Starting phenix.real_space_refine on Sat Feb 17 11:22:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c1q_16380/02_2024/8c1q_16380_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c1q_16380/02_2024/8c1q_16380.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c1q_16380/02_2024/8c1q_16380.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c1q_16380/02_2024/8c1q_16380.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c1q_16380/02_2024/8c1q_16380_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c1q_16380/02_2024/8c1q_16380_updated.pdb" } resolution = 2.82 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= 0.003 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 10 5.49 5 S 109 5.16 5 C 12060 2.51 5 N 2937 2.21 5 O 3334 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 416": "NH1" <-> "NH2" Residue "A TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 483": "OE1" <-> "OE2" Residue "A PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 515": "OD1" <-> "OD2" Residue "A PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 542": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 590": "NH1" <-> "NH2" Residue "A PHE 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 623": "OE1" <-> "OE2" Residue "A ASP 634": "OD1" <-> "OD2" Residue "A PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 656": "NH1" <-> "NH2" Residue "A PHE 663": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 706": "OE1" <-> "OE2" Residue "A PHE 792": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 418": "OE1" <-> "OE2" Residue "B TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 427": "OE1" <-> "OE2" Residue "B ASP 443": "OD1" <-> "OD2" Residue "B GLU 462": "OE1" <-> "OE2" Residue "B TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 515": "OD1" <-> "OD2" Residue "B ARG 541": "NH1" <-> "NH2" Residue "B PHE 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 586": "OD1" <-> "OD2" Residue "B PHE 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 612": "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 TYR 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 724": "OD1" <-> "OD2" Residue "B PHE 792": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 398": "OE1" <-> "OE2" Residue "C PHE 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 515": "OD1" <-> "OD2" Residue "C PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 542": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 590": "NH1" <-> "NH2" Residue "C PHE 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 623": "OE1" <-> "OE2" Residue "C PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 656": "NH1" <-> "NH2" Residue "C PHE 663": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 698": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 701": "OE1" <-> "OE2" Residue "C GLU 706": "OE1" <-> "OE2" Residue "C PHE 792": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 415": "OD1" <-> "OD2" Residue "D GLU 418": "OE1" <-> "OE2" Residue "D TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 443": "OD1" <-> "OD2" Residue "D TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 462": "OE1" <-> "OE2" Residue "D ASP 486": "OD1" <-> "OD2" Residue "D PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 515": "OD1" <-> "OD2" Residue "D PHE 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 623": "OE1" <-> "OE2" Residue "D GLU 630": "OE1" <-> "OE2" Residue "D TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 706": "OE1" <-> "OE2" Residue "D ASP 715": "OD1" <-> "OD2" Residue "D PHE 792": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 55": "OE1" <-> "OE2" Residue "E GLU 70": "OE1" <-> "OE2" Residue "E PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 56": "OE1" <-> "OE2" Residue "F PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "F GLU 190": "OE1" <-> "OE2" Residue "F TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 55": "OE1" <-> "OE2" Residue "G GLU 70": "OE1" <-> "OE2" Residue "G PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 56": "OE1" <-> "OE2" Residue "H PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" 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" Residue "H GLU 190": "OE1" <-> "OE2" Residue "H TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18462 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 