" O CYS L 274 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N CYS L 274 " --> pdb=" O SER L 293 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'L' and resid 189 through 192 removed outlier: 3.638A pdb=" N THR L 197 " --> pdb=" O TYR L 192 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'L' and resid 303 through 307 Processing sheet with id= BH, first strand: chain 'L' and resid 324 through 334 1512 hydrogen bonds defined for protein. 3900 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 17.68 Time building geometry restraints manager: 21.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 8203 1.33 - 1.45: 10900 1.45 - 1.58: 24637 1.58 - 1.70: 60 1.70 - 1.83: 528 Bond restraints: 44328 Sorted by residual: bond pdb=" C2' MGP C1003 " pdb=" C3' MGP C1003 " ideal model delta sigma weight residual 1.239 1.523 -0.284 2.00e-02 2.50e+03 2.02e+02 bond pdb=" C2' MGP K1003 " pdb=" C3' MGP K1003 " ideal model delta sigma weight residual 1.239 1.523 -0.284 2.00e-02 2.50e+03 2.01e+02 bond pdb=" C2' MGP A1003 " pdb=" C3' MGP A1003 " ideal model delta sigma weight residual 1.239 1.522 -0.283 2.00e-02 2.50e+03 2.01e+02 bond pdb=" C2' MGP I1003 " pdb=" C3' MGP I1003 " ideal model delta sigma weight residual 1.239 1.522 -0.283 2.00e-02 2.50e+03 2.01e+02 bond pdb=" C2' MGP B1003 " pdb=" C3' MGP B1003 " ideal model delta sigma weight residual 1.239 1.522 -0.283 2.00e-02 2.50e+03 2.00e+02 ... (remaining 44323 not shown) Histogram of bond angle deviations from ideal: 92.91 - 101.59: 108 101.59 - 110.27: 9517 110.27 - 118.95: 26655 118.95 - 127.64: 23432 127.64 - 136.32: 480 Bond angle restraints: 60192 Sorted by residual: angle pdb=" C1' MGP J1003 " pdb=" N9 MGP J1003 " pdb=" C8 MGP J1003 " ideal model delta sigma weight residual 106.96 126.46 -19.50 3.00e+00 1.11e-01 4.22e+01 angle pdb=" C1' MGP L1003 " pdb=" N9 MGP L1003 " pdb=" C8 MGP L1003 " ideal model delta sigma weight residual 106.96 126.45 -19.49 3.00e+00 1.11e-01 4.22e+01 angle pdb=" C1' MGP C1003 " pdb=" N9 MGP C1003 " pdb=" C8 MGP C1003 " ideal model delta sigma weight residual 106.96 126.44 -19.48 3.00e+00 1.11e-01 4.22e+01 angle pdb=" C1' MGP B1003 " pdb=" N9 MGP B1003 " pdb=" C8 MGP B1003 " ideal model delta sigma weight residual 106.96 126.42 -19.46 3.00e+00 1.11e-01 4.21e+01 angle pdb=" C1' MGP E1003 " pdb=" N9 MGP E1003 " pdb=" C8 MGP E1003 " ideal model delta sigma weight residual 106.96 126.42 -19.46 3.00e+00 1.11e-01 4.21e+01 ... (remaining 60187 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 22830 17.85 - 35.70: 2718 35.70 - 53.55: 792 53.55 - 71.40: 132 71.40 - 89.25: 72 Dihedral angle restraints: 26544 sinusoidal: 10572 harmonic: 15972 Sorted by residual: dihedral pdb=" CA SER H 66 " pdb=" C SER H 66 " pdb=" N ALA H 67 " pdb=" CA ALA H 67 " ideal model delta harmonic sigma weight residual 180.00 160.52 19.48 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA SER L 66 " pdb=" C SER L 66 " pdb=" N ALA L 67 " pdb=" CA ALA L 67 " ideal model delta harmonic sigma weight residual 180.00 160.55 19.45 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA SER J 66 " pdb=" C SER J 66 " pdb=" N ALA J 67 " pdb=" CA ALA J 67 " ideal model delta harmonic sigma weight residual 180.00 160.56 19.44 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 26541 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 4003 0.044 - 0.089: 1917 0.089 - 0.133: 721 0.133 - 0.178: 79 0.178 - 0.222: 12 Chirality restraints: 6732 Sorted by residual: chirality pdb=" C2' MGP C1003 " pdb=" C1' MGP C1003 " pdb=" C3' MGP C1003 " pdb=" O2' MGP C1003 " both_signs ideal model delta sigma weight residual False -2.41 -2.64 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" C2' MGP J1003 " pdb=" C1' MGP J1003 " pdb=" C3' MGP J1003 " pdb=" O2' MGP J1003 " both_signs ideal model delta sigma weight residual False -2.41 -2.63 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" C2' MGP L1003 " pdb=" C1' MGP L1003 " pdb=" C3' MGP L1003 " pdb=" O2' MGP L1003 " both_signs ideal model delta sigma weight residual False -2.41 -2.63 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 6729 not shown) Planarity restraints: 7560 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL I 125 " 0.048 5.00e-02 4.00e+02 7.30e-02 8.53e+00 pdb=" N PRO I 126 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO I 126 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO I 126 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL F 125 " -0.048 5.00e-02 4.00e+02 7.29e-02 8.50e+00 pdb=" N PRO F 126 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO F 126 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO F 126 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL J 125 " 0.048 5.00e-02 4.00e+02 7.29e-02 8.49e+00 pdb=" N PRO J 126 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO J 126 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO J 126 " 0.040 5.00e-02 4.00e+02 ... (remaining 7557 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 284 2.58 - 3.16: 34226 3.16 - 3.74: 68591 3.74 - 4.32: 102717 4.32 - 4.90: 159563 Nonbonded interactions: 365381 Sorted by model distance: nonbonded pdb="MG MG I1004 " pdb=" O HOH I1110 " model vdw 2.005 2.170 nonbonded pdb="MG MG A1004 " pdb=" O HOH A1110 " model vdw 2.005 2.170 nonbonded pdb="MG MG D1004 " pdb=" O HOH D1110 " model vdw 2.005 2.170 nonbonded pdb="MG MG C1004 " pdb=" O HOH C1110 " model vdw 2.006 2.170 nonbonded pdb="MG MG H1004 " pdb=" O HOH H1110 " model vdw 2.006 2.170 ... (remaining 365376 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 235 or resid 237 through 288 or resid 290 throug \ h 473 or resid 1001 through 1004)) selection = (chain 'B' and (resid 2 through 235 or resid 237 through 288 or resid 290 throug \ h 473 or resid 1001 through 1004)) selection = (chain 'C' and (resid 2 through 235 or resid 237 through 288 or resid 290 throug \ h 473 or resid 1001 through 1004)) selection = (chain 'D' and (resid 2 through 235 or resid 237 through 288 or resid 290 throug \ h 473 or resid 1001 through 1004)) selection = (chain 'E' and (resid 2 through 235 or resid 237 through 288 or resid 290 throug \ h 473 or resid 1001 through 1004)) selection = (chain 'F' and (resid 2 through 235 or resid 237 through 288 or resid 290 throug \ h 473 or resid 1001 through 1004)) selection = (chain 'G' and (resid 2 through 235 or resid 237 through 288 or resid 290 throug \ h 473 or resid 1001 through 1004)) selection = (chain 'H' and (resid 2 through 235 or resid 237 through 288 or resid 290 throug \ h 473 or resid 1001 through 1004)) selection = (chain 'I' and (resid 2 through 235 or resid 237 through 288 or resid 290 throug \ h 473 or resid 1001 through 1004)) selection = (chain 'J' and (resid 2 through 235 or resid 237 through 288 or resid 290 throug \ h 473 or resid 1001 through 1004)) selection = (chain 'K' and (resid 2 through 235 or resid 237 through 288 or resid 290 throug \ h 473 or resid 1001 through 1004)) selection = (chain 'L' and (resid 2 through 235 or resid 237 through 288 or resid 290 throug \ h 473 or resid 1001 through 1004)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 12 6.06 5 P 36 5.49 5 Mg 12 5.21 5 S 348 5.16 5 C 27228 2.51 5 N 7584 2.21 5 O 9912 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 9.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 29.820 Check model and map are aligned: 0.670 Convert atoms to be neutral: 0.340 Process input model: 150.790 Find NCS groups from input model: 3.740 Set up NCS constraints: 0.510 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 209.