Starting phenix.real_space_refine on Sun Mar 17 13:31:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c1p_16379/03_2024/8c1p_16379_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c1p_16379/03_2024/8c1p_16379.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c1p_16379/03_2024/8c1p_16379.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c1p_16379/03_2024/8c1p_16379.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c1p_16379/03_2024/8c1p_16379_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c1p_16379/03_2024/8c1p_16379_updated.pdb" } resolution = 2.9 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 P 2 5.49 5 S 118 5.16 5 Cl 4 4.86 5 C 11663 2.51 5 N 2850 2.21 5 O 3212 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 415": "OD1" <-> "OD2" Residue "A GLU 427": "OE1" <-> "OE2" Residue "A TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 449": "NH1" <-> "NH2" Residue "A GLU 482": "OE1" <-> "OE2" Residue "A PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 542": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 566": "OE1" <-> "OE2" Residue "A PHE 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 586": "OD1" <-> "OD2" Residue "A ARG 590": "NH1" <-> "NH2" Residue "A PHE 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 663": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 696": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 711": "NH1" <-> "NH2" Residue "A ASP 724": "OD1" <-> "OD2" Residue "A GLU 751": "OE1" <-> "OE2" Residue "A PHE 810": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 423": "OE1" <-> "OE2" Residue "B TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 443": "OD1" <-> "OD2" Residue "B TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 449": "NH1" <-> "NH2" Residue "B GLU 482": "OE1" <-> "OE2" Residue "B GLU 483": "OE1" <-> "OE2" Residue "B PHE 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 633": "OE1" <-> "OE2" Residue "B TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 663": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 684": "OE1" <-> "OE2" Residue "B TYR 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 418": "OE1" <-> "OE2" Residue "C GLU 427": "OE1" <-> "OE2" Residue "C TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 449": "NH1" <-> "NH2" Residue "C GLU 482": "OE1" <-> "OE2" Residue "C PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 566": "OE1" <-> "OE2" Residue "C PHE 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 586": "OD1" <-> "OD2" Residue "C ARG 590": "NH1" <-> "NH2" Residue "C PHE 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 663": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 696": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 701": "OE1" <-> "OE2" Residue "C ASP 756": "OD1" <-> "OD2" Residue "C PHE 810": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 427": "OE1" <-> "OE2" Residue "D TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 449": "NH1" <-> "NH2" Residue "D TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 482": "OE1" <-> "OE2" Residue "D GLU 483": "OE1" <-> "OE2" Residue "D ASP 486": "OD1" <-> "OD2" Residue "D PHE 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 690": "NH1" <-> "NH2" Residue "D TYR 696": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 701": "OE1" <-> "OE2" Residue "D TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 31": "OD1" <-> "OD2" Residue "E TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 41": "NH1" <-> "NH2" Residue "E PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 126": "OE1" <-> "OE2" Residue "E TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 202": "OE1" <-> "OE2" Residue "F PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 31": "OD1" <-> "OD2" Residue "F TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 92": "OD1" <-> "OD2" Residue "F PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 126": "OE1" <-> "OE2" Residue "F TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 31": "OD1" <-> "OD2" Residue "G TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 41": "NH1" <-> "NH2" Residue "G PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 126": "OE1" <-> "OE2" Residue "G TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 202": "OE1" <-> "OE2" Residue "H PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 31": "OD1" <-> "OD2" Residue "H TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 92": "OD1" <-> "OD2" Residue "H PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 126": "OE1" <-> "OE2" Residue "H TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17849 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 2942 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 399, 2915 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 385} Chain breaks: 2 Unresolved non-hydrogen bonds: 221 Unresolved non-hydrogen angles: 259 Unresolved non-hydrogen dihedrals: 186 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'GLU:plan': 15, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 131 Conformer: "B" Number of residues, atoms: 399, 2915 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 385} Chain breaks: 2 Unresolved non-hydrogen bonds: 221 Unresolved non-hydrogen angles: 259 Unresolved non-hydrogen dihedrals: 186 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'GLU:plan': 15, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 131 bond proxies already assigned to first conformer: 2954 Chain: "B" Number of atoms: 3021 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 399, 2984 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 385} Chain breaks: 2 Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 181 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'GLU:plan': 10, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 97 Conformer: "B" Number of residues, atoms: 399, 2984 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 385} Chain breaks: 2 Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 181 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'GLU:plan': 10, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 97 bond proxies already assigned to first conformer: 3011 Chain: "C" Number of atoms: 2949 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 399, 2931 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 385} Chain breaks: 2 Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 238 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 4, 'GLU:plan': 13, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 110 Conformer: "B" Number of residues, atoms: 399, 2931 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 385} Chain breaks: 2 Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 238 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 4, 'GLU:plan': 13, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 110 bond proxies already assigned to first conformer: 2979 Chain: "D" Number of atoms: 3005 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 399, 2968 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 385} Chain breaks: 2 Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 6, 'GLU:plan': 11, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 111 Conformer: "B" Number of residues, atoms: 399, 2968 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 385} Chain breaks: 2 Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 6, 'GLU:plan': 11, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 111 bond proxies already assigned to first conformer: 2994 Chain: "E" Number of atoms: 1361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1361 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 2, 'TRANS': 172} Chain breaks: 3 Chain: "F" Number of atoms: 1372 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 175, 1361 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 2, 'TRANS': 172} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 175, 1361 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 2, 'TRANS': 172} Chain breaks: 3 bond proxies already assigned to first conformer: 1380 Chain: "G" Number of atoms: 1361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1361 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 2, 'TRANS': 172} Chain breaks: 3 Chain: "H" Number of atoms: 1366 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 175, 1355 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 172} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 175, 1355 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 172} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 1374 Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 71 Unusual residues: {'CYZ': 1, 'OLC': 1, 'PLM': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "B" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 87 Unusual residues: {'CYZ': 1, 'OLC': 1, 'PLM': 2} Classifications: {'peptide': 1, 'undetermined': 4} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "C" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 71 Unusual residues: {'CYZ': 1, 'OLC': 1, 'PLM': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "D" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 87 Unusual residues: {'CYZ': 1, 'OLC': 1, 'PLM': 2} Classifications: {'peptide': 1, 'undetermined': 4} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "E" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 19 residue: pdb=" N AGLN A 583 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A 583 " occ=0.50 residue: pdb=" N AGLY A 584 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A 584 " occ=0.50 residue: pdb=" N ACYS A 585 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS A 585 " occ=0.50 residue: pdb=" N AASP A 586 " occ=0.50 ... (14 atoms not shown) pdb=" OD2BASP A 586 " occ=0.50 residue: pdb=" N APHE B 570 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE B 570 " occ=0.50 residue: pdb=" N AGLY B 584 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY B 584 " occ=0.50 residue: pdb=" N ACYS B 585 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS B 585 " occ=0.50 residue: pdb=" N AASP B 586 " occ=0.50 ... (14 atoms not shown) pdb=" OD2BASP B 586 " occ=0.50 residue: pdb=" N AILE B 587 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE B 587 " occ=0.50 residue: pdb=" N AGLY C 584 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY C 584 " occ=0.50 residue: pdb=" N ACYS C 585 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS C 585 " occ=0.50 residue: pdb=" N AASP C 586 " occ=0.50 ... (14 atoms not shown) pdb=" OD2BASP C 586 " occ=0.50 ... (remaining 7 not shown) Time building chain proxies: 15.16, per 1000 atoms: 0.85 Number of scatterers: 17849 At special positions: 0 Unit cell: (118.944, 118.944, 138.768, 