3179 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 405, 3150 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 390} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 34 Conformer: "B" Number of residues, atoms: 405, 3150 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 390} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 3187 Chain: "B" Number of atoms: 3012 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 400, 2977 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 385} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 207 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 5, 'GLU:plan': 10, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 107 Conformer: "B" Number of residues, atoms: 400, 2977 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 385} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 207 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 5, 'GLU:plan': 10, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 107 bond proxies already assigned to first conformer: 3005 Chain: "C" Number of atoms: 3116 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 406, 3087 Classifications: {'peptide': 406} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 391} Chain breaks: 2 Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 107 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 3, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 65 Conformer: "B" Number of residues, atoms: 406, 3087 Classifications: {'peptide': 406} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 391} Chain breaks: 2 Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 107 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 3, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 65 bond proxies already assigned to first conformer: 3124 Chain: "D" Number of atoms: 3152 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 400, 3117 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 385} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 Conformer: "B" Number of residues, atoms: 400, 3117 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 385} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 bond proxies already assigned to first conformer: 3147 Chain: "E" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1367 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 2, 'TRANS': 173} Chain breaks: 3 Chain: "F" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1367 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 2, 'TRANS': 173} Chain breaks: 3 Chain: "G" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1367 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 2, 'TRANS': 173} Chain breaks: 3 Chain: "H" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1367 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 2, 'TRANS': 173} Chain breaks: 3 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 70 Unusual residues: {'OLC': 1, 'PLM': 1, 'ZK1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 70 Unusual residues: {'OLC': 1, 'PLM': 1, 'ZK1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 70 Unusual residues: {'OLC': 1, 'PLM': 1, 'ZK1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 70 Unusual residues: {'OLC': 1, 'PLM': 1, 'ZK1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "F" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 26 Chain: "G" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "H" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 26 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 16 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 A 619 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 619 " 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 APHE B 619 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE B 619 " 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 residue: pdb=" N APHE C 619 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE C 619 " occ=0.50 ... (remaining 4 not shown) Time building chain proxies: 15.74, per 1000 atoms: 0.85 Number of scatterers: 18462 At special positions: 0 Unit cell: (117.66, 121.9, 135.68, 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) S 109 16.00 P 10 15.00 F 12 9.00 O 3334 8.00 N 2937 7.00 C 12060 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 