Starting phenix.real_space_refine on Sun Mar 24 16:53:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aov_15553/03_2024/8aov_15553_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aov_15553/03_2024/8aov_15553.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aov_15553/03_2024/8aov_15553.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aov_15553/03_2024/8aov_15553.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aov_15553/03_2024/8aov_15553_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aov_15553/03_2024/8aov_15553_updated.pdb" } resolution = 2.48 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= 0.002 sd= 0.111 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: 6 Type Number sf(0) Gaussians Zn 12 6.06 5 P 36 5.49 5 S 348 5.16 5 C 26880 2.51 5 N 7440 2.21 5 O 8184 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 26": "OE1" <-> "OE2" Residue "A GLU 234": "OE1" <-> "OE2" Residue "A PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 26": "OE1" <-> "OE2" Residue "C GLU 54": "OE1" <-> "OE2" Residue "C ASP 146": "OD1" <-> "OD2" Residue "C TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 58": "OD1" <-> "OD2" Residue "E TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 146": "OD1" <-> "OD2" Residue "G GLU 234": "OE1" <-> "OE2" Residue "G PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 349": "OE1" <-> "OE2" Residue "I GLU 26": "OE1" <-> "OE2" Residue "I ASP 58": "OD1" <-> "OD2" Residue "I ASP 146": "OD1" <-> "OD2" Residue "I GLU 202": "OE1" <-> "OE2" Residue "I GLU 234": "OE1" <-> "OE2" Residue "I TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 58": "OD1" <-> "OD2" Residue "K TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 26": "OE1" <-> "OE2" Residue "M TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 9": "OD1" <-> "OD2" Residue "O GLU 26": "OE1" <-> "OE2" Residue "O ASP 146": "OD1" <-> "OD2" Residue "O TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 446": "OE1" <-> "OE2" Residue "Q GLU 26": "OE1" <-> "OE2" Residue "Q GLU 54": "OE1" <-> "OE2" Residue "Q ASP 138": "OD1" <-> "OD2" Residue "Q TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 26": "OE1" <-> "OE2" Residue "S PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 9": "OD1" <-> "OD2" Residue "V ASP 75": "OD1" <-> "OD2" Residue "V ASP 146": "OD1" <-> "OD2" Residue "V TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 250": "OE1" <-> "OE2" Residue "V TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 54": "OE1" <-> "OE2" Residue "X ASP 58": "OD1" <-> "OD2" Residue "X ASP 146": "OD1" <-> "OD2" Residue "X TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 42900 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 3523 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 446, 3461 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 3 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 27 Conformer: "B" Number of residues, atoms: 446, 3461 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 3 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 27 bond proxies already assigned to first conformer: 3465 Chain: "C" Number of atoms: 3523 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 446, 3461 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 3 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 27 Conformer: "B" Number of residues, atoms: 446, 3461 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 3 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 27 bond proxies already assigned to first conformer: 3465 Chain: "E" Number of atoms: 3523 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 446, 3461 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 3 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 27 Conformer: "B" Number of residues, atoms: 446, 3461 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 3 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 27 bond proxies already assigned to first conformer: 3465 Chain: "G" Number of atoms: 3523 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 446, 3461 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 3 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 27 Conformer: "B" Number of residues, atoms: 446, 3461 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 3 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 27 bond proxies already assigned to first conformer: 3465 Chain: "I" Number of atoms: 3523 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 446, 3461 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 3 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 27 Conformer: "B" Number of residues, atoms: 446, 3461 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 3 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 27 bond proxies already assigned to first conformer: 3465 Chain: "K" Number of atoms: 3523 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 446, 3461 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 3 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 27 Conformer: "B" Number of residues, atoms: 446, 3461 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 3 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 27 bond proxies already assigned to first conformer: 3465 Chain: "M" Number of atoms: 3523 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 446, 3461 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 3 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 27 Conformer: "B" Number of residues, atoms: 446, 3461 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 3 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 27 bond proxies already assigned to first conformer: 3465 Chain: "O" Number of atoms: 3523 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 446, 3461 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 3 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 27 Conformer: "B" Number of residues, atoms: 446, 3461 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 3 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 27 bond proxies already assigned to first conformer: 3465 Chain: "Q" Number of atoms: 3523 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 446, 3461 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 3 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 27 Conformer: "B" Number of residues, atoms: 446, 3461 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 3 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 27 bond proxies already assigned to first conformer: 3465 Chain: "S" Number of atoms: 3523 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 446, 3461 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 3 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 27 Conformer: "B" Number of residues, atoms: 446, 3461 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 3 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 27 bond proxies already assigned to first conformer: 3465 Chain: "V" Number of atoms: 3523 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 446, 3461 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 3 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 27 Conformer: "B" Number of residues, atoms: 446, 3461 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 3 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 27 bond proxies already assigned to first conformer: 3465 Chain: "X" Number of atoms: 3523 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 446, 3461 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 3 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 27 Conformer: "B" Number of residues, atoms: 446, 3461 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 3 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 27 bond proxies already assigned to first conformer: 3465 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' ZN': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' ZN': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' ZN': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' ZN': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' ZN': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' ZN': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' ZN': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' ZN': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' ZN': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' ZN': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' ZN': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' ZN': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "C" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "E" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "G" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "I" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "K" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "M" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "O" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "Q" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "S" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "V" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "X" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1001 SG CYS A 134 128.478 174.947 63.496 1.00103.91 S ATOM 1053 SG CYS A 141 131.458 173.166 63.285 1.00 76.30 S ATOM 4524 SG CYS C 134 85.473 180.460 63.754 1.00100.14 S ATOM 4576 SG CYS C 141 89.040 180.040 63.330 1.00 77.44 S ATOM 8047 SG CYS E 134 45.794 163.452 63.896 1.00105.72 S ATOM 8099 SG CYS E 141 48.734 164.586 63.380 1.00 86.80 S ATOM 11570 SG CYS G 134 20.083 128.414 63.432 1.00103.43 S ATOM 11622 SG CYS G 141 21.990 131.544 63.252 1.00 72.60 S ATOM 15093 SG CYS I 134 14.523 85.452 63.765 1.00105.75 S ATOM 15145 SG CYS I 141 14.988 89.040 63.332 1.00 74.74 S ATOM 18616 SG CYS K 134 31.986 46.008 63.484 1.00102.75 S ATOM 18668 SG CYS K 141 30.369 48.930 63.256 1.00 88.78 S ATOM 22139 SG CYS M 134 66.609 20.355 63.332 1.00102.10 S ATOM 22191 SG CYS M 141 63.523 21.899 63.295 1.00 77.08 S ATOM 25662 SG CYS O 134 109.571 14.547 63.781 1.00100.18 S ATOM 25714 SG CYS O 141 106.009 15.032 63.296 1.00 71.75 S ATOM 29185 SG CYS Q 134 149.056 31.884 63.563 1.00100.99 S ATOM 29237 SG CYS Q 141 146.073 30.278 63.300 1.00 86.75 S ATOM 32708 SG CYS S 134 175.537 66.363 64.012 1.00113.88 S ATOM 32760 SG CYS S 141 173.213 63.615 63.309 1.00 77.91 S ATOM 36231 SG CYS V 134 180.189 109.369 63.553 1.00 93.65 S ATOM 36283 SG CYS V 141 180.041 105.903 63.304 1.00 76.77 S ATOM 39754 SG CYS X 134 162.941 149.065 63.407 1.00 99.75 S ATOM 39806 SG CYS X 141 164.736 146.107 63.319 1.00 88.17 S Residues with excluded nonbonded symmetry interactions: 71 residue: pdb=" N ALEU A 50 " occ=0.31 ... (14 atoms not shown) pdb=" CD2BLEU A 50 " occ=0.69 residue: pdb=" N AARG A 71 " occ=0.53 ... (20 atoms not shown) pdb=" NH2BARG A 71 " occ=0.47 residue: pdb=" N AARG A 76 " occ=0.35 ... (20 atoms not shown) pdb=" NH2BARG A 76 " occ=0.65 residue: pdb=" N AVAL A 239 " occ=0.53 ... (12 atoms not shown) pdb=" CG2BVAL A 239 " occ=0.47 residue: pdb=" N AASP A 310 " occ=0.51 ... (14 atoms not shown) pdb=" OD2BASP A 310 " occ=0.49 residue: pdb=" N AGLU A 353 " occ=0.45 ... (16 atoms not shown) pdb=" OE2BGLU A 353 " occ=0.55 residue: pdb=" N ALEU C 50 " occ=0.09 ... (14 atoms not shown) pdb=" CD2BLEU C 50 " occ=0.91 residue: pdb=" N AARG C 71 " occ=0.49 ... (20 atoms not shown) pdb=" NH2BARG C 71 " occ=0.51 residue: pdb=" N AARG C 76 " occ=0.54 ... (20 atoms not shown) pdb=" NH2BARG C 76 " occ=0.46 residue: pdb=" N AVAL C 239 " occ=0.62 ... (12 atoms not shown) pdb=" CG2BVAL C 239 " occ=0.38 residue: pdb=" N AASP C 310 " occ=0.45 ... (14 atoms not shown) pdb=" OD2BASP C 310 " occ=0.55 residue: pdb=" N AGLU C 353 " occ=0.55 ... (16 atoms not shown) pdb=" OE2BGLU C 353 " occ=0.45 ... (remaining 59 not shown) Time building chain proxies: 40.34, per 1000 atoms: 0.94 Number of scatterers: 42900 At special positions: 0 Unit cell: (196.1, 196.1, 93.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 12 29.99 S 348 16.00 P 36 15.00 O 8184 8.00 N 7440 7.00 C 26880 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: 18.53 Conformation dependent library (CDL) restraints added in 16.