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) Cl 4 17.00 S 118 16.00 P 2 15.00 O 3212 8.00 N 2850 7.00 C 11663 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 714 " - pdb=" SG CYS A 769 " distance=2.03 Simple disulfide: pdb=" SG CYS B 714 " - pdb=" SG CYS B 769 " distance=2.06 Simple disulfide: pdb=" SG CYS C 714 " - pdb=" SG CYS C 769 " distance=2.03 Simple disulfide: pdb=" SG CYS D 714 " - pdb=" SG CYS D 769 " distance=2.02 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 68 " distance=2.02 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.05 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.02 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.06 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 68 " distance=2.01 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " distance=2.05 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 68 " distance=2.01 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: 6.53 Conformation dependent library (CDL) restraints added in 5.9 seconds 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4238 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 88 helices and 26 sheets defined 53.9% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.68 Creating SS restraints... Processing helix chain 'A' and resid 408 through 410 No H-bonds generated for 'chain 'A' and resid 408 through 410' Processing helix chain 'A' and resid 414 through 416 No H-bonds generated for 'chain 'A' and resid 414 through 416' Processing helix chain 'A' and resid 420 through 432 Processing helix chain 'A' and resid 458 through 465 Processing helix chain 'A' and resid 479 through 482 No H-bonds generated for 'chain 'A' and resid 479 through 482' Processing helix chain 'A' and resid 512 through 514 No H-bonds generated for 'chain 'A' and resid 512 through 514' Processing helix chain 'A' and resid 519 through 542 Processing helix chain 'A' and resid 569 through 580 Processing helix chain 'A' and resid 592 through 619 Processing helix chain 'A' and resid 632 through 637 Processing helix chain 'A' and resid 650 through 656 Processing helix chain 'A' and resid 661 through 672 removed outlier: 3.529A pdb=" N SER A 672 " --> pdb=" O THR A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 690 Processing helix chain 'A' and resid 702 through 710 Processing helix chain 'A' and resid 739 through 751 Processing helix chain 'A' and resid 754 through 763 Processing helix chain 'A' and resid 785 through 814 removed outlier: 5.120A pdb=" N GLY A 790 " --> pdb=" O SER A 786 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL A 791 " --> pdb=" O ASN A 787 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE A 792 " --> pdb=" O VAL A 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 416 No H-bonds generated for 'chain 'B' and resid 414 through 416' Processing helix chain 'B' and resid 420 through 432 Processing helix chain 'B' and resid 458 through 465 Processing helix chain 'B' and resid 479 through 482 No H-bonds generated for 'chain 'B' and resid 479 through 482' Processing helix chain 'B' and resid 512 through 514 No H-bonds generated for 'chain 'B' and resid 512 through 514' Processing helix chain 'B' and resid 519 through 542 Processing helix chain 'B' and resid 569 through 580 Processing helix chain 'B' and resid 592 through 613 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 632 through 637 Processing helix chain 'B' and resid 650 through 656 Processing helix chain 'B' and resid 661 through 672 removed outlier: 3.652A pdb=" N SER B 672 " --> pdb=" O THR B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 691 Processing helix chain 'B' and resid 702 through 710 Processing helix chain 'B' and resid 739 through 751 Processing helix chain 'B' and resid 754 through 763 Processing helix chain 'B' and resid 785 through 814 removed outlier: 5.146A pdb=" N GLY B 790 " --> pdb=" O SER B 786 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL B 791 " --> pdb=" O ASN B 787 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 410 No H-bonds generated for 'chain 'C' and resid 408 through 410' Processing helix chain 'C' and resid 414 through 416 No H-bonds generated for 'chain 'C' and resid 414 through 416' Processing helix chain 'C' and resid 420 through 432 Processing helix chain 'C' and resid 458 through 465 Processing helix chain 'C' and resid 479 through 482 No H-bonds generated for 'chain 'C' and resid 479 through 482' Processing helix chain 'C' and resid 512 through 514 No H-bonds generated for 'chain 'C' and resid 512 through 514' Processing helix chain 'C' and resid 519 through 542 Processing helix chain 'C' and resid 569 through 580 Processing helix chain 'C' and resid 592 through 620 Processing helix chain 'C' and resid 632 through 637 Processing helix chain 'C' and resid 650 through 656 Processing helix chain 'C' and resid 661 through 671 Processing helix chain 'C' and resid 682 through 690 Processing helix chain 'C' and resid 702 through 710 Processing helix chain 'C' and resid 739 through 751 Processing helix chain 'C' and resid 754 through 764 Processing helix chain 'C' and resid 785 through 814 removed outlier: 5.140A pdb=" N GLY C 790 " --> pdb=" O SER C 786 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL C 791 " --> pdb=" O ASN C 787 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE C 792 " --> pdb=" O VAL C 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 416 Processing helix chain 'D' and resid 420 through 432 Processing helix chain 'D' and resid 458 through 465 Processing helix chain 'D' and resid 479 through 482 No H-bonds generated for 'chain 'D' and resid 479 through 482' Processing helix chain 'D' and resid 512 through 514 No H-bonds generated for 'chain 'D' and resid 512 through 514' Processing helix chain 'D' and resid 519 through 542 Processing helix chain 'D' and resid 569 through 580 Processing helix chain 'D' and resid 592 through 613 Processing helix chain 'D' and resid 616 through 620 Processing helix chain 'D' and resid 632 through 637 Processing helix chain 'D' and resid 650 through 656 Processing helix chain 'D' and resid 661 through 672 removed outlier: 3.626A pdb=" N SER D 672 " --> pdb=" O THR D 668 " (cutoff:3.500A) Processing helix chain 'D' and resid 682 through 691 Processing helix chain 'D' and resid 702 through 710 Processing helix chain 'D' and resid 739 through 751 Processing helix chain 'D' and resid 754 through 763 Processing helix chain 'D' and resid 785 through 814 removed outlier: 5.128A pdb=" N GLY D 790 " --> pdb=" O SER D 786 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL D 791 " --> pdb=" O ASN D 787 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 29 Processing helix chain 'E' and resid 93 through 104 Processing helix chain 'E' and resid 106 through 127 removed outlier: 3.890A pdb=" N GLU E 126 " --> pdb=" O VAL E 122 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE E 127 " --> pdb=" O ALA E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 160 removed outlier: 3.564A pdb=" N ILE E 157 " --> pdb=" O ILE E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 206 Processing helix chain 'F' and resid 6 through 29 Processing helix chain 'F' and resid 93 through 104 Processing helix chain 'F' and resid 106 through 127 removed outlier: 3.909A pdb=" N GLU F 126 " --> pdb=" O VAL F 122 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N PHE F 127 " --> pdb=" O ALA F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 160 removed outlier: 3.577A pdb=" N ILE F 157 " --> pdb=" O ILE F 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 206 Processing helix chain 'G' and resid 6 through 29 Processing helix chain 'G' and resid 93 through 104 Processing helix chain 'G' and resid 106 through 127 removed outlier: 3.896A pdb=" N GLU G 126 " --> pdb=" O VAL G 122 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N PHE G 127 " --> pdb=" O ALA G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 160 removed outlier: 3.565A pdb=" N ILE G 157 " --> pdb=" O ILE G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 206 Processing helix chain 'H' and resid 6 through 29 Processing helix chain 'H' and resid 93 through 104 Processing helix chain 'H' and resid 106 through 127 removed outlier: 3.912A pdb=" N GLU H 126 " --> pdb=" O VAL H 122 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N PHE H 127 " --> pdb=" O ALA H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 160 removed outlier: 3.574A pdb=" N ILE H 157 " --> pdb=" O ILE H 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 206 Processing sheet with id= A, first strand: chain 'A' and resid 391 through 395 Processing sheet with id= B, first strand: chain 'A' and resid 447 through 450 removed outlier: 3.779A pdb=" N ALA A 448 " --> pdb=" O ASN A 457 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA A 455 " --> pdb=" O ASP A 450 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 485 through 487 Processing sheet with id= D, first strand: chain 'A' and resid 492 through 494 removed outlier: 4.091A pdb=" N MET A 492 " --> pdb=" O TYR A 728 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 716 through 719 removed outlier: 4.183A pdb=" N ILE A 498 " --> pdb=" O VAL A 719 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N LYS A 501 " --> pdb=" O TYR A 696 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N TYR A 696 " --> pdb=" O LYS A 501 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA A 642 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N LEU A 699 " --> pdb=" O ALA A 642 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLY A 644 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N GLU A 701 " --> pdb=" O GLY A 644 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 391 through 395 Processing sheet with id= G, first strand: chain 'B' and resid 485 through 487 Processing sheet with id= H, first strand: chain 'B' and resid 492 through 494 removed outlier: 3.940A pdb=" N MET B 492 " --> pdb=" O TYR B 728 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 716 through 719 removed outlier: 4.262A pdb=" N ILE B 498 " --> pdb=" O VAL B 719 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LYS B 501 " --> pdb=" O TYR B 696 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N TYR B 696 " --> pdb=" O LYS B 501 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ALA B 642 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU B 699 " --> pdb=" O ALA B 642 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLY B 644 " --> pdb=" O LEU B 699 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N GLU B 701 " --> pdb=" O GLY B 644 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 390 through 395 removed outlier: 6.792A pdb=" N SER C 435 " --> pdb=" O TYR C 391 