714 " - pdb=" SG CYS A 769 " distance=2.02 Simple disulfide: pdb=" SG CYS B 714 " - pdb=" SG CYS B 769 " distance=2.03 Simple disulfide: pdb=" SG CYS C 714 " - pdb=" SG CYS C 769 " distance=2.02 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=2.00 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.06 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.06 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 68 " distance=2.00 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " distance=2.06 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 68 " distance=2.06 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 77 " distance=2.03 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: 7.73 Conformation dependent library (CDL) restraints added in 5.1 seconds 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4258 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 83 helices and 18 sheets defined 53.9% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.45 Creating SS restraints... 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 464 Processing helix chain 'A' and resid 479 through 484 removed outlier: 3.915A pdb=" N VAL A 484 " --> pdb=" O VAL A 480 " (cutoff:3.500A) 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 541 Processing helix chain 'A' and resid 569 through 580 Processing helix chain 'A' and resid 592 through 624 removed outlier: 3.567A pdb=" N ARG A 624 " --> pdb=" O LEU A 620 " (cutoff:3.500A) 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 671 Processing helix chain 'A' and resid 682 through 692 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 813 removed outlier: 3.748A pdb=" N ALA A 789 " --> pdb=" O SER A 786 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N GLY A 790 " --> pdb=" O ASN A 787 " (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 459 through 464 Processing helix chain 'B' and resid 479 through 484 removed outlier: 3.887A pdb=" N VAL B 484 " --> pdb=" O VAL B 480 " (cutoff:3.500A) 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 541 Processing helix chain 'B' and resid 569 through 580 Processing helix chain 'B' and resid 592 through 621 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 671 Processing helix chain 'B' and resid 682 through 691 Processing helix chain 'B' and resid 702 through 710 Processing helix chain 'B' and resid 738 through 752 Processing helix chain 'B' and resid 754 through 763 Processing helix chain 'B' and resid 785 through 814 removed outlier: 3.546A pdb=" N ALA B 789 " --> pdb=" O SER B 786 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N GLY B 790 " --> pdb=" O ASN B 787 " (cutoff:3.500A) 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 459 through 464 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 541 Processing helix chain 'C' and resid 569 through 580 Processing helix chain 'C' and resid 592 through 624 removed outlier: 3.618A pdb=" N ARG C 624 " --> pdb=" O LEU C 620 " (cutoff:3.500A) 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 692 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 763 Processing helix chain 'C' and resid 785 through 813 removed outlier: 3.735A pdb=" N ALA C 789 " --> pdb=" O SER C 786 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N GLY C 790 " --> pdb=" O ASN C 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 416 No H-bonds generated for 'chain 'D' and resid 414 through 416' Processing helix chain 'D' and resid 420 through 432 Processing helix chain 'D' and resid 458 through 464 Processing helix chain 'D' and resid 479 through 484 removed outlier: 3.850A pdb=" N VAL D 484 " --> pdb=" O VAL D 480 " (cutoff:3.500A) 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 541 Processing helix chain 'D' and resid 569 through 580 Processing helix chain 'D' and resid 592 through 621 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 671 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 752 Processing helix chain 'D' and resid 754 through 763 Processing helix chain 'D' and resid 785 through 814 removed outlier: 3.553A pdb=" N ALA D 789 " --> pdb=" O SER D 786 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLY D 790 " --> 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 103 Processing helix chain 'E' and resid 106 through 127 removed outlier: 4.243A