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" NE2 HIS A 79 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 141 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 134 " pdb=" ZN C 601 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 141 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 134 " pdb="ZN ZN C 601 " - pdb=" NE2 HIS C 79 " pdb=" ZN E 601 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 141 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 134 " pdb="ZN ZN E 601 " - pdb=" NE2 HIS E 79 " pdb=" ZN G 601 " pdb="ZN ZN G 601 " - pdb=" NE2 HIS G 79 " pdb="ZN ZN G 601 " - pdb=" SG CYS G 134 " pdb="ZN ZN G 601 " - pdb=" SG CYS G 141 " pdb=" ZN I 601 " pdb="ZN ZN I 601 " - pdb=" SG CYS I 141 " pdb="ZN ZN I 601 " - pdb=" SG CYS I 134 " pdb="ZN ZN I 601 " - pdb=" NE2 HIS I 79 " pdb=" ZN K 601 " pdb="ZN ZN K 601 " - pdb=" NE2 HIS K 79 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 141 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 134 " pdb=" ZN M 601 " pdb="ZN ZN M 601 " - pdb=" NE2 HIS M 79 " pdb="ZN ZN M 601 " - pdb=" SG CYS M 134 " pdb="ZN ZN M 601 " - pdb=" SG CYS M 141 " pdb=" ZN O 601 " pdb="ZN ZN O 601 " - pdb=" SG CYS O 141 " pdb="ZN ZN O 601 " - pdb=" SG CYS O 134 " pdb="ZN ZN O 601 " - pdb=" NE2 HIS O 79 " pdb=" ZN Q 601 " pdb="ZN ZN Q 601 " - pdb=" NE2 HIS Q 79 " pdb="ZN ZN Q 601 " - pdb=" SG CYS Q 134 " pdb="ZN ZN Q 601 " - pdb=" SG CYS Q 141 " pdb=" ZN S 601 " pdb="ZN ZN S 601 " - pdb=" SG CYS S 134 " pdb="ZN ZN S 601 " - pdb=" SG CYS S 141 " pdb="ZN ZN S 601 " - pdb=" NE2 HIS S 79 " pdb=" ZN V 601 " pdb="ZN ZN V 601 " - pdb=" SG CYS V 141 " pdb="ZN ZN V 601 " - pdb=" SG CYS V 134 " pdb="ZN ZN V 601 " - pdb=" NE2 HIS V 79 " pdb=" ZN X 601 " pdb="ZN ZN X 601 " - pdb=" NE2 HIS X 79 " pdb="ZN ZN X 601 " - pdb=" SG CYS X 134 " pdb="ZN ZN X 601 " - pdb=" SG CYS X 141 " 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10320 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 180 helices and 60 sheets defined 30.5% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.94 Creating SS restraints... Processing helix chain 'A' and resid 14 through 21 Processing helix chain 'A' and resid 38 through 54 Processing helix chain 'A' and resid 68 through 70 No H-bonds generated for 'chain 'A' and resid 68 through 70' Processing helix chain 'A' and resid 90 through 103 Processing helix chain 'A' and resid 112 through 124 Processing helix chain 'A' and resid 158 through 168 removed outlier: 3.686A 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: 3.707A pdb=" N TRP A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 341 Processing helix chain 'A' and resid 345 through 347 No H-bonds generated for 'chain 'A' and resid 345 through 347' Processing helix chain 'A' and resid 352 through 363 Processing helix chain 'A' and resid 381 through 403 Proline residue: A 385 - end of helix Processing helix chain 'A' and resid 462 through 471 removed outlier: 3.690A pdb=" N LEU A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 21 Processing helix chain 'C' and resid 38 through 54 Processing helix chain 'C' and resid 68 through 70 No H-bonds generated for 'chain 'C' and resid 68 through 70' Processing helix chain 'C' and resid 90 through 103 Processing helix chain 'C' and resid 112 through 124 Processing helix chain 'C' and resid 158 through 168 removed outlier: 3.701A 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: 3.731A pdb=" N TRP C 258 " --> pdb=" O LEU C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 341 Processing helix chain 'C' and resid 345 through 347 No H-bonds generated for 'chain 'C' and resid 345 through 347' Processing helix chain 'C' and resid 352 through 363 Processing helix chain 'C' and resid 381 through 403 Proline residue: C 385 - end of helix Processing helix chain 'C' and resid 462 through 471 removed outlier: 3.655A pdb=" N LEU C 471 " --> pdb=" O ARG C 467 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 21 Processing helix chain 'E' and resid 38 through 54 Processing helix chain 'E' and resid 68 through 71 Processing helix chain 'E' and resid 90 through 103 Processing helix chain 'E' and resid 112 through 124 Processing helix chain 'E' and resid 158 through 166 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: 3.754A pdb=" N TRP E 258 " --> pdb=" O LEU E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 341 Processing helix chain 'E' and resid 345 through 347 No H-bonds generated for 'chain 'E' and resid 345 through 347' Processing helix chain 'E' and resid 352 through 363 Processing helix chain 'E' and resid 381 through 403 Proline residue: E 385 - end of helix Processing helix chain 'E' and resid 462 through 471 removed outlier: 3.653A pdb=" N LEU E 471 " --> pdb=" O ARG E 467 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 21 Processing helix chain 'G' and resid 38 through 54 Processing helix chain 'G' and resid 68 through 70 No H-bonds generated for 'chain 'G' and resid 68 through 70' Processing helix chain 'G' and resid 90 through 103 Processing helix chain 'G' and resid 112 through 124 Processing helix chain 'G' and resid 158 through 168 removed outlier: 3.702A 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: 3.679A pdb=" N TRP G 258 " --> pdb=" O LEU G 254 " (cutoff:3.500A) Processing helix chain 'G' and resid 336 through 342 Processing helix chain 'G' and resid 345 through 347 No H-bonds generated for 'chain 'G' and resid 345 through 347' Processing helix chain 'G' and resid 352 through 363 Processing helix chain 'G' and resid 381 through 403 Proline residue: G 385 - end of helix Processing helix chain 'G' and resid 462 through 471 removed outlier: 3.743A pdb=" N LEU G 471 " --> pdb=" O ARG G 467 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 21 Processing helix chain 'I' and resid 38 through 54 Processing helix chain 'I' and resid 68 through 70 No H-bonds generated for 'chain 'I' and resid 68 through 70' Processing helix chain 'I' and resid 90 through 103 Processing helix chain 'I' and resid 112 through 124 Processing helix chain 'I' and resid 158 through 166 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: 3.742A pdb=" N TRP I 258 " --> pdb=" O LEU I 254 " (cutoff:3.500A) Processing helix chain 'I' and resid 336 through 342 Processing helix chain 'I' and resid 345 through 347 No H-bonds generated for 'chain 'I' and resid 345 through 347' Processing helix chain 'I' and resid 352 through 362 Processing helix chain 'I' and resid 381 through 403 Proline residue: I 385 - end of helix Processing helix chain 'I' and resid 462 through 471 removed outlier: 3.689A pdb=" N LEU I 471 " --> pdb=" O ARG I 467 " (cutoff:3.500A) Processing helix chain 'K' and resid 14 through 21 Processing helix chain 'K' and resid 38 through 54 Processing helix chain 'K' and resid 68 through 70 No H-bonds generated for 'chain 'K' and resid 68 through 70' Processing helix chain 'K' and resid 90 through 103 Processing helix chain 'K' and resid 112 through 124 Processing helix chain 'K' and resid 158 through 166 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: 3.749A pdb=" N TRP K 258 " --> pdb=" O LEU K 254 " (cutoff:3.500A) Processing helix chain 'K' and resid 336 through 341 Processing helix chain 'K' and resid 345 through 347 No H-bonds generated for 'chain 'K' and resid 345 through 347' Processing helix chain 'K' and resid 352 through 363 Processing helix chain 'K' and resid 381 through 403 Proline residue: K 385 - end of helix Processing helix chain 'K' and resid 462 through 471 removed outlier: 3.639A pdb=" N LEU K 471 " --> pdb=" O ARG K 467 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 21 Processing helix chain 'M' and resid 38 through 54 Processing helix chain 'M' and resid 68 through 70 No H-bonds generated for 'chain 'M' and resid 68 through 70' Processing helix chain 'M' and resid 90 through 103 Processing helix chain 'M' and resid 112 through 124 Processing helix chain 'M' and resid 158 through 166 Processing helix chain 'M' and resid 181 through 184 No H-bonds generated for 'chain 'M' and resid 181 through 184' Processing helix chain 'M' and resid 193 through 195 No H-bonds generated for 'chain 'M' and resid 193 through 195' Processing helix chain 'M' and resid 202 through 204 No H-bonds generated for 'chain 'M' and resid 202 through 204' Processing helix chain 'M' and resid 252 through 258 removed outlier: 3.673A pdb=" N TRP M 258 " --> pdb=" O LEU M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 336 through 341 Processing helix chain 'M' and resid 345 through 347 No H-bonds generated for 'chain 'M' and resid 345 through 347' Processing helix chain 'M' and resid 352 through 363 Processing helix chain 'M' and resid 381 through 403 Proline residue: M 385 - end of helix Processing helix chain 'M' and resid 462 through 471 removed outlier: 3.542A pdb=" N LEU M 471 " --> pdb=" O ARG M 467 " (cutoff:3.500A) Processing helix chain 'O' and resid 14 through 21 Processing helix chain 'O' and resid 38 through 54 Processing helix chain 'O' and resid 68 through 70 No H-bonds generated for 'chain 'O' and resid 68 through 70' Processing helix chain 'O' and resid 90 through 102 Processing helix chain 'O' and resid 112 through 124 Processing helix chain 'O' and resid 158 through 166 Processing helix chain 'O' and resid 181 through 184 No H-bonds generated for 'chain 'O' and resid 181 through 184' Processing helix chain 'O' and resid 193 through 195 No H-bonds generated for 'chain 'O' and resid 193 through 195' Processing helix chain 'O' and resid 202 through 204 No H-bonds generated for 'chain 'O' and resid 202 through 204' Processing helix chain 'O' and resid 252 through 258 removed outlier: 3.685A pdb=" N TRP O 258 " --> pdb=" O LEU O 254 " (cutoff:3.500A) Processing helix chain 'O' and resid 336 through 342 Processing helix chain 'O' and resid 345 through 347 No H-bonds generated for 'chain 'O' and resid 345 through 347' Processing helix chain 'O' and resid 352 through 363 Processing helix chain 'O' and resid 381 through 403 Proline residue: O 385 - end of helix Processing helix chain 'O' and resid 462 through 471 removed outlier: 3.659A pdb=" N LEU O 471 " --> pdb=" O ARG O 467 " (cutoff:3.500A) Processing helix chain 'Q' and resid 14 through 21 Processing helix chain 'Q' and resid 38 through 54 Processing helix chain 'Q' and resid 68 through 71 Processing helix chain 'Q' and resid 90 through 103 Processing helix chain 'Q' and resid 112 through 124 Processing helix chain 'Q' and resid 158 through 168 removed outlier: 3.699A pdb=" N LYS Q 168 " --> pdb=" O HIS Q 164 " (cutoff:3.500A) Processing helix chain 'Q' and resid 181 through 184 No H-bonds generated for 'chain 'Q' and resid 181 through 184' Processing helix chain 'Q' and resid 193 through 195 No H-bonds generated for 'chain 'Q' and resid 193 through 195' Processing helix chain 'Q' and resid 202 through 204 No H-bonds generated for 'chain 'Q' and resid 202 through 204' Processing helix chain 'Q' and resid 252 through 258 removed outlier: 3.801A pdb=" N TRP Q 258 " --> pdb=" O LEU Q 254 " (cutoff:3.500A) Processing helix chain 'Q' and resid 336 through 341 Processing helix chain 'Q' and resid 345 through 347 No H-bonds generated for 'chain 'Q' and resid 345 through 347' Processing helix chain 'Q' and resid 352 through 363 Processing helix chain 'Q' and resid 381 through 403 Proline residue: Q 385 - end of helix Processing helix chain 'Q' and resid 462 through 471 removed outlier: 3.534A pdb=" N LEU Q 471 " --> pdb=" O ARG Q 467 " (cutoff:3.500A) Processing helix chain 'S' and resid 14 through 21 Processing helix chain 'S' and resid 38 through 54 Processing helix chain 'S' and resid 68 through 71 Processing helix chain 'S' and resid 90 through 101 Processing helix chain 'S' and resid 112 through 124 Processing helix chain 'S' and resid 158 through 168 removed outlier: 3.715A pdb=" N LYS S 168 " --> pdb=" O HIS S 164 " (cutoff:3.500A) Processing helix chain 'S' and resid 181 through 184 No H-bonds generated for 'chain 'S' and resid 181 through 184' Processing helix chain 'S' and resid 193 through 195 No H-bonds generated for 'chain 'S' and resid 193 through 195' Processing helix chain 'S' and resid 202 through 204 No H-bonds generated for 'chain 'S' and resid 202 through 204' Processing helix chain 'S' and resid 252 through 258 removed outlier: 3.705A pdb=" N TRP S 258 " --> pdb=" O LEU S 254 " (cutoff:3.500A) Processing helix chain 'S' and resid 336 through 341 Processing helix chain 'S' and resid 345 through 347 No H-bonds generated for 'chain 'S' and resid 345 through 347' Processing helix chain 'S' and resid 352 through 363 Processing helix chain 'S' and resid 381 through 403 Proline residue: S 385 - end of helix Processing helix chain 'S' and resid 462 through 471 removed outlier: 3.734A pdb=" N LEU S 471 " --> pdb=" O ARG S 467 " (cutoff:3.500A) Processing helix chain 'V' and resid 14 through 21 Processing helix chain 'V' and resid 38 through 54 Processing helix chain 'V' and resid 68 through 70 No H-bonds generated for 'chain 'V' and resid 68 through 70' Processing helix chain 'V' and resid 90 through 103 Processing helix chain 'V' and resid 112 through 124 Processing helix chain 'V' and resid 158 through 166 Processing helix chain 'V' and resid 181 through 184 No H-bonds generated for 'chain 'V' and resid 181 through 184' Processing helix chain 'V' and resid 193 through 195 No H-bonds generated for 'chain 'V' and resid 193 through 195' Processing helix chain 'V' and resid 202 through 204 No H-bonds generated for 'chain 'V' and resid 202 through 204' Processing helix chain 'V' and resid 252 through 258 removed outlier: 3.762A pdb=" N TRP V 258 " --> pdb=" O LEU V 254 " (cutoff:3.500A) Processing helix chain 'V' and resid 336 through 341 Processing helix chain 'V' and resid 345 through 347 No H-bonds generated for 'chain 'V' and resid 345 through 347' Processing helix chain 'V' and resid 352 through 363 Processing helix chain 'V' and resid 381 through 403 Proline residue: V 385 - end of helix Processing helix chain 'V' and resid 462 through 471 removed outlier: 3.708A pdb=" N LEU V 471 " --> pdb=" O ARG V 467 " (cutoff:3.500A) Processing helix chain 'X' and resid 14 through 21 Processing helix chain 'X' and resid 38 through 54 Processing helix chain 'X' and resid 68 through 70 No H-bonds generated for 'chain 'X' and resid 68 through 70' Processing helix chain 'X' and resid 90 through 101 Processing helix chain 'X' and resid 112 through 124 Processing helix chain 'X' and resid 158 through 166 Processing helix chain 'X' and resid 181 through 184 No H-bonds generated for 'chain 'X' and resid 181 through 184' Processing helix chain 'X' and resid 193 through 195 No H-bonds generated for 'chain 'X' and resid 193 through 195' Processing helix chain 'X' and resid 202 through 204 No H-bonds generated for 'chain 'X' and resid 202 through 204' Processing helix chain 'X' and resid 252 through 258 removed outlier: 3.769A pdb=" N TRP X 258 " --> pdb=" O LEU X 254 " (cutoff:3.500A) Processing helix chain 'X' and resid 336 through 341 Processing helix chain 'X' and resid 345 through 347 No H-bonds generated for 'chain 'X' and resid 345 through 347' Processing helix chain 'X' and resid 352 through 363 Processing helix chain 'X' and resid 381 through 403 Proline residue: X 385 - end of helix Processing helix chain 'X' and resid 462 through 471 removed outlier: 3.635A pdb=" N LEU X 471 " --> pdb=" O ARG X 467 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 