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N VAL C 393 " --> pdb=" O SER C 435 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ARG C 437 " --> pdb=" O VAL C 393 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N THR C 395 " --> pdb=" O ARG C 437 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLU C 439 " --> pdb=" O THR C 395 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'C' and resid 447 through 450 removed outlier: 3.859A pdb=" N ALA C 448 " --> pdb=" O ASN C 457 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA C 455 " --> pdb=" O ASP C 450 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 485 through 487 Processing sheet with id= M, first strand: chain 'C' and resid 492 through 494 removed outlier: 3.936A pdb=" N MET C 492 " --> pdb=" O TYR C 728 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 716 through 719 removed outlier: 4.282A pdb=" N ILE C 498 " --> pdb=" O VAL C 719 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N LYS C 501 " --> pdb=" O TYR C 696 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N TYR C 696 " --> pdb=" O LYS C 501 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA C 642 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N LEU C 699 " --> pdb=" O ALA C 642 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLY C 644 " --> pdb=" O LEU C 699 " (cutoff:3.500A) removed outlier: 8.872A pdb=" N GLU C 701 " --> pdb=" O GLY C 644 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 391 through 395 Processing sheet with id= P, first strand: chain 'D' and resid 485 through 487 Processing sheet with id= Q, first strand: chain 'D' and resid 492 through 494 removed outlier: 3.919A pdb=" N MET D 492 " --> pdb=" O TYR D 728 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 716 through 719 removed outlier: 4.176A pdb=" N ILE D 498 " --> pdb=" O VAL D 719 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LYS D 501 " --> pdb=" O TYR D 696 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N TYR D 696 " --> pdb=" O LYS D 501 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA D 642 " --> pdb=" O ALA D 697 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N LEU D 699 " --> pdb=" O ALA D 642 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLY D 644 " --> pdb=" O LEU D 699 " (cutoff:3.500A) removed outlier: 8.900A pdb=" N GLU D 701 " --> pdb=" O GLY D 644 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 34 through 36 Processing sheet with id= T, first strand: chain 'E' and resid 59 through 61 Processing sheet with id= U, first strand: chain 'F' and resid 34 through 36 Processing sheet with id= V, first strand: chain 'F' and resid 59 through 61 Processing sheet with id= W, first strand: chain 'G' and resid 34 through 36 Processing sheet with id= X, first strand: chain 'G' and resid 59 through 61 Processing sheet with id= Y, first strand: chain 'H' and resid 34 through 36 Processing sheet with id= Z, first strand: chain 'H' and resid 59 through 61 971 hydrogen bonds defined for protein. 2600 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: 5.18 Time building geometry restraints manager: 7.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2918 1.32 - 1.45: 6070 1.45 - 1.58: 9004 1.58 - 1.71: 12 1.71 - 1.84: 184 Bond restraints: 18188 Sorted by residual: bond pdb=" C LEU D 646 " pdb=" N GLU D 647 " ideal model delta sigma weight residual 1.330 1.272 0.058 1.47e-02 4.63e+03 1.57e+01 bond pdb=" CA SER H 144 " pdb=" CB SER H 144 " ideal model delta sigma weight residual 1.528 1.474 0.055 1.56e-02 4.11e+03 1.24e+01 bond pdb=" CA SER F 144 " pdb=" CB SER F 144 " ideal model delta sigma weight residual 1.528 1.476 0.052 1.56e-02 4.11e+03 1.12e+01 bond pdb=" CG HIS F 60 " pdb=" CD2 HIS F 60 " ideal model delta sigma weight residual 1.354 1.318 0.036 1.10e-02 8.26e+03 1.04e+01 bond pdb=" CA SER C 533 " pdb=" CB SER C 533 " ideal model delta sigma weight residual 1.528 1.478 0.051 1.59e-02 3.96e+03 1.01e+01 ... (remaining 18183 not shown) Histogram of bond angle deviations from ideal: 92.59 - 101.08: 56 101.08 - 109.57: 2239 109.57 - 118.06: 11495 118.06 - 126.55: 10627 126.55 - 135.04: 228 Bond angle restraints: 24645 Sorted by residual: angle pdb=" O LEU D 646 " pdb=" C LEU D 646 " pdb=" N GLU D 647 " ideal model delta sigma weight residual 123.22 115.79 7.43 1.14e+00 7.69e-01 4.25e+01 angle pdb=" CA GLN C 583 " pdb=" C GLN C 583 " pdb=" N BGLY C 584 " ideal model delta sigma weight residual 119.07 112.02 7.05 1.20e+00 6.94e-01 3.45e+01 angle pdb=" CA HIS H 132 " pdb=" CB HIS H 132 " pdb=" CG HIS H 132 " ideal model delta sigma weight residual 113.80 119.37 -5.57 1.00e+00 1.00e+00 3.11e+01 angle pdb=" C LEU H 69 " pdb=" CA LEU H 69 " pdb=" CB LEU H 69 " ideal model delta sigma weight residual 109.38 118.64 -9.26 1.68e+00 3.54e-01 3.04e+01 angle pdb=" O GLN C 583 " pdb=" C GLN C 583 " pdb=" N BGLY C 584 " ideal model delta sigma weight residual 122.19 127.73 -5.54 1.03e+00 9.43e-01 2.89e+01 ... (remaining 24640 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.42: 10195 32.42 - 64.84: 364 64.84 - 97.26: 31 97.26 - 129.68: 18 129.68 - 162.10: 2 Dihedral angle restraints: 10610 sinusoidal: 3970 harmonic: 6640 Sorted by residual: dihedral pdb=" CB CYS C 714 " pdb=" SG CYS C 714 " pdb=" SG CYS C 769 " pdb=" CB CYS C 769 " ideal model delta sinusoidal sigma weight residual -86.00 -172.80 86.80 1 1.00e+01 1.00e-02 9.06e+01 dihedral pdb=" CB CYS D 714 " pdb=" SG CYS D 714 " pdb=" SG CYS D 769 " pdb=" CB CYS D 769 " ideal model delta sinusoidal sigma weight residual 93.00 165.74 -72.74 1 1.00e+01 1.00e-02 6.75e+01 dihedral pdb=" CB CYS B 714 " pdb=" SG CYS B 714 " pdb=" SG CYS B 769 " pdb=" CB CYS B 769 " ideal model delta sinusoidal sigma weight residual 93.00 165.10 -72.10 1 1.00e+01 1.00e-02 6.65e+01 ... (remaining 10607 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.156: 2605 0.156 - 0.312: 194 0.312 - 0.468: 9 0.468 - 0.624: 1 0.624 - 0.780: 1 Chirality restraints: 2810 Sorted by residual: chirality pdb=" CA LEU H 69 " pdb=" N LEU H 69 " pdb=" C LEU H 69 " pdb=" CB LEU H 69 " both_signs ideal model delta sigma weight residual False 2.51 1.73 0.78 2.00e-01 2.50e+01 1.52e+01 chirality pdb=" CA HIS H 132 " pdb=" N HIS H 132 " pdb=" C HIS H 132 " pdb=" CB HIS H 132 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.71e+00 chirality pdb=" CB THR C 395 " pdb=" CA THR C 395 " pdb=" OG1 THR C 395 " pdb=" CG2 THR C 395 " both_signs ideal model delta sigma weight residual False 2.55 2.09 0.47 2.00e-01 2.50e+01 5.43e+00 ... (remaining 2807 not shown) Planarity restraints: 3013 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 OLC A1403 " -0.091 2.00e-02 2.50e+03 7.77e-02 6.03e+01 pdb=" C11 OLC A1403 " 0.080 2.00e-02 2.50e+03 pdb=" C8 OLC A1403 " 0.074 2.00e-02 2.50e+03 pdb=" C9 OLC A1403 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 602 " 0.067 2.00e-02 2.50e+03 3.35e-02 2.80e+01 pdb=" CG TRP D 602 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TRP D 602 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP D 602 " -0.034 2.00e-02 2.50e+03 pdb=" NE1 TRP D 602 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP D 602 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP D 602 " -0.038 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 602 " 0.015 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 602 " -0.021 2.00e-02 2.50e+03 pdb=" CH2 TRP D 602 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 583 " -0.025 2.00e-02 2.50e+03 5.12e-02 2.62e+01 pdb=" C GLN B 583 " 0.089 2.00e-02 2.50e+03 pdb=" O GLN B 583 " -0.033 2.00e-02 2.50e+03 pdb=" N BGLY B 584 " -0.030 2.00e-02 2.50e+03 ... (remaining 3010 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4297 2.81 - 3.33: 17822 3.33 - 3.86: 30855 3.86 - 4.38: 35263 4.38 - 4.90: 60133 Nonbonded interactions: 148370 Sorted by model distance: nonbonded pdb=" O GLY C 419 " pdb=" OE1 GLU C 423 " model vdw 2.288 3.040 nonbonded pdb=" O ILE C 396 " pdb=" CG1 VAL C 402 " model vdw 2.334 3.460 nonbonded pdb=" N GLY D 790 " pdb=" O HOH D1501 " model vdw 2.342 2.520 nonbonded pdb=" O GLY D 419 " pdb=" OE1 GLU D 423 " model vdw 2.343 3.040 nonbonded pdb=" N BASP A 586 " pdb=" OD1BASP A 586 " model vdw 2.345 2.520 ... (remaining 148365 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 389 through 391 and (name N or name CA or name C or name \ O or name CB )) or resid 392 through 414 or (resid 415 through 416 and (name N o \ r name CA or name C or name O or name CB )) or resid 417 through 429 or (resid 4 \ 30 and (name N or name CA or name C or name O or name CB )) or resid 431 through \ 569 or resid 571 through 582 or resid 588 through 664 or (resid 665 and (name N \ or name CA or name C or name O or name CB )) or resid 666 through 779 or (resid \ 780 and (name N or name CA or name C or name O or name CB )) or resid 781 throu \ gh 815 or resid 1401 through 1404)) selection = (chain 'B' and ((resid 389 through 391 and (name N or name CA or name C or name \ O or name CB )) or resid 392 through 398 or (resid 399 and (name N or name CA or \ name C or name O or name CB )) or resid 400 through 403 or (resid 404 and (name \ N or name CA or name C or name O or name CB )) or resid 405 through 415 or (res \ id 416 and (name N or name CA or name C or name O or name CB )) or resid 417 thr \ ough 429 or (resid 430 and (name N or name CA or name C or name O or name CB )) \ or resid 431 through 461 or (resid 462 and (name N or name CA or name C or name \ O or name CB )) or resid 463 through 500 or (resid 501 through 502 and (name N o \ r name CA or name C or name O or name CB )) or resid 503 or (resid 504 through 5 \ 07 and (name N or name CA or name C or name O or name CB )) or resid 508 through \ 569 or resid 571 through 582 or resid 588 through 622 or (resid 623 through 627 \ and (name N or name CA or name C or name O or name CB )) or resid 628 or (resid \ 629 through 630 and (name N or name CA or name C or name O or name CB )) or res \ id 631 through 632 or (resid 633 through 634 and (name N or name CA or name C or \ name O or name CB )) or resid 635 through 658 or (resid 659 and (name N or name \ CA or name C or name O or name CB )) or resid 660 through 664 or (resid 665 and \ (name N or name CA or name C or name O or name CB )) or resid 666 through 683 o \ r (resid 684 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 85 through 690 or (resid 691 through 693 and (name N or name CA or name C or nam \ e O or name CB )) or resid 694 through 705 or (resid 706 and (name N or name CA \ or name C or name O or name CB )) or resid 707 through 815 or resid 1401 or (res \ id 1402 and (name CA or name CB or name C1 or name C2 or name C3 or name C4 or n \ ame C5 or name C6 or name C7 or name C8 or name C9 or name O1 or name O2 )) or r \ esid 1403 