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 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 : 0.010 0.284 44328 Z= 0.693 Angle : 1.050 19.496 60192 Z= 0.538 Chirality : 0.056 0.222 6732 Planarity : 0.006 0.073 7560 Dihedral : 17.456 89.252 16200 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer Outliers : 2.08 % 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: -0.12 (0.11), residues: 5388 helix: 1.68 (0.13), residues: 1644 sheet: 0.64 (0.15), residues: 1080 loop : -1.61 (0.11), residues: 2664 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 428 time to evaluate : 5.234 Fit side-chains outliers start: 96 outliers final: 77 residues processed: 511 average time/residue: 1.6363 time to fit residues: 1027.3084 Evaluate side-chains 466 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 389 time to evaluate : 5.331 Switching outliers to nearest non-outliers outliers start: 77 outliers final: 76 residues processed: 1 average time/residue: 0.3653 time to fit residues: 7.9309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 455 optimal weight: 0.0040 chunk 409 optimal weight: 6.9990 chunk 227 optimal weight: 0.0570 chunk 139 optimal weight: 6.9990 chunk 276 optimal weight: 1.9990 chunk 218 optimal weight: 0.9990 chunk 423 optimal weight: 0.7980 chunk 163 optimal weight: 0.7980 chunk 257 optimal weight: 1.9990 chunk 315 optimal weight: 10.0000 chunk 490 optimal weight: 8.9990 overall best weight: 0.5312 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 ASN C 95 ASN D 95 ASN E 95 ASN F 95 ASN G 95 ASN H 95 ASN I 95 ASN K 95 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 44328 Z= 0.156 Angle : 0.596 12.094 60192 Z= 0.296 Chirality : 0.043 0.131 6732 Planarity : 0.005 0.056 7560 Dihedral : 5.169 54.405 6024 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer Outliers : 2.88 % 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: 0.47 (0.11), residues: 5388 helix: 2.23 (0.13), residues: 1644 sheet: 0.97 (0.14), residues: 1248 loop : -1.45 (0.11), residues: 2496 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 426 time to evaluate : 5.441 Fit side-chains outliers start: 133 outliers final: 71 residues processed: 543 average time/residue: 1.5442 time to fit residues: 1043.1855 Evaluate side-chains 452 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 381 time to evaluate : 5.370 Switching outliers to nearest non-outliers outliers start: 71 outliers final: 69 residues processed: 2 average time/residue: 0.3690 time to fit residues: 8.6061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 272 optimal weight: 4.9990 chunk 152 optimal weight: 5.9990 chunk 408 optimal weight: 0.8980 chunk 333 optimal weight: 0.9990 chunk 135 optimal weight: 10.0000 chunk 491 optimal weight: 0.0870 chunk 530 optimal weight: 3.9990 chunk 437 optimal weight: 2.9990 chunk 487 optimal weight: 0.4980 chunk 167 optimal weight: 0.8980 chunk 394 optimal weight: 3.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN B 95 ASN C 95 ASN D 95 ASN E 95 ASN F 95 ASN G 95 ASN H 95 ASN J 95 ASN K 95 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 44328 Z= 0.153 Angle : 0.590 13.160 60192 Z= 0.294 Chirality : 0.043 0.132 6732 Planarity : 0.005 0.050 7560 Dihedral : 4.962 51.161 6024 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer Outliers : 2.68 % 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: 0.53 (0.11), residues: 5388 helix: 2.41 (0.13), residues: 1644 sheet: 1.00 (0.14), residues: 1176 loop : -1.43 (0.11), residues: 2568 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 374 time to evaluate : 5.167 Fit side-chains outliers start: 124 outliers final: 79 residues processed: 486 average time/residue: 1.6023 time to fit residues: 967.7459 Evaluate side-chains 451 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 372 time to evaluate : 5.162 Switching outliers to nearest non-outliers outliers start: 79 outliers final: 75 residues processed: 4 average time/residue: 0.3641 time to fit residues: 9.8943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 485 optimal weight: 0.9990 chunk 369 optimal weight: 3.9990 chunk 254 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 234 optimal weight: 4.9990 chunk 329 optimal weight: 4.9990 