Starting phenix.real_space_refine (version: 1.21rc1) on Wed Jul 19 10:35:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fgg_31580/07_2023/7fgg_31580_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fgg_31580/07_2023/7fgg_31580.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fgg_31580/07_2023/7fgg_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_31580/07_2023/7fgg_31580_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fgg_31580/07_2023/7fgg_31580_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fgg_31580/07_2023/7fgg_31580.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fgg_31580/07_2023/7fgg_31580.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fgg_31580/07_2023/7fgg_31580_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fgg_31580/07_2023/7fgg_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 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. 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-1.21rc1-5013/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: 39.81, per 1000 atoms: 0.88 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: 17.68 Conformation dependent library (CDL) restraints added in 11.3 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: 4.74 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: 18.08 Time building geometry restraints manager: 18.43 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 101.20 126.46 -25.26 3.00e+00 1.11e-01 7.09e+01 angle pdb=" C1' MGP L1003 " pdb=" N9 MGP L1003 " pdb=" C8 MGP L1003 " ideal model delta sigma weight residual 101.20 126.45 -25.25 3.00e+00 1.11e-01 7.08e+01 angle pdb=" C1' MGP C1003 " pdb=" N9 MGP C1003 " pdb=" C8 MGP C1003 " ideal model delta sigma weight residual 101.20 126.44 -25.24 3.00e+00 1.11e-01 7.08e+01 angle pdb=" C1' MGP B1003 " pdb=" N9 MGP B1003 " pdb=" C8 MGP B1003 " ideal model delta sigma weight residual 101.20 126.42 -25.22 3.00e+00 1.11e-01 7.07e+01 angle pdb=" C1' MGP E1003 " pdb=" N9 MGP E1003 " pdb=" C8 MGP E1003 " ideal model delta sigma weight residual 101.20 126.42 -25.22 3.00e+00 1.11e-01 7.07e+01 ... (remaining 60187 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 22842 17.85 - 35.70: 2706 35.70 - 53.55: 780 53.55 - 71.40: 144 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: 3985 0.044 - 0.088: 1923 0.088 - 0.132: 728 0.132 - 0.176: 84 0.176 - 0.221: 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 1.22e+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 1.17e+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 1.16e+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 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: 6.830 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: 27.870 Check model and map are aligned: 0.770 Set scattering table: 0.430 Process input model: 141.680 Find NCS groups from input model: 3.710 Set up NCS constraints: 0.510 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 195.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 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= 0.688 Angle : 1.083 25.256 60192 Z= 0.545 Chirality : 0.056 0.221 6732 Planarity : 0.006 0.073 7560 Dihedral : 17.473 89.252 16200 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 2.63 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 : 5.557 Fit side-chains outliers start: 96 outliers final: 77 residues processed: 511 average time/residue: 1.7135 time to fit residues: 1069.1121 Evaluate side-chains 466 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 389 time to evaluate : 5.417 Switching outliers to nearest non-outliers outliers start: 77 outliers final: 76 residues processed: 1 average time/residue: 0.4118 time to fit residues: 7.9705 ------------------------------------------------------------------------------- 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: 0.7680 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 44328 Z= 0.155 Angle : 0.554 7.179 60192 Z= 0.287 Chirality : 0.043 0.129 6732 Planarity : 0.005 0.056 7560 Dihedral : 5.101 50.185 6024 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer Outliers : 2.94 % 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: 2.32 (0.13), residues: 1632 sheet: 1.05 (0.14), residues: 1236 loop : -1.46 (0.11), residues: 2520 *********************** 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 555 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 419 time to evaluate : 4.896 Fit side-chains outliers start: 136 outliers final: 72 residues processed: 539 average time/residue: 1.6167 time to fit residues: 1076.2282 Evaluate side-chains 455 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 383 time to evaluate : 5.662 Switching outliers to nearest non-outliers outliers start: 72 outliers final: 70 residues