pdb=" N GLU E 126 " --> pdb=" O VAL E 122 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N PHE E 127 " --> pdb=" O ALA E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 161 Processing helix chain 'E' and resid 177 through 208 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 126 removed outlier: 3.829A pdb=" N GLU F 126 " --> pdb=" O VAL F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 161 removed outlier: 4.035A pdb=" N ALA F 161 " --> pdb=" O SER F 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 208 removed outlier: 3.748A pdb=" N ARG F 208 " --> pdb=" O HIS F 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 29 Processing helix chain 'G' and resid 93 through 103 Processing helix chain 'G' and resid 106 through 127 removed outlier: 4.240A pdb=" N GLU G 126 " --> pdb=" O VAL G 122 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N PHE G 127 " --> pdb=" O ALA G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 161 Processing helix chain 'G' and resid 177 through 208 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 126 removed outlier: 3.834A pdb=" N GLU H 126 " --> pdb=" O VAL H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 161 removed outlier: 4.041A pdb=" N ALA H 161 " --> pdb=" O SER H 158 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 208 removed outlier: 3.751A pdb=" N ARG H 208 " --> pdb=" O HIS H 204 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 390 through 392 removed outlier: 6.558A pdb=" N SER A 435 " --> pdb=" O TYR A 391 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 485 through 487 Processing sheet with id= C, first strand: chain 'A' and resid 492 through 494 removed outlier: 3.548A pdb=" N MET A 492 " --> pdb=" O TYR A 728 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 716 through 719 removed outlier: 4.120A pdb=" N ILE A 498 " --> pdb=" O VAL A 719 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N LYS A 501 " --> pdb=" O TYR A 696 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N TYR A 696 " --> pdb=" O LYS A 501 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA A 642 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N LEU A 699 " --> pdb=" O ALA A 642 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLY A 644 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 9.247A pdb=" N GLU A 701 " --> pdb=" O GLY A 644 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 448 through 450 removed outlier: 3.620A pdb=" N ALA B 455 " --> pdb=" O ASP B 450 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 492 through 494 removed outlier: 3.531A pdb=" N MET B 492 " --> pdb=" O TYR B 728 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 716 through 719 removed outlier: 4.077A pdb=" N ILE B 498 " --> pdb=" O VAL B 719 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N LYS B 501 " --> pdb=" O TYR B 696 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N TYR B 696 " --> pdb=" O LYS B 501 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ALA B 642 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N LEU B 699 " --> pdb=" O ALA B 642 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLY B 644 " --> pdb=" O LEU B 699 " (cutoff:3.500A) removed outlier: 9.578A pdb=" N GLU B 701 " --> pdb=" O GLY B 644 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 390 through 395 removed outlier: 6.375A pdb=" N SER C 435 " --> pdb=" O TYR C 391 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N VAL C 393 " --> pdb=" O SER C 435 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ARG C 437 " --> pdb=" O VAL C 393 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N THR C 395 " --> pdb=" O ARG C 437 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N GLU C 439 " --> pdb=" O THR C 395 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'C' and resid 485 through 487 Processing sheet with id= J, first strand: chain 'C' and resid 492 through 494 removed outlier: 3.617A pdb=" N MET C 492 " --> pdb=" O TYR C 728 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 716 through 719 removed outlier: 4.133A pdb=" N ILE C 498 " --> pdb=" O VAL C 719 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LYS C 501 " --> pdb=" O TYR C 696 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N TYR C 696 " --> pdb=" O LYS C 501 