Starting phenix.real_space_refine on Sun Mar 24 22:03:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jce_36159/03_2024/8jce_36159_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jce_36159/03_2024/8jce_36159.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jce_36159/03_2024/8jce_36159.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jce_36159/03_2024/8jce_36159.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jce_36159/03_2024/8jce_36159_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jce_36159/03_2024/8jce_36159_updated.pdb" } resolution = 2.41 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.026 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 48 5.49 5 Mg 12 5.21 5 S 348 5.16 5 C 27420 2.51 5 N 7584 2.21 5 O 8880 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 9": "OD1" <-> "OD2" Residue "A GLU 26": "OE1" <-> "OE2" Residue "A GLU 28": "OE1" <-> "OE2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 109": "OD1" <-> "OD2" Residue "A PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 310": "OD1" <-> "OD2" Residue "A GLU 405": "OE1" <-> "OE2" Residue "B ASP 9": "OD1" <-> "OD2" Residue "B ASP 11": "OD1" <-> "OD2" Residue "B GLU 26": "OE1" <-> "OE2" Residue "B GLU 28": "OE1" <-> "OE2" Residue "B ASP 109": "OD1" <-> "OD2" Residue "B PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 277": "OD1" <-> "OD2" Residue "B ASP 310": "OD1" <-> "OD2" Residue "B PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 412": "OE1" <-> "OE2" Residue "B PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 11": "OD1" <-> "OD2" Residue "C GLU 26": "OE1" <-> "OE2" Residue "C GLU 28": "OE1" <-> "OE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 310": "OD1" <-> "OD2" Residue "C PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 405": "OE1" <-> "OE2" Residue "C GLU 412": "OE1" <-> "OE2" Residue "D ASP 9": "OD1" <-> "OD2" Residue "D GLU 26": "OE1" <-> "OE2" Residue "D GLU 28": "OE1" <-> "OE2" Residue "D PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 109": "OD1" <-> "OD2" Residue "D PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 310": "OD1" <-> "OD2" Residue "D GLU 405": "OE1" <-> "OE2" Residue "E ASP 9": "OD1" <-> "OD2" Residue "E ASP 11": "OD1" <-> "OD2" Residue "E GLU 26": "OE1" <-> "OE2" Residue "E GLU 28": "OE1" <-> "OE2" Residue "E PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 58": "OD1" <-> "OD2" Residue "E GLU 91": "OE1" <-> "OE2" Residue "E ASP 109": "OD1" <-> "OD2" Residue "E PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 310": "OD1" <-> "OD2" Residue "E PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 412": "OE1" <-> "OE2" Residue "E PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 11": "OD1" <-> "OD2" Residue "F GLU 26": "OE1" <-> "OE2" Residue "F PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 310": "OD1" <-> "OD2" Residue "F PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 405": "OE1" <-> "OE2" Residue "F GLU 412": "OE1" <-> "OE2" Residue "G ASP 9": "OD1" <-> "OD2" Residue "G GLU 26": "OE1" <-> "OE2" Residue "G GLU 28": "OE1" <-> "OE2" Residue "G PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 109": "OD1" <-> "OD2" Residue "G PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 277": "OD1" <-> "OD2" Residue "G TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 310": "OD1" <-> "OD2" Residue "G GLU 405": "OE1" <-> "OE2" Residue "H ASP 9": "OD1" <-> "OD2" Residue "H ASP 11": "OD1" <-> "OD2" Residue "H GLU 26": "OE1" <-> "OE2" Residue "H GLU 28": "OE1" <-> "OE2" Residue "H PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 58": "OD1" <-> "OD2" Residue "H ASP 109": "OD1" <-> "OD2" Residue "H PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 277": "OD1" <-> "OD2" Residue "H ASP 310": "OD1" <-> "OD2" Residue "H PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 412": "OE1" <-> "OE2" Residue "H PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 11": "OD1" <-> "OD2" Residue "I GLU 26": "OE1" <-> "OE2" Residue "I GLU 28": "OE1" <-> "OE2" Residue "I PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 310": "OD1" <-> "OD2" Residue "I GLU 405": "OE1" <-> "OE2" Residue "J ASP 9": "OD1" <-> "OD2" Residue "J GLU 26": "OE1" <-> "OE2" Residue "J GLU 28": "OE1" <-> "OE2" Residue "J PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 58": "OD1" <-> "OD2" Residue "J ASP 109": "OD1" <-> "OD2" Residue "J PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 277": "OD1" <-> "OD2" Residue "J TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 310": "OD1" <-> "OD2" Residue "J ASP 354": "OD1" <-> "OD2" Residue "J GLU 405": "OE1" <-> "OE2" Residue "K ASP 11": "OD1" <-> "OD2" Residue "K GLU 26": "OE1" <-> "OE2" Residue "K GLU 28": "OE1" <-> "OE2" Residue "K PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 58": "OD1" <-> "OD2" Residue "K GLU 91": "OE1" <-> "OE2" Residue "K ASP 109": "OD1" <-> "OD2" Residue "K PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 277": "OD1" <-> "OD2" Residue "K ASP 310": "OD1" <-> "OD2" Residue "K PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 405": "OE1" <-> "OE2" Residue "K GLU 412": "OE1" <-> "OE2" Residue "K PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 11": "OD1" <-> "OD2" Residue "L GLU 26": "OE1" <-> "OE2" Residue "L GLU 28": "OE1" <-> "OE2" Residue "L PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 310": "OD1" <-> "OD2" Residue "L GLU 405": "OE1" <-> "OE2" Residue "L GLU 412": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 44304 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 3543 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 453, 3537 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 453, 3537 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3605 Chain: "B" Number of atoms: 3543 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 453, 3537 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 453, 3537 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3605 Chain: "C" Number of atoms: 3543 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 453, 3537 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 453, 3537 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3605 Chain: "D" Number of atoms: 3543 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 453, 3537 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 453, 3537 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3605 Chain: "E" Number of atoms: 3543 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 453, 3537 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 453, 3537 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3605 Chain: "F" Number of atoms: 3543 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 453, 3537 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 453, 3537 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3605 Chain: "G" Number of atoms: 3543 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 453, 3537 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 453, 3537 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3605 Chain: "H" Number of atoms: 3543 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 453, 3537 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 453, 3537 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3605 Chain: "I" Number of atoms: 3543 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 453, 3537 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 453, 3537 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3605 Chain: "J" Number of atoms: 3543 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 453, 3537 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 453, 3537 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3605 Chain: "K" Number of atoms: 3543 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 453, 3537 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 453, 3537 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3605 Chain: "L" Number of atoms: 3543 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 453, 3537 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 453, 3537 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 3 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3605 Chain: "A" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 100 Unusual residues: {' MG': 1, ' ZN': 1, 'YG4': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain: "B" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 100 Unusual residues: {' MG': 1, ' ZN': 1, 'YG4': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain: "C" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 100 Unusual residues: {' MG': 1, ' ZN': 1, 'YG4': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain: "D" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 100 Unusual residues: {' MG': 1, ' ZN': 1, 'YG4': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain: "E" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 100 Unusual residues: {' MG': 1, ' ZN': 1, 'YG4': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain: "F" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 100 Unusual residues: {' MG': 1, ' ZN': 1, 'YG4': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain: "G" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 100 Unusual residues: {' MG': 1, ' ZN': 1, 'YG4': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain: "H" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 100 Unusual residues: {' MG': 1, ' ZN': 1, 'YG4': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain: "I" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 100 Unusual residues: {' MG': 1, ' ZN': 1, 'YG4': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain: "J" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 100 Unusual residues: {' MG': 1, ' ZN': 1, 'YG4': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain: "K" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 100 Unusual residues: {' MG': 1, ' ZN': 1, 'YG4': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain: "L" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 100 Unusual residues: {' MG': 1, ' ZN': 1, 'YG4': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain: "A" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Chain: "C" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Chain: "E" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Chain: "F" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "G" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Chain: "H" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Chain: "I" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "J" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Chain: "K" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Chain: "L" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1019 SG CYS A 134 20.276 131.099 61.518 1.00 77.67 S ATOM 1071 SG CYS A 141 20.951 135.121 60.817 1.00 74.94 S ATOM 4562 SG CYS B 134 17.158 86.013 61.522 1.00 77.73 S ATOM 4614 SG CYS B 141 15.854 89.824 60.792 1.00 71.40 S ATOM 8105 SG CYS C 134 37.093 45.420 61.509 1.00 77.84 S ATOM 8157 SG CYS C 141 33.968 48.043 60.817 1.00 71.12 S