4 through 6 Processing sheet with id= B, first strand: chain 'A' and resid 77 through 81 removed outlier: 6.622A pdb=" N VAL A 147 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ILE A 64 " --> pdb=" O VAL A 147 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE A 149 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU A 172 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N TYR A 150 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N TYR A 174 " --> pdb=" O TYR A 150 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ARG A 289 " --> pdb=" O THR A 278 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N THR A 278 " --> pdb=" O ARG A 289 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N THR A 291 " --> pdb=" O CYS A 276 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N CYS A 276 " --> pdb=" O THR A 291 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N SER A 293 " --> pdb=" O CYS A 274 " (cutoff:3.500A) removed outlier: 5.053A 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: 3.961A 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 'C' and resid 4 through 6 Processing sheet with id= G, first strand: chain 'C' and resid 77 through 81 removed outlier: 6.549A pdb=" N VAL C 147 " --> pdb=" O LEU C 62 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ILE C 64 " --> pdb=" O VAL C 147 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE C 149 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU C 172 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N TYR C 150 " --> pdb=" O LEU C 172 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TYR C 174 " --> pdb=" O TYR C 150 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ARG C 289 " --> pdb=" O THR C 278 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N THR C 278 " --> pdb=" O ARG C 289 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N THR C 291 " --> pdb=" O CYS C 276 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N CYS C 276 " --> pdb=" O THR C 291 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N SER C 293 " --> pdb=" O CYS C 274 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N CYS C 274 " --> pdb=" O SER C 293 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 189 through 192 Processing sheet with id= I, first strand: chain 'C' and resid 303 through 308 removed outlier: 3.924A pdb=" N THR C 437 " --> pdb=" O HIS C 308 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 324 through 334 Processing sheet with id= K, first strand: chain 'E' and resid 4 through 6 Processing sheet with id= L, first strand: chain 'E' and resid 77 through 81 removed outlier: 6.544A pdb=" N VAL E 147 " --> pdb=" O LEU E 62 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ILE E 64 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE E 149 " --> pdb=" O ILE E 64 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU E 172 " --> pdb=" O ALA E 148 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N TYR E 150 " --> pdb=" O LEU E 172 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N TYR E 174 " --> pdb=" O TYR E 150 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ARG E 289 " --> pdb=" O THR E 278 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N THR E 278 " --> pdb=" O ARG E 289 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N THR E 291 " --> pdb=" O CYS E 276 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N CYS E 276 " --> pdb=" O THR E 291 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N SER E 293 " --> pdb=" O CYS E 274 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N CYS E 274 " --> pdb=" O SER E 293 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 189 through 192 Processing sheet with id= N, first strand: chain 'E' and resid 303 through 308 removed outlier: 3.919A pdb=" N THR E 437 " --> pdb=" O HIS E 308 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 324 through 334 Processing sheet with id= P, first strand: chain 'G' and resid 4 through 6 Processing sheet with id= Q, first strand: chain 'G' and resid 77 through 79 removed outlier: 6.616A pdb=" N VAL G 147 " --> pdb=" O LEU G 62 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ILE G 64 " --> pdb=" O VAL G 147 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE G 149 " --> pdb=" O ILE G 64 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU G 172 " --> pdb=" O ALA G 148 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N TYR G 150 " --> pdb=" O LEU G 172 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TYR G 174 " --> pdb=" O TYR G 150 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ARG G 289 " --> pdb=" O THR G 278 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N THR G 278 " --> pdb=" O ARG G 289 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N THR G 291 " --> pdb=" O CYS G 276 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N CYS G 276 " --> pdb=" O THR G 291 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N SER G 293 " --> pdb=" O CYS G 274 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N CYS G 274 " --> pdb=" O SER G 293 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'G' and resid 189 through 192 Processing sheet with id= S, first strand: chain 'G' and resid 303 through 308 removed outlier: 3.925A pdb=" N THR G 437 " --> pdb=" O HIS G 308 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'G' and resid 324 through 334 Processing sheet with id= U, first strand: chain 'I' and resid 4 through 6 Processing sheet with id= V, first strand: chain 'I' and resid 77 through 79 removed outlier: 6.589A pdb=" N VAL I 147 " --> pdb=" O LEU I 62 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N ILE I 64 " --> pdb=" O VAL I 147 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE I 149 " --> pdb=" O ILE I 64 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU I 172 " --> pdb=" O ALA I 148 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N TYR I 150 " --> pdb=" O LEU I 172 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N TYR I 174 " --> pdb=" O TYR I 150 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ARG I 289 " --> pdb=" O THR I 278 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N THR I 278 " --> pdb=" O ARG I 289 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N THR I 291 " --> pdb=" O CYS I 276 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N CYS I 276 " --> pdb=" O THR I 291 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N SER I 293 " --> pdb=" O CYS I 274 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N CYS I 274 " --> pdb=" O SER I 293 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'I' and resid 189 through 192 Processing sheet with id= X, first strand: chain 'I' and resid 303 through 308 removed outlier: 3.942A pdb=" N THR I 437 " --> pdb=" O HIS I 308 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'I' and resid 324 through 334 Processing sheet with id= Z, first strand: chain 'K' and resid 4 through 6 Processing sheet with id= AA, first strand: chain 'K' and resid 61 through 64 removed outlier: 6.581A pdb=" N VAL K 147 " --> pdb=" O LEU K 62 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N ILE K 64 " --> pdb=" O VAL K 147 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ILE K 149 " --> pdb=" O ILE K 64 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU K 172 " --> pdb=" O ALA K 148 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N TYR K 150 " --> pdb=" O LEU K 172 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N TYR K 174 " --> pdb=" O TYR K 150 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ARG K 289 " --> pdb=" O THR K 278 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N THR K 278 " --> pdb=" O ARG K 289 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N THR K 291 " --> pdb=" O CYS K 276 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N CYS K 276 " --> pdb=" O THR K 291 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N SER K 293 " --> pdb=" O CYS K 274 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N CYS K 274 " --> pdb=" O SER K 293 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'K' and resid 189 through 192 Processing sheet with id= AC, first strand: chain 'K' and resid 303 through 308 removed outlier: 3.909A pdb=" N THR K 437 " --> pdb=" O HIS K 308 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'K' and resid 324 through 334 Processing sheet with id= AE, first strand: chain 'M' and resid 4 through 6 Processing sheet with id= AF, first strand: chain 'M' and resid 77 through 81 removed outlier: 6.639A pdb=" N VAL M 147 " --> pdb=" O LEU M 62 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ILE M 64 " --> pdb=" O VAL M 147 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE M 149 " --> pdb=" O ILE M 64 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU M 172 " --> pdb=" O ALA M 148 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N TYR M 150 " --> pdb=" O LEU M 172 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TYR M 174 " --> pdb=" O TYR M 150 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ARG M 289 " --> pdb=" O THR M 278 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N THR M 278 " --> pdb=" O ARG M 289 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N THR M 291 " --> pdb=" O CYS M 276 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N CYS M 276 " --> pdb=" O THR M 291 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N SER M 293 " --> pdb=" O CYS M 274 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N CYS M 274 " --> pdb=" O SER M 293 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'M' and resid 189 through 192 Processing sheet with id= AH, first strand: chain 'M' and resid 303 through 308 removed outlier: 3.958A pdb=" N THR M 437 " --> pdb=" O HIS M 308 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'M' and resid 324 through 334 Processing sheet with id= AJ, first strand: chain 'O' and resid 4 through 6 Processing sheet with id= AK, first strand: chain 'O' and resid 77 through 81 removed outlier: 6.622A pdb=" N VAL O 147 " --> pdb=" O LEU O 62 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N ILE O 64 " --> pdb=" O VAL O 147 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE O 149 " --> pdb=" O ILE O 64 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU O 172 " --> pdb=" O ALA O 148 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N TYR O 150 " --> pdb=" O LEU O 172 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TYR O 174 " --> pdb=" O TYR O 150 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ARG O 289 " --> pdb=" O THR O 278 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N THR O 278 " --> pdb=" O ARG O 289 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N THR O 291 " --> pdb=" O CYS O 276 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N CYS O 276 " --> pdb=" O THR O 291 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N SER O 293 " --> pdb=" O CYS O 274 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N CYS O 274 " --> pdb=" O SER O 293 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'O' and resid 189 through 192 Processing sheet with id= AM, first strand: chain 'O' and resid 303 through 308 removed outlier: 3.910A pdb=" N THR O 437 " --> pdb=" O HIS O 308 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'O' and resid 324 through 334 Processing sheet with id= AO, first strand: chain 'Q' and resid 4 through 6 Processing sheet with id= AP, first strand: chain 'Q' and resid 77 through 81 removed outlier: 6.509A pdb=" N VAL Q 147 " --> pdb=" O LEU Q 62 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ILE Q 64 " --> pdb=" O VAL Q 147 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE Q 149 " --> pdb=" O ILE Q 64 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU Q 172 " --> pdb=" O ALA Q 148 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N TYR Q 150 " --> pdb=" O LEU Q 172 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N TYR Q 174 " --> pdb=" O TYR Q 150 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ARG Q 289 " --> pdb=" O THR Q 278 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N THR Q 278 " --> pdb=" O ARG Q 289 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N THR Q 291 " --> pdb=" O CYS Q 276 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N CYS Q 276 " --> pdb=" O THR Q 291 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N SER Q 293 " --> pdb=" O CYS Q 274 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N CYS Q 274 " --> pdb=" O SER Q 293 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'Q' and resid 189 through 192 Processing sheet with id= AR, first strand: chain 'Q' and resid 303 through 308 removed outlier: 3.923A pdb=" N THR Q 437 " --> pdb=" O HIS Q 308 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'Q' and resid 324 through 334 Processing sheet with id= AT, first strand: chain 'S' and resid 4 through 6 Processing sheet with id= AU, first strand: chain 'S' and resid 77 through 81 removed outlier: 6.598A pdb=" N VAL S 147 " --> pdb=" O LEU S 62 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ILE S 64 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE S 149 " --> pdb=" O ILE S 64 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU S 172 " --> pdb=" O ALA S 148 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N TYR S 150 " --> pdb=" O LEU S 172 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N TYR S 174 " --> pdb=" O TYR S 150 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ARG S 289 " --> pdb=" O THR S 278 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N THR S 278 " --> pdb=" O ARG S 289 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N THR S 291 " --> pdb=" O CYS S 276 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N CYS S 276 " --> pdb=" O THR S 291 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N SER S 293 " --> pdb=" O CYS S 274 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N CYS S 274 " --> pdb=" O SER S 293 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'S' and resid 189 through 192 Processing sheet with id= AW, first strand: chain 'S' and resid 303 through 308 removed outlier: 3.976A pdb=" N THR S 437 " --> pdb=" O HIS S 308 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'S' and resid 324 through 334 Processing sheet with id= AY, first strand: chain 'V' and resid 4 through 6 Processing sheet with id= AZ, first strand: chain 'V' and resid 77 through 81 removed outlier: 6.617A pdb=" N VAL V 147 " --> pdb=" O LEU V 62 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ILE V 64 " --> pdb=" O VAL V 147 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE V 149 " --> pdb=" O ILE V 64 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU V 172 " --> pdb=" O ALA V 148 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N TYR V 150 " --> pdb=" O LEU V 172 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TYR V 174 " --> pdb=" O TYR V 150 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ARG V 289 " --> pdb=" O THR V 278 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N THR V 278 " --> pdb=" O ARG V 289 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N THR V 291 " --> pdb=" O CYS V 276 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N CYS V 276 " --> pdb=" O THR V 291 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N SER V 293 " --> pdb=" O CYS V 274 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N CYS V 274 " --> pdb=" O SER V 293 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'V' and resid 189 through 192 Processing sheet with id= BB, first strand: chain 'V' and resid 303 through 308 removed outlier: 3.927A pdb=" N THR V 437 " --> pdb=" O HIS V 308 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'V' and resid 324 through 334 Processing sheet with id= BD, first strand: chain 'X' and resid 4 through 6 Processing sheet with id= BE, first strand: chain 'X' and resid 77 through 81 removed outlier: 6.554A pdb=" N VAL X 147 " --> pdb=" O LEU X 62 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ILE X 64 " --> pdb=" O VAL X 147 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ILE X 149 " --> pdb=" O ILE X 64 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU X 172 " --> pdb=" O ALA X 148 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N TYR X 150 " --> pdb=" O LEU X 172 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N TYR X 174 " --> pdb=" O TYR X 150 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ARG X 289 " --> pdb=" O THR X 278 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N THR X 278 " --> pdb=" O ARG X 289 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N THR X 291 " --> pdb=" O CYS X 276 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N CYS X 276 " --> pdb=" O THR X 291 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N SER X 293 " --> pdb=" O CYS X 274 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N CYS X 274 " --> pdb=" O SER X 293 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'X' and resid 189 through 192 Processing sheet with id= BG, first strand: chain 'X' and resid 303 through 308 removed outlier: 3.926A pdb=" N THR X 437 " --> pdb=" O HIS X 308 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'X' and resid 324 through 334 1622 hydrogen bonds defined for protein. 4032 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: 16.77 Time building geometry restraints manager: 20.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 13826 1.35 - 1.47: 10173 1.47 - 1.59: 19081 1.59 - 1.71: 60 1.71 - 1.83: 504 Bond restraints: 43644 Sorted by residual: bond pdb=" C ASP I 89 " pdb=" N PRO I 90 " ideal model delta sigma weight residual 1.336 1.359 -0.023 1.20e-02 6.94e+03 3.79e+00 bond pdb=" CB MET K 73 " pdb=" CG MET K 73 " ideal model delta sigma weight residual 1.520 1.565 -0.045 3.00e-02 1.11e+03 2.24e+00 bond pdb=" CA MET C 73 " pdb=" CB MET C 73 " ideal model delta sigma weight residual 1.527 1.543 -0.016 1.15e-02 7.56e+03 1.92e+00 bond pdb=" CA MET K 73 " pdb=" CB MET K 73 " ideal model delta sigma weight residual 1.527 1.542 -0.015 1.15e-02 7.56e+03 1.80e+00 bond pdb=" CA ASP C 89 " pdb=" C ASP C 89 " ideal model delta sigma weight residual 1.525 1.553 -0.028 2.10e-02 2.27e+03 1.78e+00 ... (remaining 43639 not shown) Histogram of bond angle deviations from ideal: 96.78 - 104.23: 756 104.23 - 111.68: 20812 111.68 - 119.12: 14705 119.12 - 126.57: 22422 126.57 - 134.01: 669 Bond angle restraints: 59364 Sorted by residual: angle pdb=" CB MET K 123 " pdb=" CG MET K 123 " pdb=" SD MET K 123 " ideal model delta sigma weight residual 112.70 125.46 -12.76 3.00e+00 1.11e-01 1.81e+01 angle pdb=" CB MET K 73 " pdb=" CG MET K 73 " pdb=" SD MET K 73 " ideal model delta sigma weight residual 112.70 124.54 -11.84 3.00e+00 1.11e-01 1.56e+01 angle pdb=" N ASP C 89 " pdb=" CA ASP C 89 " pdb=" C ASP C 89 " ideal model delta sigma weight residual 111.00 119.55 -8.55 2.80e+00 1.28e-01 9.33e+00 angle pdb=" CA LYS C 231 " pdb=" CB LYS C 231 " pdb=" CG LYS C 231 " ideal model delta sigma weight residual 114.10 120.17 -6.07 2.00e+00 2.50e-01 9.21e+00 angle pdb=" CB MET Q 123 " pdb=" CG MET Q 123 " pdb=" SD MET Q 123 " ideal model delta sigma weight residual 112.70 120.81 -8.11 3.00e+00 1.11e-01 7.30e+00 ... (remaining 59359 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.90: 25582 33.90 - 67.81: 805 67.81 - 101.71: 37 101.71 - 135.62: 0 135.62 - 169.52: 12 Dihedral angle restraints: 26436 sinusoidal: 10428 harmonic: 16008 Sorted by residual: dihedral pdb=" C8 GTP I 602 " pdb=" C1' GTP I 602 " pdb=" N9 GTP I 602 " pdb=" O4' GTP I 602 " ideal model delta sinusoidal sigma weight residual 104.59 -85.88 -169.52 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" C8 GTP X 602 " pdb=" C1' GTP X 602 " pdb=" N9 GTP X 602 " pdb=" O4' GTP X 602 " ideal model delta sinusoidal sigma weight residual 104.59 -86.71 -168.70 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" C8 GTP Q 602 " pdb=" C1' GTP Q 602 " pdb=" N9 GTP Q 602 " pdb=" O4' GTP Q 602 " ideal model delta sinusoidal sigma weight residual 104.59 -86.88 -168.53 1 2.00e+01 2.50e-03 4.75e+01 ... (remaining 26433 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 4636 0.036 - 0.073: 1422 0.073 - 0.109: 514 0.109 - 0.145: 158 0.145 - 0.181: 2 Chirality restraints: 6732 Sorted by residual: chirality pdb=" CA ASP C 89 " pdb=" N ASP C 89 " pdb=" C ASP C 89 " pdb=" CB ASP C 89 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.23e-01 chirality pdb=" CB ILE G 440 " pdb=" CA ILE G 440 " pdb=" CG1 ILE G 440 " pdb=" CG2 ILE G 440 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.88e-01 chirality pdb=" CB ILE V 440 " pdb=" CA ILE V 440 " pdb=" CG1 ILE V 440 " pdb=" CG2 ILE V 440 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 4.93e-01 ... (remaining 6729 not shown) Planarity restraints: 7488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP O 56 " 0.037 5.00e-02 4.00e+02 5.55e-02 4.93e+00 pdb=" N PRO O 57 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO O 57 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO O 57 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP V 56 " -0.035 5.00e-02 4.00e+02 5.23e-02 4.37e+00 pdb=" N PRO V 57 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO V 57 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO V 57 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU I 234 " 0.034 5.00e-02 4.00e+02 5.20e-02 4.32e+00 pdb=" N PRO I 235 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO I 235 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO I 235 " 0.029 5.00e-02 4.00e+02 ... (remaining 7485 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 536 2.61 - 3.19: 36741 3.19 - 3.76: 74527 3.76 - 4.33: 105413 4.33 - 4.90: 168030 Nonbonded interactions: 385247 Sorted by model distance: nonbonded pdb=" OE1 GLU X 129 " pdb="ZN ZN X 601 " model vdw 2.044 2.230 nonbonded pdb=" OE1 GLU G 129 " pdb="ZN ZN G 601 " model vdw 2.057 2.230 nonbonded pdb=" OE1 GLU K 129 " pdb="ZN ZN K 601 " model vdw 2.093 2.230 nonbonded pdb=" OD2 ASP S 63 " pdb=" OG SER S 66 " model vdw 2.111 2.440 nonbonded pdb=" OD2 ASP O 63 " pdb=" OG SER O 66 " model vdw 2.113 2.440 ... (remaining 385242 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 3 through 19 or resid 21 through 49 or resid 51 through 70 \ or resid 72 through 75 or resid 77 through 238 or resid 240 through 309 or resi \ d 311 through 352 or resid 354 through 472 or resid 601 through 602)) selection = (chain 'C' and (resid 3 through 19 or resid 21 through 49 or resid 51 through 70 \ or resid 72 through 75 or resid 77 through 238 or resid 240 through 309 or resi \ d 311 through 352 or resid 354 through 472 or resid 601 through 602)) selection = (chain 'E' and (resid 3 through 19 or resid 21 through 49 or resid 51 through 70 \ or resid 72 through 75 or resid 77 through 238 or resid 240 through 309 or resi \ d 311 through 352 or resid 354 through 472 or resid 601 through 602)) selection = (chain 'G' and (resid 3 through 19 or resid 21 through 49 or resid 51 through 70 \ or resid 72 through 75 or resid 77 through 238 or resid 240 through 309 or resi \ d 311 through 352 or resid 354 through 472 or resid 601 through 602)) selection = (chain 'I' and (resid 3 through 19 or resid 21 through 49 or resid 51 through 70 \ or resid 72 through 75 or resid 77 through 238 or resid 240 through 309 or resi \ d 311 through 352 or resid 354 through 472 or resid 601 through 602)) selection = (chain 'K' and (resid 3 through 19 or resid 21 through 49 or resid 51 through 70 \ or resid 72 through 75 or resid 77 through 238 or resid 240 through 309 or resi \ d 311 through 352 or resid 354 through 472 or resid 601 through 602)) selection = (chain 'M' and (resid 3 through 19 or resid 21 through 49 or resid 51 through 70 \ or resid 72 through 75 or resid 77 through 238 or resid 240 through 309 or resi \ d 311 through 352 or resid 354 through 472 or resid 601 through 602)) selection = (chain 'O' and (resid 3 through 19 or resid 21 through 49 or resid 51 through 70 \ or resid 72 through 75 or resid 77 through 238 or resid 240 through 309 or resi \ d 311 through 352 or resid 354 through 472 or resid 601 through 602)) selection = (chain 'Q' and (resid 3 through 19 or resid 21 through 49 or resid 51 through 70 \ or resid 72 through 75 or resid 77 through 238 or resid 240 through 309 or resi \ d 311 through 352 or resid 354 through 472 or resid 601 through 602)) selection = (chain 'S' and (resid 3 through 19 or resid 21 through 49 or resid 51 through 70 \ or resid 72 through 75 or resid 77 through 238 or resid 240 through 309 or resi \ d 311 through 352 or resid 354 through 472 or resid 601 through 602)) selection = (chain 'V' and (resid 3 through 19 or resid 21 through 49 or resid 51 through 70 \ or resid 72 through 75 or resid 77 through 238 or resid 240 through 309 or resi \ d 311 through 352 or resid 354 through 472 or resid 601 through 602)) selection = (chain 'X' and (resid 3 through 19 or resid 21 through 49 or resid 51 through 70 \ or resid 72 through 75 or resid 77 through 238 or resid 240 through 309 or resi \ d 311 through 352 or resid 354 through 472 or resid 601 through 602)) } 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=0.00 max=1.00 mean=0.98 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: 2.780 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: 15.770 Check model and map are aligned: 0.740 Set scattering table: 0.470 Process input model: 155.190 Find NCS groups from input model: 3.310 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 189.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 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 : 0.003 0.045 43644 Z= 0.193 Angle : 0.568 12.760 59364 Z= 0.291 Chirality : 0.042 0.181 6732 Planarity : 0.005 0.055 7488 Dihedral : 16.267 169.524 16116 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.01 % Allowed : 19.49 % Favored : 78.50 % 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 (0.11), residues: 5484 helix: 0.72 (0.12), residues: 1968 sheet: 0.32 (0.17), residues: 804 loop : -1.12 (0.11), residues: 2712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 258 HIS 0.007 0.001 HIS E 79 PHE 0.018 0.002 PHE S 264 TYR 0.015 0.001 TYR O 382 ARG 0.004 0.000 ARG I 289 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 4536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 367 time to evaluate : 3.827 Fit side-chains REVERT: A 72 MET cc_start: 0.5806 (pmm) cc_final: 0.5583 (ptp) REVERT: A 73 MET cc_start: 0.7292 (ppp) cc_final: 0.6931 (ptm) REVERT: C 73 MET cc_start: 0.6371 (ptp) cc_final: 0.5843 (ptp) REVERT: I 408 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8206 (mt) REVERT: S 357 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8323 (mttp) REVERT: X 72 MET cc_start: 0.6274 (pmm) cc_final: 0.5698 (ptm) REVERT: X 73 MET cc_start: 0.6721 (ptt) cc_final: 0.6441 (ptp) outliers start: 73 outliers final: 63 residues processed: 434 average time/residue: 1.2702 time to fit residues: 703.3662 Evaluate side-chains 421 residues out of total 4536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 356 time to evaluate : 4.