processed: 2 average time/residue: 0.3958 time to fit residues: 8.7030 ------------------------------------------------------------------------------- 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: 5.9990 chunk 152 optimal weight: 0.9990 chunk 408 optimal weight: 0.0970 chunk 333 optimal weight: 0.1980 chunk 135 optimal weight: 10.0000 chunk 491 optimal weight: 0.8980 chunk 530 optimal weight: 3.9990 chunk 437 optimal weight: 0.9980 chunk 487 optimal weight: 0.9980 chunk 167 optimal weight: 0.7980 chunk 394 optimal weight: 0.0980 overall best weight: 0.4178 ------------------------------------------------------------------------------- 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: 0.7667 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 44328 Z= 0.138 Angle : 0.518 8.132 60192 Z= 0.264 Chirality : 0.042 0.127 6732 Planarity : 0.005 0.049 7560 Dihedral : 4.835 53.578 6024 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer Outliers : 2.40 % 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: 0.70 (0.11), residues: 5388 helix: 2.50 (0.14), residues: 1632 sheet: 1.11 (0.14), residues: 1248 loop : -1.35 (0.11), residues: 2508 *********************** 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 487 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 376 time to evaluate : 4.930 Fit side-chains outliers start: 111 outliers final: 68 residues processed: 482 average time/residue: 1.7053 time to fit residues: 1007.5022 Evaluate side-chains 433 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 365 time to evaluate : 5.067 Switching outliers to nearest non-outliers outliers start: 68 outliers final: 67 residues processed: 1 average time/residue: 0.3801 time to fit residues: 7.6351 ------------------------------------------------------------------------------- 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: 1.9990 chunk 369 optimal weight: 5.9990 chunk 254 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 234 optimal weight: 3.9990 chunk 329 optimal weight: 0.7980 chunk 493 optimal weight: 10.0000 chunk 521 optimal weight: 1.9990 chunk 257 optimal weight: 7.9990 chunk 467 optimal weight: 10.0000 chunk 140 optimal weight: 6.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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: 0.7810 moved from start: 0.1789 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= 0.279 Angle : 0.736 10.643 60192 Z= 0.394 Chirality : 0.049 0.219 6732 Planarity : 0.005 0.047 7560 Dihedral : 5.498 56.287 6024 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer Outliers : 2.49 % 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: 2.25 (0.13), residues: 1632 sheet: 1.30 (0.16), residues: 936 loop : -1.46 (0.10), residues: 2820 *********************** 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 494 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 379 time to evaluate : 5.216 Fit side-chains outliers start: 115 outliers final: 78 residues processed: 481 average time/residue: 1.7589 time to fit residues: 1033.0816 Evaluate side-chains 453 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 375 time to evaluate : 5.348 Switching outliers to nearest non-outliers outliers start: 78 outliers final: 73 residues processed: 5 average time/residue: 0.4044 time to fit residues: 11.2367 ------------------------------------------------------------------------------- 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: 10.0000 chunk 7 optimal weight: 10.0000 chunk 388 optimal weight: 0.9980 chunk 215 optimal weight: 4.9990 chunk 445 optimal weight: 2.9990 chunk 360 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 266 optimal weight: 0.5980 chunk 468 optimal weight: 0.4980 chunk 131 optimal weight: 1.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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: 0.7767 moved from start: 0.1913 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= 0.189 Angle : 0.615 8.965 60192 Z= 0.326 Chirality : 0.045 0.150 6732 Planarity : 0.005 0.047 7560 Dihedral : 5.310 55.776 6024 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer Outliers : 2.47 % 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: 0.50 (0.11), residues: 5388 helix: 2.45 (0.13), residues: 1632 sheet: 1.16 (0.15), residues: 1056 loop : -1.46 (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 503 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 389 time to evaluate : 5.530 Fit side-chains outliers start: 114 outliers final: 86 residues processed: 489 average time/residue: 1.7207 time to fit residues: 1034.8742 Evaluate side-chains 474 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 388 time to evaluate : 4.983 Switching outliers to nearest non-outliers outliers start: 86 