chunk 493 optimal weight: 10.0000 chunk 521 optimal weight: 4.9990 chunk 257 optimal weight: 7.9990 chunk 467 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN B 95 ASN C 95 ASN D 95 ASN E 95 ASN F 95 ASN G 95 ASN H 95 ASN I 95 ASN J 95 ASN K 95 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 44328 Z= 0.269 Angle : 0.751 13.904 60192 Z= 0.394 Chirality : 0.049 0.149 6732 Planarity : 0.005 0.047 7560 Dihedral : 5.416 50.105 6024 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer Outliers : 2.66 % 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: 0.37 (0.11), residues: 5388 helix: 2.30 (0.13), residues: 1644 sheet: 1.26 (0.16), residues: 936 loop : -1.49 (0.10), residues: 2808 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 382 time to evaluate : 5.678 Fit side-chains outliers start: 123 outliers final: 79 residues processed: 492 average time/residue: 1.6187 time to fit residues: 980.3375 Evaluate side-chains 458 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 379 time to evaluate : 5.726 Switching outliers to nearest non-outliers outliers start: 79 outliers final: 74 residues processed: 5 average time/residue: 0.3825 time to fit residues: 10.7622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 434 optimal weight: 5.9990 chunk 296 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 388 optimal weight: 0.8980 chunk 215 optimal weight: 4.9990 chunk 445 optimal weight: 0.0370 chunk 360 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 266 optimal weight: 1.9990 chunk 468 optimal weight: 0.4980 chunk 131 optimal weight: 1.9990 overall best weight: 1.0862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN B 95 ASN C 95 ASN D 95 ASN E 95 ASN F 95 ASN G 95 ASN H 95 ASN I 95 ASN J 95 ASN K 95 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 44328 Z= 0.172 Angle : 0.622 12.990 60192 Z= 0.317 Chirality : 0.044 0.132 6732 Planarity : 0.005 0.047 7560 Dihedral : 5.137 50.590 6024 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer Outliers : 2.34 % 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: 0.52 (0.11), residues: 5388 helix: 2.47 (0.13), residues: 1632 sheet: 1.20 (0.15), residues: 1056 loop : -1.47 (0.11), residues: 2700 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 388 time to evaluate : 5.125 Fit side-chains outliers start: 108 outliers final: 89 residues processed: 485 average time/residue: 1.5973 time to fit residues: 959.7792 Evaluate side-chains 472 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 383 time to evaluate : 5.654 Switching outliers to nearest non-outliers outliers start: 89 outliers final: 82 residues processed: 7 average time/residue: 0.3979 time to fit residues: 13.2594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 175 optimal weight: 4.9990 chunk 470 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 306 optimal weight: 8.9990 chunk 128 optimal weight: 2.9990 chunk 522 optimal weight: 5.9990 chunk 433 optimal weight: 3.9990 chunk 241 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 172 optimal weight: 0.8980 chunk 274 optimal weight: 9.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN B 95 ASN C 95 ASN D 95 ASN E 95 ASN F 95 ASN G 95 ASN H 95 ASN I 95 ASN J 95 ASN K 95 ASN L 95 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 44328 Z= 0.290 Angle : 0.778 14.099 60192 Z= 0.410 Chirality : 0.049 0.153 6732 Planarity : 0.005 0.047 7560 Dihedral : 5.452 48.686 6024 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer Outliers : 2.45 % 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: 0.30 (0.11), residues: 5388 helix: 2.24 (0.13), residues: 1644 sheet: 1.15 (0.16), residues: 936 loop : -1.50 (0.10), residues: 2808 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 383 time to evaluate : 5.416 Fit side-chains outliers start: 113 outliers final: 81 residues processed: 484 average time/residue: 1.6237 time to fit residues: 973.2979 Evaluate side-chains 