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 458 SER Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 74 SER Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 274 CYS Chi-restraints excluded: chain I residue 345 ILE Chi-restraints excluded: chain I residue 386 VAL Chi-restraints excluded: chain I residue 408 LEU Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 274 CYS Chi-restraints excluded: chain K residue 296 LEU Chi-restraints excluded: chain K residue 345 ILE Chi-restraints excluded: chain K residue 410 VAL Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain O residue 44 SER Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 305 VAL Chi-restraints excluded: chain O residue 345 ILE Chi-restraints excluded: chain Q residue 60 THR Chi-restraints excluded: chain Q residue 74 SER Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 89 ASP Chi-restraints excluded: chain Q residue 315 CYS Chi-restraints excluded: chain Q residue 345 ILE Chi-restraints excluded: chain Q residue 410 VAL Chi-restraints excluded: chain S residue 81 VAL Chi-restraints excluded: chain S residue 89 ASP Chi-restraints excluded: chain S residue 153 VAL Chi-restraints excluded: chain S residue 196 SER Chi-restraints excluded: chain S residue 262 SER Chi-restraints excluded: chain S residue 274 CYS Chi-restraints excluded: chain S residue 305 VAL Chi-restraints excluded: chain S residue 330 VAL Chi-restraints excluded: chain S residue 357 LYS Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 296 LEU Chi-restraints excluded: chain V residue 315 CYS Chi-restraints excluded: chain V residue 345 ILE Chi-restraints excluded: chain X residue 60 THR Chi-restraints excluded: chain X residue 81 VAL Chi-restraints excluded: chain X residue 274 CYS Chi-restraints excluded: chain X residue 285 TYR Chi-restraints excluded: chain X residue 345 ILE Chi-restraints excluded: chain X residue 410 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 445 optimal weight: 8.9990 chunk 400 optimal weight: 0.9990 chunk 222 optimal weight: 3.9990 chunk 136 optimal weight: 0.8980 chunk 269 optimal weight: 10.0000 chunk 213 optimal weight: 0.6980 chunk 413 optimal weight: 0.8980 chunk 160 optimal weight: 0.6980 chunk 251 optimal weight: 7.9990 chunk 308 optimal weight: 7.9990 chunk 479 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 HIS ** I 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.0269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 43644 Z= 0.190 Angle : 0.537 9.157 59364 Z= 0.271 Chirality : 0.042 0.172 6732 Planarity : 0.004 0.044 7488 Dihedral : 9.635 169.808 6265 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.93 % Allowed : 18.02 % 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: -0.25 (0.11), residues: 5484 helix: 0.83 (0.13), residues: 1968 sheet: 0.35 (0.17), residues: 804 loop : -1.07 (0.11), residues: 2712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 258 HIS 0.004 0.001 HIS I 308 PHE 0.017 0.002 PHE I 183 TYR 0.014 0.001 TYR O 195 ARG 0.004 0.000 ARG I 289 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 4536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 370 time to evaluate : 4.780 Fit side-chains REVERT: A 72 MET cc_start: 0.5823 (pmm) cc_final: 0.5584 (ptp) REVERT: A 73 MET cc_start: 0.7382 (OUTLIER) cc_final: 0.7045 (ptm) REVERT: A 123 MET cc_start: 0.5895 (OUTLIER) cc_final: 0.4899 (tpp) REVERT: A 146 ASP cc_start: 0.7997 (OUTLIER) cc_final: 0.7461 (p0) REVERT: C 73 MET cc_start: 0.6761 (ptp) cc_final: 0.6208 (ptp) REVERT: G 345 ILE cc_start: 0.9011 (OUTLIER) cc_final: 0.8575 (tp) REVERT: I 58 ASP cc_start: 0.6600 (OUTLIER) cc_final: 0.6192 (m-30) REVERT: I 72 MET cc_start: 0.5645 (pmm) cc_final: 0.5233 (ptp) REVERT: I 73 MET cc_start: 0.7136 (OUTLIER) cc_final: 0.6563 (ptp) REVERT: I 146 ASP cc_start: 0.7989 (OUTLIER) cc_final: 0.7535 (p0) REVERT: I 408 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8215 (mt) REVERT: M 123 MET cc_start: 0.5537 (mmt) cc_final: 0.5274 (mmp) REVERT: M 146 ASP cc_start: 0.7911 (OUTLIER) cc_final: 0.7341 (p0) REVERT: M 234 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.8006 (mt-10) REVERT: O 123 MET cc_start: 0.5447 (mmm) cc_final: 0.4673 (mmp) REVERT: O 146 ASP cc_start: 0.8096 (OUTLIER) cc_final: 0.7567 (p0) REVERT: Q 72 MET cc_start: 0.5668 (ptm) cc_final: 0.5403 (pmm) REVERT: S 234 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.8100 (mt-10) outliers start: 114 outliers final: 56 residues processed: 450 average time/residue: 1.2408 time to fit residues: 715.0802 Evaluate side-chains 427 residues out of total 4536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 359 time to evaluate : 4.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 274 CYS Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain I residue 73 MET Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 146 ASP Chi-restraints excluded: chain I residue 345 ILE Chi-restraints excluded: chain I residue 408 LEU Chi-restraints excluded: chain K residue 58 ASP Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 345 ILE Chi-restraints excluded: chain K residue 410 VAL Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 146 ASP Chi-restraints excluded: chain M residue 234 GLU Chi-restraints excluded: chain M residue 253 LYS Chi-restraints excluded: chain M residue 274 CYS Chi-restraints excluded: chain O residue 58 ASP Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 274 CYS Chi-restraints excluded: chain O residue 345 ILE Chi-restraints excluded: chain Q residue 58 ASP Chi-restraints excluded: chain Q residue 60 THR Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 234 GLU Chi-restraints excluded: chain Q residue 315 CYS Chi-restraints excluded: chain Q residue 345 ILE Chi-restraints excluded: chain Q residue 386 VAL Chi-restraints excluded: chain S residue 81 VAL Chi-restraints excluded: chain S residue 153 VAL Chi-restraints excluded: chain S residue 234 GLU Chi-restraints excluded: chain S residue 246 THR Chi-restraints excluded: chain S residue 274 CYS Chi-restraints excluded: chain V residue 58 ASP Chi-restraints excluded: chain V residue 66 SER Chi-restraints excluded: chain V residue 74 SER Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 89 ASP Chi-restraints excluded: chain V residue 296 LEU Chi-restraints excluded: chain V residue 315 CYS Chi-restraints excluded: chain V residue 345 ILE Chi-restraints excluded: chain X residue 58 ASP Chi-restraints excluded: chain X residue 60 THR Chi-restraints excluded: chain X residue 81 VAL Chi-restraints excluded: chain X residue 274 CYS Chi-restraints excluded: chain X residue 285 TYR Chi-restraints excluded: chain X residue 345 ILE Chi-restraints excluded: chain X residue 386 VAL Chi-restraints excluded: chain X residue 410 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 266 optimal weight: 3.9990 chunk 148 optimal weight: 7.9990 chunk 399 optimal weight: 3.9990 chunk 326 optimal weight: 3.9990 chunk 132 optimal weight: 7.9990 chunk 480 optimal weight: 3.9990 chunk 518 optimal weight: 0.9990 chunk 427 optimal weight: 4.9990 chunk 476 optimal weight: 2.9990 chunk 163 optimal weight: 6.9990 chunk 385 optimal weight: 0.5980 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 381 ASN ** I 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 203 GLN ** O 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.0702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 43644 Z= 0.399 Angle : 0.633 9.343 59364 Z= 0.324 Chirality : 0.046 0.180 6732 Planarity : 0.005 0.044 7488 Dihedral : 9.939 172.830 6229 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.59 % Allowed : 17.45 % Favored : 78.96 % 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 (0.11), residues: 5484 helix: 0.69 (0.12), residues: 1956 sheet: 0.37 (0.17), residues: 804 loop : -1.10 (0.11), residues: 2724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 258 HIS 0.007 0.002 HIS K 37 PHE 0.023 0.003 PHE S 183 TYR 0.020 0.002 TYR O 195 ARG 0.007 0.001 ARG M 252 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 4536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 369 time to evaluate : 4.948 Fit side-chains REVERT: A 146 ASP cc_start: 0.8005 (OUTLIER) cc_final: 0.7503 (p0) REVERT: A 250 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7521 (mm-30) REVERT: C 73 MET cc_start: 0.6837 (ptp) cc_final: 0.6340 (ptt) REVERT: C 146 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.7417 (p0) REVERT: G 146 ASP cc_start: 0.7951 (OUTLIER) cc_final: 0.7416 (p0) REVERT: G 234 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8125 (mt-10) REVERT: I 58 ASP cc_start: 0.6457 (OUTLIER) cc_final: 0.6214 (m-30) REVERT: I 72 MET cc_start: 0.5634 (pmm) cc_final: 0.5152 (ptp) REVERT: I 73 MET cc_start: 0.7136 (OUTLIER) cc_final: 0.6148 (ppp) REVERT: I 146 ASP cc_start: 0.7983 (OUTLIER) cc_final: 0.7457 (p0) REVERT: I 228 MET cc_start: 0.6400 (OUTLIER) cc_final: 0.6006 (pmm) REVERT: I 402 MET cc_start: 0.8375 (mtm) cc_final: 0.7973 (mtm) REVERT: M 123 MET cc_start: 0.5673 (mmt) cc_final: 0.5376 (mmp) REVERT: M 146 ASP cc_start: 0.7995 (OUTLIER) cc_final: 0.7447 (p0) REVERT: M 234 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8116 (mt-10) REVERT: O 123 MET cc_start: 0.5425 (mmm) cc_final: 0.4755 (mmp) REVERT: O 146 ASP cc_start: 0.8137 (OUTLIER) cc_final: 0.7520 (p0) REVERT: Q 72 MET cc_start: 0.5647 (ptm) cc_final: 0.5337 (pmm) REVERT: S 146 ASP cc_start: 0.7950 (OUTLIER) cc_final: 0.7448 (p0) REVERT: S 234 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8134 (mt-10) REVERT: V 146 ASP cc_start: 0.8223 (OUTLIER) cc_final: 0.7589 (p0) REVERT: X 146 ASP cc_start: 0.8000 (OUTLIER) cc_final: 0.7798 (p0) outliers start: 137 outliers final: 71 residues processed: 470 average time/residue: 1.2733 time to fit residues: 766.5027 Evaluate side-chains 453 residues out of total 4536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 366 time to evaluate : 4.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 396 LYS Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 315 CYS Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 146 ASP Chi-restraints excluded: chain G residue 232 LYS Chi-restraints excluded: chain G residue 234 GLU Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain I residue 73 MET Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 146 ASP Chi-restraints excluded: chain I residue 228 MET Chi-restraints excluded: chain I residue 315 CYS Chi-restraints excluded: chain I residue 345 ILE Chi-restraints excluded: chain I residue 408 LEU Chi-restraints excluded: chain K residue 58 ASP Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 74 SER Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 315 CYS Chi-restraints excluded: chain K residue 345 ILE Chi-restraints excluded: chain K residue 410 VAL Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 146 ASP Chi-restraints excluded: chain M residue 234 GLU Chi-restraints excluded: chain M residue 253 LYS Chi-restraints excluded: chain M residue 345 ILE Chi-restraints excluded: chain O residue 58 ASP Chi-restraints excluded: chain O residue 74 SER Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 274 CYS Chi-restraints excluded: chain O residue 315 CYS Chi-restraints excluded: chain O residue 345 ILE Chi-restraints excluded: chain O residue 402 MET Chi-restraints excluded: chain Q residue 58 ASP Chi-restraints excluded: chain Q residue 60 THR Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 234 GLU Chi-restraints excluded: chain Q residue 315 CYS Chi-restraints excluded: chain Q residue 345 ILE Chi-restraints excluded: chain Q residue 386 VAL Chi-restraints excluded: chain Q residue 410 VAL Chi-restraints excluded: chain S residue 81 VAL Chi-restraints excluded: chain S residue 146 ASP Chi-restraints excluded: chain S residue 153 VAL Chi-restraints excluded: chain S residue 234 GLU Chi-restraints excluded: chain S residue 246 THR Chi-restraints excluded: chain S residue 274 CYS Chi-restraints excluded: chain V residue 44 SER Chi-restraints excluded: chain V residue 58 ASP Chi-restraints excluded: chain V residue 66 SER Chi-restraints excluded: chain V residue 74 SER Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 146 ASP Chi-restraints excluded: chain V residue 296 LEU Chi-restraints excluded: chain V residue 315 CYS Chi-restraints excluded: chain V residue 345 ILE Chi-restraints excluded: chain X residue 58 ASP Chi-restraints excluded: chain X residue 60 THR Chi-restraints excluded: chain X residue 81 VAL Chi-restraints excluded: chain X residue 146 ASP Chi-restraints excluded: chain X residue 274 CYS Chi-restraints excluded: chain X residue 285 TYR Chi-restraints excluded: chain X residue 345 ILE Chi-restraints excluded: chain X residue 386 VAL Chi-restraints excluded: chain X residue 410 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 474 optimal weight: 2.9990 chunk 361 optimal weight: 6.9990 chunk 249 optimal weight: 0.5980 chunk 53 optimal weight: 8.9990 chunk 229 optimal weight: 9.9990 chunk 322 optimal weight: 3.9990 chunk 482 optimal weight: 2.9990 chunk 510 optimal weight: 0.9980 chunk 251 optimal weight: 0.9990 chunk 456 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 381 ASN ** O 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.0692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 43644 Z= 0.294 Angle : 0.585 10.497 59364 Z= 0.298 Chirality : 0.044 0.165 6732 Planarity : 0.005 0.043 7488 Dihedral : 9.840 172.136 6229 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.61 % Allowed : 17.45 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.11), residues: 5484 helix: 0.97 (0.13), residues: 1884 sheet: 0.40 (0.17), residues: 804 loop : -1.05 (0.11), residues: 2796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 258 HIS 0.005 0.001 HIS I 308 PHE 0.019 0.002 PHE A 183 TYR 0.016 0.002 TYR O 195 ARG 0.005 0.000 ARG C 252 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 4536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 367 time to evaluate : 4.820 Fit side-chains REVERT: A 72 MET cc_start: 0.5606 (pmm) cc_final: 0.5329 (ptp) REVERT: A 123 MET cc_start: 0.5541 (mmp) cc_final: 0.4700 (tpp) REVERT: A 146 ASP cc_start: 0.7999 (OUTLIER) cc_final: 0.7486 (p0) REVERT: A 250 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7424 (mm-30) REVERT: C 73 MET cc_start: 0.6753 (ptp) cc_final: 0.6286 (ptp) REVERT: C 146 ASP cc_start: 0.8098 (OUTLIER) cc_final: 0.7391 (p0) REVERT: G 123 MET cc_start: 0.5476 (mmp) cc_final: 0.5208 (mmp) REVERT: G 146 ASP cc_start: 0.7944 (OUTLIER) cc_final: 0.7422 (p0) REVERT: G 234 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.8116 (mt-10) REVERT: I 58 ASP cc_start: 0.6475 (OUTLIER) cc_final: 0.6262 (m-30) REVERT: I 72 MET cc_start: 0.5537 (pmm) cc_final: 0.5150 (ptp) REVERT: I 73 MET cc_start: 0.7169 (OUTLIER) cc_final: 0.6159 (ppp) REVERT: I 146 ASP cc_start: 0.7970 (OUTLIER) cc_final: 0.7462 (p0) REVERT: I 228 MET cc_start: 0.6392 (OUTLIER) cc_final: 0.6020 (pmm) REVERT: I 402 MET cc_start: 0.8347 (mtm) cc_final: 0.7936 (mtm) REVERT: M 123 MET cc_start: 0.5824 (mmt) cc_final: 0.5555 (mmp) REVERT: M 146 ASP cc_start: 0.7983 (OUTLIER) cc_final: 0.7418 (p0) REVERT: M 234 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8093 (mt-10) REVERT: O 123 MET cc_start: 0.5439 (mmm) cc_final: 0.4821 (mmp) REVERT: O 146 ASP cc_start: 0.8147 (OUTLIER) cc_final: 0.7466 (p0) REVERT: O 232 LYS cc_start: 0.7814 (pttp) cc_final: 0.7590 (ptmm) REVERT: Q 72 MET cc_start: 0.5677 (ptm) cc_final: 0.5362 (pmm) REVERT: S 146 ASP cc_start: 0.7951 (OUTLIER) cc_final: 0.7437 (p0) REVERT: V 146 ASP cc_start: 0.8216 (OUTLIER) cc_final: 0.7591 (p0) outliers start: 137 outliers final: 80 residues processed: 470 average time/residue: 1.2937 time to fit residues: 777.5670 Evaluate side-chains 461 residues out of total 4536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 367 time to evaluate : 4.