outliers final: 78 residues processed: 8 average time/residue: 0.3989 time to fit residues: 12.7220 ------------------------------------------------------------------------------- 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: 8.9990 chunk 470 optimal weight: 0.3980 chunk 103 optimal weight: 4.9990 chunk 306 optimal weight: 0.0020 chunk 128 optimal weight: 2.9990 chunk 522 optimal weight: 6.9990 chunk 433 optimal weight: 9.9990 chunk 241 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 172 optimal weight: 0.7980 chunk 274 optimal weight: 6.9990 overall best weight: 1.2392 ------------------------------------------------------------------------------- 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: 0.7756 moved from start: 0.1985 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= 0.178 Angle : 0.598 8.859 60192 Z= 0.315 Chirality : 0.044 0.145 6732 Planarity : 0.005 0.047 7560 Dihedral : 5.239 56.925 6024 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer Outliers : 2.14 % 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: 0.55 (0.11), residues: 5388 helix: 2.49 (0.13), residues: 1632 sheet: 1.18 (0.15), residues: 1056 loop : -1.43 (0.11), residues: 2700 *********************** 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 486 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 387 time to evaluate : 5.892 Fit side-chains outliers start: 99 outliers final: 73 residues processed: 479 average time/residue: 1.7089 time to fit residues: 1004.6584 Evaluate side-chains 457 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 384 time to evaluate : 5.070 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 72 residues processed: 1 average time/residue: 0.4157 time to fit residues: 7.6461 ------------------------------------------------------------------------------- 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: 3.9990 chunk 58 optimal weight: 9.9990 chunk 297 optimal weight: 0.7980 chunk 381 optimal weight: 2.9990 chunk 295 optimal weight: 0.7980 chunk 439 optimal weight: 0.7980 chunk 291 optimal weight: 5.9990 chunk 520 optimal weight: 2.9990 chunk 325 optimal weight: 0.0970 chunk 317 optimal weight: 3.9990 chunk 240 optimal weight: 0.8980 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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: 0.7713 moved from start: 0.2100 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= 0.146 Angle : 0.544 8.038 60192 Z= 0.281 Chirality : 0.043 0.128 6732 Planarity : 0.005 0.046 7560 Dihedral : 5.053 56.771 6024 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer Outliers : 1.93 % 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: 0.64 (0.11), residues: 5388 helix: 2.57 (0.13), residues: 1632 sheet: 1.26 (0.15), residues: 1056 loop : -1.38 (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 472 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 383 time to evaluate : 4.973 Fit side-chains outliers start: 89 outliers final: 76 residues processed: 465 average time/residue: 1.6809 time to fit residues: 961.7656 Evaluate side-chains 450 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 374 time to evaluate : 5.379 Switching outliers to nearest non-outliers outliers start: 76 outliers final: 71 residues processed: 5 average time/residue: 0.4238 time to fit residues: 12.6662 ------------------------------------------------------------------------------- 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: 8.9990 chunk 310 optimal weight: 5.9990 chunk 156 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 chunk 100 optimal weight: 0.0370 chunk 330 optimal weight: 0.1980 chunk 354 optimal weight: 1.9990 chunk 257 optimal weight: 1.9990 chunk 48 optimal weight: 0.0870 chunk 409 optimal weight: 6.9990 overall best weight: 0.8640 ------------------------------------------------------------------------------- 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: 0.7727 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 44328 Z= 0.155 Angle : 0.562 8.296 60192 Z= 0.291 Chirality : 0.043 0.130 6732 Planarity : 0.005 0.046 7560 Dihedral : 5.066 57.355 6024 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer Outliers : 1.99 % 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: 0.67 (0.11), residues: 5388 helix: 2.59 (0.13), residues: 1632 sheet: 1.26 (0.15), residues: 1056 loop : -1.36 (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 464 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 372 time to evaluate : 5.305 Fit side-chains outliers start: 92 outliers final: 74 residues processed: 457 average time/residue: 1.7090 time to fit residues: 959.6771 Evaluate side-chains 450 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 376 time to evaluate : 4.924 Switching