ATOM 11648 SG CYS D 134 74.601 20.266 61.521 1.00 77.78 S ATOM 11700 SG CYS D 141 70.579 20.941 60.818 1.00 75.09 S ATOM 15191 SG CYS E 134 119.679 17.158 61.523 1.00 77.58 S ATOM 15243 SG CYS E 141 115.873 15.847 60.793 1.00 71.62 S ATOM 18734 SG CYS F 134 160.280 37.085 61.510 1.00 77.76 S ATOM 18786 SG CYS F 141 157.649 33.970 60.813 1.00 70.84 S ATOM 22277 SG CYS G 134 185.436 74.590 61.523 1.00 77.43 S ATOM 22329 SG CYS G 141 184.762 70.570 60.819 1.00 74.90 S ATOM 25820 SG CYS H 134 188.557 119.679 61.526 1.00 77.73 S ATOM 25872 SG CYS H 141 189.852 115.862 60.790 1.00 71.72 S ATOM 29363 SG CYS I 134 168.604 160.290 61.515 1.00 77.79 S ATOM 29415 SG CYS I 141 171.725 157.648 60.813 1.00 70.94 S ATOM 32906 SG CYS J 134 131.110 185.426 61.520 1.00 77.55 S ATOM 32958 SG CYS J 141 135.130 184.752 60.818 1.00 74.97 S ATOM 36449 SG CYS K 134 86.021 188.547 61.525 1.00 77.52 S ATOM 36501 SG CYS K 141 89.835 189.842 60.792 1.00 71.38 S ATOM 39992 SG CYS L 134 45.427 168.606 61.508 1.00 77.81 S ATOM 40044 SG CYS L 141 48.058 171.723 60.813 1.00 70.83 S Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" N ACYS A 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS A 236 " 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 ACYS C 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS C 236 " 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 ACYS E 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS E 236 " 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 ACYS G 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS G 236 " occ=0.50 residue: pdb=" N ACYS H 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS H 236 " occ=0.50 residue: pdb=" N ACYS I 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS I 236 " occ=0.50 residue: pdb=" N ACYS J 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS J 236 " occ=0.50 residue: pdb=" N ACYS K 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS K 236 " occ=0.50 residue: pdb=" N ACYS L 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS L 236 " occ=0.50 Time building chain proxies: 40.59, per 1000 atoms: 0.92 Number of scatterers: 44304 At special positions: 0 Unit cell: (206.55, 206.55, 90.1, 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 48 15.00 Mg 12 11.99 O 8880 8.00 N 7584 7.00 C 27420 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: 17.59 Conformation dependent library (CDL) restraints added in 14.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" NE2 HIS A 79 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 141 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 134 " pdb=" ZN B 602 " pdb="ZN ZN B 602 " - pdb=" NE2 HIS B 79 " pdb="ZN ZN B 602 " - pdb=" SG CYS B 141 " pdb="ZN ZN B 602 " - pdb=" SG CYS B 134 " pdb=" ZN C 602 " pdb="ZN ZN C 602 " - pdb=" NE2 HIS C 79 " pdb="ZN ZN C 602 " - pdb=" SG CYS C 141 " pdb="ZN ZN C 602 " - pdb=" SG CYS C 134 " pdb=" ZN D 602 " pdb="ZN ZN D 602 " - pdb=" NE2 HIS D 79 " pdb="ZN ZN D 602 " - pdb=" SG CYS D 141 " pdb="ZN ZN D 602 " - pdb=" SG CYS D 134 " pdb=" ZN E 602 " pdb="ZN ZN E 602 " - pdb=" NE2 HIS E 79 " pdb="ZN ZN E 602 " - pdb=" SG CYS E 141 " pdb="ZN ZN E 602 " - pdb=" SG CYS E 134 " pdb=" ZN F 602 " pdb="ZN ZN F 602 " - pdb=" NE2 HIS F 79 " pdb="ZN ZN F 602 " - pdb=" SG CYS F 141 " pdb="ZN ZN F 602 " - pdb=" SG CYS F 134 " pdb=" ZN G 602 " pdb="ZN ZN G 602 " - pdb=" NE2 HIS G 79 " pdb="ZN ZN G 602 " - pdb=" SG CYS G 141 " pdb="ZN ZN G 602 " - pdb=" SG CYS G 134 " pdb=" ZN H 602 " pdb="ZN ZN H 602 " - pdb=" NE2 HIS H 79 " pdb="ZN ZN H 602 " - pdb=" SG CYS H 141 " pdb="ZN ZN H 602 " - pdb=" SG CYS H 134 " pdb=" ZN I 602 " pdb="ZN ZN I 602 " - pdb=" NE2 HIS I 79 " pdb="ZN ZN I 602 " - pdb=" SG CYS I 141 " pdb="ZN ZN I 602 " - pdb=" SG CYS I 134 " pdb=" ZN J 602 " pdb="ZN ZN J 602 " - pdb=" NE2 HIS J 79 " pdb="ZN ZN J 602 " - pdb=" SG CYS J 141 " pdb="ZN ZN J 602 " - pdb=" SG CYS J 134 " pdb=" ZN K 602 " pdb="ZN ZN K 602 " - pdb=" NE2 HIS K 79 " pdb="ZN ZN K 602 " - pdb=" SG CYS K 141 " pdb="ZN ZN K 602 " - pdb=" SG CYS K 134 " pdb=" ZN L 602 " pdb="ZN ZN L 602 " - pdb=" NE2 HIS L 79 " pdb="ZN ZN L 602 " - pdb=" SG CYS L 141 " pdb="ZN ZN L 602 " - pdb=" SG CYS L 134 " 10752 Ramachandran restraints generated. 5376 Oldfield, 0 Emsley, 5376 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10368 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 180 helices and 60 sheets defined 30.6% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.57 Creating SS restraints... Processing helix chain 'A' and resid 13 through 21 removed outlier: 3.701A pdb=" N LYS A 16 " --> pdb=" O ALA A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 54 removed outlier: 3.541A pdb=" N LYS A 49 " --> pdb=" O HIS A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 71 Processing helix chain 'A' and resid 89 through 101 Processing helix chain 'A' and resid 112 through 124 Processing helix chain 'A' and resid 158 through 168 removed outlier: 4.035A 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: 3.937A 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 402 Proline residue: A 385 - end of helix removed outlier: 3.629A pdb=" N ALA A 388 " --> pdb=" O PRO A 385 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN A 389 " --> pdb=" O VAL A 386 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS A 393 " --> pdb=" O ALA A 390 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA A 395 " --> pdb=" O SER A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 472 Processing helix chain 'B' and resid 13 through 21 removed outlier: 3.716A pdb=" N LYS B 16 " --> pdb=" O ALA B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 54 removed outlier: 3.547A pdb=" N LYS B 49 " --> pdb=" O HIS B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 71 Processing helix chain 'B' and resid 89 through 101 Processing helix chain 'B' and resid 112 through 124 Processing helix chain 'B' and resid 158 through 168 removed outlier: 4.119A 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: 3.932A pdb=" N TRP B 258 " --> pdb=" O LEU B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 342 removed outlier: 3.518A pdb=" N MET B 342 " --> pdb=" O ILE B 338 " (cutoff:3.500A) 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 402 Proline residue: B 385 - end of helix removed outlier: 3.582A pdb=" N ALA B 388 " --> pdb=" O PRO B 385 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN B 389 " --> pdb=" O VAL B 386 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS B 393 " --> pdb=" O ALA B 390 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA B 395 " --> pdb=" O SER B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 472 Processing helix chain 'C' and resid 13 through 21 removed outlier: 3.712A pdb=" N LYS C 16 " --> pdb=" O ALA C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 54 removed outlier: 3.589A pdb=" N LYS C 49 " --> pdb=" O HIS C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 71 Processing helix chain 'C' and resid 89 through 101 Processing helix chain 'C' and resid 112 through 124 Processing helix chain 'C' and resid 158 through 168 removed outlier: 4.168A 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: 3.967A pdb=" N TRP C 258 " --> pdb=" O LEU C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 342 removed outlier: 3.535A pdb=" N MET C 342 " --> pdb=" O ILE C 338 " (cutoff:3.500A) 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 402 Proline residue: C 385 - end of helix removed outlier: 3.526A pdb=" N ALA C 388 " --> pdb=" O PRO C 385 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN C 389 " --> pdb=" O VAL C 386 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA C 395 " --> pdb=" O SER C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 472 Processing helix chain 'D' and resid 13 through 21 removed outlier: 3.705A pdb=" N LYS D 16 " --> pdb=" O ALA D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 54 removed outlier: 3.542A pdb=" N LYS D 49 " --> pdb=" O HIS D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 71 Processing helix chain 'D' and resid 89 through 101 Processing helix chain 'D' and resid 112 through 124 Processing helix chain 'D' and resid 158 through 168 removed outlier: 4.035A 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: 3.930A pdb=" N TRP D 258 " --> pdb=" O LEU D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 342 removed outlier: 3.515A pdb=" N MET D 342 " --> pdb=" O ILE D 338 " (cutoff:3.500A) 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 402 Proline residue: D 385 - end of helix removed outlier: 3.628A pdb=" N ALA D 388 " --> pdb=" O PRO D 385 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN D 389 " --> pdb=" O VAL D 386 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS D 393 " --> pdb=" O ALA D 390 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA D 395 " --> pdb=" O SER D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 472 Processing helix chain 'E' and resid 13 through 21 removed outlier: 3.766A pdb=" N LYS E 16 " --> pdb=" O ALA E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 54 removed outlier: 3.547A pdb=" N LYS E 49 " --> pdb=" O HIS E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 71 Processing helix chain 'E' and resid 89 through 101 Processing helix chain 'E' and resid 112 through 124 Processing helix chain 'E' and resid 158 through 168 removed outlier: 4.117A 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: 3.931A pdb=" N TRP E 258 " --> pdb=" O LEU E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 342 removed outlier: 3.516A pdb=" N MET E 342 " --> pdb=" O ILE E 338 " (cutoff:3.500A) 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 402 Proline residue: E 385 - end of helix removed outlier: 3.580A pdb=" N ALA E 388 " --> pdb=" O PRO E 385 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN E 389 " --> pdb=" O VAL E 386 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS E 393 " --> pdb=" O ALA E 390 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA E 395 " --> pdb=" O SER E 392 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 472 Processing helix chain 'F' and resid 13 through 21 removed outlier: 3.712A pdb=" N LYS F 16 " --> pdb=" O ALA F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 54 removed outlier: 3.593A pdb=" N LYS F 49 " --> pdb=" O HIS F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 71 Processing helix chain 'F' and resid 89 through 101 Processing helix chain 'F' and resid 112 through 124 Processing helix chain 'F' and resid 158 through 168 removed outlier: 4.164A 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: 3.967A pdb=" N TRP F 258 " --> pdb=" O LEU F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 342 removed outlier: 3.537A pdb=" N MET F 342 " --> pdb=" O ILE F 338 " (cutoff:3.500A) 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 402 Proline residue: F 385 - end of helix removed outlier: 3.519A pdb=" N ALA F 388 " --> pdb=" O PRO F 385 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN F 389 " --> pdb=" O VAL F 386 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA F 395 " --> pdb=" O SER F 392 " (cutoff:3.500A) Processing helix chain 'F' and resid 462 through 472 Processing helix chain 'G' and resid 13 through 21 removed outlier: 3.704A pdb=" N LYS G 16 " --> pdb=" O ALA G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 54 removed outlier: 3.540A pdb=" N LYS G 49 " --> pdb=" O HIS G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 71 Processing helix chain 'G' and resid 89 through 101 Processing helix chain 'G' and resid 112 through 124 Processing helix chain 'G' and resid 158 through 168 removed outlier: 4.029A 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: 3.935A 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 402 Proline residue: G 385 - end of helix removed outlier: 3.625A pdb=" N ALA G 388 " --> pdb=" O PRO G 385 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN G 389 " --> pdb=" O VAL G 386 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS G 393 " --> pdb=" O ALA G 390 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA G 395 " --> pdb=" O SER G 392 " (cutoff:3.500A) Processing helix chain 'G' and resid 462 through 472 Processing helix chain 'H' and resid 13 through 21 removed outlier: 3.734A pdb=" N LYS H 16 " --> pdb=" O ALA H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 54 removed outlier: 3.549A pdb=" N LYS H 49 " --> pdb=" O HIS H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 71 Processing helix chain 'H' and resid 89 through 101 Processing helix chain 'H' and resid 112 through 124 Processing helix chain 'H' and resid 158 through 168 removed outlier: 4.115A 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: 3.933A pdb=" N TRP H 258 " --> pdb=" O LEU H 254 " (cutoff:3.500A) Processing helix chain 'H' and resid 336 through 342 removed outlier: 3.519A pdb=" N MET H 342 " --> pdb=" O ILE H 338 " (cutoff:3.500A) 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 402 Proline residue: H 385 - end of helix removed outlier: 3.567A pdb=" N ALA H 388 " --> pdb=" O PRO H 385 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN H 389 " --> pdb=" O VAL H 386 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS H 393 " --> pdb=" O ALA H 390 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA H 395 " --> pdb=" O SER H 392 " (cutoff:3.500A) Processing helix chain 'H' and resid 462 through 472 Processing helix chain 'I' and resid 13 through 21 removed outlier: 3.716A pdb=" N LYS I 16 " --> pdb=" O ALA I 13 " (cutoff:3.500A) Processing helix chain 'I' and resid 38 through 54 removed outlier: 3.591A pdb=" N LYS I 49 " --> pdb=" O HIS I 45 " (cutoff:3.500A) Processing helix chain 'I' and resid 68 through 71 Processing helix chain 'I' and resid 89 through 101 Processing helix chain 'I' and resid 112 through 124 Processing helix chain 'I' and resid 158 through 168 removed outlier: 4.167A 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: 3.969A pdb=" N TRP I 258 " --> pdb=" O LEU I 254 " (cutoff:3.500A) Processing helix chain 'I' and resid 336 through 342 removed outlier: 3.534A pdb=" N MET I 342 " --> pdb=" O ILE I 338 " (cutoff:3.500A) 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 402 Proline residue: I 385 - end of helix removed outlier: 3.517A pdb=" N ALA I 388 " --> pdb=" O PRO I 385 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN I 389 " --> pdb=" O VAL I 386 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA I 395 " --> pdb=" O SER I 392 " (cutoff:3.500A) Processing helix chain 'I' and resid 462 through 472 Processing helix chain 'J' and resid 13 through 21 removed outlier: 3.701A pdb=" N LYS J 16 " --> pdb=" O ALA J 13 " (cutoff:3.500A) Processing helix chain 'J' and resid 38 through 54 removed outlier: 3.539A pdb=" N LYS J 49 " --> pdb=" O HIS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 68 through 71 Processing helix chain 'J' and resid 89 through 101 Processing helix chain 'J' and resid 112 through 124 Processing helix chain 'J' and resid 158 through 168 removed outlier: 4.031A 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: 3.936A 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 402 Proline residue: J 385 - end of helix removed outlier: 3.625A pdb=" N ALA J 388 " --> pdb=" O PRO J 385 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN J 389 " --> pdb=" O VAL J 386 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS J 393 " --> pdb=" O ALA J 390 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA J 395 " --> pdb=" O SER J 392 " (cutoff:3.500A) Processing helix chain 'J' and resid 462 through 472 Processing helix chain 'K' and resid 13 through 21 removed outlier: 3.713A pdb=" N LYS K 16 " --> pdb=" O ALA K 13 " (cutoff:3.500A) Processing helix chain 'K' and resid 38 through 54 removed outlier: 3.549A pdb=" N LYS K 49 " --> pdb=" O HIS K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 68 through 71 Processing helix chain 'K' and resid 89 through 101 Processing helix chain 'K' and resid 112 through 124 Processing helix chain 'K' and resid 158 through 168 removed outlier: 4.121A 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: 3.934A pdb=" N TRP K 258 " --> pdb=" O LEU K 254 " (cutoff:3.500A) Processing helix chain 'K' and resid 336 through 342 removed outlier: 3.527A pdb=" N MET K 342 " --> pdb=" O ILE K 338 " (cutoff:3.500A) 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 402 Proline residue: K 385 - end of helix removed outlier: 3.583A pdb=" N ALA K 388 " --> pdb=" O PRO K 385 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN K 389 " --> pdb=" O VAL K 386 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS K 393 " --> pdb=" O ALA K 390 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA K 395 " --> pdb=" O SER K 392 " (cutoff:3.500A) Processing helix chain 'K' and resid 462 through 472 Processing helix chain 'L' and resid 13 through 21 removed outlier: 3.716A pdb=" N LYS L 16 " --> pdb=" O ALA L 13 " (cutoff:3.500A) Processing helix chain 'L' and resid 38 through 54 removed outlier: 3.585A pdb=" N LYS L 49 " --> pdb=" O HIS L 45 " (cutoff:3.500A) Processing helix chain 'L' and resid 68 through 71 Processing helix chain 'L' and resid 89 through 101 Processing helix chain 'L' and resid 112 through 124 Processing helix chain 'L' and resid 158 through 168 removed outlier: 4.182A 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: 3.968A pdb=" N TRP L 258 " --> pdb=" O LEU L 254 " (cutoff:3.500A) Processing helix chain 'L' and resid 336 through 342 removed outlier: 3.544A pdb=" N MET L 342 " --> pdb=" O ILE L 338 " (cutoff:3.500A) 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 402 Proline residue: L 385 - end of helix removed outlier: 3.527A pdb=" N ALA L 388 " --> pdb=" O PRO L 385 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN L 389 " --> pdb=" O VAL L 386 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA L 395 " --> pdb=" O SER L 392 " (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: 6.090A pdb=" N GLU A 26 " --> pdb=" O VAL A 4 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N VAL A 6 " --> pdb=" O GLU A 26 " (cutoff:3.500A) removed outlier: 6.464A 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: 6.731A pdb=" N VAL A 147 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ILE A 64 " --> pdb=" O VAL A 147 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE A 149 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU A 172 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N TYR A 150 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TYR A 174 " --> pdb=" O TYR A 150 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL A 280 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ARG A 289 " --> pdb=" O THR A 278 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N THR A 278 " --> pdb=" O ARG A 289 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N THR A 291 " --> pdb=" O CYS A 276 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N CYS A 276 " --> pdb=" O THR A 291 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N SER A 293 " --> pdb=" O CYS A 274 " (cutoff:3.500A) removed outlier: 5.452A 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 Processing sheet with id= D, first strand: chain 'A' and resid 303 through 308 removed outlier: 4.070A pdb=" N THR A 437 " --> pdb=" O HIS A 308 " (cutoff:3.500A) 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: 6.073A pdb=" N GLU B 26 " --> pdb=" O VAL B 4 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N VAL B 6 " --> pdb=" O GLU B 26 " (cutoff:3.500A) removed outlier: 6.495A 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: 6.742A pdb=" N VAL B 147 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ILE B 64 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE B 149 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU B 172 " --> pdb=" O ALA B 148 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N TYR B 150 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N TYR B 174 " --> pdb=" O TYR B 150 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL B 280 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ARG B 289 " --> pdb=" O THR B 278 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N THR B 278 " --> pdb=" O ARG B 289 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N THR B 291 " --> pdb=" O CYS B 276 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N CYS B 276 " --> pdb=" O THR B 291 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N SER B 293 " --> pdb=" O CYS B 274 " (cutoff:3.500A) removed outlier: 5.429A 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 Processing sheet with id= I, first strand: chain 'B' and resid 303 through 308 removed outlier: 3.983A pdb=" N THR B 437 " --> pdb=" O HIS B 308 " (cutoff:3.500A) 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: 6.156A pdb=" N GLU C 26 " --> pdb=" O VAL C 4 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N VAL C 6 " --> pdb=" O GLU C 26 " (cutoff:3.500A) removed outlier: 6.499A 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: 6.746A pdb=" N VAL C 147 " --> pdb=" O LEU C 62 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ILE C 64 " --> pdb=" O VAL C 147 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE C 149 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU C 172 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N TYR C 150 " --> pdb=" O LEU C 172 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N TYR C 174 " --> pdb=" O TYR C 150 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY C 177 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL C 280 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ARG C 289 " --> pdb=" O THR C 278 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N THR C 278 " --> pdb=" O ARG C 289 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N THR C 291 " --> pdb=" O CYS C 276 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N CYS C 276 " --> pdb=" O THR C 291 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N SER C 293 " --> pdb=" O CYS C 274 " (cutoff:3.500A) removed outlier: 5.481A 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 Processing sheet with id= N, first strand: chain 'C' and resid 303 through 308 