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA C 642 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N LEU C 699 " --> pdb=" O ALA C 642 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N GLY C 644 " --> pdb=" O LEU C 699 " (cutoff:3.500A) removed outlier: 9.357A pdb=" N GLU C 701 " --> pdb=" O GLY C 644 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 391 through 393 Processing sheet with id= M, first strand: chain 'D' and resid 492 through 494 removed outlier: 3.514A pdb=" N MET D 492 " --> pdb=" O TYR D 728 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 716 through 719 removed outlier: 4.076A pdb=" N ILE D 498 " --> pdb=" O VAL D 719 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N LYS D 501 " --> pdb=" O TYR D 696 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N TYR D 696 " --> pdb=" O LYS D 501 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA D 642 " --> pdb=" O ALA D 697 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N LEU D 699 " --> pdb=" O ALA D 642 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLY D 644 " --> pdb=" O LEU D 699 " (cutoff:3.500A) removed outlier: 9.507A pdb=" N GLU D 701 " --> pdb=" O GLY D 644 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 59 through 61 Processing sheet with id= P, first strand: chain 'F' and resid 173 through 175 Processing sheet with id= Q, first strand: chain 'G' and resid 59 through 61 Processing sheet with id= R, first strand: chain 'H' and resid 173 through 175 993 hydrogen bonds defined for protein. 2506 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: 5.46 Time building geometry restraints manager: 8.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 2837 1.29 - 1.43: 5269 1.43 - 1.57: 10555 1.57 - 1.71: 12 1.71 - 1.85: 174 Bond restraints: 18847 Sorted by residual: bond pdb=" C LEU B 616 " pdb=" O LEU B 616 " ideal model delta sigma weight residual 1.237 1.154 0.082 1.19e-02 7.06e+03 4.80e+01 bond pdb=" CAO ZK1 A 901 " pdb=" PBA ZK1 A 901 " ideal model delta sigma weight residual 1.896 1.779 0.117 2.00e-02 2.50e+03 3.42e+01 bond pdb=" CAO ZK1 D 901 " pdb=" PBA ZK1 D 901 " ideal model delta sigma weight residual 1.896 1.795 0.101 2.00e-02 2.50e+03 2.57e+01 bond pdb=" CA SER D 611 " pdb=" CB SER D 611 " ideal model delta sigma weight residual 1.528 1.458 0.070 1.56e-02 4.11e+03 2.04e+01 bond pdb=" CA SER C 576 " pdb=" CB SER C 576 " ideal model delta sigma weight residual 1.528 1.464 0.065 1.56e-02 4.11e+03 1.71e+01 ... (remaining 18842 not shown) Histogram of bond angle deviations from ideal: 96.49 - 104.33: 199 104.33 - 112.16: 8344 112.16 - 120.00: 9131 120.00 - 127.84: 7639 127.84 - 135.68: 143 Bond angle restraints: 25456 Sorted by residual: angle pdb=" N GLN B 583 " pdb=" CA GLN B 583 " pdb=" C GLN B 583 " ideal model delta sigma weight residual 109.63 99.18 10.45 1.49e+00 4.50e-01 4.92e+01 angle pdb=" C GLU B 684 " pdb=" CA GLU B 684 " pdb=" CB GLU B 684 " ideal model delta sigma weight residual 110.85 121.97 -11.12 1.70e+00 3.46e-01 4.28e+01 angle pdb=" CA ASP B 724 " pdb=" CB ASP B 724 " pdb=" CG ASP B 724 " ideal model delta sigma weight residual 112.60 118.63 -6.03 1.00e+00 1.00e+00 3.63e+01 angle pdb=" CA PHE D 570 " pdb=" CB PHE D 570 " pdb=" CG PHE D 570 " ideal model delta sigma weight residual 113.80 119.80 -6.00 1.00e+00 1.00e+00 3.60e+01 angle pdb=" CA ASP A 724 " pdb=" CB ASP A 724 " pdb=" CG ASP A 724 " ideal model delta sigma weight residual 112.60 118.10 -5.50 1.00e+00 1.00e+00 3.02e+01 ... (remaining 25451 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.16: 10172 21.16 - 42.31: 702 42.31 - 63.47: 178 63.47 - 84.63: 30 84.63 - 105.78: 12 Dihedral angle restraints: 11094 sinusoidal: 4410 harmonic: 6684 Sorted by residual: dihedral pdb=" CA BCYS D 585 " pdb=" C BCYS D 585 " pdb=" N BASP D 586 " pdb=" CA BASP D 586 " ideal model delta harmonic sigma weight residual -180.00 -150.22 -29.78 0 5.00e+00 4.00e-02 3.55e+01 dihedral pdb=" C GLU B 684 " pdb=" N GLU B 684 " pdb=" CA GLU B 684 " pdb=" CB GLU B 684 " ideal model delta harmonic sigma weight residual -122.60 -137.15 14.55 0 2.50e+00 1.60e-01 3.39e+01 dihedral pdb=" CA BCYS A 585 " pdb=" C BCYS A 585 " pdb=" N BASP A 586 " pdb=" CA BASP A 586 " ideal model delta harmonic sigma weight residual -180.00 -155.86 -24.14 0 5.00e+00 4.00e-02 2.33e+01 ... (remaining 