outliers to nearest non-outliers outliers start: 74 outliers final: 70 residues processed: 4 average time/residue: 0.9021 time to fit residues: 11.8431 ------------------------------------------------------------------------------- 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: 9.9990 chunk 498 optimal weight: 2.9990 chunk 454 optimal weight: 8.9990 chunk 485 optimal weight: 1.9990 chunk 291 optimal weight: 3.9990 chunk 211 optimal weight: 0.9990 chunk 380 optimal weight: 7.9990 chunk 148 optimal weight: 10.0000 chunk 438 optimal weight: 2.9990 chunk 458 optimal weight: 20.0000 chunk 483 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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: 0.7785 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 44328 Z= 0.225 Angle : 0.669 9.667 60192 Z= 0.355 Chirality : 0.047 0.181 6732 Planarity : 0.005 0.045 7560 Dihedral : 5.380 58.559 6024 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % 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: 0.48 (0.11), residues: 5388 helix: 2.49 (0.13), residues: 1632 sheet: 1.26 (0.16), residues: 936 loop : -1.44 (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 467 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 377 time to evaluate : 5.073 Fit side-chains outliers start: 90 outliers final: 71 residues processed: 464 average time/residue: 1.7487 time to fit residues: 995.1868 Evaluate side-chains 452 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 381 time to evaluate : 5.533 Switching outliers to nearest non-outliers outliers start: 71 outliers final: 69 residues processed: 2 average time/residue: 0.9662 time to fit residues: 10.0660 ------------------------------------------------------------------------------- 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: 2.9990 chunk 512 optimal weight: 7.9990 chunk 313 optimal weight: 10.0000 chunk 243 optimal weight: 0.3980 chunk 356 optimal weight: 0.9980 chunk 537 optimal weight: 3.9990 chunk 495 optimal weight: 10.0000 chunk 428 optimal weight: 0.0570 chunk 44 optimal weight: 0.9990 chunk 330 optimal weight: 0.9990 chunk 262 optimal weight: 2.9990 overall best weight: 0.6902 ------------------------------------------------------------------------------- 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: 0.7716 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 44328 Z= 0.149 Angle : 0.552 8.122 60192 Z= 0.285 Chirality : 0.043 0.129 6732 Planarity : 0.005 0.046 7560 Dihedral : 5.095 57.409 6024 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer Outliers : 1.65 % 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: 0.64 (0.11), residues: 5388 helix: 2.56 (0.13), residues: 1632 sheet: 1.23 (0.15), residues: 1056 loop : -1.36 (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 464 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 388 time to evaluate : 5.253 Fit side-chains outliers start: 76 outliers final: 66 residues processed: 464 average time/residue: 1.7291 time to fit residues: 1002.9582 Evaluate side-chains 443 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 377 time to evaluate : 5.137 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 66 residues processed: 0 time to fit residues: 7.0244 ------------------------------------------------------------------------------- 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: 0.7980 chunk 456 optimal weight: 10.0000 chunk 131 optimal weight: 0.4980 chunk 395 optimal weight: 2.9990 chunk 63 optimal weight: 0.0980 chunk 119 optimal weight: 0.7980 chunk 429 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 440 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3717 r_free = 0.3717 target = 0.143420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.105375 restraints weight = 159149.838| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.60 r_work: 0.3026 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2915 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2915 r_free = 0.2915 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2915 r_free = 0.2915 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2915 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 44328 Z= 0.165 Angle : 0.581 8.558 60192 Z= 0.303 Chirality : 0.044 0.134 6732 Planarity : 0.005 0.046 7560 Dihedral : 5.147 58.066 6024 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % 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: 0.66 (0.11), residues: 5388 helix: 2.59 (0.13), residues: 1632 sheet: 1.22 (0.15), residues: 1056 loop : -1.36 (0.11), residues: 2700 =============================================================================== Job complete usr+sys time: 16684.18 seconds wall clock time: 298 minutes 41.84 seconds (17921.84 seconds total)