removed outlier: 4.085A pdb=" N THR C 437 " --> pdb=" O HIS C 308 " (cutoff:3.500A) 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: 6.092A pdb=" N GLU D 26 " --> pdb=" O VAL D 4 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N VAL D 6 " --> pdb=" O GLU D 26 " (cutoff:3.500A) removed outlier: 6.466A 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: 6.730A pdb=" N VAL D 147 " --> pdb=" O LEU D 62 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ILE D 64 " --> pdb=" O VAL D 147 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE D 149 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU D 172 " --> pdb=" O ALA D 148 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N TYR D 150 " --> pdb=" O LEU D 172 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TYR D 174 " --> pdb=" O TYR D 150 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL D 280 " --> pdb=" O VAL D 287 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ARG D 289 " --> pdb=" O THR D 278 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N THR D 278 " --> pdb=" O ARG D 289 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N THR D 291 " --> pdb=" O CYS D 276 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N CYS D 276 " --> pdb=" O THR D 291 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N SER D 293 " --> pdb=" O CYS D 274 " (cutoff:3.500A) removed outlier: 5.450A 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 Processing sheet with id= S, first strand: chain 'D' and resid 303 through 308 removed outlier: 4.068A pdb=" N THR D 437 " --> pdb=" O HIS D 308 " (cutoff:3.500A) 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: 6.072A pdb=" N GLU E 26 " --> pdb=" O VAL E 4 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N VAL E 6 " --> pdb=" O GLU E 26 " (cutoff:3.500A) removed outlier: 6.491A 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: 6.739A pdb=" N VAL E 147 " --> pdb=" O LEU E 62 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ILE E 64 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE E 149 " --> pdb=" O ILE E 64 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU E 172 " --> pdb=" O ALA E 148 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N TYR E 150 " --> pdb=" O LEU E 172 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N TYR E 174 " --> pdb=" O TYR E 150 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL E 280 " --> pdb=" O VAL E 287 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ARG E 289 " --> pdb=" O THR E 278 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N THR E 278 " --> pdb=" O ARG E 289 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N THR E 291 " --> pdb=" O CYS E 276 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N CYS E 276 " --> pdb=" O THR E 291 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N SER E 293 " --> pdb=" O CYS E 274 " (cutoff:3.500A) removed outlier: 5.433A 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 Processing sheet with id= X, first strand: chain 'E' and resid 303 through 308 removed outlier: 3.981A pdb=" N THR E 437 " --> pdb=" O HIS E 308 " (cutoff:3.500A) 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: 6.157A pdb=" N GLU F 26 " --> pdb=" O VAL F 4 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N VAL F 6 " --> pdb=" O GLU F 26 " (cutoff:3.500A) removed outlier: 6.501A 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: 6.742A pdb=" N VAL F 147 " --> pdb=" O LEU F 62 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ILE F 64 " --> pdb=" O VAL F 147 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE F 149 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU F 172 " --> pdb=" O ALA F 148 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N TYR F 150 " --> pdb=" O LEU F 172 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N TYR F 174 " --> pdb=" O TYR F 150 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY F 177 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL F 280 " --> pdb=" O VAL F 287 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ARG F 289 " --> pdb=" O THR F 278 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N THR F 278 " --> pdb=" O ARG F 289 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N THR F 291 " --> pdb=" O CYS F 276 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N CYS F 276 " --> pdb=" O THR F 291 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N SER F 293 " --> pdb=" O CYS F 274 " (cutoff:3.500A) removed outlier: 5.484A 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 Processing sheet with id= AC, first strand: chain 'F' and resid 303 through 308 removed outlier: 4.086A pdb=" N THR F 437 " --> pdb=" O HIS F 308 " (cutoff:3.500A) 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: 6.104A pdb=" N GLU G 26 " --> pdb=" O VAL G 4 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N VAL G 6 " --> pdb=" O GLU G 26 " (cutoff:3.500A) removed outlier: 6.463A 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: 6.724A pdb=" N VAL G 147 " --> pdb=" O LEU G 62 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ILE G 64 " --> pdb=" O VAL G 147 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE G 149 " --> pdb=" O ILE G 64 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU G 172 " --> pdb=" O ALA G 148 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N TYR G 150 " --> pdb=" O LEU G 172 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N TYR G 174 " --> pdb=" O TYR G 150 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL G 280 " --> pdb=" O VAL G 287 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ARG G 289 " --> pdb=" O THR G 278 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N THR G 278 " --> pdb=" O ARG G 289 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N THR G 291 " --> pdb=" O CYS G 276 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N CYS G 276 " --> pdb=" O THR G 291 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N SER G 293 " --> pdb=" O CYS G 274 " (cutoff:3.500A) removed outlier: 5.449A 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 Processing sheet with id= AH, first strand: chain 'G' and resid 303 through 308 removed outlier: 4.054A pdb=" N THR G 437 " --> pdb=" O HIS G 308 " (cutoff:3.500A) 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: 6.076A pdb=" N GLU H 26 " --> pdb=" O VAL H 4 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N VAL H 6 " --> pdb=" O GLU H 26 " (cutoff:3.500A) removed outlier: 6.497A 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: 6.740A pdb=" N VAL H 147 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ILE H 64 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE H 149 " --> pdb=" O ILE H 64 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU H 172 " --> pdb=" O ALA H 148 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N TYR H 150 " --> pdb=" O LEU H 172 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N TYR H 174 " --> pdb=" O TYR H 150 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL H 280 " --> pdb=" O VAL H 287 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ARG H 289 " --> pdb=" O THR H 278 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N THR H 278 " --> pdb=" O ARG H 289 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N THR H 291 " --> pdb=" O CYS H 276 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N CYS H 276 " --> pdb=" O THR H 291 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N SER H 293 " --> pdb=" O CYS H 274 " (cutoff:3.500A) removed outlier: 5.432A 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 Processing sheet with id= AM, first strand: chain 'H' and resid 303 through 308 removed outlier: 3.984A pdb=" N THR H 437 " --> pdb=" O HIS H 308 " (cutoff:3.500A) 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: 6.152A pdb=" N GLU I 26 " --> pdb=" O VAL I 4 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N VAL I 6 " --> pdb=" O GLU I 26 " (cutoff:3.500A) removed outlier: 6.498A 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: 6.751A pdb=" N VAL I 147 " --> pdb=" O LEU I 62 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ILE I 64 " --> pdb=" O VAL I 147 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE I 149 " --> pdb=" O ILE I 64 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU I 172 " --> pdb=" O ALA I 148 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N TYR I 150 " --> pdb=" O LEU I 172 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N TYR I 174 " --> pdb=" O TYR I 150 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY I 177 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL I 280 " --> pdb=" O VAL I 287 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ARG I 289 " --> pdb=" O THR I 278 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N THR I 278 " --> pdb=" O ARG I 289 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N THR I 291 " --> pdb=" O CYS I 276 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N CYS I 276 " --> pdb=" O THR I 291 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N SER I 293 " --> pdb=" O CYS I 274 " (cutoff:3.500A) removed outlier: 5.475A 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 Processing sheet with id= AR, first strand: chain 'I' and resid 303 through 308 removed outlier: 4.083A pdb=" N THR I 437 " --> pdb=" O HIS I 308 " (cutoff:3.500A) 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: 6.105A pdb=" N GLU J 26 " --> pdb=" O VAL J 4 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N VAL J 6 " --> pdb=" O GLU J 26 " (cutoff:3.500A) removed outlier: 6.462A 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: 6.723A pdb=" N VAL J 147 " --> pdb=" O LEU J 62 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ILE J 64 " --> pdb=" O VAL J 147 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE J 149 " --> pdb=" O ILE J 64 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU J 172 " --> pdb=" O ALA J 148 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N TYR J 150 " --> pdb=" O LEU J 172 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N TYR J 174 " --> pdb=" O TYR J 150 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL J 280 " --> pdb=" O VAL J 287 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ARG J 289 " --> pdb=" O THR J 278 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N THR J 278 " --> pdb=" O ARG J 289 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N THR J 291 " --> pdb=" O CYS J 276 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N CYS J 276 " --> pdb=" O THR J 291 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N SER J 293 " --> pdb=" O CYS J 274 " (cutoff:3.500A) removed outlier: 5.449A 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 Processing sheet with id= AW, first strand: chain 'J' and resid 303 through 308 removed outlier: 4.054A pdb=" N THR J 437 " --> pdb=" O HIS J 308 " (cutoff:3.500A) 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: 6.078A pdb=" N GLU K 26 " --> pdb=" O VAL K 4 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N VAL K 6 " --> pdb=" O GLU K 26 " (cutoff:3.500A) removed