or resid 1405)) selection = (chain 'C' and ((resid 389 through 391 and (name N or name CA or name C or name \ O or name CB )) or resid 392 through 398 or (resid 399 and (name N or name CA or \ name C or name O or name CB )) or resid 400 through 415 or (resid 416 and (name \ N or name CA or name C or name O or name CB )) or resid 417 through 466 or (res \ id 467 through 469 and (name N or name CA or name C or name O or name CB )) or r \ esid 470 through 569 or resid 571 through 582 or resid 588 through 633 or (resid \ 634 and (name N or name CA or name C or name O or name CB )) or resid 635 throu \ gh 691 or (resid 692 through 693 and (name N or name CA or name C or name O or n \ ame CB )) or resid 694 through 705 or (resid 706 and (name N or name CA or name \ C or name O or name CB )) or resid 707 through 708 or (resid 709 and (name N or \ name CA or name C or name O or name CB )) or resid 710 through 779 or (resid 780 \ and (name N or name CA or name C or name O or name CB )) or resid 781 through 8 \ 15 or resid 1401 through 1404)) selection = (chain 'D' and (resid 389 through 466 or (resid 467 through 469 and (name N or n \ ame CA or name C or name O or name CB )) or resid 470 through 500 or (resid 501 \ through 502 and (name N or name CA or name C or name O or name CB )) or resid 50 \ 3 or (resid 504 through 507 and (name N or name CA or name C or name O or name C \ B )) or resid 508 through 569 or resid 571 through 582 or resid 588 through 622 \ or (resid 623 through 627 and (name N or name CA or name C or name O or name CB \ )) or resid 628 or (resid 629 through 630 and (name N or name CA or name C or na \ me O or name CB )) or resid 631 through 646 or (resid 647 through 648 and (name \ N or name CA or name C or name O or name CB )) or resid 649 through 658 or (resi \ d 659 and (name N or name CA or name C or name O or name CB )) or resid 660 thro \ ugh 664 or (resid 665 and (name N or name CA or name C or name O or name CB )) o \ r resid 666 through 691 or (resid 692 through 693 and (name N or name CA or name \ C or name O or name CB )) or resid 694 through 705 or (resid 706 and (name N or \ name CA or name C or name O or name CB )) or resid 707 through 708 or (resid 70 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 710 through \ 779 or (resid 780 and (name N or name CA or name C or name O or name CB )) or re \ sid 781 through 815 or resid 1401 or (resid 1402 and (name CA or name CB or name \ C1 or name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 \ or name C9 or name O1 or name O2 )) or resid 1403 or resid 1405)) } ncs_group { reference = (chain 'E' and (resid 5 through 40 or (resid 41 and (name N or name CA or name C \ or name O or name CB )) or resid 42 through 183 or resid 185 through 209)) selection = (chain 'F' and (resid 5 through 40 or (resid 41 and (name N or name CA or name C \ or name O or name CB )) or resid 42 through 183 or resid 185 through 209)) selection = (chain 'G' and (resid 5 through 40 or (resid 41 and (name N or name CA or name C \ or name O or name CB )) or resid 42 through 183 or resid 185 through 209)) selection = (chain 'H' and (resid 5 through 183 or resid 185 through 209)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 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: 1.210 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: 0.010 Extract box with map and model: 5.930 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 54.970 Find NCS groups from input model: 1.320 Set up NCS constraints: 0.110 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:11.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 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 : 0.009 0.077 18188 Z= 0.587 Angle : 1.473 10.156 24645 Z= 0.979 Chirality : 0.091 0.780 2810 Planarity : 0.010 0.154 3013 Dihedral : 17.094 162.101 6339 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.88 % Favored : 96.07 % Rotamer: Outliers : 4.44 % Allowed : 6.34 % Favored : 89.23 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.15), residues: 2275 helix: -0.25 (0.13), residues: 1333 sheet: -2.17 (0.27), residues: 266 loop : -1.84 (0.20), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.010 TRP D 602 HIS 0.008 0.002 HIS F 132 PHE 0.045 0.008 PHE A 537 TYR 0.042 0.008 TYR B 417 ARG 0.060 0.005 ARG A 711 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 360 time to evaluate : 1.770 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 396 ILE cc_start: 0.7786 (tt) cc_final: 0.7381 (mt) REVERT: A 398 GLU cc_start: 0.7306 (tp30) cc_final: 0.6969 (tp30) REVERT: A 403 MET cc_start: 0.5753 (mtm) cc_final: 0.5325 (mtp) REVERT: A 459 MET cc_start: 0.7215 (mtm) cc_final: 0.6724 (mtm) REVERT: A 566 GLU cc_start: 0.7382 (pp20) cc_final: 0.7070 (mm-30) REVERT: A 590 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.7825 (mpp-170) REVERT: A 637 LYS cc_start: 0.4758 (mmtt) cc_final: 0.4549 (mttm) REVERT: A 690 ARG cc_start: 0.5199 (OUTLIER) cc_final: 0.4819 (mtt90) REVERT: A 724 ASP cc_start: 0.8759 (p0) cc_final: 0.8401 (p0) REVERT: A 726 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7765 (pttp) REVERT: A 803 MET cc_start: 0.8386 (mtm) cc_final: 0.8112 (mtm) REVERT: B 403 MET cc_start: 0.6754 (mtm) cc_final: 0.6074 (mtp) REVERT: B 416 ARG cc_start: 0.5522 (ttp-170) cc_final: 0.5189 (ttp-110) REVERT: B 462 GLU cc_start: 0.6678 (mt-10) cc_final: 0.6291 (tt0) REVERT: B 483 GLU cc_start: 0.6878 (mt-10) cc_final: 0.6416 (mp0) REVERT: B 590 ARG cc_start: 0.8673 (mtm180) cc_final: 0.8261 (mtp180) REVERT: B 615 ASN cc_start: 0.7472 (m-40) cc_final: 0.6879 (t0) REVERT: B 653 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7578 (mp0) REVERT: B 665 LYS cc_start: 0.7017 (ttmm) cc_final: 0.6402 (mmmm) REVERT: B 707 TYR cc_start: 0.7458 (t80) cc_final: 0.7011 (t80) REVERT: B 807 LEU cc_start: 0.7107 (OUTLIER) cc_final: 0.6514 (tp) REVERT: C 403 MET cc_start: 0.6056 (mtm) cc_final: 0.5541 (mtm) REVERT: C 566 GLU cc_start: 0.7718 (pp20) cc_final: 0.7413 (mm-30) REVERT: C 581 MET cc_start: 0.9027 (mmt) cc_final: 0.8818 (mmt) REVERT: C 709 GLU cc_start: 0.7574 (tt0) cc_final: 0.7320 (tt0) REVERT: D 443 ASP cc_start: 0.5641 (m-30) cc_final: 0.5416 (m-30) REVERT: D 465 TYR cc_start: 0.6101 (m-10) cc_final: 0.5618 (m-10) REVERT: D 467 ARG cc_start: 0.6626 (mpt-90) cc_final: 0.6294 (mpt-90) REVERT: D 482 GLU cc_start: 0.6737 (tp30) cc_final: 0.6446 (tp30) REVERT: D 499 MET cc_start: 0.8882 (ttm) cc_final: 0.8644 (ttp) REVERT: D 507 LYS cc_start: 0.6958 (ptpt) cc_final: 0.6684 (pttp) REVERT: D 566 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7126 (tp30) REVERT: D 638 GLN cc_start: 0.5793 (pp30) cc_final: 0.5304 (pp30) REVERT: D 645 THR cc_start: 0.8072 (m) cc_final: 0.7462 (t) REVERT: D 653 GLU cc_start: 0.7535 (tp30) cc_final: 0.7174 (tp30) REVERT: D 657 ARG cc_start: 0.7298 (ttp-170) cc_final: 0.7027 (mtp85) REVERT: D 754 VAL cc_start: 0.7600 (t) cc_final: 0.7392 (p) REVERT: D 761 LYS cc_start: 0.6943 (tmmt) cc_final: 0.6529 (tptp) REVERT: D 807 LEU cc_start: 0.6740 (OUTLIER) cc_final: 0.6240 (tt) REVERT: E 24 MET cc_start: 0.7434 (tpt) cc_final: 0.7213 (tpt) REVERT: E 31 ASP cc_start: 0.7698 (OUTLIER) cc_final: 0.7382 (m-30) REVERT: E 68 CYS cc_start: 0.6873 (m) cc_final: 0.6617 (t) REVERT: F 24 MET cc_start: 0.8526 (tpt) cc_final: 0.7745 (tpt) REVERT: F 37 ARG cc_start: 0.6037 (mtt-85) cc_final: 0.5698 (mmt90) REVERT: F 96 TYR cc_start: 0.6675 (t80) cc_final: 0.6372 (t80) REVERT: F 99 ARG cc_start: 0.6966 (OUTLIER) cc_final: 0.6727 (mmt180) REVERT: F 207 LEU cc_start: 0.3786 (OUTLIER) cc_final: 0.3433 (pt) REVERT: G 5 ASP cc_start: 0.2420 (OUTLIER) cc_final: 0.2208 (t0) REVERT: G 11 LEU cc_start: 0.7119 (tp) cc_final: 0.6756 (mm) REVERT: G 24 MET cc_start: 0.7910 (tpt) cc_final: 0.7267 (tpp) REVERT: G 30 THR cc_start: 0.8055 (OUTLIER) cc_final: 0.7810 (p) REVERT: G 31 ASP cc_start: 0.7807 (OUTLIER) cc_final: 0.7223 (m-30) REVERT: G 41 ARG cc_start: 0.2626 (OUTLIER) cc_final: 0.2264 (ttt-90) REVERT: G 60 HIS cc_start: 0.7067 (p90) cc_final: 0.6658 (p-80) REVERT: G 65 ARG cc_start: 0.6323 (mtm-85) cc_final: 0.5360 (mpt180) REVERT: G 79 LYS cc_start: 0.5812 (ttmm) cc_final: 0.5388 (tttp) REVERT: G 99 ARG cc_start: 0.6671 (mmp-170) cc_final: 0.6281 (mtt-85) REVERT: G 190 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8355 (mm-30) REVERT: H 12 ILE cc_start: 0.7953 (mt) cc_final: 0.7651 (mm) REVERT: H 14 THR cc_start: 0.8344 (t) cc_final: 0.8083 (m) REVERT: H 58 MET cc_start: 0.5912 (tpt) cc_final: 0.5407 (mmm) REVERT: H 67 CYS cc_start: 0.7540 (m) cc_final: 0.7136 (m) REVERT: H 78 LYS cc_start: 0.6798 (OUTLIER) cc_final: 0.6574 (ptmt) REVERT: H 99 ARG cc_start: 0.7294 (OUTLIER) cc_final: 0.6890 (mmm160) REVERT: H 174 SER cc_start: 0.8623 (OUTLIER) cc_final: 0.8360 (m) REVERT: A 1404 GLU cc_start: 0.7000 (mt-10) cc_final: 0.6580 (mm-30) REVERT: C 1404 GLU cc_start: 0.6413 (mt-10) cc_final: 0.5907 (mm-30) outliers start: 74 outliers final: 11 residues processed: 405 average time/residue: 1.2945 time to fit residues: 584.1293 Evaluate side-chains 287 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 260 time to evaluate : 1.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 590 ARG Chi-restraints excluded: chain A residue 690 ARG Chi-restraints excluded: chain A residue 726 LYS Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 479 LEU Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 566 GLU Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain F residue 99 ARG Chi-restraints excluded: chain F residue 174 SER Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain G residue 5 ASP Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 41 ARG Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 99 ARG Chi-restraints excluded: chain H residue 132 HIS Chi-restraints excluded: chain H residue 174 SER Chi-restraints excluded: chain H residue 207 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 0.6980 chunk 169 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 114 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 175 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 203 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 HIS A 743 ASN B 743 ASN C 582 GLN D 752 GLN E 160 ASN F 132 HIS F 204 HIS F 206 GLN G 160 ASN G 204 HIS H 132 HIS H 204 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18188 Z= 0.164 Angle : 0.505 9.398 24645 Z= 0.274 Chirality : 0.039 0.179 2810 Planarity : 0.004 0.034 3013 Dihedral : 13.323 167.305 2899 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 3.05 % Allowed : 14.00 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 0.68 (0.17), residues: 2275 helix: 1.66 (0.14), residues: 1339 sheet: -1.75 (0.32), residues: 204 loop : -1.15 (0.20), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 