464 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 383 time to evaluate : 5.368 Switching outliers to nearest non-outliers outliers start: 81 outliers final: 77 residues processed: 4 average time/residue: 0.3842 time to fit residues: 10.2347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 503 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 297 optimal weight: 0.8980 chunk 381 optimal weight: 1.9990 chunk 295 optimal weight: 8.9990 chunk 439 optimal weight: 0.3980 chunk 291 optimal weight: 4.9990 chunk 520 optimal weight: 3.9990 chunk 325 optimal weight: 9.9990 chunk 317 optimal weight: 6.9990 chunk 240 optimal weight: 0.8980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN B 95 ASN C 95 ASN D 95 ASN E 95 ASN F 95 ASN G 95 ASN H 95 ASN I 95 ASN J 95 ASN K 95 ASN L 95 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 44328 Z= 0.191 Angle : 0.656 13.271 60192 Z= 0.338 Chirality : 0.045 0.134 6732 Planarity : 0.005 0.047 7560 Dihedral : 5.243 49.564 6024 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer Outliers : 2.19 % 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: 0.47 (0.11), residues: 5388 helix: 2.43 (0.13), residues: 1632 sheet: 1.10 (0.15), residues: 1056 loop : -1.47 (0.11), residues: 2700 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 388 time to evaluate : 5.127 Fit side-chains outliers start: 101 outliers final: 78 residues processed: 481 average time/residue: 1.6307 time to fit residues: 970.6963 Evaluate side-chains 458 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 380 time to evaluate : 5.298 Switching outliers to nearest non-outliers outliers start: 78 outliers final: 74 residues processed: 4 average time/residue: 0.6388 time to fit residues: 11.0969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 321 optimal weight: 9.9990 chunk 207 optimal weight: 0.9990 chunk 310 optimal weight: 3.9990 chunk 156 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 100 optimal weight: 0.0870 chunk 330 optimal weight: 8.9990 chunk 354 optimal weight: 4.9990 chunk 257 optimal weight: 1.9990 chunk 48 optimal weight: 0.0270 chunk 409 optimal weight: 8.9990 overall best weight: 1.4222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN B 95 ASN C 95 ASN D 95 ASN E 95 ASN F 95 ASN G 95 ASN H 95 ASN I 95 ASN J 95 ASN K 95 ASN L 95 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 44328 Z= 0.190 Angle : 0.653 13.283 60192 Z= 0.335 Chirality : 0.045 0.133 6732 Planarity : 0.005 0.047 7560 Dihedral : 5.194 49.071 6024 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer Outliers : 1.95 % 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 (0.11), residues: 5388 helix: 2.45 (0.13), residues: 1632 sheet: 1.11 (0.15), residues: 1056 loop : -1.45 (0.11), residues: 2700 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 384 time to evaluate : 5.866 Fit side-chains outliers start: 90 outliers final: 81 residues processed: 465 average time/residue: 1.6282 time to fit residues: 937.3051 Evaluate side-chains 457 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 376 time to evaluate : 5.483 Switching outliers to nearest non-outliers outliers start: 81 outliers final: 73 residues processed: 8 average time/residue: 0.9168 time to fit residues: 17.4932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 473 optimal weight: 5.9990 chunk 498 optimal weight: 0.5980 chunk 454 optimal weight: 8.9990 chunk 485 optimal weight: 5.9990 chunk 291 optimal weight: 5.9990 chunk 211 optimal weight: 0.9990 chunk 380 optimal weight: 7.9990 chunk 148 optimal weight: 9.9990 chunk 438 optimal weight: 2.9990 chunk 458 optimal weight: 2.9990 chunk 483 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN B 95 ASN C 95 ASN D 95 ASN E 95 ASN F 95 ASN G 95 ASN H 95 ASN I 95 ASN J 95 ASN K 95 ASN L 95 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 44328 Z= 0.233 Angle : 0.715 13.769 60192 Z= 0.372 Chirality : 0.047 0.137 