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 396 LYS Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 315 CYS Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain G residue 16 LYS Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 146 ASP Chi-restraints excluded: chain G residue 234 GLU Chi-restraints excluded: chain G residue 315 CYS Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain I residue 73 MET Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 146 ASP Chi-restraints excluded: chain I residue 228 MET Chi-restraints excluded: chain I residue 274 CYS Chi-restraints excluded: chain I residue 315 CYS Chi-restraints excluded: chain I residue 345 ILE Chi-restraints excluded: chain I residue 408 LEU Chi-restraints excluded: chain K residue 58 ASP Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 74 SER Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 274 CYS Chi-restraints excluded: chain K residue 315 CYS Chi-restraints excluded: chain K residue 345 ILE Chi-restraints excluded: chain K residue 386 VAL Chi-restraints excluded: chain K residue 410 VAL Chi-restraints excluded: chain M residue 16 LYS Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 146 ASP Chi-restraints excluded: chain M residue 234 GLU Chi-restraints excluded: chain M residue 253 LYS Chi-restraints excluded: chain M residue 315 CYS Chi-restraints excluded: chain M residue 345 ILE Chi-restraints excluded: chain O residue 58 ASP Chi-restraints excluded: chain O residue 74 SER Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 274 CYS Chi-restraints excluded: chain O residue 315 CYS Chi-restraints excluded: chain O residue 345 ILE Chi-restraints excluded: chain O residue 402 MET Chi-restraints excluded: chain Q residue 58 ASP Chi-restraints excluded: chain Q residue 60 THR Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 234 GLU Chi-restraints excluded: chain Q residue 274 CYS Chi-restraints excluded: chain Q residue 315 CYS Chi-restraints excluded: chain Q residue 345 ILE Chi-restraints excluded: chain Q residue 386 VAL Chi-restraints excluded: chain Q residue 410 VAL Chi-restraints excluded: chain S residue 81 VAL Chi-restraints excluded: chain S residue 146 ASP Chi-restraints excluded: chain S residue 246 THR Chi-restraints excluded: chain S residue 274 CYS Chi-restraints excluded: chain V residue 44 SER Chi-restraints excluded: chain V residue 58 ASP Chi-restraints excluded: chain V residue 66 SER Chi-restraints excluded: chain V residue 74 SER Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 146 ASP Chi-restraints excluded: chain V residue 274 CYS Chi-restraints excluded: chain V residue 296 LEU Chi-restraints excluded: chain V residue 315 CYS Chi-restraints excluded: chain V residue 345 ILE Chi-restraints excluded: chain X residue 58 ASP Chi-restraints excluded: chain X residue 60 THR Chi-restraints excluded: chain X residue 81 VAL Chi-restraints excluded: chain X residue 274 CYS Chi-restraints excluded: chain X residue 285 TYR Chi-restraints excluded: chain X residue 345 ILE Chi-restraints excluded: chain X residue 386 VAL Chi-restraints excluded: chain X residue 410 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 425 optimal weight: 0.9980 chunk 289 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 380 optimal weight: 1.9990 chunk 210 optimal weight: 0.6980 chunk 435 optimal weight: 0.0040 chunk 352 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 260 optimal weight: 7.9990 chunk 458 optimal weight: 0.7980 chunk 128 optimal weight: 7.9990 overall best weight: 0.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 165 GLN ** I 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.0608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 43644 Z= 0.195 Angle : 0.536 10.516 59364 Z= 0.271 Chirality : 0.042 0.159 6732 Planarity : 0.004 0.041 7488 Dihedral : 9.619 170.946 6228 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.22 % Allowed : 17.83 % Favored : 78.96 % 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: -0.21 (0.11), residues: 5484 helix: 0.88 (0.13), residues: 1956 sheet: 0.36 (0.17), residues: 804 loop : -1.05 (0.11), residues: 2724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 258 HIS 0.003 0.001 HIS I 308 PHE 0.015 0.002 PHE A 183 TYR 0.012 0.001 TYR O 195 ARG 0.003 0.000 ARG C 252 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 4536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 379 time to evaluate : 5.065 Fit side-chains REVERT: A 72 MET cc_start: 0.5614 (pmm) cc_final: 0.5367 (ptp) REVERT: A 146 ASP cc_start: 0.7981 (OUTLIER) cc_final: 0.7469 (p0) REVERT: A 250 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7351 (mm-30) REVERT: C 73 MET cc_start: 0.6700 (ptp) cc_final: 0.6267 (ptp) REVERT: C 146 ASP cc_start: 0.8178 (OUTLIER) cc_final: 0.7445 (p0) REVERT: G 123 MET cc_start: 0.5648 (mmp) cc_final: 0.5301 (mmp) REVERT: I 73 MET cc_start: 0.7127 (OUTLIER) cc_final: 0.6124 (ppp) REVERT: I 146 ASP cc_start: 0.7963 (OUTLIER) cc_final: 0.7480 (p0) REVERT: I 228 MET cc_start: 0.6441 (OUTLIER) cc_final: 0.6073 (pmm) REVERT: I 402 MET cc_start: 0.8273 (mtm) cc_final: 0.7885 (mtm) REVERT: I 408 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8294 (mt) REVERT: K 73 MET cc_start: 0.7108 (OUTLIER) cc_final: 0.6358 (ppp) REVERT: M 123 MET cc_start: 0.5801 (mmt) cc_final: 0.5527 (mmp) REVERT: O 123 MET cc_start: 0.5364 (mmm) cc_final: 0.4800 (mmp) REVERT: Q 72 MET cc_start: 0.5850 (ptm) cc_final: 0.5554 (pmm) REVERT: Q 228 MET cc_start: 0.6439 (ppp) cc_final: 0.6163 (pmm) REVERT: S 234 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8121 (mt-10) outliers start: 119 outliers final: 72 residues processed: 464 average time/residue: 1.3099 time to fit residues: 780.1489 Evaluate side-chains 452 residues out of total 4536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 371 time to evaluate : 4.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 315 CYS Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 315 CYS Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 73 MET Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 146 ASP Chi-restraints excluded: chain I residue 228 MET Chi-restraints excluded: chain I residue 345 ILE Chi-restraints excluded: chain I residue 408 LEU Chi-restraints excluded: chain K residue 58 ASP Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 73 MET Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 274 CYS Chi-restraints excluded: chain K residue 315 CYS Chi-restraints excluded: chain K residue 345 ILE Chi-restraints excluded: chain K residue 386 VAL Chi-restraints excluded: chain K residue 410 VAL Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 253 LYS Chi-restraints excluded: chain M residue 315 CYS Chi-restraints excluded: chain O residue 58 ASP Chi-restraints excluded: chain O residue 74 SER Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 274 CYS Chi-restraints excluded: chain O residue 345 ILE Chi-restraints excluded: chain O residue 402 MET Chi-restraints excluded: chain Q residue 58 ASP Chi-restraints excluded: chain Q residue 60 THR Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 234 GLU Chi-restraints excluded: chain Q residue 274 CYS Chi-restraints excluded: chain Q residue 315 CYS Chi-restraints excluded: chain Q residue 345 ILE Chi-restraints excluded: chain Q residue 386 VAL Chi-restraints excluded: chain Q residue 410 VAL Chi-restraints excluded: chain S residue 81 VAL Chi-restraints excluded: chain S residue 234 GLU Chi-restraints excluded: chain S residue 246 THR Chi-restraints excluded: chain S residue 274 CYS Chi-restraints excluded: chain V residue 44 SER Chi-restraints excluded: chain V residue 58 ASP Chi-restraints excluded: chain V residue 66 SER Chi-restraints excluded: chain V residue 74 SER Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 274 CYS Chi-restraints excluded: chain V residue 296 LEU Chi-restraints excluded: chain V residue 331 CYS Chi-restraints excluded: chain V residue 345 ILE Chi-restraints excluded: chain V residue 410 VAL Chi-restraints excluded: chain X residue 16 LYS Chi-restraints excluded: chain X residue 58 ASP Chi-restraints excluded: chain X residue 60 THR Chi-restraints excluded: chain X residue 81 VAL Chi-restraints excluded: chain X residue 274 CYS Chi-restraints excluded: chain X residue 285 TYR Chi-restraints excluded: chain X residue 315 CYS Chi-restraints excluded: chain X residue 345 ILE Chi-restraints excluded: chain X residue 386 VAL Chi-restraints excluded: chain X residue 410 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 171 optimal weight: 0.9980 chunk 459 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 299 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 510 optimal weight: 2.9990 chunk 424 optimal weight: 0.9990 chunk 236 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 168 optimal weight: 0.0040 chunk 268 optimal weight: 0.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 165 GLN ** I 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.0641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 43644 Z= 0.182 Angle : 0.526 10.833 59364 Z= 0.266 Chirality : 0.041 0.157 6732 Planarity : 0.004 0.040 7488 Dihedral : 9.493 170.287 6227 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.08 % Allowed : 18.20 % Favored : 78.72 % 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: 5484 helix: 0.98 (0.13), residues: 1956 sheet: 0.32 (0.17), residues: 804 loop : -1.02 (0.11), residues: 2724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 258 HIS 0.003 0.001 HIS C 37 PHE 0.014 0.002 PHE A 183 TYR 0.012 0.001 TYR O 195 ARG 0.003 0.000 ARG C 252 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 4536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 372 time to evaluate : 4.032 Fit side-chains REVERT: A 72 MET cc_start: 0.5781 (pmm) cc_final: 0.5517 (ptp) REVERT: A 146 ASP cc_start: 0.7984 (OUTLIER) cc_final: 0.7465 (p0) REVERT: C 73 MET cc_start: 0.6659 (ptp) cc_final: 0.6209 (ptp) REVERT: C 146 ASP cc_start: 0.8140 (OUTLIER) cc_final: 0.7413 (p0) REVERT: E 72 MET cc_start: 0.6167 (ptm) cc_final: 0.5551 (pmm) REVERT: G 123 MET cc_start: 0.5703 (mmp) cc_final: 0.5401 (mmp) REVERT: I 72 MET cc_start: 0.5994 (ptp) cc_final: 0.5740 (pmm) REVERT: I 146 ASP cc_start: 0.8047 (OUTLIER) cc_final: 0.7581 (p0) REVERT: I 228 MET cc_start: 0.6408 (OUTLIER) cc_final: 0.6048 (pmm) REVERT: I 402 MET cc_start: 0.8211 (mtm) cc_final: 0.7829 (mtm) REVERT: I 408 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8253 (mt) REVERT: K 73 MET cc_start: 0.7042 (OUTLIER) cc_final: 0.6285 (ppp) REVERT: M 123 MET cc_start: 0.5727 (mmt) cc_final: 0.5416 (mmp) REVERT: O 123 MET cc_start: 0.5393 (mmm) cc_final: 0.4955 (mmp) REVERT: O 146 ASP cc_start: 0.8166 (OUTLIER) cc_final: 0.7478 (p0) REVERT: Q 72 MET cc_start: 0.6012 (ptm) cc_final: 0.5708 (pmm) REVERT: Q 228 MET cc_start: 0.6496 (ppp) cc_final: 0.6217 (pmm) REVERT: S 234 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8113 (mt-10) REVERT: X 228 MET cc_start: 0.6574 (ppp) cc_final: 0.6309 (pmm) outliers start: 113 outliers final: 80 residues processed: 457 average time/residue: 1.2918 time to fit residues: 759.7651 Evaluate side-chains 457 residues out of total 4536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 369 time to evaluate : 5.