11091 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 2092 0.092 - 0.185: 631 0.185 - 0.277: 80 0.277 - 0.369: 7 0.369 - 0.462: 1 Chirality restraints: 2811 Sorted by residual: chirality pdb=" CA GLU B 684 " pdb=" N GLU B 684 " pdb=" C GLU B 684 " pdb=" CB GLU B 684 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.33e+00 chirality pdb=" CB VAL B 791 " pdb=" CA VAL B 791 " pdb=" CG1 VAL B 791 " pdb=" CG2 VAL B 791 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" CB VAL D 791 " pdb=" CA VAL D 791 " pdb=" CG1 VAL D 791 " pdb=" CG2 VAL D 791 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.23e+00 ... (remaining 2808 not shown) Planarity restraints: 3111 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV H1302 " -0.106 2.00e-02 2.50e+03 1.11e-01 1.22e+02 pdb=" C29 POV H1302 " 0.092 2.00e-02 2.50e+03 pdb="C210 POV H1302 " 0.127 2.00e-02 2.50e+03 pdb="C211 POV H1302 " -0.114 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV F1302 " -0.097 2.00e-02 2.50e+03 9.70e-02 9.41e+01 pdb=" C29 POV F1302 " 0.099 2.00e-02 2.50e+03 pdb="C210 POV F1302 " 0.095 2.00e-02 2.50e+03 pdb="C211 POV F1302 " -0.097 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 583 " -0.043 2.00e-02 2.50e+03 8.60e-02 7.40e+01 pdb=" C GLN D 583 " 0.149 2.00e-02 2.50e+03 pdb=" O GLN D 583 " -0.055 2.00e-02 2.50e+03 pdb=" N BGLY D 584 " -0.051 2.00e-02 2.50e+03 ... (remaining 3108 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 776 2.72 - 3.26: 19155 3.26 - 3.81: 30134 3.81 - 4.35: 38094 4.35 - 4.90: 63788 Nonbonded interactions: 151947 Sorted by model distance: nonbonded pdb=" O PHE C 654 " pdb=" OG SER C 658 " model vdw 2.171 2.440 nonbonded pdb=" NH1 ARG B 690 " pdb=" OD1 ASP B 715 " model vdw 2.184 2.520 nonbonded pdb=" NH2 ARG A 711 " pdb=" O LYS A 766 " model vdw 2.204 2.520 nonbonded pdb=" N AASP D 586 " pdb=" OD1AASP D 586 " model vdw 2.223 2.520 nonbonded pdb=" N BASP D 586 " pdb=" OD1BASP D 586 " model vdw 2.239 2.520 ... (remaining 151942 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 390 through 391 or (resid 392 and (name N or name CA or na \ me C or name O or name CB or name CG1)) or resid 393 through 398 or (resid 399 a \ nd (name N or name CA or name C or name O or name CB or name CG )) or resid 400 \ through 403 or (resid 404 and (name N or name CA or name C or name O or name CB \ or name CG )) or resid 405 or (resid 406 and (name N or name CA or name C or nam \ e O or name CB )) or resid 407 through 408 or (resid 409 through 410 and (name N \ or name CA or name C or name O or name CB )) or resid 411 or (resid 412 and (na \ me N or name CA or name C or name O or name CB )) or resid 413 through 414 or (r \ esid 415 and (name N or name CA or name C or name O or name CB )) or resid 416 t \ hrough 422 or (resid 423 and (name N or name CA or name C or name O or name CB o \ r name CG )) or resid 424 through 429 or (resid 430 and (name N or name CA or na \ me C or name O or name CB )) or resid 431 through 433 or (resid 434 and (name N \ or name CA or name C or name O or name CB or name CG )) or (resid 435 and (name \ N or name CA or name C or name O or name CB )) or resid 436 or (resid 437 and (n \ ame N or name CA or name C or name O or name CB )) or resid 438 or (resid 439 an \ d (name N or name CA or name C or name O or name CB or name CG )) or resid 440 t \ hrough 441 or (resid 442 and (name N or name CA or name C or name O or name CB ) \ ) or resid 443 through 448 or (resid 449 through 452 and (name N or name CA or n \ ame C or name O or name CB )) or resid 453 or (resid 454 through 455 and (name N \ or name CA or name C or name O or name CB )) or resid 456 or (resid 457 and (na \ me N or name CA or name C or name O or name CB )) or resid 458 through 466 or (r \ esid 467 through 468 and (name N or name CA or name C or name O or name CB )) or \ resid 469 through 504 or (resid 505 and (name N or name CA or name C or name O \ or name CB )) or resid 506 or (resid 507 and (name N or name CA or name C or nam \ e O or name CB )) or resid 508 through 546 or resid 567 through 581 or resid 583 \ or resid 587 through 618 or resid 620 through 637 or (resid 638 through 640 and \ (name N or name CA or name C or name O or name CB )) or resid 641 through 646 o \ r (resid 647 and (name N or name CA or name C or name O or name CB or name