602 HIS 0.002 0.001 HIS E 60 PHE 0.017 0.001 PHE C 570 TYR 0.015 0.001 TYR D 669 ARG 0.006 0.001 ARG C 656 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 298 time to evaluate : 1.893 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 396 ILE cc_start: 0.7794 (tt) cc_final: 0.7439 (mt) REVERT: A 403 MET cc_start: 0.5555 (mtm) cc_final: 0.5024 (mtp) REVERT: A 431 HIS cc_start: 0.6654 (m-70) cc_final: 0.6373 (m-70) REVERT: A 445 LYS cc_start: 0.6217 (mttm) cc_final: 0.5990 (mttm) REVERT: A 446 TYR cc_start: 0.7512 (m-80) cc_final: 0.7295 (m-80) REVERT: A 459 MET cc_start: 0.6831 (mtm) cc_final: 0.6529 (mtm) REVERT: A 566 GLU cc_start: 0.7488 (pp20) cc_final: 0.7201 (mm-30) REVERT: A 590 ARG cc_start: 0.8657 (mmm-85) cc_final: 0.7673 (mtt90) REVERT: A 803 MET cc_start: 0.8334 (mtm) cc_final: 0.8068 (mtm) REVERT: B 401 TYR cc_start: 0.7442 (m-80) cc_final: 0.7055 (m-80) REVERT: B 459 MET cc_start: 0.6891 (mtm) cc_final: 0.6674 (mtm) REVERT: B 462 GLU cc_start: 0.6803 (mt-10) cc_final: 0.6481 (tt0) REVERT: B 590 ARG cc_start: 0.8713 (mtm180) cc_final: 0.8229 (mtt180) REVERT: B 615 ASN cc_start: 0.7571 (m-40) cc_final: 0.6958 (t0) REVERT: B 653 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7522 (mp0) REVERT: B 665 LYS cc_start: 0.6926 (ttmm) cc_final: 0.6567 (tmtp) REVERT: B 707 TYR cc_start: 0.7344 (t80) cc_final: 0.6781 (t80) REVERT: B 711 ARG cc_start: 0.4833 (mmp80) cc_final: 0.4262 (mmp80) REVERT: B 748 LYS cc_start: 0.7074 (mtmt) cc_final: 0.6823 (mtpm) REVERT: B 807 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.6688 (tp) REVERT: C 398 GLU cc_start: 0.7074 (tp30) cc_final: 0.6785 (mm-30) REVERT: C 403 MET cc_start: 0.5927 (mtm) cc_final: 0.5450 (mtm) REVERT: C 486 ASP cc_start: 0.7478 (m-30) cc_final: 0.7014 (t0) REVERT: C 499 MET cc_start: 0.8068 (ttm) cc_final: 0.7822 (ttp) REVERT: C 653 GLU cc_start: 0.7665 (mm-30) cc_final: 0.6711 (pt0) REVERT: D 403 MET cc_start: 0.6956 (mtm) cc_final: 0.6729 (mtm) REVERT: D 467 ARG cc_start: 0.6460 (mpt-90) cc_final: 0.5978 (mpt-90) REVERT: D 499 MET cc_start: 0.8807 (ttm) cc_final: 0.8569 (ttp) REVERT: D 507 LYS cc_start: 0.6840 (ptpt) cc_final: 0.6545 (pttp) REVERT: D 566 GLU cc_start: 0.7630 (pp20) cc_final: 0.7164 (mm-30) REVERT: D 638 GLN cc_start: 0.5870 (pp30) cc_final: 0.5477 (pm20) REVERT: D 653 GLU cc_start: 0.7501 (tp30) cc_final: 0.6886 (tp30) REVERT: D 807 LEU cc_start: 0.6908 (OUTLIER) cc_final: 0.6443 (tt) REVERT: E 24 MET cc_start: 0.7328 (tpt) cc_final: 0.7112 (tpt) REVERT: E 31 ASP cc_start: 0.7364 (OUTLIER) cc_final: 0.6750 (m-30) REVERT: E 58 MET cc_start: 0.6116 (OUTLIER) cc_final: 0.5863 (tpt) REVERT: E 68 CYS cc_start: 0.7101 (m) cc_final: 0.6793 (t) REVERT: E 97 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7515 (mt) REVERT: E 204 HIS cc_start: 0.6174 (OUTLIER) cc_final: 0.5955 (t70) REVERT: F 24 MET cc_start: 0.8394 (tpt) cc_final: 0.7677 (tpt) REVERT: F 37 ARG cc_start: 0.5918 (mtt-85) cc_final: 0.5563 (mmt90) REVERT: F 96 TYR cc_start: 0.6944 (t80) cc_final: 0.6680 (t80) REVERT: F 99 ARG cc_start: 0.7109 (OUTLIER) cc_final: 0.6687 (mmt180) REVERT: F 207 LEU cc_start: 0.3845 (OUTLIER) cc_final: 0.3486 (pt) REVERT: G 11 LEU cc_start: 0.7393 (tp) cc_final: 0.6956 (mm) REVERT: G 31 ASP cc_start: 0.7633 (OUTLIER) cc_final: 0.6935 (m-30) REVERT: G 41 ARG cc_start: 0.2911 (OUTLIER) cc_final: 0.2511 (ttt-90) REVERT: G 65 ARG cc_start: 0.6256 (mtm-85) cc_final: 0.5964 (mtt-85) REVERT: G 79 LYS cc_start: 0.5900 (ttmm) cc_final: 0.5578 (tttm) REVERT: G 99 ARG cc_start: 0.6668 (mmp-170) cc_final: 0.6225 (mtt-85) REVERT: H 12 ILE cc_start: 0.7808 (mt) cc_final: 0.7560 (mm) REVERT: H 67 CYS cc_start: 0.7565 (m) cc_final: 0.7215 (m) REVERT: H 99 ARG cc_start: 0.7417 (mmt-90) cc_final: 0.6927 (mmm160) REVERT: H 174 SER cc_start: 0.8622 (t) cc_final: 0.8371 (m) REVERT: H 207 LEU cc_start: 0.4383 (OUTLIER) cc_final: 0.4166 (mt) outliers start: 50 outliers final: 14 residues processed: 325 average time/residue: 1.2496 time to fit residues: 455.5996 Evaluate side-chains 286 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 261 time to evaluate : 1.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 725 SER Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 99 ARG Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 41 ARG Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 204 HIS Chi-restraints excluded: chain H residue 207 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 113 optimal weight: 0.0010 chunk 63 optimal weight: 7.9990 chunk 169 optimal weight: 4.9990 chunk 138 optimal weight: 0.9990 chunk 56 optimal weight: 0.0670 chunk 203 optimal weight: 1.9990 chunk 220 optimal weight: 4.9990 chunk 181 optimal weight: 7.9990 chunk 202 optimal weight: 0.9980 chunk 69 optimal weight: 10.0000 chunk 163 optimal weight: 6.9990 overall best weight: 0.8128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 GLN C 582 GLN D 752 GLN E 149 ASN G 204 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 18188 Z= 0.146 Angle : 0.468 7.107 24645 Z= 0.252 Chirality : 0.038 0.151 2810 Planarity : 0.004 0.038 3013 Dihedral : 11.922 161.555 2865 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.51 % Allowed : 14.75 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.17), residues: 2275 helix: 2.05 (0.14), residues: 1337 sheet: -1.44 (0.29), residues: 240 loop : -0.98 (0.21), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 456 HIS 0.013 0.001 HIS H 204 PHE 0.015 0.001 PHE C 570 TYR 0.020 0.001 TYR C 434 ARG 0.007 0.000 ARG G 37 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 288 time to evaluate : 1.886 Fit side-chains REVERT: A 396 ILE cc_start: 0.7794 (tt) cc_final: 0.7443 (mt) REVERT: A 403 MET cc_start: 0.5633 (mtm) cc_final: 0.5093 (mtp) REVERT: A 431 HIS cc_start: 0.6626 (m-70) cc_final: 0.6415 (m-70) REVERT: A 445 LYS cc_start: 0.6127 (mttm) cc_final: 0.5898 (mttm) REVERT: A 565 ASN cc_start: 0.6350 (t0) cc_final: 0.5977 (t0) REVERT: A 566 GLU cc_start: 0.7445 (pp20) cc_final: 0.7156 (mm-30) REVERT: A 590 ARG cc_start: 0.8712 (mmm-85) cc_final: 0.7732 (mtt90) REVERT: A 710 GLN cc_start: 0.5782 (mm-40) cc_final: 0.5566 (mt0) REVERT: A 784 SER cc_start: 0.8264 (p) cc_final: 0.8059 (m) REVERT: A 803 MET cc_start: 0.8371 (mtm) cc_final: 0.8046 (mtm) REVERT: B 459 MET cc_start: 0.6715 (mtm) cc_final: 0.6469 (mtm) REVERT: B 483 GLU cc_start: 0.6981 (mt-10) cc_final: 0.6421 (mp0) REVERT: B 590 ARG cc_start: 0.8742 (mtm180) cc_final: 0.8263 (mtt180) REVERT: B 615 ASN cc_start: 0.7629 (m-40) cc_final: 0.6969 (t0) REVERT: B 653 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7465 (mp0) REVERT: B 711 ARG cc_start: 0.4838 (mmp80) cc_final: 0.4327 (mmp80) REVERT: B 748 LYS cc_start: 0.7131 (mtmt) cc_final: 0.6856 (mtpm) REVERT: B 807 LEU cc_start: 0.7361 (OUTLIER) cc_final: 0.6697 (tp) REVERT: C 398 GLU cc_start: 0.7057 (tp30) cc_final: 0.6811 (mm-30) REVERT: C 403 MET cc_start: 0.5947 (mtm) cc_final: 0.5473 (mtm) REVERT: C 438 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7658 (tt) REVERT: C 486 ASP cc_start: 0.7425 (m-30) cc_final: 0.6921 (t0) REVERT: C 499 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.7911 (ttp) REVERT: C 653 GLU cc_start: 0.7721 (mm-30) cc_final: 0.6803 (pt0) REVERT: C 657 ARG cc_start: 0.7860 (ptp90) cc_final: 0.7602 (ptp-110) REVERT: D 403 MET cc_start: 0.6954 (mtm) cc_final: 0.6624 (mtm) REVERT: D 465 TYR cc_start: 0.5855 (m-10) cc_final: 0.5548 (m-10) REVERT: D 499 MET cc_start: 0.8731 (ttm) cc_final: 0.8515 (ttp) REVERT: D 507 LYS cc_start: 0.6814 (ptpt) cc_final: 0.6534 (pttp) REVERT: D 566 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7193 (mm-30) REVERT: D 638 GLN cc_start: 0.5891 (pp30) cc_final: 0.5237 (pp30) REVERT: D 641 ILE cc_start: 0.7198 (mt) cc_final: 0.6948 (mt) REVERT: D 650 SER cc_start: 0.8156 (t) cc_final: 0.7791 (m) REVERT: D 653 GLU cc_start: 0.7440 (tp30) cc_final: 0.6825 (tp30) REVERT: D 657 ARG cc_start: 0.7649 (mtm110) cc_final: 0.6957 (mtp180) REVERT: D 807 LEU cc_start: 0.6795 (OUTLIER) cc_final: 0.6263 (tt) REVERT: E 58 MET cc_start: 0.5999 (OUTLIER) cc_final: 0.5702 (tpt) REVERT: E 68 CYS cc_start: 0.7114 (m) cc_final: 0.6871 (t) REVERT: E 202 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.6340 (mp0) REVERT: F 24 MET cc_start: 0.8297 (tpt) cc_final: 0.7637 (tpt) REVERT: F 37 ARG cc_start: 0.6004 (mtt-85) cc_final: 0.5638 (mmt90) REVERT: F 96 TYR cc_start: 0.6919 (t80) cc_final: 0.6695 (t80) REVERT: F 99 ARG cc_start: 0.7105 (mmt90) cc_final: 0.6702 (mmt90) REVERT: F 207 LEU cc_start: 0.3594 (OUTLIER) cc_final: 0.3329 (pp) REVERT: G 31 ASP cc_start: 0.7894 (OUTLIER) cc_final: 0.7655 (p0) REVERT: G 41 ARG cc_start: 0.2948 (OUTLIER) cc_final: 0.2533 (mtp180) REVERT: G 65 ARG cc_start: 0.6405 (mtm-85) cc_final: 0.6032 (mtt-85) REVERT: G 79 LYS cc_start: 0.5860 (ttmm) cc_final: 0.5469 (tttp) REVERT: G 99 ARG cc_start: 0.6680 (mmp-170) cc_final: 0.6255 (mtt-85) REVERT: H 67 CYS cc_start: 0.7575 (m) cc_final: 0.7251 (m) REVERT: H 174 SER cc_start: 0.8591 (t) cc_final: 0.8366 (m) outliers start: 58 outliers final: 26 residues processed: 318 average time/residue: 1.2030 time to fit residues: 429.0937 Evaluate side-chains 292 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 256 time to evaluate : 1.