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 315 CYS Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 315 CYS Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 146 ASP Chi-restraints excluded: chain I residue 228 MET Chi-restraints excluded: chain I residue 274 CYS Chi-restraints excluded: chain I residue 345 ILE Chi-restraints excluded: chain I residue 408 LEU Chi-restraints excluded: chain K residue 58 ASP Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 73 MET Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 89 ASP Chi-restraints excluded: chain K residue 274 CYS Chi-restraints excluded: chain K residue 315 CYS Chi-restraints excluded: chain K residue 345 ILE Chi-restraints excluded: chain K residue 386 VAL Chi-restraints excluded: chain K residue 410 VAL Chi-restraints excluded: chain M residue 58 ASP Chi-restraints excluded: chain M residue 73 MET Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 253 LYS Chi-restraints excluded: chain M residue 315 CYS Chi-restraints excluded: chain O residue 58 ASP Chi-restraints excluded: chain O residue 74 SER Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 274 CYS Chi-restraints excluded: chain O residue 315 CYS Chi-restraints excluded: chain O residue 331 CYS Chi-restraints excluded: chain O residue 345 ILE Chi-restraints excluded: chain Q residue 58 ASP Chi-restraints excluded: chain Q residue 60 THR Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 234 GLU Chi-restraints excluded: chain Q residue 274 CYS Chi-restraints excluded: chain Q residue 315 CYS Chi-restraints excluded: chain Q residue 345 ILE Chi-restraints excluded: chain Q residue 386 VAL Chi-restraints excluded: chain Q residue 410 VAL Chi-restraints excluded: chain S residue 81 VAL Chi-restraints excluded: chain S residue 234 GLU Chi-restraints excluded: chain S residue 246 THR Chi-restraints excluded: chain S residue 274 CYS Chi-restraints excluded: chain V residue 44 SER Chi-restraints excluded: chain V residue 58 ASP Chi-restraints excluded: chain V residue 66 SER Chi-restraints excluded: chain V residue 74 SER Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 274 CYS Chi-restraints excluded: chain V residue 296 LEU Chi-restraints excluded: chain V residue 315 CYS Chi-restraints excluded: chain V residue 331 CYS Chi-restraints excluded: chain V residue 345 ILE Chi-restraints excluded: chain V residue 410 VAL Chi-restraints excluded: chain X residue 16 LYS Chi-restraints excluded: chain X residue 58 ASP Chi-restraints excluded: chain X residue 60 THR Chi-restraints excluded: chain X residue 81 VAL Chi-restraints excluded: chain X residue 274 CYS Chi-restraints excluded: chain X residue 285 TYR Chi-restraints excluded: chain X residue 315 CYS Chi-restraints excluded: chain X residue 345 ILE Chi-restraints excluded: chain X residue 386 VAL Chi-restraints excluded: chain X residue 410 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 492 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 291 optimal weight: 5.9990 chunk 373 optimal weight: 9.9990 chunk 289 optimal weight: 6.9990 chunk 430 optimal weight: 0.9990 chunk 285 optimal weight: 10.0000 chunk 508 optimal weight: 1.9990 chunk 318 optimal weight: 3.9990 chunk 310 optimal weight: 0.8980 chunk 234 optimal weight: 0.6980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 165 GLN ** I 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.0739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 43644 Z= 0.245 Angle : 0.557 11.402 59364 Z= 0.282 Chirality : 0.042 0.158 6732 Planarity : 0.004 0.039 7488 Dihedral : 9.624 171.620 6226 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.19 % Allowed : 18.04 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.11), residues: 5484 helix: 0.96 (0.13), residues: 1944 sheet: 0.37 (0.17), residues: 804 loop : -0.98 (0.11), residues: 2736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 258 HIS 0.004 0.001 HIS I 308 PHE 0.018 0.002 PHE G 183 TYR 0.014 0.002 TYR O 195 ARG 0.004 0.000 ARG Q 252 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 4536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 372 time to evaluate : 4.593 Fit side-chains REVERT: A 72 MET cc_start: 0.5785 (pmm) cc_final: 0.5512 (ptp) REVERT: A 73 MET cc_start: 0.7307 (OUTLIER) cc_final: 0.6825 (ptm) REVERT: A 146 ASP cc_start: 0.7956 (OUTLIER) cc_final: 0.7443 (p0) REVERT: C 73 MET cc_start: 0.6579 (ptp) cc_final: 0.6175 (ptp) REVERT: C 75 ASP cc_start: 0.7242 (OUTLIER) cc_final: 0.7014 (p0) REVERT: C 146 ASP cc_start: 0.8181 (OUTLIER) cc_final: 0.7417 (p0) REVERT: E 72 MET cc_start: 0.6201 (ptm) cc_final: 0.5553 (pmm) REVERT: G 123 MET cc_start: 0.5691 (mmp) cc_final: 0.5387 (mmp) REVERT: I 72 MET cc_start: 0.6004 (ptp) cc_final: 0.5736 (pmm) REVERT: I 146 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7547 (p0) REVERT: I 402 MET cc_start: 0.8281 (mtm) cc_final: 0.7886 (mtm) REVERT: I 408 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8276 (mt) REVERT: K 73 MET cc_start: 0.7002 (OUTLIER) cc_final: 0.6237 (ppp) REVERT: M 123 MET cc_start: 0.5727 (mmt) cc_final: 0.5407 (mmp) REVERT: O 72 MET cc_start: 0.5836 (pmm) cc_final: 0.5510 (ptp) REVERT: O 123 MET cc_start: 0.5400 (mmm) cc_final: 0.4827 (mmp) REVERT: O 146 ASP cc_start: 0.8164 (OUTLIER) cc_final: 0.7477 (p0) REVERT: Q 72 MET cc_start: 0.6021 (ptm) cc_final: 0.5709 (pmm) REVERT: S 234 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8193 (mt-10) REVERT: V 72 MET cc_start: 0.5791 (pmm) cc_final: 0.5405 (ptp) REVERT: V 146 ASP cc_start: 0.8169 (OUTLIER) cc_final: 0.7519 (p0) REVERT: V 402 MET cc_start: 0.8231 (mtm) cc_final: 0.7813 (mtm) REVERT: X 228 MET cc_start: 0.6554 (ppp) cc_final: 0.6318 (pmm) REVERT: X 267 LYS cc_start: 0.8162 (mtpt) cc_final: 0.7921 (mtpp) outliers start: 118 outliers final: 81 residues processed: 467 average time/residue: 1.2776 time to fit residues: 761.2139 Evaluate side-chains 460 residues out of total 4536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 369 time to evaluate : 4.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 315 CYS Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 315 CYS Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 146 ASP Chi-restraints excluded: chain I residue 274 CYS Chi-restraints excluded: chain I residue 315 CYS Chi-restraints excluded: chain I residue 345 ILE Chi-restraints excluded: chain I residue 408 LEU Chi-restraints excluded: chain K residue 58 ASP Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 73 MET Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 274 CYS Chi-restraints excluded: chain K residue 315 CYS Chi-restraints excluded: chain K residue 345 ILE Chi-restraints excluded: chain K residue 386 VAL Chi-restraints excluded: chain K residue 410 VAL Chi-restraints excluded: chain M residue 58 ASP Chi-restraints excluded: chain M residue 73 MET Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 253 LYS Chi-restraints excluded: chain M residue 315 CYS Chi-restraints excluded: chain O residue 58 ASP Chi-restraints excluded: chain O residue 74 SER Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 274 CYS Chi-restraints excluded: chain O residue 315 CYS Chi-restraints excluded: chain O residue 331 CYS Chi-restraints excluded: chain O residue 345 ILE Chi-restraints excluded: chain O residue 410 VAL Chi-restraints excluded: chain Q residue 58 ASP Chi-restraints excluded: chain Q residue 60 THR Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 234 GLU Chi-restraints excluded: chain Q residue 274 CYS Chi-restraints excluded: chain Q residue 315 CYS Chi-restraints excluded: chain Q residue 345 ILE Chi-restraints excluded: chain Q residue 386 VAL Chi-restraints excluded: chain Q residue 410 VAL Chi-restraints excluded: chain S residue 81 VAL Chi-restraints excluded: chain S residue 234 GLU Chi-restraints excluded: chain S residue 246 THR Chi-restraints excluded: chain S residue 274 CYS Chi-restraints excluded: chain V residue 44 SER Chi-restraints excluded: chain V residue 58 ASP Chi-restraints excluded: chain V residue 66 SER Chi-restraints excluded: chain V residue 74 SER Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 146 ASP Chi-restraints excluded: chain V residue 274 CYS Chi-restraints excluded: chain V residue 296 LEU Chi-restraints excluded: chain V residue 315 CYS Chi-restraints excluded: chain V residue 331 CYS Chi-restraints excluded: chain V residue 345 ILE Chi-restraints excluded: chain V residue 410 VAL Chi-restraints excluded: chain X residue 58 ASP Chi-restraints excluded: chain X residue 60 THR Chi-restraints excluded: chain X residue 81 VAL Chi-restraints excluded: chain X residue 274 CYS Chi-restraints excluded: chain X residue 285 TYR Chi-restraints excluded: chain X residue 315 CYS Chi-restraints excluded: chain X residue 345 ILE Chi-restraints excluded: chain X residue 386 VAL Chi-restraints excluded: chain X residue 410 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 314 optimal weight: 0.6980 chunk 203 optimal weight: 0.9980 chunk 303 optimal weight: 7.9990 chunk 153 optimal weight: 8.9990 chunk 99 optimal weight: 20.0000 chunk 98 optimal weight: 2.9990 chunk 323 optimal weight: 1.9990 chunk 346 optimal weight: 0.6980 chunk 251 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 400 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 165 GLN ** I 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.0768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 43644 Z= 0.239 Angle : 0.557 12.147 59364 Z= 0.282 Chirality : 0.042 0.158 6732 Planarity : 0.004 0.039 7488 Dihedral : 9.618 171.672 6226 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.97 % Allowed : 18.24 % Favored : 78.78 % 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: -0.03 (0.11), residues: 5484 helix: 1.18 (0.13), residues: 1884 sheet: 0.36 (0.17), residues: 804 loop : -0.99 (0.11), residues: 2796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 258 HIS 0.004 0.001 HIS I 308 PHE 0.018 0.002 PHE G 183 TYR 0.014 0.002 TYR G 150 ARG 0.005 0.000 ARG I 142 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 4536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 369 time to evaluate : 4.544 Fit side-chains REVERT: A 72 MET cc_start: 0.5782 (pmm) cc_final: 0.5490 (ptp) REVERT: A 73 MET cc_start: 0.7322 (OUTLIER) cc_final: 0.6835 (ptm) REVERT: A 146 ASP cc_start: 0.7942 (OUTLIER) cc_final: 0.7428 (p0) REVERT: A 250 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7383 (mm-30) REVERT: C 73 MET cc_start: 0.6561 (ptp) cc_final: 0.6150 (ptp) REVERT: C 75 ASP cc_start: 0.7220 (OUTLIER) cc_final: 0.6987 (p0) REVERT: E 72 MET cc_start: 0.6235 (ptm) cc_final: 0.5551 (pmm) REVERT: G 123 MET cc_start: 0.5684 (mmp) cc_final: 0.5413 (mmp) REVERT: G 234 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.8101 (mt-10) REVERT: I 72 MET cc_start: 0.6048 (ptp) cc_final: 0.5719 (pmm) REVERT: I 146 ASP cc_start: 0.8022 (OUTLIER) cc_final: 0.7495 (p0) REVERT: I 228 MET cc_start: 0.6423 (OUTLIER) cc_final: 0.6050 (pmm) REVERT: I 402 MET cc_start: 0.8278 (mtm) cc_final: 0.7875 (mtm) REVERT: I 408 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8290 (mt) REVERT: K 73 MET cc_start: 0.6949 (OUTLIER) cc_final: 0.6220 (ppp) REVERT: M 123 MET cc_start: 0.5741 (mmt) cc_final: 0.5404 (mmp) REVERT: M 234 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.8105 (mt-10) REVERT: O 72 MET cc_start: 0.5842 (pmm) cc_final: 0.5514 (ptp) REVERT: O 123 MET cc_start: 0.5439 (mmm) cc_final: 0.4889 (mmp) REVERT: O 146 ASP cc_start: 0.8166 (OUTLIER) cc_final: 0.7477 (p0) REVERT: Q 232 LYS cc_start: 0.7960 (pttp) cc_final: 0.7582 (ptmt) REVERT: S 234 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8189 (mt-10) REVERT: V 72 MET cc_start: 0.5795 (pmm) cc_final: 0.5413 (ptp) REVERT: V 402 MET cc_start: 0.8232 (mtm) cc_final: 0.7810 (mtm) REVERT: X 228 MET cc_start: 0.6548 (ppp) cc_final: 0.6320 (pmm) REVERT: X 267 LYS cc_start: 0.8142 (mtpt) cc_final: 0.7900 (mtpp) outliers start: 108 outliers final: 83 residues processed: 451 average time/residue: 1.3164 time to fit residues: 753.4544 Evaluate side-chains 460 residues out of total 4536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 365 time to evaluate : 4.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 396 LYS Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 315 CYS Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 234 GLU Chi-restraints excluded: chain G residue 315 CYS Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 146 ASP Chi-restraints excluded: chain I residue 228 MET Chi-restraints excluded: chain I residue 274 CYS Chi-restraints excluded: chain I residue 315 CYS Chi-restraints excluded: chain I residue 345 ILE Chi-restraints excluded: chain I residue 408 LEU Chi-restraints excluded: chain K residue 58 ASP Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 73 MET Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 274 CYS Chi-restraints excluded: chain K residue 315 CYS Chi-restraints excluded: chain K residue 345 ILE Chi-restraints excluded: chain K residue 386 VAL Chi-restraints excluded: chain K residue 410 VAL Chi-restraints excluded: chain M residue 58 ASP Chi-restraints excluded: chain M residue 73 MET Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 234 GLU Chi-restraints excluded: chain M residue 253 LYS Chi-restraints excluded: chain M residue 315 CYS Chi-restraints excluded: chain O residue 58 ASP Chi-restraints excluded: chain O residue 74 SER Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 274 CYS Chi-restraints excluded: chain O residue 315 CYS Chi-restraints excluded: chain O residue 331 CYS Chi-restraints excluded: chain O residue 345 ILE Chi-restraints excluded: chain O residue 402 MET Chi-restraints excluded: chain O residue 410 VAL Chi-restraints excluded: chain Q residue 58 ASP Chi-restraints excluded: chain Q residue 60 THR Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 234 GLU Chi-restraints excluded: chain Q residue 274 CYS Chi-restraints excluded: chain Q residue 315 CYS Chi-restraints excluded: chain Q residue 345 ILE Chi-restraints excluded: chain Q residue 386 VAL Chi-restraints excluded: chain Q residue 410 VAL Chi-restraints excluded: chain S residue 81 VAL Chi-restraints excluded: chain S residue 234 GLU Chi-restraints excluded: chain S residue 246 THR Chi-restraints excluded: chain S residue 274 CYS Chi-restraints excluded: chain V residue 58 ASP Chi-restraints excluded: chain V residue 66 SER Chi-restraints excluded: chain V residue 74 SER Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 274 CYS Chi-restraints excluded: chain V residue 296 LEU Chi-restraints excluded: chain V residue 315 CYS Chi-restraints excluded: chain V residue 331 CYS Chi-restraints excluded: chain V residue 345 ILE Chi-restraints excluded: chain V residue 