CG )) \ or resid 648 through 656 or (resid 657 and (name N or name CA or name C or name \ O or name CB )) or resid 658 or (resid 659 and (name N or name CA or name C or \ name O or name CB )) or resid 660 through 663 or (resid 664 and (name N or name \ CA or name C or name O or name CB )) or resid 665 or (resid 666 and (name N or n \ ame CA or name C or name O or name CB )) or resid 667 through 670 or (resid 671 \ and (name N or name CA or name C or name O or name CB )) or resid 672 through 67 \ 3 or (resid 674 and (name N or name CA or name C or name O or name CB )) or resi \ d 675 through 679 or (resid 680 and (name N or name CA or name C or name O or na \ me CB )) or resid 681 through 682 or (resid 683 and (name N or name CA or name C \ or name O or name CB )) or resid 684 through 685 or (resid 686 and (name N or n \ ame CA or name C or name O or name CB )) or resid 687 through 694 or (resid 695 \ and (name N or name CA or name C or name O or name CB )) or resid 696 through 70 \ 0 or (resid 701 and (name N or name CA or name C or name O or name CB )) or resi \ d 702 through 733 or (resid 734 and (name N or name CA or name C or name O or na \ me CB )) or resid 735 through 747 or (resid 748 and (name N or name CA or name C \ or name O or name CB )) or resid 749 through 750 or (resid 751 through 752 and \ (name N or name CA or name C or name O or name CB )) or resid 753 or (resid 754 \ and (name N or name CA or name C or name O or name CB or name CG1)) or resid 755 \ through 756 or (resid 757 and (name N or name CA or name C or name O or name CB \ )) or resid 758 through 770 or (resid 772 through 773 and (name N or name CA or \ name C or name O or name CB )) or resid 779 through 815 or resid 901 through 90 \ 3)) selection = (chain 'B' and (resid 390 through 456 or (resid 457 and (name N or name CA or na \ me C or name O or name CB )) or resid 458 through 504 or (resid 505 and (name N \ or name CA or name C or name O or name CB )) or resid 506 or (resid 507 and (nam \ e N or name CA or name C or name O or name CB )) or resid 508 through 545 or (re \ sid 566 and (name N or name CA or name C or name O or name CB )) or resid 567 th \ rough 581 or resid 583 or resid 587 through 618 or resid 620 through 658 or (res \ id 659 and (name N or name CA or name C or name O or name CB )) or resid 660 thr \ ough 663 or (resid 664 and (name N or name CA or name C or name O or name CB )) \ or resid 665 or (resid 666 and (name N or name CA or name C or name O or name CB \ )) or resid 667 through 685 or (resid 686 and (name N or name CA or name C or n \ ame O or name CB )) or resid 687 through 753 or (resid 754 and (name N or name C \ A or name C or name O or name CB or name CG1)) or resid 755 through 777 or (resi \ d 778 and (name N or name CA or name C or name O or name CB )) or resid 779 thro \ ugh 813 or (resid 814 through 815 and (name N or name CA or name C or name O or \ name CB )) or resid 901 through 903)) selection = (chain 'C' and (resid 390 through 391 or (resid 392 and (name N or name CA or na \ me C or name O or name CB or name CG1)) or resid 393 through 398 or (resid 399 a \ nd (name N or name CA or name C or name O or name CB or name CG )) or resid 400 \ through 403 or (resid 404 and (name N or name CA or name C or name O or name CB \ or name CG )) or resid 405 through 409 or (resid 410 and (name N or name CA or n \ ame C or name O or name CB )) or resid 411 or (resid 412 and (name N or name CA \ or name C or name O or name CB )) or resid 413 through 414 or (resid 415 and (na \ me N or name CA or name C or name O or name CB )) or resid 416 through 422 or (r \ esid 423 and (name N or name CA or name C or name O or name CB or name CG )) or \ resid 424 through 429 or (resid 430 and (name N or name CA or name C or name O o \ r name CB )) or resid 431 through 433 or (resid 434 and (name N or name CA or na \ me C or name O or name CB or name CG )) or (resid 435 and (name N or name CA or \ name C or name O or name CB )) or resid 436 through 438 or (resid 439 and (name \ N or name CA or name C or name O or name CB or name CG )) or resid 440 through 4 \ 41 or (resid 442 and (name N or name CA or name C or name O or name CB )) or res \ id 443 through 448 or (resid 449 through 452 and (name N or name CA or name C or \ name O or name CB )) or resid 453 