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 499 MET Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 725 SER Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 566 GLU Chi-restraints excluded: chain D residue 615 ASN Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 67 CYS Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 41 ARG Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain H residue 97 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 201 optimal weight: 0.6980 chunk 153 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 204 optimal weight: 2.9990 chunk 216 optimal weight: 10.0000 chunk 106 optimal weight: 5.9990 chunk 193 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 582 GLN D 752 GLN F 204 HIS ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 18188 Z= 0.306 Angle : 0.569 7.937 24645 Z= 0.303 Chirality : 0.042 0.211 2810 Planarity : 0.005 0.044 3013 Dihedral : 12.411 111.006 2855 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 4.49 % Allowed : 14.52 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.17), residues: 2275 helix: 1.55 (0.14), residues: 1333 sheet: -1.49 (0.32), residues: 188 loop : -1.06 (0.20), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 456 HIS 0.006 0.002 HIS G 60 PHE 0.020 0.002 PHE C 570 TYR 0.019 0.002 TYR F 180 ARG 0.008 0.001 ARG B 624 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 264 time to evaluate : 1.926 Fit side-chains REVERT: A 396 ILE cc_start: 0.7816 (tt) cc_final: 0.7497 (mt) REVERT: A 403 MET cc_start: 0.5583 (mtm) cc_final: 0.4984 (mtp) REVERT: A 431 HIS cc_start: 0.6546 (m-70) cc_final: 0.6311 (m90) REVERT: A 565 ASN cc_start: 0.6390 (t0) cc_final: 0.6017 (t0) REVERT: A 566 GLU cc_start: 0.7367 (pp20) cc_final: 0.7046 (mm-30) REVERT: A 590 ARG cc_start: 0.8727 (mmm-85) cc_final: 0.7743 (mtt90) REVERT: A 708 ILE cc_start: 0.7258 (OUTLIER) cc_final: 0.7037 (mp) REVERT: A 803 MET cc_start: 0.8388 (mtm) cc_final: 0.8069 (mtm) REVERT: B 427 GLU cc_start: 0.6645 (tp30) cc_final: 0.6353 (mm-30) REVERT: B 459 MET cc_start: 0.6964 (mtm) cc_final: 0.6692 (mtm) REVERT: B 615 ASN cc_start: 0.7725 (m-40) cc_final: 0.7074 (t0) REVERT: B 624 ARG cc_start: 0.6507 (ptp-110) cc_final: 0.6289 (ptp-110) REVERT: B 711 ARG cc_start: 0.5332 (mmp80) cc_final: 0.4824 (mmp-170) REVERT: C 403 MET cc_start: 0.5745 (mtm) cc_final: 0.5238 (mtm) REVERT: C 438 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7704 (tt) REVERT: C 736 SER cc_start: 0.6913 (t) cc_final: 0.6642 (t) REVERT: D 403 MET cc_start: 0.6917 (mtm) cc_final: 0.6613 (mtm) REVERT: D 499 MET cc_start: 0.8836 (ttm) cc_final: 0.8611 (ttp) REVERT: D 507 LYS cc_start: 0.6883 (ptpt) cc_final: 0.6599 (pttp) REVERT: D 566 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7191 (mm-30) REVERT: D 638 GLN cc_start: 0.6323 (pp30) cc_final: 0.5572 (pp30) REVERT: D 639 THR cc_start: 0.6585 (OUTLIER) cc_final: 0.6351 (m) REVERT: D 641 ILE cc_start: 0.7230 (mt) cc_final: 0.7013 (mt) REVERT: D 650 SER cc_start: 0.8198 (t) cc_final: 0.7850 (m) REVERT: D 653 GLU cc_start: 0.7445 (tp30) cc_final: 0.6782 (tp30) REVERT: D 748 LYS cc_start: 0.6452 (OUTLIER) cc_final: 0.6163 (ttmt) REVERT: D 807 LEU cc_start: 0.6668 (OUTLIER) cc_final: 0.6245 (tm) REVERT: E 31 ASP cc_start: 0.7430 (OUTLIER) cc_final: 0.6943 (m-30) REVERT: E 58 MET cc_start: 0.5767 (mmm) cc_final: 0.5501 (tpt) REVERT: E 79 LYS cc_start: 0.6602 (ttmm) cc_final: 0.6086 (ttpp) REVERT: E 97 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7509 (mt) REVERT: E 202 GLU cc_start: 0.6835 (OUTLIER) cc_final: 0.6337 (mp0) REVERT: F 24 MET cc_start: 0.8264 (tpt) cc_final: 0.7870 (tpt) REVERT: F 37 ARG cc_start: 0.6191 (mtt-85) cc_final: 0.5730 (mmt90) REVERT: F 79 LYS cc_start: 0.7117 (mttm) cc_final: 0.6492 (tmmm) REVERT: F 96 TYR cc_start: 0.6888 (t80) cc_final: 0.6674 (t80) REVERT: F 99 ARG cc_start: 0.7039 (mmt90) cc_final: 0.6675 (mmt90) REVERT: G 31 ASP cc_start: 0.7893 (OUTLIER) cc_final: 0.7033 (m-30) REVERT: G 41 ARG cc_start: 0.3046 (OUTLIER) cc_final: 0.2556 (mtp180) REVERT: G 65 ARG cc_start: 0.6394 (mtm-85) cc_final: 0.6063 (mtt-85) REVERT: G 76 VAL cc_start: 0.6353 (t) cc_final: 0.6120 (p) REVERT: G 79 LYS cc_start: 0.5998 (ttmm) cc_final: 0.5617 (tttp) REVERT: G 99 ARG cc_start: 0.6762 (mmp-170) cc_final: 0.6367 (mtt-85) REVERT: G 204 HIS cc_start: 0.6478 (OUTLIER) cc_final: 0.6255 (t-90) REVERT: H 14 THR cc_start: 0.8296 (t) cc_final: 0.8033 (m) REVERT: H 67 CYS cc_start: 0.7622 (m) cc_final: 0.7324 (m) outliers start: 73 outliers final: 32 residues processed: 308 average time/residue: 1.2716 time to fit residues: 443.9693 Evaluate side-chains 293 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 249 time to evaluate : 1.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 443 ASP Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 725 SER Chi-restraints excluded: chain D residue 443 ASP Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 566 GLU Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 748 LYS Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 24 MET Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 41 ARG Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 174 SER Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 180 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 161 optimal weight: 3.9990 chunk 89 optimal weight: 9.9990 chunk 184 optimal weight: 0.7980 chunk 149 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 194 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 752 GLN E 205 GLN G 160 ASN ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18188 Z= 0.195 Angle : 0.492 7.054 24645 Z= 0.263 Chirality : 0.039 0.176 2810 Planarity : 0.004 0.044 3013 Dihedral : 11.513 105.451 2853 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.86 % Allowed : 16.36 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 0.83 (0.17), residues: 2275 helix: 1.69 (0.14), residues: 1335 sheet: -1.19 (0.32), residues: 214 loop : -1.02 (0.21), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 456 HIS 0.005 0.001 HIS F 204 PHE 0.016 0.001 PHE C 570 TYR 0.018 0.002 TYR C 434 ARG 0.007 0.000 ARG C 449 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 263 time to evaluate : 1.989 Fit side-chains REVERT: A 396 ILE cc_start: 0.7820 (tt) cc_final: 0.7520 (mt) REVERT: A 403 MET cc_start: 0.5522 (mtm) cc_final: 0.4925 (mtp) REVERT: A 431 HIS cc_start: 0.6559 (m-70) cc_final: 0.6335 (m90) REVERT: A 565 ASN cc_start: 0.6307 (t0) cc_final: 0.6019 (t0) REVERT: A 566 GLU cc_start: 0.7407 (pp20) cc_final: 0.7063 (mm-30) REVERT: A 590 ARG cc_start: 0.8738 (mmm-85) cc_final: 0.7749 (mtt90) REVERT: A 803 MET cc_start: 0.8381 (mtm) cc_final: 0.8055 (mtm) REVERT: B 403 MET cc_start: 0.6643 (mtm) cc_final: 0.5890 (mtp) REVERT: B 459 MET cc_start: 0.6944 (mtm) cc_final: 0.6602 (mtm) REVERT: B 483 GLU cc_start: 0.6968 (mt-10) cc_final: 0.6403 (mp0) REVERT: B 615 ASN cc_start: 0.7607 (m-40) cc_final: 0.7011 (t0) REVERT: B 624 ARG cc_start: 0.6419 (ptp-110) cc_final: 0.6169 (ptp-110) REVERT: B 711 ARG cc_start: 0.5238 (mmp80) cc_final: 0.4703 (mmp-170) REVERT: C 403 MET cc_start: 0.5867 (mtm) cc_final: 0.5388 (mtm) REVERT: C 438 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7716 (tt) REVERT: C 736 SER cc_start: 0.6992 (t) cc_final: 0.6754 (t) REVERT: D 403 MET cc_start: 0.6906 (mtm) cc_final: 0.6548 (mtm) REVERT: D 499 MET cc_start: 0.8838 (ttm) cc_final: 0.8600 (ttp) REVERT: D 507 LYS cc_start: 0.6818 (ptpt) cc_final: 0.6517 (pttp) REVERT: D 542 PHE cc_start: 0.4356 (OUTLIER) cc_final: 0.4103 (t80) REVERT: D 566 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7166 (mm-30) REVERT: D 638 GLN cc_start: 0.6339 (pp30) cc_final: 0.5580 (pp30) REVERT: D 639 THR cc_start: 0.6588 (OUTLIER) cc_final: 0.6334 (m) REVERT: D 641 ILE cc_start: 0.7247 (mt) cc_final: 0.7016 (mt) REVERT: D 650 SER cc_start: 0.8138 (t) cc_final: 0.7838 (m) REVERT: D 653 GLU cc_start: 0.7461 (tp30) cc_final: 0.6804 (tp30) REVERT: D 748 LYS cc_start: 0.6401 (OUTLIER) cc_final: 0.6119 (ttmt) REVERT: D 807 LEU cc_start: 0.6700 (OUTLIER) cc_final: 0.6186 (tm) REVERT: E 31 ASP cc_start: 0.7383 (OUTLIER) cc_final: 0.6998 (m-30) REVERT: E 41 ARG cc_start: 0.5242 (OUTLIER) cc_final: 0.4403 (tpt90) REVERT: E 58 MET cc_start: 0.5773 (mmm) cc_final: 0.5454 (mmm) REVERT: E 79 LYS cc_start: 0.6627 (ttmm) cc_final: 0.6113 (ttpp) REVERT: E 97 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7511 (mt) REVERT: E 202 GLU cc_start: 0.6752 (OUTLIER) cc_final: 0.6242 (mp0) REVERT: F 37 ARG cc_start: 0.6269 (mtt-85) cc_final: 0.5815 (mmt90) REVERT: F 79 LYS cc_start: 0.7015 (mttm) cc_final: 0.6467 (tmmm) REVERT: F 96 TYR cc_start: 0.6947 (t80) cc_final: 0.6709 (t80) REVERT: F 99 ARG cc_start: 0.7095 (mmt90) cc_final: 0.6719 (mmt90) REVERT: G 31 ASP cc_start: 0.7853 (OUTLIER) cc_final: 0.7554 (p0) REVERT: G 41 ARG cc_start: 0.3098 (OUTLIER) cc_final: 0.2662 (mtp180) REVERT: G 65 ARG cc_start: 0.6389 (mtm-85) cc_final: 0.6099 (mtt-85) REVERT: G 76 VAL cc_start: 0.6241 (t) cc_final: 0.5994 (p) REVERT: G 79 LYS cc_start: 0.5990 (ttmm) cc_final: 0.5587 (tttp) REVERT: G 99 ARG cc_start: 0.6718 (mmp-170) cc_final: 0.6301 (mtt-85) REVERT: G 184 PHE cc_start: 0.7358 (m-80) cc_final: 0.6925 (m-80) REVERT: H 67 CYS cc_start: 0.7601 (m) cc_final: 0.7325 (m) REVERT: H 202 GLU cc_start: 0.7062 (mt-10) cc_final: 0.6684 (mm-30) outliers start: 61 outliers final: 29 residues processed: 298 average time/residue: 1.2669 time to fit residues: 423.3877 Evaluate side-chains 295 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 254 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 725 SER Chi-restraints excluded: chain D residue 443 ASP Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 566 GLU Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 748 LYS Chi-restraints excluded: chain D residue 765 ASP Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 41 ARG Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain G residue 24 MET Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 41 ARG Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 72 optimal weight: 3.9990 chunk 194 optimal weight: 10.0000 chunk 42 optimal weight: 8.9990 chunk 127 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 216 optimal weight: 9.9990 chunk 179 optimal weight: 10.0000 chunk 100 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 113 optimal weight: 4.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 752 GLN E 205 GLN F 204 HIS ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 18188 Z= 0.339 Angle : 0.586 7.430 24645 Z= 0.311 Chirality : 0.043 0.252 2810 Planarity : 0.005 0.047 3013 Dihedral : 12.278 112.164 2853 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 4.49 % Allowed : 15.96 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.17), residues: 2275 helix: 1.34 (0.14), residues: 1329 sheet: -1.49 (0.33), residues: 186 loop : -1.17 (0.20), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 667 HIS 0.006 0.002 HIS F 60 PHE 0.019 0.002 PHE A 604 TYR 0.021 0.002 TYR G 32 ARG 0.005 0.001 ARG C 541 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 256 time to evaluate : 1.936 Fit side-chains REVERT: A 396 ILE cc_start: 0.7786 (tt) cc_final: 0.7498 (OUTLIER) REVERT: A 565 ASN cc_start: 0.6323 (t0) cc_final: 0.6011 (t0) REVERT: A 566 GLU cc_start: 0.7440 (pp20) cc_final: 0.7055 (mm-30) REVERT: A 590 ARG cc_start: 0.8747 (mmm-85) cc_final: 0.7756 (mtt90) REVERT: A 803 MET cc_start: 0.8406 (mtm) cc_final: 0.8099 (mtm) REVERT: B 403 MET cc_start: 0.6649 (mtm) cc_final: 0.6039 (mtp) REVERT: B 459 MET cc_start: 0.7120 (mtm) cc_final: 0.6660 (mtm) REVERT: B 483 GLU cc_start: 0.6972 (mt-10) cc_final: 0.6406 (mp0) REVERT: B 615 ASN cc_start: 0.7752 (m-40) cc_final: 0.7158 (t0) REVERT: C 403 MET cc_start: 0.5776 (mtm) cc_final: 0.5223 (mtm) REVERT: C 438 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7751 (tt) REVERT: C 736 SER cc_start: 0.6862 (t) cc_final: 0.6569 (t) REVERT: D 403 MET cc_start: 0.6839 (mtm) cc_final: 0.6331 (mtm) REVERT: D 638 GLN cc_start: 0.6556 (pp30) cc_final: 0.5688 (pp30) REVERT: D 639 THR cc_start: 0.6666 (OUTLIER) cc_final: 0.6417 (m) REVERT: D 641 ILE cc_start: 0.7223 (mt) cc_final: 0.7013 (mt) REVERT: D 650 SER cc_start: 0.8124 (t) cc_final: 0.7781 (m) REVERT: D 653 GLU cc_start: 0.7517 (tp30) cc_final: 0.6849 (tp30) REVERT: D 748 LYS cc_start: 0.6440 (OUTLIER) cc_final: 0.6133 (ttmt) REVERT: D 807 LEU cc_start: 0.6651 (OUTLIER) cc_final: 0.6218 (tm) REVERT: E 31 ASP cc_start: 0.7335 (OUTLIER) cc_final: 0.7087 (m-30) REVERT: E 58 MET cc_start: 0.5660 (mmm) cc_final: 0.5350 (mmm) REVERT: E 79 LYS cc_start: 0.6695 (ttmm) cc_final: 0.6192 (ttpp) REVERT: E 97 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7508 (mt) REVERT: E 202 GLU cc_start: 0.6808 (OUTLIER) cc_final: 0.6326 (mp0) REVERT: F 37 ARG cc_start: 0.6201 (mtt-85) cc_final: 0.5781 (mmt90) REVERT: F 79 LYS cc_start: 0.7148 (mttm) cc_final: 0.6522 (tmmm) REVERT: F 96 TYR cc_start: 0.6770 (t80) cc_final: 0.6481 (t80) REVERT: F 99 ARG cc_start: 0.7040 (mmt90) cc_final: 0.6695 (mmt180) REVERT: G 41 ARG cc_start: 0.3049 (OUTLIER) cc_final: 0.2654 (mtp180) REVERT: G 65 ARG cc_start: 0.6156 (mtm-85) cc_final: 0.5875 (mtt-85) REVERT: G 79 LYS cc_start: 0.5987 (ttmm) cc_final: 0.5660 (tttp) REVERT: G 99 ARG cc_start: 0.6793 (mmp-170) cc_final: 0.6413 (mtt-85) REVERT: G 129 ARG cc_start: 0.4622 (ttm110) cc_final: 0.4075 (mpp80) REVERT: H 14 THR cc_start: 0.8211 (t) cc_final: 0.7964 (m) REVERT: H 37 ARG cc_start: 0.5729 (mtt-85) cc_final: 0.5520 (mmt90) REVERT: H 67 CYS cc_start: 0.7585 (m) cc_final: 0.7281 (m) REVERT: H 202 GLU cc_start: 0.7009 (mt-10) cc_final: 0.6658 (mm-30) outliers start: 72 outliers final: 40 residues processed: 299 average time/residue: 1.2902 time to fit residues: 430.6276 Evaluate side-chains 296 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 249 time to evaluate : 2.