outlier: 6.492A 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: 6.740A pdb=" N VAL K 147 " --> pdb=" O LEU K 62 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ILE K 64 " --> pdb=" O VAL K 147 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE K 149 " --> pdb=" O ILE K 64 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU K 172 " --> pdb=" O ALA K 148 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N TYR K 150 " --> pdb=" O LEU K 172 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N TYR K 174 " --> pdb=" O TYR K 150 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL K 280 " --> pdb=" O VAL K 287 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ARG K 289 " --> pdb=" O THR K 278 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N THR K 278 " --> pdb=" O ARG K 289 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N THR K 291 " --> pdb=" O CYS K 276 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N CYS K 276 " --> pdb=" O THR K 291 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N SER K 293 " --> pdb=" O CYS K 274 " (cutoff:3.500A) removed outlier: 5.431A 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 Processing sheet with id= BB, first strand: chain 'K' and resid 303 through 308 removed outlier: 3.984A pdb=" N THR K 437 " --> pdb=" O HIS K 308 " (cutoff:3.500A) 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: 6.153A pdb=" N GLU L 26 " --> pdb=" O VAL L 4 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N VAL L 6 " --> pdb=" O GLU L 26 " (cutoff:3.500A) removed outlier: 6.496A 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: 6.745A pdb=" N VAL L 147 " --> pdb=" O LEU L 62 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ILE L 64 " --> pdb=" O VAL L 147 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE L 149 " --> pdb=" O ILE L 64 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU L 172 " --> pdb=" O ALA L 148 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N TYR L 150 " --> pdb=" O LEU L 172 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N TYR L 174 " --> pdb=" O TYR L 150 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY L 177 " --> pdb=" O VAL L 286 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL L 280 " --> pdb=" O VAL L 287 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG L 289 " --> pdb=" O THR L 278 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N THR L 278 " --> pdb=" O ARG L 289 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N THR L 291 " --> pdb=" O CYS L 276 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N CYS L 276 " --> pdb=" O THR L 291 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N SER L 293 " --> pdb=" O CYS L 274 " (cutoff:3.500A) removed outlier: 5.476A 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 Processing sheet with id= BG, first strand: chain 'L' and resid 303 through 308 removed outlier: 4.082A pdb=" N THR L 437 " --> pdb=" O HIS L 308 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'L' and resid 324 through 334 1503 hydrogen bonds defined for protein. 3669 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 17.51 Time building geometry restraints manager: 18.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13912 1.34 - 1.46: 8300 1.46 - 1.58: 21876 1.58 - 1.69: 96 1.69 - 1.81: 528 Bond restraints: 44712 Sorted by residual: bond pdb=" O8 YG4 G 604 " pdb=" P1 YG4 G 604 " ideal model delta sigma weight residual 1.656 1.599 0.057 2.00e-02 2.50e+03 8.09e+00 bond pdb=" O8 YG4 E 604 " pdb=" P1 YG4 E 604 " ideal model delta sigma weight residual 1.656 1.599 0.057 2.00e-02 2.50e+03 8.07e+00 bond pdb=" O8 YG4 B 604 " pdb=" P1 YG4 B 604 " ideal model delta sigma weight residual 1.656 1.600 0.056 2.00e-02 2.50e+03 7.97e+00 bond pdb=" O8 YG4 K 604 " pdb=" P1 YG4 K 604 " ideal model delta sigma weight residual 1.656 1.600 0.056 2.00e-02 2.50e+03 7.96e+00 bond pdb=" O8 YG4 J 604 " pdb=" P1 YG4 J 604 " ideal model delta sigma weight residual 1.656 1.600 0.056 2.00e-02 2.50e+03 7.95e+00 ... (remaining 44707 not shown) Histogram of bond angle deviations from ideal: 90.53 - 99.24: 24 99.24 - 107.94: 2233 107.94 - 116.65: 29749 116.65 - 125.35: 27855 125.35 - 134.06: 955 Bond angle restraints: 60816 Sorted by residual: angle pdb=" CG SAH B 603 " pdb=" SD SAH B 603 " pdb=" C5' SAH B 603 " ideal model delta sigma weight residual 101.77 90.53 11.24 3.00e+00 1.11e-01 1.40e+01 angle pdb=" CG SAH E 603 " pdb=" SD SAH E 603 " pdb=" C5' SAH E 603 " ideal model delta sigma weight residual 101.77 90.55 11.22 3.00e+00 1.11e-01 1.40e+01 angle pdb=" CG SAH H 603 " pdb=" SD SAH H 603 " pdb=" C5' SAH H 603 " ideal model delta sigma weight residual 101.77 90.55 11.22 3.00e+00 1.11e-01 1.40e+01 angle pdb=" CG SAH K 603 " pdb=" SD SAH K 603 " pdb=" C5' SAH K 603 " ideal model delta sigma weight residual 101.77 90.56 11.21 3.00e+00 1.11e-01 1.40e+01 angle pdb=" CG SAH F 603 " pdb=" SD SAH F 603 " pdb=" C5' SAH F 603 " ideal model delta sigma weight residual 101.77 90.56 11.21 3.00e+00 1.11e-01 1.40e+01 ... (remaining 60811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.00: 26157 34.00 - 68.00: 1234 68.00 - 102.00: 209 102.00 - 136.00: 8 136.00 - 170.00: 16 Dihedral angle restraints: 27624 sinusoidal: 11628 harmonic: 15996 Sorted by residual: dihedral pdb=" C14 YG4 L 604 " pdb=" O16 YG4 L 604 " pdb=" P4 YG4 L 604 " pdb=" O18 YG4 L 604 " ideal model delta sinusoidal sigma weight residual 184.82 14.82 170.00 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C14 YG4 F 604 " pdb=" O16 YG4 F 604 " pdb=" P4 YG4 F 604 " pdb=" O18 YG4 F 604 " ideal model delta sinusoidal sigma weight residual 184.82 14.87 169.95 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C14 YG4 C 604 " pdb=" O16 YG4 C 604 " pdb=" P4 YG4 C 604 " pdb=" O18 YG4 C 604 " ideal model delta sinusoidal sigma weight residual 184.82 14.91 169.91 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 27621 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 5940 0.064 - 0.128: 845 0.128 - 0.192: 31 0.192 - 0.257: 24 0.257 - 0.321: 12 Chirality restraints: 6852 Sorted by residual: chirality pdb=" C16 YG4 A1003 " pdb=" C15 YG4 A1003 " pdb=" N6 YG4 A1003 " pdb=" O15 YG4 A1003 " both_signs ideal model delta sigma weight residual False 2.46 2.14 0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" C16 YG4 D 604 " pdb=" C15 YG4 D 604 " pdb=" N6 YG4 D 604 " pdb=" O15 YG4 D 604 " both_signs ideal model delta sigma weight residual False 2.46 2.14 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" C16 YG4 G 604 " pdb=" C15 YG4 G 604 " pdb=" N6 YG4 G 604 " pdb=" O15 YG4 G 604 " both_signs ideal model delta sigma weight residual False 2.46 2.15 0.32 2.00e-01 2.50e+01 2.53e+00 ... (remaining 6849 not shown) Planarity restraints: 7548 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C27 YG4 F 604 " -0.056 2.00e-02 2.50e+03 2.67e-02 1.60e+01 pdb=" C28 YG4 F 604 " 0.006 2.00e-02 2.50e+03 pdb=" C29 YG4 F 604 " -0.006 2.00e-02 2.50e+03 pdb=" C30 YG4 F 604 " 0.017 2.00e-02 2.50e+03 pdb=" C31 YG4 F 604 " 0.032 2.00e-02 2.50e+03 pdb=" N11 YG4 F 604 " 0.016 2.00e-02 2.50e+03 pdb=" N12 YG4 F 604 " -0.011 2.00e-02 2.50e+03 pdb=" O24 YG4 F 604 " 0.028 2.00e-02 2.50e+03 pdb=" O25 YG4 F 604 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C27 YG4 L 604 " 0.056 2.00e-02 2.50e+03 2.66e-02 1.60e+01 pdb=" C28 YG4 L 604 " -0.006 2.00e-02 2.50e+03 pdb=" C29 YG4 L 604 " 0.006 2.00e-02 2.50e+03 pdb=" C30 YG4 L 604 " -0.016 2.00e-02 2.50e+03 pdb=" C31 YG4 L 604 " -0.032 2.00e-02 2.50e+03 pdb=" N11 YG4 L 604 " -0.017 2.00e-02 2.50e+03 pdb=" N12 YG4 L 604 " 0.011 2.00e-02 2.50e+03 pdb=" O24 YG4 L 604 " -0.028 2.00e-02 2.50e+03 pdb=" O25 YG4 L 604 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C27 YG4 C 604 " 0.056 2.00e-02 2.50e+03 2.66e-02 1.59e+01 pdb=" C28 YG4 C 604 " -0.006 2.00e-02 2.50e+03 pdb=" C29 YG4 C 604 " 0.005 2.00e-02 2.50e+03 pdb=" C30 YG4 C 604 " -0.016 2.00e-02 2.50e+03 pdb=" C31 YG4 C 604 " -0.032 2.00e-02 2.50e+03 pdb=" N11 YG4 C 604 " -0.016 2.00e-02 2.50e+03 pdb=" N12 YG4 C 604 " 0.011 2.00e-02 2.50e+03 pdb=" O24 YG4 C 604 " -0.028 2.00e-02 2.50e+03 pdb=" O25 YG4 C 604 " 0.026 2.00e-02 2.50e+03 ... (remaining 7545 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 304 2.60 - 3.17: 33137 3.17 - 3.75: 62739 3.75 - 4.32: 96913 4.32 - 4.90: 156469 Nonbonded interactions: 349562 Sorted by model distance: nonbonded pdb="MG MG H 601 " pdb=" O HOH G 703 " model vdw 2.023 2.170 nonbonded pdb="MG MG E 601 " pdb=" O HOH D 703 " model vdw 2.025 2.170 nonbonded pdb="MG MG B 601 " pdb=" O HOH A1103 " model vdw 2.025 2.170 nonbonded pdb="MG MG K 601 " pdb=" O HOH J 703 " model vdw 2.025 2.170 nonbonded pdb="MG MG J 601 " pdb=" O HOH I 712 " model vdw 2.032 2.170 ... (remaining 349557 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 474)) selection = (chain 'B' and (resid 2 through 235 or resid 237 through 474)) selection = (chain 'C' and (resid 2 through 235 or resid 237 through 474)) selection = (chain 'D' and (resid 2 through 235 or resid 237 through 474)) selection = (chain 'E' and (resid 2 through 235 or resid 237 through 474)) selection = (chain 'F' and (resid 2 through 235 or resid 237 through 474)) selection = (chain 'G' and (resid 2 through 235 or resid 237 through 474)) selection = (chain 'H' and (resid 2 through 235 or resid 237 through 474)) selection = (chain 'I' and (resid 2 through 235 or resid 237 through 474)) selection = (chain 'J' and (resid 2 through 235 or resid 237 through 474)) selection = (chain 'K' and (resid 2 through 235 or resid 237 through 474)) selection = (chain 'L' and (resid 2 through 235 or resid 237 through 474)) } 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: 7.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 25.730 Check model and map are aligned: 0.660 Set scattering table: 0.380 Process input model: 146.820 Find NCS groups from input model: 3.650 Set up NCS constraints: 0.260 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: 0.020 Load rotamer database and sin/cos tables:13.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 198.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 44712 Z= 0.308 Angle : 0.750 11.236 60816 Z= 0.332 Chirality : 0.047 0.321 6852 Planarity : 0.005 0.046 7548 Dihedral : 20.044 169.999 17256 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.59 % Allowed : 20.23 % Favored : 79.18 % 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: -0.35 (0.10), residues: 5376 helix: 0.74 (0.12), residues: 1572 sheet: 0.78 (0.15), residues: 1140 loop : -1.32 (0.10), residues: 2664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 199 HIS 0.002 0.001 HIS D 259 PHE 0.010 0.001 PHE F 183 TYR 0.012 0.001 TYR L 285 ARG 0.002 0.000 ARG F 20 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10752 Ramachandran restraints generated. 5376 Oldfield, 0 Emsley, 5376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10752 Ramachandran restraints generated. 