410 VAL Chi-restraints excluded: chain X residue 58 ASP Chi-restraints excluded: chain X residue 60 THR Chi-restraints excluded: chain X residue 81 VAL Chi-restraints excluded: chain X residue 274 CYS Chi-restraints excluded: chain X residue 285 TYR Chi-restraints excluded: chain X residue 315 CYS Chi-restraints excluded: chain X residue 345 ILE Chi-restraints excluded: chain X residue 386 VAL Chi-restraints excluded: chain X residue 410 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 462 optimal weight: 4.9990 chunk 487 optimal weight: 0.1980 chunk 444 optimal weight: 0.9980 chunk 474 optimal weight: 0.6980 chunk 285 optimal weight: 9.9990 chunk 206 optimal weight: 0.9980 chunk 372 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 chunk 428 optimal weight: 0.8980 chunk 448 optimal weight: 9.9990 chunk 472 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 120 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.0755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 43644 Z= 0.175 Angle : 0.526 12.337 59364 Z= 0.265 Chirality : 0.041 0.160 6732 Planarity : 0.004 0.039 7488 Dihedral : 9.443 170.370 6226 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.91 % Allowed : 18.29 % Favored : 78.81 % 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: -0.10 (0.11), residues: 5484 helix: 1.06 (0.13), residues: 1944 sheet: 0.33 (0.17), residues: 804 loop : -1.02 (0.11), residues: 2736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 258 HIS 0.003 0.001 HIS C 37 PHE 0.015 0.002 PHE G 183 TYR 0.011 0.001 TYR O 195 ARG 0.008 0.000 ARG I 142 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 4536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 366 time to evaluate : 5.046 Fit side-chains REVERT: A 72 MET cc_start: 0.5838 (pmm) cc_final: 0.5551 (ptp) REVERT: A 73 MET cc_start: 0.7320 (OUTLIER) cc_final: 0.6857 (ptm) REVERT: A 250 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7328 (mm-30) REVERT: C 73 MET cc_start: 0.6543 (ptp) cc_final: 0.6129 (ptp) REVERT: E 72 MET cc_start: 0.6168 (ptm) cc_final: 0.5501 (pmm) REVERT: G 123 MET cc_start: 0.5605 (mmp) cc_final: 0.5296 (mmp) REVERT: G 234 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.8037 (mt-10) REVERT: I 72 MET cc_start: 0.6090 (ptp) cc_final: 0.5751 (pmm) REVERT: I 234 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8164 (mt-10) REVERT: I 402 MET cc_start: 0.8192 (mtm) cc_final: 0.7805 (mtm) REVERT: I 408 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8253 (mt) REVERT: M 123 MET cc_start: 0.5725 (mmt) cc_final: 0.5380 (mmp) REVERT: M 234 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.8068 (mt-10) REVERT: O 72 MET cc_start: 0.5846 (pmm) cc_final: 0.5532 (ptp) REVERT: O 123 MET cc_start: 0.5618 (mmm) cc_final: 0.5002 (mmp) REVERT: O 146 ASP cc_start: 0.8171 (OUTLIER) cc_final: 0.7480 (p0) REVERT: Q 228 MET cc_start: 0.6509 (ppp) cc_final: 0.6250 (pmm) REVERT: S 234 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8165 (mt-10) REVERT: V 72 MET cc_start: 0.5801 (pmm) cc_final: 0.5440 (ptp) REVERT: V 73 MET cc_start: 0.7252 (OUTLIER) cc_final: 0.6955 (ptt) REVERT: V 402 MET cc_start: 0.8167 (mtm) cc_final: 0.7724 (mtm) REVERT: X 228 MET cc_start: 0.6495 (ppp) cc_final: 0.6258 (pmm) REVERT: X 267 LYS cc_start: 0.8136 (mtpt) cc_final: 0.7903 (mtpp) outliers start: 105 outliers final: 76 residues processed: 445 average time/residue: 1.2894 time to fit residues: 735.4619 Evaluate side-chains 446 residues out of total 4536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 362 time to evaluate : 5.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 315 CYS Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 234 GLU Chi-restraints excluded: chain G residue 315 CYS Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 274 CYS Chi-restraints excluded: chain I residue 315 CYS Chi-restraints excluded: chain I residue 345 ILE Chi-restraints excluded: chain I residue 408 LEU Chi-restraints excluded: chain K residue 58 ASP Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 274 CYS Chi-restraints excluded: chain K residue 315 CYS Chi-restraints excluded: chain K residue 345 ILE Chi-restraints excluded: chain K residue 386 VAL Chi-restraints excluded: chain K residue 410 VAL Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 234 GLU Chi-restraints excluded: chain M residue 253 LYS Chi-restraints excluded: chain M residue 315 CYS Chi-restraints excluded: chain O residue 58 ASP Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 274 CYS Chi-restraints excluded: chain O residue 315 CYS Chi-restraints excluded: chain O residue 331 CYS Chi-restraints excluded: chain O residue 345 ILE Chi-restraints excluded: chain O residue 402 MET Chi-restraints excluded: chain O residue 410 VAL Chi-restraints excluded: chain Q residue 58 ASP Chi-restraints excluded: chain Q residue 60 THR Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 234 GLU Chi-restraints excluded: chain Q residue 274 CYS Chi-restraints excluded: chain Q residue 315 CYS Chi-restraints excluded: chain Q residue 345 ILE Chi-restraints excluded: chain Q residue 386 VAL Chi-restraints excluded: chain Q residue 410 VAL Chi-restraints excluded: chain S residue 81 VAL Chi-restraints excluded: chain S residue 234 GLU Chi-restraints excluded: chain S residue 246 THR Chi-restraints excluded: chain S residue 274 CYS Chi-restraints excluded: chain S residue 315 CYS Chi-restraints excluded: chain V residue 58 ASP Chi-restraints excluded: chain V residue 66 SER Chi-restraints excluded: chain V residue 73 MET Chi-restraints excluded: chain V residue 74 SER Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 274 CYS Chi-restraints excluded: chain V residue 296 LEU Chi-restraints excluded: chain V residue 315 CYS Chi-restraints excluded: chain V residue 331 CYS Chi-restraints excluded: chain V residue 345 ILE Chi-restraints excluded: chain V residue 410 VAL Chi-restraints excluded: chain X residue 58 ASP Chi-restraints excluded: chain X residue 60 THR Chi-restraints excluded: chain X residue 81 VAL Chi-restraints excluded: chain X residue 285 TYR Chi-restraints excluded: chain X residue 315 CYS Chi-restraints excluded: chain X residue 345 ILE Chi-restraints excluded: chain X residue 386 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 311 optimal weight: 4.9990 chunk 501 optimal weight: 0.6980 chunk 306 optimal weight: 2.9990 chunk 237 optimal weight: 0.7980 chunk 348 optimal weight: 6.9990 chunk 526 optimal weight: 0.8980 chunk 484 optimal weight: 8.9990 chunk 418 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 323 optimal weight: 0.7980 chunk 256 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 120 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.0817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 43644 Z= 0.178 Angle : 0.524 12.645 59364 Z= 0.264 Chirality : 0.041 0.157 6732 Planarity : 0.004 0.038 7488 Dihedral : 9.397 170.256 6224 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.52 % Allowed : 18.57 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.11), residues: 5484 helix: 1.06 (0.13), residues: 1956 sheet: 0.32 (0.17), residues: 804 loop : -1.00 (0.11), residues: 2724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 258 HIS 0.003 0.001 HIS C 37 PHE 0.016 0.002 PHE G 183 TYR 0.011 0.001 TYR O 195 ARG 0.007 0.000 ARG C 142 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 4536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 361 time to evaluate : 5.301 Fit side-chains REVERT: A 26 GLU cc_start: 0.7412 (tp30) cc_final: 0.7182 (tp30) REVERT: A 72 MET cc_start: 0.5852 (pmm) cc_final: 0.5541 (ptp) REVERT: A 73 MET cc_start: 0.7324 (OUTLIER) cc_final: 0.6868 (ptm) REVERT: A 250 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7332 (mm-30) REVERT: C 73 MET cc_start: 0.6533 (ptp) cc_final: 0.6112 (ptp) REVERT: E 72 MET cc_start: 0.6212 (ptm) cc_final: 0.5523 (pmm) REVERT: G 123 MET cc_start: 0.5609 (mmp) cc_final: 0.5286 (mmp) REVERT: G 234 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.8071 (mt-10) REVERT: I 72 MET cc_start: 0.6133 (ptp) cc_final: 0.5784 (pmm) REVERT: I 402 MET cc_start: 0.8185 (mtm) cc_final: 0.7817 (mtm) REVERT: I 408 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8245 (mt) REVERT: M 123 MET cc_start: 0.5651 (mmt) cc_final: 0.5288 (mmp) REVERT: M 234 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8087 (mt-10) REVERT: O 72 MET cc_start: 0.5842 (pmm) cc_final: 0.5531 (ptp) REVERT: O 123 MET cc_start: 0.5659 (mmm) cc_final: 0.5067 (mmp) REVERT: Q 228 MET cc_start: 0.6471 (ppp) cc_final: 0.6208 (pmm) REVERT: S 123 MET cc_start: 0.6327 (mmp) cc_final: 0.6093 (mmp) REVERT: S 234 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8163 (mt-10) REVERT: V 72 MET cc_start: 0.5802 (pmm) cc_final: 0.5448 (ptp) REVERT: V 73 MET cc_start: 0.7222 (OUTLIER) cc_final: 0.6898 (ptt) REVERT: V 402 MET cc_start: 0.8176 (mtm) cc_final: 0.7744 (mtm) REVERT: X 228 MET cc_start: 0.6461 (ppp) cc_final: 0.6231 (pmm) REVERT: X 267 LYS cc_start: 0.8129 (mtpt) cc_final: 0.7898 (mtpp) outliers start: 87 outliers final: 73 residues processed: 429 average time/residue: 1.3529 time to fit residues: 738.8762 Evaluate side-chains 440 residues out of total 4536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 360 time to evaluate : 4.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 315 CYS Chi-restraints excluded: chain E residue 345 ILE Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 410 VAL Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 234 GLU Chi-restraints excluded: chain G residue 315 CYS Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 274 CYS Chi-restraints excluded: chain I residue 315 CYS Chi-restraints excluded: chain I residue 345 ILE Chi-restraints excluded: chain I residue 408 LEU Chi-restraints excluded: chain K residue 58 ASP Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 74 SER Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 274 CYS Chi-restraints excluded: chain K residue 315 CYS Chi-restraints excluded: chain K residue 345 ILE Chi-restraints excluded: chain K residue 386 VAL Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 234 GLU Chi-restraints excluded: chain M residue 253 LYS Chi-restraints excluded: chain M residue 315 CYS Chi-restraints excluded: chain O residue 58 ASP Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 274 CYS Chi-restraints excluded: chain O residue 331 CYS Chi-restraints excluded: chain O residue 345 ILE Chi-restraints excluded: chain O residue 402 MET Chi-restraints excluded: chain O residue 410 VAL Chi-restraints excluded: chain Q residue 58 ASP Chi-restraints excluded: chain Q residue 60 THR Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 234 GLU Chi-restraints excluded: chain Q residue 274 CYS Chi-restraints excluded: chain Q residue 315 CYS Chi-restraints excluded: chain Q residue 345 ILE Chi-restraints excluded: chain Q residue 386 VAL Chi-restraints excluded: chain Q residue 410 VAL Chi-restraints excluded: chain S residue 81 VAL Chi-restraints excluded: chain S residue 234 GLU Chi-restraints excluded: chain S residue 246 THR Chi-restraints excluded: chain S residue 274 CYS Chi-restraints excluded: chain S residue 315 CYS Chi-restraints excluded: chain V residue 58 ASP Chi-restraints excluded: chain V residue 66 SER Chi-restraints excluded: chain V residue 73 MET Chi-restraints excluded: chain V residue 74 SER Chi-restraints excluded: chain V residue 81 VAL Chi-restraints excluded: chain V residue 274 CYS Chi-restraints excluded: chain V residue 296 LEU Chi-restraints excluded: chain V residue 315 CYS Chi-restraints excluded: chain V residue 331 CYS Chi-restraints excluded: chain V residue 345 ILE Chi-restraints excluded: chain V residue 410 VAL Chi-restraints excluded: chain X residue 58 ASP Chi-restraints excluded: chain X residue 60 THR Chi-restraints excluded: chain X residue 81 VAL Chi-restraints excluded: chain X residue 285 TYR Chi-restraints excluded: chain X residue 315 CYS Chi-restraints excluded: chain X residue 345 ILE Chi-restraints excluded: chain X residue 386 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 332 optimal weight: 5.9990 chunk 446 optimal weight: 0.8980 chunk 128 optimal weight: 6.9990 chunk 386 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 116 optimal weight: 6.9990 chunk 419 optimal weight: 0.7980 chunk 175 optimal weight: 0.7980 chunk 430 optimal weight: 0.0170 chunk 53 optimal weight: 0.9990 chunk 77 optimal weight: 0.3980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 120 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.177454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.141315 restraints weight = 245075.230| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 4.44 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3620 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3620 r_free = 0.3620 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3619 r_free = 0.3619 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3619 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.0861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 43644 Z= 0.162 Angle : 0.515 12.636 59364 Z= 0.258 Chirality : 0.041 0.157 6732 Planarity : 0.004 0.039 7488 Dihedral : 9.304 169.670 6223 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.47 % Allowed : 18.68 % Favored : 78.85 % 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: -0.03 (0.11), residues: 5484 helix: 1.11 (0.13), residues: 1956 sheet: 0.34 (0.17), residues: 804 loop : -0.98 (0.11), residues: 2724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 421 HIS 0.004 0.001 HIS C 37 PHE 0.015 0.001 PHE G 183 TYR 0.010 0.001 TYR O 195 ARG 0.007 0.000 ARG C 142 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12395.17 seconds wall clock time: 223 minutes 35.63 seconds (13415.63 seconds total)