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 443 ASP Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 434 TYR Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 725 SER Chi-restraints excluded: chain D residue 443 ASP Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 748 LYS Chi-restraints excluded: chain D residue 765 ASP Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 24 MET Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 41 ARG Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 208 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 158 optimal weight: 6.9990 chunk 122 optimal weight: 7.9990 chunk 182 optimal weight: 3.9990 chunk 121 optimal weight: 9.9990 chunk 215 optimal weight: 4.9990 chunk 135 optimal weight: 0.6980 chunk 131 optimal weight: 3.9990 chunk 99 optimal weight: 0.5980 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 752 GLN E 205 GLN F 204 HIS ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18188 Z= 0.242 Angle : 0.527 7.818 24645 Z= 0.280 Chirality : 0.040 0.205 2810 Planarity : 0.004 0.046 3013 Dihedral : 11.802 107.997 2853 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.86 % Allowed : 17.11 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 0.56 (0.17), residues: 2275 helix: 1.47 (0.14), residues: 1331 sheet: -1.26 (0.32), residues: 214 loop : -1.12 (0.21), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 762 HIS 0.005 0.001 HIS F 204 PHE 0.016 0.002 PHE C 570 TYR 0.022 0.002 TYR G 32 ARG 0.009 0.001 ARG B 624 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 267 time to evaluate : 2.039 Fit side-chains REVERT: A 396 ILE cc_start: 0.7796 (tt) cc_final: 0.7534 (OUTLIER) REVERT: A 565 ASN cc_start: 0.6265 (t0) cc_final: 0.6021 (t0) REVERT: A 566 GLU cc_start: 0.7448 (pp20) cc_final: 0.7047 (mm-30) REVERT: A 590 ARG cc_start: 0.8752 (mmm-85) cc_final: 0.7766 (mtt90) REVERT: A 803 MET cc_start: 0.8390 (mtm) cc_final: 0.8077 (mtm) REVERT: B 403 MET cc_start: 0.6699 (mtm) cc_final: 0.5911 (mtp) REVERT: B 459 MET cc_start: 0.7065 (mtm) cc_final: 0.6630 (mtm) REVERT: B 483 GLU cc_start: 0.6983 (mt-10) cc_final: 0.6392 (mp0) REVERT: B 615 ASN cc_start: 0.7737 (m-40) cc_final: 0.7159 (t0) REVERT: B 624 ARG cc_start: 0.6595 (ptp-110) cc_final: 0.6382 (ptp-110) REVERT: C 398 GLU cc_start: 0.6898 (tp30) cc_final: 0.6564 (mm-30) REVERT: C 403 MET cc_start: 0.5723 (mtm) cc_final: 0.5195 (mtm) REVERT: C 438 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7749 (tt) REVERT: C 736 SER cc_start: 0.6938 (t) cc_final: 0.6647 (t) REVERT: C 738 LEU cc_start: 0.6952 (OUTLIER) cc_final: 0.6638 (mt) REVERT: D 403 MET cc_start: 0.6882 (mtm) cc_final: 0.6455 (mtm) REVERT: D 459 MET cc_start: 0.6889 (mtm) cc_final: 0.6549 (mmm) REVERT: D 465 TYR cc_start: 0.5803 (m-10) cc_final: 0.5581 (m-10) REVERT: D 615 ASN cc_start: 0.8079 (m-40) cc_final: 0.7774 (m110) REVERT: D 638 GLN cc_start: 0.6580 (pp30) cc_final: 0.5738 (pp30) REVERT: D 639 THR cc_start: 0.6688 (OUTLIER) cc_final: 0.6445 (m) REVERT: D 641 ILE cc_start: 0.7232 (mt) cc_final: 0.7022 (mt) REVERT: D 650 SER cc_start: 0.8153 (t) cc_final: 0.7834 (m) REVERT: D 653 GLU cc_start: 0.7431 (tp30) cc_final: 0.6721 (tp30) REVERT: D 701 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8264 (mt-10) REVERT: D 748 LYS cc_start: 0.6409 (OUTLIER) cc_final: 0.6102 (ttmt) REVERT: D 807 LEU cc_start: 0.6621 (OUTLIER) cc_final: 0.6168 (tm) REVERT: E 58 MET cc_start: 0.5709 (mmm) cc_final: 0.5441 (mmm) REVERT: E 79 LYS cc_start: 0.6630 (ttmm) cc_final: 0.6119 (ttpp) REVERT: E 97 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7515 (mt) REVERT: E 202 GLU cc_start: 0.6754 (OUTLIER) cc_final: 0.6246 (mp0) REVERT: F 37 ARG cc_start: 0.6189 (mtt-85) cc_final: 0.5771 (mmt90) REVERT: F 79 LYS cc_start: 0.7067 (mttm) cc_final: 0.6483 (tmmm) REVERT: F 96 TYR cc_start: 0.6787 (t80) cc_final: 0.6577 (t80) REVERT: F 99 ARG cc_start: 0.7036 (mmt90) cc_final: 0.6752 (mmt90) REVERT: G 11 LEU cc_start: 0.7306 (tt) cc_final: 0.6931 (mm) REVERT: G 41 ARG cc_start: 0.3078 (OUTLIER) cc_final: 0.2761 (mtp180) REVERT: G 65 ARG cc_start: 0.6117 (mtm-85) cc_final: 0.5784 (mtt-85) REVERT: G 79 LYS cc_start: 0.6020 (ttmm) cc_final: 0.5684 (tttp) REVERT: G 99 ARG cc_start: 0.6777 (mmp-170) cc_final: 0.6379 (mtt-85) REVERT: G 129 ARG cc_start: 0.4568 (ttm110) cc_final: 0.4049 (mpp80) REVERT: H 37 ARG cc_start: 0.5738 (mtt-85) cc_final: 0.5505 (mmt90) REVERT: H 67 CYS cc_start: 0.7547 (m) cc_final: 0.7248 (m) REVERT: H 202 GLU cc_start: 0.7088 (mt-10) cc_final: 0.6702 (mm-30) outliers start: 61 outliers final: 39 residues processed: 303 average time/residue: 1.2622 time to fit residues: 427.7758 Evaluate side-chains 308 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 261 time to evaluate : 1.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 443 ASP Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 725 SER Chi-restraints excluded: chain C residue 738 LEU Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain D residue 443 ASP Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 701 GLU Chi-restraints excluded: chain D residue 748 LYS Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain G residue 24 MET Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 41 ARG Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 133 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 65 optimal weight: 0.4980 chunk 42 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 106 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 169 optimal weight: 6.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 752 GLN E 205 GLN ** H 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18188 Z= 0.200 Angle : 0.500 7.509 24645 Z= 0.266 Chirality : 0.039 0.184 2810 Planarity : 0.004 0.046 3013 Dihedral : 11.427 105.858 2851 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.34 % Allowed : 17.86 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 0.71 (0.17), residues: 2275 helix: 1.62 (0.14), residues: 1327 sheet: -1.14 (0.33), residues: 210 loop : -1.11 (0.21), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 667 HIS 0.004 0.001 HIS H 204 PHE 0.014 0.001 PHE C 570 TYR 0.023 0.001 TYR G 32 ARG 0.009 0.000 ARG B 624 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 268 time to evaluate : 1.800 Fit side-chains REVERT: A 396 ILE cc_start: 0.7801 (tt) cc_final: 0.7529 (mt) REVERT: A 566 GLU cc_start: 0.7436 (pp20) cc_final: 0.7093 (mm-30) REVERT: A 590 ARG cc_start: 0.8759 (mmm-85) cc_final: 0.7767 (mtt90) REVERT: A 665 LYS cc_start: 0.6996 (OUTLIER) cc_final: 0.6785 (tttp) REVERT: A 803 MET cc_start: 0.8387 (mtm) cc_final: 0.8057 (mtm) REVERT: B 403 MET cc_start: 0.6637 (mtm) cc_final: 0.5922 (mtp) REVERT: B 459 MET cc_start: 0.6985 (mtm) cc_final: 0.6613 (mtm) REVERT: B 483 GLU cc_start: 0.7007 (mt-10) cc_final: 0.6451 (mp0) REVERT: B 615 ASN cc_start: 0.7781 (m-40) cc_final: 0.7180 (t0) REVERT: B 624 ARG cc_start: 0.6606 (ptp-110) cc_final: 0.6314 (ptp-110) REVERT: B 711 ARG cc_start: 0.5196 (mmm-85) cc_final: 0.4680 (mmp-170) REVERT: C 398 GLU cc_start: 0.6956 (tp30) cc_final: 0.6756 (mm-30) REVERT: C 403 MET cc_start: 0.5826 (mtm) cc_final: 0.5303 (mtm) REVERT: C 438 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7763 (tt) REVERT: C 736 SER cc_start: 0.6954 (t) cc_final: 0.6706 (t) REVERT: C 738 LEU cc_start: 0.6893 (OUTLIER) cc_final: 0.6612 (mt) REVERT: D 403 MET cc_start: 0.6929 (mtm) cc_final: 0.6484 (mtm) REVERT: D 459 MET cc_start: 0.6904 (mtm) cc_final: 0.6599 (mmm) REVERT: D 615 ASN cc_start: 0.8085 (m-40) cc_final: 0.7780 (m110) REVERT: D 638 GLN cc_start: 0.6577 (pp30) cc_final: 0.5766 (pp30) REVERT: D 639 THR cc_start: 0.6683 (OUTLIER) cc_final: 0.6442 (m) REVERT: D 650 SER cc_start: 0.8154 (t) cc_final: 0.7833 (m) REVERT: D 653 GLU cc_start: 0.7468 (tp30) cc_final: 0.6730 (tp30) REVERT: D 748 LYS cc_start: 0.6398 (OUTLIER) cc_final: 0.6100 (ttmt) REVERT: D 807 LEU cc_start: 0.6684 (OUTLIER) cc_final: 0.6169 (tm) REVERT: E 58 MET cc_start: 0.5639 (mmm) cc_final: 0.5352 (mmm) REVERT: E 79 LYS cc_start: 0.6730 (ttmm) cc_final: 0.6197 (ttpp) REVERT: E 97 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7512 (mt) REVERT: E 202 GLU cc_start: 0.6753 (OUTLIER) cc_final: 0.6242 (mp0) REVERT: F 37 ARG cc_start: 0.6193 (mtt-85) cc_final: 0.5778 (mmt90) REVERT: F 74 ARG cc_start: 0.6149 (ttm170) cc_final: 0.5750 (ttm110) REVERT: F 79 LYS cc_start: 0.7094 (mttm) cc_final: 0.6503 (tmmm) REVERT: F 96 TYR cc_start: 0.6790 (t80) cc_final: 0.6587 (t80) REVERT: F 99 ARG cc_start: 0.7004 (mmt90) cc_final: 0.6736 (mmt90) REVERT: G 11 LEU cc_start: 0.7268 (tt) cc_final: 0.6884 (mm) REVERT: G 41 ARG cc_start: 0.3027 (OUTLIER) cc_final: 0.2730 (mtp180) REVERT: G 65 ARG cc_start: 0.6123 (mtm-85) cc_final: 0.5795 (mtt-85) REVERT: G 79 LYS cc_start: 0.5967 (ttmm) cc_final: 0.5621 (tttp) REVERT: G 99 ARG cc_start: 0.6777 (mmp-170) cc_final: 0.6344 (mtt-85) REVERT: G 129 ARG cc_start: 0.4566 (ttm110) cc_final: 0.3992 (mpp80) REVERT: G 204 HIS cc_start: 0.6743 (OUTLIER) cc_final: 0.6480 (t-90) REVERT: H 37 ARG cc_start: 0.5740 (mtt-85) cc_final: 0.5515 (mmt90) REVERT: H 67 CYS cc_start: 0.7549 (m) cc_final: 0.7268 (m) REVERT: H 202 GLU