5376 Oldfield, 0 Emsley, 5376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 4668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 260 time to evaluate : 5.330 Fit side-chains outliers start: 27 outliers final: 19 residues processed: 287 average time/residue: 1.7174 time to fit residues: 601.3939 Evaluate side-chains 268 residues out of total 4668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 249 time to evaluate : 5.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 396 LYS Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 396 LYS Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain G residue 396 LYS Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 214 SER Chi-restraints excluded: chain J residue 214 SER Chi-restraints excluded: chain J residue 396 LYS Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 214 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 455 optimal weight: 8.9990 chunk 409 optimal weight: 0.8980 chunk 227 optimal weight: 5.9990 chunk 139 optimal weight: 0.8980 chunk 276 optimal weight: 0.9990 chunk 218 optimal weight: 2.9990 chunk 423 optimal weight: 0.0010 chunk 163 optimal weight: 2.9990 chunk 257 optimal weight: 0.9990 chunk 315 optimal weight: 10.0000 chunk 490 optimal weight: 0.0670 overall best weight: 0.5726 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN A 377 ASN B 95 ASN C 95 ASN D 95 ASN D 377 ASN E 95 ASN F 53 GLN F 95 ASN G 377 ASN H 95 ASN I 53 GLN I 95 ASN J 95 ASN J 377 ASN K 95 ASN L 53 GLN L 95 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.0871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 44712 Z= 0.141 Angle : 0.557 10.181 60816 Z= 0.274 Chirality : 0.042 0.175 6852 Planarity : 0.005 0.041 7548 Dihedral : 17.101 151.816 7219 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.67 % Allowed : 19.93 % Favored : 79.40 % 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: 0.14 (0.11), residues: 5376 helix: 1.59 (0.13), residues: 1572 sheet: 0.91 (0.14), residues: 1188 loop : -1.29 (0.11), residues: 2616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 470 HIS 0.004 0.001 HIS L 45 PHE 0.010 0.001 PHE F 264 TYR 0.008 0.001 TYR E 382 ARG 0.001 0.000 ARG I 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10752 Ramachandran restraints generated. 5376 Oldfield, 0 Emsley, 5376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10752 Ramachandran restraints generated. 5376 Oldfield, 0 Emsley, 5376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 4668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 259 time to evaluate : 5.393 Fit side-chains REVERT: A 441 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.7972 (mp10) REVERT: B 400 LYS cc_start: 0.8377 (ttmm) cc_final: 0.8112 (mtpt) REVERT: D 441 GLN cc_start: 0.8704 (OUTLIER) cc_final: 0.7976 (mp10) REVERT: E 364 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7663 (mt0) REVERT: E 400 LYS cc_start: 0.8375 (ttmm) cc_final: 0.8113 (mtpt) REVERT: H 364 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7693 (mt0) REVERT: K 364 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7671 (mt0) outliers start: 31 outliers final: 2 residues processed: 287 average time/residue: 1.9039 time to fit residues: 654.3159 Evaluate side-chains 259 residues out of total 4668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 252 time to evaluate : 4.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain D residue 441 GLN Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 364 GLN Chi-restraints excluded: chain H residue 364 GLN Chi-restraints excluded: chain K residue 364 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 272 optimal weight: 0.7980 chunk 152 optimal weight: 10.0000 chunk 408 optimal weight: 0.4980 chunk 333 optimal weight: 5.9990 chunk 135 optimal weight: 10.0000 chunk 491 optimal weight: 1.9990 chunk 530 optimal weight: 3.9990 chunk 437 optimal weight: 0.5980 chunk 487 optimal weight: 0.6980 chunk 167 optimal weight: 0.1980 chunk 394 optimal weight: 0.0000 overall best weight: 0.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN A 377 ASN B 95 ASN C 95 ASN D 95 ASN D 377 ASN E 95 ASN F 95 ASN G 377 ASN H 95 ASN I 95 ASN J 95 ASN J 377 ASN K 95 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 44712 Z= 0.119 Angle : 0.518 10.182 60816 Z= 0.246 Chirality : 0.041 0.222 6852 Planarity : 0.004 0.039 7548 Dihedral : 15.196 143.625 7188 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.91 % Allowed : 19.50 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.11), residues: 5376 helix: 1.83 (0.14), residues: 1584 sheet: 1.12 (0.14), residues: 1164 loop : -1.23 (0.11), residues: 2628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 470 HIS 0.002 0.000 HIS C 164 PHE 0.010 0.001 PHE C 264 TYR 0.006 0.001 TYR E 382 ARG 0.002 0.000 ARG E 411 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10752 Ramachandran restraints generated. 5376 Oldfield, 0 Emsley, 5376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10752 Ramachandran restraints generated. 5376 Oldfield, 0 Emsley, 5376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 4668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 269 time to evaluate : 5.326 Fit side-chains REVERT: B 400 LYS cc_start: 0.8335 (ttmm) cc_final: 0.8082 (mtpt) REVERT: C 285 TYR cc_start: 0.8806 (OUTLIER) cc_final: 0.6021 (m-80) REVERT: E 364 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7537 (mt0) REVERT: E 400 LYS cc_start: 0.8336 (ttmm) cc_final: 0.8076 (mtpt) REVERT: F 285 TYR cc_start: 0.8811 (OUTLIER) cc_final: 0.6026 (m-80) REVERT: H 364 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7531 (mt0) REVERT: K 364 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7545 (mt0) REVERT: L 285 TYR cc_start: 0.8872 (OUTLIER) cc_final: 0.6084 (m-80) outliers start: 42 outliers final: 12 residues processed: 308 average time/residue: 1.7921 time to fit residues: 667.4347 Evaluate side-chains 273 residues out of total 4668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 255 time to evaluate : 5.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 364 GLN Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain H residue 194 SER Chi-restraints excluded: chain H residue 364 GLN Chi-restraints excluded: chain J residue 109 ASP Chi-restraints excluded: chain J residue 232 LYS Chi-restraints excluded: chain K residue 109 ASP Chi-restraints excluded: chain K residue 194 SER Chi-restraints excluded: chain K residue 364 GLN Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain L residue 376 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 485 optimal weight: 0.9990 chunk 369 optimal weight: 1.9990 chunk 254 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 chunk 234 optimal weight: 1.9990 chunk 329 optimal weight: 0.9990 chunk 493 optimal weight: 0.0570 chunk 521 optimal weight: 0.7980 chunk 257 optimal weight: 10.0000 chunk 467 optimal weight: 4.9990 chunk 140 optimal weight: 0.0050 overall best weight: 0.5716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN A 377 ASN B 95 ASN C 95 ASN C 111 ASN C 364 GLN D 95 ASN D 377 ASN E 95 ASN F 95 ASN F 111 ASN F 364 GLN G 377 ASN H 95 ASN I 95 ASN I 111 ASN I 364 GLN J 95 ASN J 377 ASN K 95 ASN L 111 ASN L 364 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 44712 Z= 0.122 Angle : 0.521 10.121 60816 Z= 0.247 Chirality : 0.041 0.185 6852 Planarity : 0.004 0.038 7548 Dihedral : 14.405 132.208 7188 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.76 % Allowed : 19.91 % Favored : 79.33 % 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: 5376 helix: 2.10 (0.14), residues: 1572 sheet: 1.23 (0.14), residues: 1164 loop : -1.20 (0.11), residues: 2640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 470 HIS 0.002 0.000 HIS G 164 PHE 0.011 0.001 PHE L 264 TYR 0.007 0.001 TYR A 382 ARG 0.002 0.000 ARG C 110 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10752 Ramachandran restraints generated. 5376 Oldfield, 0 Emsley, 5376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10752 Ramachandran restraints generated. 5376 Oldfield, 0 Emsley, 5376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 4668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 275 time to evaluate : 5.452 Fit side-chains REVERT: B 400 LYS cc_start: 0.8300 (ttmm) cc_final: 0.8049 (mtpt) REVERT: C 285 TYR cc_start: 0.8876 (OUTLIER) cc_final: 0.6038 (m-80) REVERT: D 441 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.7767 (mp10) REVERT: E 364 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7525 (mt0) REVERT: F 285 TYR cc_start: 0.8889 (OUTLIER) cc_final: 0.5985 (m-80) REVERT: H 364 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7519 (mt0) REVERT: I 285 TYR cc_start: 0.8970 (OUTLIER) cc_final: 0.6081 (m-80) REVERT: K 364 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7525 (mt0) REVERT: L 285 TYR cc_start: 0.8946 (OUTLIER) cc_final: 0.6112 (m-80) outliers start: 35 outliers final: 9 residues processed: 303 average time/residue: 1.7958 time to fit residues: 659.4138 Evaluate side-chains 272 residues out of total 4668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 255 time to evaluate : 4.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain D residue 441 GLN Chi-restraints excluded: chain E residue 364 GLN Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 364 GLN Chi-restraints excluded: chain H residue 194 SER Chi-restraints excluded: chain H residue 364 GLN Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain J residue 109 ASP Chi-restraints excluded: chain K residue 109 ASP Chi-restraints excluded: chain K residue 194 SER Chi-restraints excluded: chain K residue 364 GLN Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain L residue 376 THR 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: 0.0030 chunk 7 optimal weight: 0.7980 chunk 388 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 445 optimal weight: 0.9990 chunk 360 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 266 optimal weight: 0.9980 chunk 468 optimal weight: 0.5980 chunk 131 optimal weight: 0.6980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN A 377 ASN B 95 ASN C 95 ASN C 364 GLN D 95 ASN D 377 ASN E 95 ASN F 95 ASN G 377 ASN H 95 ASN I 95 ASN I 364 GLN J 95 ASN J 377 ASN K 95 ASN L 364 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 44712 Z= 0.122 Angle : 0.516 10.116 60816 Z= 0.245 Chirality : 0.041 0.169 6852 Planarity : 0.004 0.038 7548 Dihedral : 13.953 129.571 7188 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.59 % Allowed : 20.37 % Favored : 79.05 % 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: 0.61 (0.11), residues: 5376 helix: 2.17 (0.14), residues: 1572 sheet: 1.29 (0.14), residues: 1164 loop : -1.18 (0.11), residues: 2640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 470 HIS 0.002 0.000 HIS J 164 PHE 0.010 0.001 PHE I 264 TYR 0.007 0.001 TYR A 382 ARG 0.001 0.000 ARG H 411 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10752 Ramachandran restraints generated. 5376 Oldfield, 0 Emsley, 5376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10752 Ramachandran restraints generated. 