6732 Planarity : 0.005 0.047 7560 Dihedral : 5.342 48.750 6024 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer Outliers : 1.97 % 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: 0.36 (0.11), residues: 5388 helix: 2.37 (0.13), residues: 1632 sheet: 1.16 (0.16), residues: 936 loop : -1.50 (0.10), residues: 2820 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 370 time to evaluate : 5.544 Fit side-chains outliers start: 91 outliers final: 74 residues processed: 456 average time/residue: 1.6278 time to fit residues: 921.5837 Evaluate side-chains 454 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 380 time to evaluate : 5.673 Switching outliers to nearest non-outliers outliers start: 74 outliers final: 73 residues processed: 1 average time/residue: 1.5301 time to fit residues: 9.2814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 318 optimal weight: 4.9990 chunk 512 optimal weight: 7.9990 chunk 313 optimal weight: 7.9990 chunk 243 optimal weight: 0.7980 chunk 356 optimal weight: 0.0020 chunk 537 optimal weight: 4.9990 chunk 495 optimal weight: 9.9990 chunk 428 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 330 optimal weight: 0.7980 chunk 262 optimal weight: 2.9990 overall best weight: 1.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN B 95 ASN C 95 ASN D 95 ASN E 95 ASN F 95 ASN G 95 ASN H 95 ASN I 95 ASN J 95 ASN K 95 ASN L 95 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 44328 Z= 0.185 Angle : 0.647 13.159 60192 Z= 0.331 Chirality : 0.045 0.133 6732 Planarity : 0.005 0.047 7560 Dihedral : 5.183 49.084 6024 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer Outliers : 1.67 % 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: 0.51 (0.11), residues: 5388 helix: 2.48 (0.13), residues: 1632 sheet: 1.12 (0.15), residues: 1056 loop : -1.45 (0.11), residues: 2700 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 384 time to evaluate : 5.496 Fit side-chains outliers start: 77 outliers final: 77 residues processed: 457 average time/residue: 1.5762 time to fit residues: 895.2537 Evaluate side-chains 452 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 375 time to evaluate : 5.470 Switching outliers to nearest non-outliers outliers start: 77 outliers final: 73 residues processed: 4 average time/residue: 0.7400 time to fit residues: 10.9701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 340 optimal weight: 7.9990 chunk 456 optimal weight: 10.0000 chunk 131 optimal weight: 0.7980 chunk 395 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 119 optimal weight: 0.0970 chunk 429 optimal weight: 3.9990 chunk 179 optimal weight: 0.9990 chunk 440 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN B 95 ASN C 95 ASN D 95 ASN E 95 ASN F 95 ASN G 95 ASN H 95 ASN I 95 ASN J 95 ASN K 95 ASN L 95 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.141920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.103686 restraints weight = 157347.415| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.61 r_work: 0.2996 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3700 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3700 r_free = 0.3700 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3700 r_free = 0.3700 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3700 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 44328 Z= 0.200 Angle : 0.671 13.413 60192 Z= 0.345 Chirality : 0.045 0.134 6732 Planarity : 0.005 0.047 7560 Dihedral : 5.231 48.811 6024 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer Outliers : 1.71 % 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: 0.48 (0.11), residues: 5388 helix: 2.45 (0.13), residues: 1632 sheet: 1.08 (0.15), residues: 1056 loop : -1.46 (0.11), residues: 2700 =============================================================================== Job complete usr+sys time: 16152.99 seconds wall clock time: 286 minutes 25.38 seconds (17185.38 seconds total)