cc_start: 0.7136 (mt-10) cc_final: 0.6693 (mm-30) outliers start: 52 outliers final: 38 residues processed: 298 average time/residue: 1.2720 time to fit residues: 423.0256 Evaluate side-chains 310 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 262 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 443 ASP Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 519 TYR Chi-restraints excluded: chain A residue 665 LYS Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 725 SER Chi-restraints excluded: chain C residue 738 LEU Chi-restraints excluded: chain D residue 443 ASP Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 719 VAL Chi-restraints excluded: chain D residue 748 LYS Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain G residue 24 MET Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 41 ARG Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 196 optimal weight: 10.0000 chunk 206 optimal weight: 4.9990 chunk 188 optimal weight: 6.9990 chunk 201 optimal weight: 1.9990 chunk 121 optimal weight: 9.9990 chunk 87 optimal weight: 1.9990 chunk 157 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 181 optimal weight: 5.9990 chunk 190 optimal weight: 5.9990 chunk 200 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 752 GLN E 205 GLN F 204 HIS ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 18188 Z= 0.377 Angle : 0.615 7.933 24645 Z= 0.325 Chirality : 0.044 0.259 2810 Planarity : 0.005 0.048 3013 Dihedral : 12.306 113.207 2851 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.51 % Allowed : 17.80 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 0.26 (0.17), residues: 2275 helix: 1.26 (0.14), residues: 1323 sheet: -1.48 (0.34), residues: 186 loop : -1.28 (0.20), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 667 HIS 0.007 0.002 HIS G 82 PHE 0.021 0.002 PHE A 604 TYR 0.029 0.002 TYR G 32 ARG 0.007 0.001 ARG B 624 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 261 time to evaluate : 1.936 Fit side-chains REVERT: A 396 ILE cc_start: 0.7791 (tt) cc_final: 0.7520 (mt) REVERT: A 566 GLU cc_start: 0.7514 (pp20) cc_final: 0.7114 (mm-30) REVERT: A 590 ARG cc_start: 0.8766 (mmm-85) cc_final: 0.7774 (mtt90) REVERT: A 679 VAL cc_start: 0.7655 (t) cc_final: 0.7341 (p) REVERT: A 803 MET cc_start: 0.8423 (mtm) cc_final: 0.8098 (mtm) REVERT: B 403 MET cc_start: 0.6550 (mtm) cc_final: 0.5998 (mtp) REVERT: B 459 MET cc_start: 0.7052 (mtm) cc_final: 0.6675 (mtm) REVERT: B 483 GLU cc_start: 0.6936 (mt-10) cc_final: 0.6351 (mp0) REVERT: B 615 ASN cc_start: 0.7713 (m-40) cc_final: 0.7084 (t0) REVERT: C 403 MET cc_start: 0.5727 (mtm) cc_final: 0.5203 (mtm) REVERT: C 736 SER cc_start: 0.6799 (t) cc_final: 0.6483 (t) REVERT: C 738 LEU cc_start: 0.6999 (OUTLIER) cc_final: 0.6687 (mt) REVERT: D 615 ASN cc_start: 0.8109 (m-40) cc_final: 0.7783 (m110) REVERT: D 638 GLN cc_start: 0.6718 (pp30) cc_final: 0.5923 (pp30) REVERT: D 650 SER cc_start: 0.8134 (t) cc_final: 0.7791 (m) REVERT: D 653 GLU cc_start: 0.7529 (tp30) cc_final: 0.6802 (tp30) REVERT: D 748 LYS cc_start: 0.6464 (OUTLIER) cc_final: 0.6156 (ttmt) REVERT: D 807 LEU cc_start: 0.6650 (OUTLIER) cc_final: 0.6218 (tm) REVERT: E 58 MET cc_start: 0.5648 (mmm) cc_final: 0.5237 (mpt) REVERT: E 65 ARG cc_start: 0.6031 (mtm-85) cc_final: 0.5600 (mtm-85) REVERT: E 79 LYS cc_start: 0.6792 (ttmm) cc_final: 0.6356 (ttpp) REVERT: E 97 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7477 (mt) REVERT: E 202 GLU cc_start: 0.6826 (OUTLIER) cc_final: 0.6331 (mp0) REVERT: F 37 ARG cc_start: 0.6166 (mtt-85) cc_final: 0.5733 (mmt90) REVERT: F 79 LYS cc_start: 0.7231 (mttm) cc_final: 0.6592 (tmmm) REVERT: F 96 TYR cc_start: 0.6790 (t80) cc_final: 0.6544 (t80) REVERT: F 99 ARG cc_start: 0.6989 (mmt90) cc_final: 0.6762 (mmt90) REVERT: G 11 LEU cc_start: 0.7257 (tt) cc_final: 0.6891 (mm) REVERT: G 65 ARG cc_start: 0.5934 (mtm-85) cc_final: 0.5696 (mtt-85) REVERT: G 79 LYS cc_start: 0.6002 (ttmm) cc_final: 0.5644 (tttp) REVERT: G 99 ARG cc_start: 0.6759 (mmp-170) cc_final: 0.6363 (mtt-85) REVERT: G 129 ARG cc_start: 0.4368 (ttm110) cc_final: 0.4167 (mtp85) REVERT: H 14 THR cc_start: 0.8223 (t) cc_final: 0.7964 (m) outliers start: 55 outliers final: 38 residues processed: 296 average time/residue: 1.3013 time to fit residues: 433.6086 Evaluate side-chains 298 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 255 time to evaluate : 2.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 443 ASP Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 725 SER Chi-restraints excluded: chain C residue 738 LEU Chi-restraints excluded: chain D residue 443 ASP Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 719 VAL Chi-restraints excluded: chain D residue 748 LYS Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 24 MET Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 132 optimal weight: 0.0170 chunk 212 optimal weight: 0.9990 chunk 129 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 223 optimal weight: 3.9990 chunk 205 optimal weight: 5.9990 chunk 177 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 137 optimal weight: 0.3980 chunk 108 optimal weight: 8.9990 overall best weight: 1.0622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 752 GLN E 205 GLN ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18188 Z= 0.168 Angle : 0.495 7.992 24645 Z= 0.263 Chirality : 0.039 0.220 2810 Planarity : 0.004 0.044 3013 Dihedral : 11.325 105.802 2847 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.59 % Allowed : 18.89 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 0.74 (0.17), residues: 2275 helix: 1.65 (0.14), residues: 1327 sheet: -1.11 (0.33), residues: 210 loop : -1.14 (0.21), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 667 HIS 0.003 0.001 HIS F 204 PHE 0.012 0.001 PHE C 570 TYR 0.026 0.001 TYR G 32 ARG 0.013 0.000 ARG B 624 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 264 time to evaluate : 1.883 Fit side-chains REVERT: A 396 ILE cc_start: 0.7799 (tt) cc_final: 0.7537 (mt) REVERT: A 566 GLU cc_start: 0.7512 (pp20) cc_final: 0.7141 (mm-30) REVERT: A 590 ARG cc_start: 0.8740 (mmm-85) cc_final: 0.7732 (mtt90) REVERT: A 803 MET cc_start: 0.8384 (mtm) cc_final: 0.8063 (mtm) REVERT: B 403 MET cc_start: 0.6698 (mtm) cc_final: 0.6090 (mtp) REVERT: B 459 MET cc_start: 0.6933 (mtm) cc_final: 0.6551 (mtm) REVERT: B 483 GLU cc_start: 0.7011 (mt-10) cc_final: 0.6429 (mp0) REVERT: B 615 ASN cc_start: 0.7694 (m-40) cc_final: 0.6937 (t0) REVERT: C 398 GLU cc_start: 0.6891 (tp30) cc_final: 0.6673 (mm-30) REVERT: C 403 MET cc_start: 0.5817 (mtm) cc_final: 0.5305 (mtm) REVERT: C 542 PHE cc_start: 0.7502 (OUTLIER) cc_final: 0.6780 (t80) REVERT: C 736 SER cc_start: 0.6964 (t) cc_final: 0.6710 (t) REVERT: C 738 LEU cc_start: 0.6911 (OUTLIER) cc_final: 0.6617 (mt) REVERT: D 403 MET cc_start: 0.6964 (mtm) cc_final: 0.6670 (mtm) REVERT: D 459 MET cc_start: 0.6865 (mtm) cc_final: 0.6401 (mmm) REVERT: D 615 ASN cc_start: 0.8032 (m-40) cc_final: 0.7739 (m110) REVERT: D 638 GLN cc_start: 0.6624 (pp30) cc_final: 0.5887 (pp30) REVERT: D 650 SER cc_start: 0.8181 (t) cc_final: 0.7867 (m) REVERT: D 653 GLU cc_start: 0.7481 (tp30) cc_final: 0.6772 (tp30) REVERT: D 748 LYS cc_start: 0.6393 (OUTLIER) cc_final: 0.6099 (ttmt) REVERT: D 807 LEU cc_start: 0.6703 (OUTLIER) cc_final: 0.6119 (tm) REVERT: E 58 MET cc_start: 0.5583 (mmm) cc_final: 0.5208 (mpt) REVERT: E 79 LYS cc_start: 0.6819 (ttmm) cc_final: 0.6405 (ttpp) REVERT: E 97 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7528 (mt) REVERT: E 202 GLU cc_start: 0.6760 (OUTLIER) cc_final: 0.6250 (mp0) REVERT: F 37 ARG cc_start: 0.6166 (mtt-85) cc_final: 0.5740 (mmt90) REVERT: F 74 ARG cc_start: 0.6035 (ttm170) cc_final: 0.5609 (ttm110) REVERT: F 79 LYS cc_start: 0.7056 (mttm) cc_final: 0.6468 (tmmm) REVERT: F 96 TYR cc_start: 0.6835 (t80) cc_final: 0.6627 (t80) REVERT: F 99 ARG cc_start: 0.6988 (mmt90) cc_final: 0.6759 (mmt90) REVERT: G 11 LEU cc_start: 0.7270 (tt) cc_final: 0.6877 (mm) REVERT: G 65 ARG cc_start: 0.6012 (mtm-85) cc_final: 0.5714 (mtt-85) REVERT: G 79 LYS cc_start: 0.5860 (ttmm) cc_final: 0.5539 (tttp) REVERT: G 99 ARG cc_start: 0.6759 (mmp-170) cc_final: 0.6330 (mtt-85) REVERT: G 184 PHE cc_start: 0.7196 (m-80) cc_final: 0.6494 (t80) REVERT: H 67 CYS cc_start: 0.7511 (m) cc_final: 0.7231 (m) REVERT: H 202 GLU cc_start: 0.7115 (mt-10) cc_final: 0.6664 (mm-30) outliers start: 39 outliers final: 30 residues processed: 285 average time/residue: 1.2635 time to fit residues: 402.8001 Evaluate side-chains 289 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 253 time to evaluate : 1.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 443 ASP Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 742 VAL Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 725 SER Chi-restraints excluded: chain C residue 738 LEU Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 541 ARG Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 719 VAL Chi-restraints excluded: chain D residue 748 LYS Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain G residue 24 MET Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 141 optimal weight: 5.9990 chunk 189 optimal weight: 6.9990 chunk 54 optimal weight: 0.0970 chunk 163 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 177 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 182 optimal weight: 1.9990 chunk 22 optimal weight: 0.0060 chunk 32 optimal weight: 6.9990 overall best weight: 2.2200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 752 GLN E 205 GLN ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.165123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.129704 restraints weight = 76906.723| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 3.51 r_work: 0.2861 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2827 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2826 r_free = 0.2826 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2826 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18188 Z= 0.261 Angle : 0.543 7.867 24645 Z= 0.287 Chirality : 0.041 0.258 2810 Planarity : 0.004 0.047 3013 Dihedral : 11.586 108.072 2847 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.82 % Allowed : 19.07 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.00 % 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: 0.58 (0.17), residues: 2275 helix: 1.49 (0.14), residues: 1327 sheet: -1.15 (0.33), residues: 210 loop : -1.16 (0.21), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 667 HIS 0.004 0.001 HIS F 60 PHE 0.016 0.002 PHE C 570 TYR 0.036 0.002 TYR C 707 ARG 0.012 0.001 ARG B 624 =============================================================================== Job complete usr+sys time: 6889.05 seconds wall clock time: 122 minutes 19.96 seconds (7339.96 seconds total)