5376 Oldfield, 0 Emsley, 5376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 4668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 259 time to evaluate : 5.002 Fit side-chains REVERT: B 123 MET cc_start: 0.8180 (mmp) cc_final: 0.7539 (mmp) REVERT: C 285 TYR cc_start: 0.8909 (OUTLIER) cc_final: 0.6008 (m-80) REVERT: C 364 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7541 (mt0) REVERT: E 364 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7506 (mt0) REVERT: F 285 TYR cc_start: 0.8921 (OUTLIER) cc_final: 0.6022 (m-80) REVERT: H 364 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7503 (mt0) REVERT: I 285 TYR cc_start: 0.9012 (OUTLIER) cc_final: 0.6175 (m-80) REVERT: K 364 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7534 (mt0) REVERT: L 285 TYR cc_start: 0.8957 (OUTLIER) cc_final: 0.6126 (m-80) REVERT: L 364 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7556 (mt0) outliers start: 27 outliers final: 6 residues processed: 280 average time/residue: 1.7276 time to fit residues: 588.3530 Evaluate side-chains 266 residues out of total 4668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 251 time to evaluate : 5.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 364 GLN Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 364 GLN Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain H residue 364 GLN Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 364 GLN Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 109 ASP Chi-restraints excluded: chain K residue 364 GLN Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain L residue 364 GLN Chi-restraints excluded: chain L residue 376 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 175 optimal weight: 0.0570 chunk 470 optimal weight: 7.9990 chunk 103 optimal weight: 6.9990 chunk 306 optimal weight: 2.9990 chunk 128 optimal weight: 0.6980 chunk 522 optimal weight: 3.9990 chunk 433 optimal weight: 5.9990 chunk 241 optimal weight: 6.9990 chunk 43 optimal weight: 9.9990 chunk 172 optimal weight: 0.2980 chunk 274 optimal weight: 7.9990 overall best weight: 1.6102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN A 364 GLN A 377 ASN B 95 ASN C 95 ASN C 111 ASN D 95 ASN D 364 GLN D 377 ASN E 95 ASN F 95 ASN F 111 ASN G 364 GLN G 377 ASN H 95 ASN I 95 ASN I 111 ASN J 95 ASN J 364 GLN J 377 ASN K 95 ASN L 95 ASN L 111 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 44712 Z= 0.187 Angle : 0.575 10.089 60816 Z= 0.282 Chirality : 0.043 0.180 6852 Planarity : 0.004 0.039 7548 Dihedral : 13.984 129.944 7188 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.59 % Allowed : 20.32 % Favored : 79.09 % 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: 5376 helix: 2.19 (0.14), residues: 1572 sheet: 1.12 (0.14), residues: 1188 loop : -1.22 (0.11), residues: 2616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 421 HIS 0.003 0.001 HIS L 164 PHE 0.014 0.001 PHE E 264 TYR 0.012 0.001 TYR F 285 ARG 0.002 0.000 ARG G 413 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10752 Ramachandran restraints generated. 5376 Oldfield, 0 Emsley, 5376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10752 Ramachandran restraints generated. 5376 Oldfield, 0 Emsley, 5376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 4668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 265 time to evaluate : 5.264 Fit side-chains REVERT: A 364 GLN cc_start: 0.7978 (OUTLIER) cc_final: 0.7482 (mt0) REVERT: A 441 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.7741 (mp10) REVERT: B 111 ASN cc_start: 0.7596 (t0) cc_final: 0.7386 (t0) REVERT: B 123 MET cc_start: 0.8293 (mmp) cc_final: 0.7617 (mmp) REVERT: B 227 ILE cc_start: 0.0266 (OUTLIER) cc_final: -0.0215 (mp) REVERT: C 285 TYR cc_start: 0.9080 (OUTLIER) cc_final: 0.6104 (m-80) REVERT: C 364 GLN cc_start: 0.7895 (mt0) cc_final: 0.7666 (mp10) REVERT: D 364 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.7478 (mt0) REVERT: D 441 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.7775 (mp10) REVERT: E 111 ASN cc_start: 0.7599 (t0) cc_final: 0.7384 (t0) REVERT: E 364 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7661 (mt0) REVERT: F 285 TYR cc_start: 0.9092 (OUTLIER) cc_final: 0.6125 (m-80) REVERT: G 364 GLN cc_start: 0.7967 (OUTLIER) cc_final: 0.7472 (mt0) REVERT: H 111 ASN cc_start: 0.7554 (t0) cc_final: 0.7340 (t0) REVERT: H 364 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7688 (mt0) REVERT: I 285 TYR cc_start: 0.9180 (OUTLIER) cc_final: 0.6314 (m-80) REVERT: J 364 GLN cc_start: 0.7982 (OUTLIER) cc_final: 0.7497 (mt0) REVERT: K 111 ASN cc_start: 0.7592 (t0) cc_final: 0.7382 (t0) REVERT: K 364 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7672 (mt0) REVERT: L 285 TYR cc_start: 0.9070 (OUTLIER) cc_final: 0.6274 (m-80) REVERT: L 364 GLN cc_start: 0.7905 (mt0) cc_final: 0.7660 (mp10) outliers start: 27 outliers final: 8 residues processed: 285 average time/residue: 1.6633 time to fit residues: 580.7221 Evaluate side-chains 282 residues out of total 4668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 260 time to evaluate : 5.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 364 GLN Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 364 GLN Chi-restraints excluded: chain D residue 441 GLN Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 364 GLN Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 364 GLN Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 364 GLN Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain J residue 109 ASP Chi-restraints excluded: chain J residue 364 GLN Chi-restraints excluded: chain K residue 109 ASP Chi-restraints excluded: chain K residue 364 GLN Chi-restraints excluded: chain L residue 285 TYR 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: 6.9990 chunk 297 optimal weight: 3.9990 chunk 381 optimal weight: 6.9990 chunk 295 optimal weight: 7.9990 chunk 439 optimal weight: 3.9990 chunk 291 optimal weight: 0.0770 chunk 520 optimal weight: 0.2980 chunk 325 optimal weight: 0.7980 chunk 317 optimal weight: 4.9990 chunk 240 optimal weight: 4.9990 overall best weight: 1.8342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN A 111 ASN A 364 GLN A 377 ASN B 95 ASN C 95 ASN C 364 GLN D 95 ASN D 111 ASN D 364 GLN D 377 ASN E 95 ASN F 95 ASN F 364 GLN G 111 ASN G 364 GLN G 377 ASN H 95 ASN I 95 ASN J 95 ASN J 111 ASN J 364 GLN J 377 ASN K 95 ASN L 95 ASN L 364 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 44712 Z= 0.206 Angle : 0.584 10.098 60816 Z= 0.288 Chirality : 0.044 0.183 6852 Planarity : 0.004 0.041 7548 Dihedral : 13.986 128.629 7188 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.85 % Allowed : 20.10 % Favored : 79.05 % 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: 0.33 (0.11), residues: 5376 helix: 2.14 (0.14), residues: 1572 sheet: 0.82 (0.15), residues: 1104 loop : -1.29 (0.11), residues: 2700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 175 HIS 0.003 0.001 HIS C 164 PHE 0.015 0.001 PHE H 264 TYR 0.013 0.001 TYR F 285 ARG 0.002 0.000 ARG F 222 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10752 Ramachandran restraints generated. 5376 Oldfield, 0 Emsley, 5376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10752 Ramachandran restraints generated. 5376 Oldfield, 0 Emsley, 5376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 4668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 256 time to evaluate : 5.306 Fit side-chains REVERT: A 441 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.7797 (mp10) REVERT: B 111 ASN cc_start: 0.7636 (t0) cc_final: 0.7400 (t0) REVERT: B 123 MET cc_start: 0.8298 (mmp) cc_final: 0.7622 (mmp) REVERT: B 227 ILE cc_start: 0.0330 (OUTLIER) cc_final: -0.0148 (mp) REVERT: C 285 TYR cc_start: 0.9137 (OUTLIER) cc_final: 0.6197 (m-80) REVERT: D 441 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.7751 (mp10) REVERT: E 111 ASN cc_start: 0.7612 (t0) cc_final: 0.7411 (t0) REVERT: E 364 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7697 (mt0) REVERT: F 285 TYR cc_start: 0.9123 (OUTLIER) cc_final: 0.6226 (m-80) REVERT: F 364 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7703 (mt0) REVERT: H 364 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7681 (mt0) REVERT: I 285 TYR cc_start: 0.9186 (OUTLIER) cc_final: 0.6382 (m-80) REVERT: K 364 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7698 (mt0) REVERT: L 285 TYR cc_start: 0.9109 (OUTLIER) cc_final: 0.6275 (m-80) REVERT: L 364 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7548 (mt0) outliers start: 39 outliers final: 8 residues processed: 283 average time/residue: 1.6963 time to fit residues: 586.1738 Evaluate side-chains 274 residues out of total 4668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 254 time to evaluate : 5.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 441 GLN Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 364 GLN Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 364 GLN Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 364 GLN Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain J residue 109 ASP Chi-restraints excluded: chain K residue 109 ASP Chi-restraints excluded: chain K residue 364 GLN Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain L residue 364 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 321 optimal weight: 8.9990 chunk 207 optimal weight: 3.9990 chunk 310 optimal weight: 6.9990 chunk 156 optimal weight: 6.9990 chunk 102 optimal weight: 0.8980 chunk 100 optimal weight: 0.0370 chunk 330 optimal weight: 7.9990 chunk 354 optimal weight: 8.9990 chunk 257 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 409 optimal weight: 6.9990 overall best weight: 2.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN A 377 ASN B 95 ASN C 95 ASN C 364 GLN D 95 ASN D 377 ASN E 95 ASN F 95 ASN G 377 ASN H 95 ASN H 111 ASN I 95 ASN I 364 GLN J 95 ASN J 377 ASN K 95 ASN K 111 ASN L 95 ASN L 364 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 44712 Z= 0.255 Angle : 0.623 10.106 60816 Z= 0.311 Chirality : 0.045 0.194 6852 Planarity : 0.005 0.041 7548 Dihedral : 14.113 128.166 7188 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.61 % Allowed : 20.37 % Favored : 79.03 % 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: 0.19 (0.11), residues: 5376 helix: 2.04 (0.14), residues: 1560 sheet: 0.73 (0.15), residues: 1104 loop : -1.35 (0.11), residues: 2712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 421 HIS 0.003 0.001 HIS G 164 PHE 0.017 0.002 PHE E 264 TYR 0.016 0.001 TYR C 285 ARG 0.002 0.000 ARG F 222 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10752 Ramachandran restraints generated. 5376 Oldfield, 0 Emsley, 5376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10752 Ramachandran restraints generated. 5376 Oldfield, 0 Emsley, 5376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 4668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 254 time to evaluate : 5.169 Fit side-chains REVERT: A 441 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.7759 (mp10) REVERT: B 111 ASN cc_start: 0.7740 (t0) cc_final: 0.7484 (t0) REVERT: B 123 MET cc_start: 0.8299 (mmp) cc_final: 0.7599 (mmp) REVERT: B 227 ILE cc_start: 0.0333 (OUTLIER) cc_final: -0.0128 (mp) REVERT: C 285 TYR cc_start: 0.9208 (OUTLIER) cc_final: 0.6331 (m-80) REVERT: C 402 MET cc_start: 0.8446 (mtp) cc_final: 0.8157 (mtp) REVERT: D 441 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.7792 (mp10) REVERT: E 111 ASN cc_start: 0.7716 (t0) cc_final: 0.7497 (t0) REVERT: E 364 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7670 (mt0) REVERT: F 285 TYR cc_start: 0.9205 (OUTLIER) cc_final: 0.6345 (m-80) REVERT: F 402 MET cc_start: 0.8455 (mtp) cc_final: 0.8167 (mtp) REVERT: H 285 TYR cc_start: 0.9419 (OUTLIER) cc_final: 0.9041 (t80) REVERT: H 364 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7691 (mt0) REVERT: I 285 TYR cc_start: 0.9234 (OUTLIER) cc_final: 0.6388 (m-80) REVERT: I 402 MET cc_start: 0.8450 (mtp) cc_final: 0.8157 (mtp) REVERT: K 364 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.7690 (mt0) REVERT: L 285 TYR cc_start: 0.9172 (OUTLIER) cc_final: 0.6428 (m-80) outliers start: 28 outliers final: 8 residues processed: 276 average time/residue: 1.8328 time to fit residues: 619.8982 Evaluate side-chains 269 residues out of total 4668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 250 time to evaluate : 5.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 441 GLN Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 364 GLN Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 364 GLN Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain J residue 109 ASP Chi-restraints excluded: chain K residue 109 ASP Chi-restraints excluded: chain K residue 364 GLN Chi-restraints excluded: chain L residue 285 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 473 optimal weight: 8.9990 chunk 498 optimal weight: 4.9990 chunk 454 optimal weight: 1.9990 chunk 485 optimal weight: 2.9990 chunk 291 optimal weight: 4.9990 chunk 211 optimal weight: 10.0000 chunk 380 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 438 optimal weight: 0.7980 chunk 458 optimal weight: 0.9990 chunk 483 optimal weight: 0.6980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN A 364 GLN A 377 ASN B 95 ASN C 95 ASN C 364 GLN D 95 ASN D 364 GLN D 377 ASN E 95 ASN F 95 ASN F 364 GLN G 364 GLN G 377 ASN H 95 ASN I 95 ASN I 364 GLN J 95 ASN J 377 ASN K 95 ASN L 95 ASN L 364 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 44712 Z= 0.181 Angle : 0.574 10.171 60816 Z= 0.282 Chirality : 0.043 0.180 6852 Planarity : 0.004 0.040 7548 Dihedral : 13.838 124.805 7188 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.59 % Allowed : 20.32 % Favored : 79.09 % 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: 0.22 (0.11), residues: 5376 helix: 2.04 (0.14), residues: 1584 sheet: 0.76 (0.15), residues: 1104 loop : -1.36 (0.11), residues: 2688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 470 HIS 0.003 0.001 HIS L 164 PHE 0.014 0.001 PHE E 264 TYR 0.011 0.001 TYR F 285 ARG 0.002 0.000 ARG G 413 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10752 Ramachandran restraints generated. 5376 Oldfield, 0 Emsley, 5376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10752 Ramachandran restraints generated. 5376 Oldfield, 0 Emsley, 5376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 4668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 254 time to evaluate : 5.385 Fit side-chains REVERT: A 441 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.7763 (mp10) REVERT: B 111 ASN cc_start: 0.7668 (t0) cc_final: 0.7427 (t0) REVERT: B 123 MET cc_start: 0.8293 (mmp) cc_final: 0.7631 (mmp) REVERT: B 227 ILE cc_start: 0.0317 (OUTLIER) cc_final: -0.0154 (mp) REVERT: C 285 TYR cc_start: 0.9143 (OUTLIER) cc_final: 0.6244 (m-80) REVERT: C 364 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7854 (mt0) REVERT: D 441 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.7769 (mp10) REVERT: E 111 ASN cc_start: 0.7668 (t0) cc_final: 0.7446 (t0) REVERT: E 123 MET cc_start: 0.8296 (mmp) cc_final: 0.7631 (mmp) REVERT: E 364 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7649 (mt0) REVERT: F 285 TYR cc_start: 0.9132 (OUTLIER) cc_final: 0.6218 (m-80) REVERT: F 364 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7690 (mt0) REVERT: G 364 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7573 (mt0) REVERT: H 285 TYR cc_start: 0.9387 (OUTLIER) cc_final: 0.8998 (t80) REVERT: H 364 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.7678 (mt0) REVERT: I 285 TYR cc_start: 0.9185 (OUTLIER) cc_final: 0.6395 (m-80) REVERT: I 364 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7847 (mt0) REVERT: K 285 TYR cc_start: 0.9387 (OUTLIER) cc_final: 0.9000 (t80) REVERT: K 364 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7664 (mt0) REVERT: L 285 TYR cc_start: 0.9111 (OUTLIER) cc_final: 0.6318 (m-80) REVERT: L 364 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7780 (mt0) outliers start: 27 outliers final: 4 residues processed: 271 average time/residue: 1.8080 time to fit residues: 603.0289 Evaluate side-chains 271 residues out of total 4668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 250 time to evaluate : 5.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 364 GLN Chi-restraints excluded: chain D residue 441 GLN Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 364 GLN Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 364 GLN Chi-restraints excluded: chain G residue 364 GLN Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 364 GLN Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 364 GLN Chi-restraints excluded: chain K residue 109 ASP Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 364 GLN Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain L residue 364 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 318 optimal weight: 3.9990 chunk 512 optimal weight: 1.9990 chunk 313 optimal weight: 0.2980 chunk 243 optimal weight: 0.8980 chunk 356 optimal weight: 3.9990 chunk 537 optimal weight: 3.9990 chunk 495 optimal weight: 10.0000 chunk 428 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 330 optimal weight: 4.9990 chunk 262 optimal weight: 0.0980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN A 364 GLN A 377 ASN B 95 ASN C 95 ASN C 111 ASN D 95 ASN D 364 GLN D 377 ASN E 95 ASN F 95 ASN F 111 ASN F 364 GLN G 364 GLN G 377 ASN H 95 ASN I 95 ASN I 111 ASN I 364 GLN J 95 ASN J 377 ASN K 95 ASN L 95 ASN L 111 ASN L 364 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.119 44712 Z= 0.209 Angle : 0.923 59.007 60816 Z= 0.517 Chirality : 0.043 0.282 6852 Planarity : 0.005 0.055 7548 Dihedral : 13.844 124.812 7188 Min Nonbonded Distance : 1.569 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.85 % Favored : 97.08 % Rotamer: Outliers : 0.54 % Allowed : 20.34 % Favored : 79.11 % Cbeta Deviations : 0.10 % 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: 0.22 (0.11), residues: 5376 helix: 2.04 (0.14), residues: 1584 sheet: 0.76 (0.15), residues: 1104 loop : -1.36 (0.11), residues: 2688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 470 HIS 0.002 0.001 HIS C 164 PHE 0.014 0.001 PHE E 264 TYR 0.011 0.001 TYR C 285 ARG 0.001 0.000 ARG G 413 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10752 Ramachandran restraints generated. 5376 Oldfield, 0 Emsley, 5376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10752 Ramachandran restraints generated. 5376 Oldfield, 0 Emsley, 5376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 4668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 250 time to evaluate : 4.747 Fit side-chains REVERT: A 364 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7503 (mt0) REVERT: A 441 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.7751 (mp10) REVERT: B 111 ASN cc_start: 0.7667 (t0) cc_final: 0.7401 (t0) REVERT: B 123 MET cc_start: 0.8292 (mmp) cc_final: 0.7629 (mmp) REVERT: B 227 ILE cc_start: 0.0307 (OUTLIER) cc_final: -0.0154 (mp) REVERT: C 285 TYR cc_start: 0.9137 (OUTLIER) cc_final: 0.6233 (m-80) REVERT: D 364 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7494 (mt0) REVERT: D 441 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.7767 (mp10) REVERT: E 111 ASN cc_start: 0.7666 (t0) cc_final: 0.7443 (t0) REVERT: E 123 MET cc_start: 0.8296 (mmp) cc_final: 0.7630 (mmp) REVERT: E 364 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7648 (mt0) REVERT: F 285 TYR cc_start: 0.9129 (OUTLIER) cc_final: 0.6218 (m-80) REVERT: H 285 TYR cc_start: 0.9385 (OUTLIER) cc_final: 0.8997 (t80) REVERT: H 364 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7676 (mt0) REVERT: I 285 TYR cc_start: 0.9191 (OUTLIER) cc_final: 0.6405 (m-80) REVERT: K 285 TYR cc_start: 0.9386 (OUTLIER) cc_final: 0.8998 (t80) REVERT: K 364 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7663 (mt0) REVERT: L 285 TYR cc_start: 0.9108 (OUTLIER) cc_final: 0.6318 (m-80) outliers start: 25 outliers final: 5 residues processed: 265 average time/residue: 1.7222 time to fit residues: 557.3706 Evaluate side-chains 269 residues out of total 4668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 250 time to evaluate : 5.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 GLN Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain D residue 109 ASP Chi-restraints excluded: chain D residue 364 GLN Chi-restraints excluded: chain D residue 441 GLN Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 364 GLN Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 364 GLN Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain K residue 109 ASP Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 364 GLN Chi-restraints excluded: chain L residue 285 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 340 optimal weight: 0.6980 chunk 456 optimal weight: 9.9990 chunk 131 optimal weight: 0.0040 chunk 395 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 119 optimal weight: 6.9990 chunk 429 optimal weight: 0.8980 chunk 179 optimal weight: 0.9990 chunk 440 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN A 377 ASN B 95 ASN C 95 ASN D 95 ASN D 377 ASN E 95 ASN F 95 ASN G 377 ASN H 95 ASN I 95 ASN J 95 ASN J 377 ASN K 95 ASN L 95 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.085380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.060458 restraints weight = 184643.303| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 3.55 r_work: 0.2606 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2608 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2608 r_free = 0.2608 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2608 r_free = 0.2608 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2608 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.327 44712 Z= 0.269 Angle : 1.024 59.200 60816 Z= 0.589 Chirality : 0.048 1.308 6852 Planarity : 0.005 0.048 7548 Dihedral : 13.844 124.813 7188 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.87 % Favored : 97.02 % Rotamer: Outliers : 0.50 % Allowed : 20.39 % Favored : 79.11 % Cbeta Deviations : 0.10 % 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: 0.22 (0.11), residues: 5376 helix: 2.04 (0.14), residues: 1584 sheet: 0.76 (0.15), residues: 1104 loop : -1.36 (0.11), residues: 2688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 470 HIS 0.002 0.001 HIS C 164 PHE 0.014 0.001 PHE E 264 TYR 0.011 0.001 TYR C 285 ARG 0.001 0.000 ARG G 413 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12039.86 seconds wall clock time: 221 minutes 18.75 seconds (13278.75 seconds total)