through 466 or (resid 467 through 468 and (na \ me N or name CA or name C or name O or name CB )) or resid 469 through 546 or re \ sid 567 through 581 or resid 583 or resid 587 through 618 or resid 620 through 6 \ 37 or (resid 638 through 640 and (name N or name CA or name C or name O or name \ CB )) or resid 641 through 646 or (resid 647 and (name N or name CA or name C or \ name O or name CB or name CG )) or resid 648 through 673 or (resid 674 and (nam \ e N or name CA or name C or name O or name CB )) or resid 675 through 679 or (re \ sid 680 and (name N or name CA or name C or name O or name CB )) or resid 681 th \ rough 700 or (resid 701 and (name N or name CA or name C or name O or name CB )) \ or resid 702 through 747 or (resid 748 and (name N or name CA or name C or name \ O or name CB )) or resid 749 through 750 or (resid 751 through 752 and (name N \ or name CA or name C or name O or name CB )) or resid 753 or (resid 754 and (nam \ e N or name CA or name C or name O or name CB or name CG1)) or resid 755 through \ 756 or (resid 757 and (name N or name CA or name C or name O or name CB )) or r \ esid 758 through 770 or (resid 772 through 773 and (name N or name CA or name C \ or name O or name CB )) or resid 779 through 815 or resid 901 through 903)) selection = (chain 'D' and (resid 390 through 391 or (resid 392 and (name N or name CA or na \ me C or name O or name CB or name CG1)) or resid 393 through 403 or (resid 404 a \ nd (name N or name CA or name C or name O or name CB or name CG )) or resid 405 \ or (resid 406 and (name N or name CA or name C or name O or name CB )) or resid \ 407 through 408 or (resid 409 through 410 and (name N or name CA or name C or na \ me O or name CB )) or resid 411 or (resid 412 and (name N or name CA or name C o \ r name O or name CB )) or resid 413 through 414 or (resid 415 and (name N or nam \ e CA or name C or name O or name CB )) or resid 416 through 422 or (resid 423 an \ d (name N or name CA or name C or name O or name CB or name CG )) or resid 424 t \ hrough 429 or (resid 430 and (name N or name CA or name C or name O or name CB ) \ ) or resid 431 through 433 or (resid 434 and (name N or name CA or name C or nam \ e O or name CB or name CG )) or (resid 435 and (name N or name CA or name C or n \ ame O or name CB )) or resid 436 or (resid 437 and (name N or name CA or name C \ or name O or name CB )) or resid 438 or (resid 439 and (name N or name CA or nam \ e C or name O or name CB or name CG )) or resid 440 through 441 or (resid 442 an \ d (name N or name CA or name C or name O or name CB )) or resid 443 through 448 \ or (resid 449 through 452 and (name N or name CA or name C or name O or name CB \ )) or resid 453 or (resid 454 through 455 and (name N or name CA or name C or na \ me O or name CB )) or resid 456 or (resid 457 and (name N or name CA or name C o \ r name O or name CB )) or resid 458 through 466 or (resid 467 through 468 and (n \ ame N or name CA or name C or name O or name CB )) or resid 469 through 504 or ( \ resid 505 and (name N or name CA or name C or name O or name CB )) or resid 506 \ or (resid 507 and (name N or name CA or name C or name O or name CB )) or resid \ 508 through 545 or (resid 566 and (name N or name CA or name C or name O or name \ CB )) or resid 567 through 581 or resid 583 or resid 587 through 618 or resid 6 \ 20 through 637 or (resid 638 through 640 and (name N or name CA or name C or nam \ e O or name CB )) or resid 641 through 646 or (resid 647 and (name N or name CA \ or name C or name O or name CB or name CG )) or resid 648 through 656 or (resid \ 657 and (name N or name CA or name C or name O or name CB )) or resid 658 or (re \ sid 659 and (name N or name CA or name C or name O or name CB )) or resid 660 th \ rough 663 or (resid 664 and (name N or name CA or name C or name O or name CB )) \ or resid 665 or (resid 666 and (name N or name CA or name C or name O or name C \ B )) or resid 667 through 670 or (resid 671 and (name N or name CA or name C or \ name O or name CB )) or resid 672 through 673 or (resid 674 and (name N or name \ CA or name C or name O or name CB )) or resid 675 through 679 or (resid 680 and \ (name N or name CA or name C or name O or name CB )) or resid 681 through 682 or \ (resid 683 and (name N or name CA or name C or name O or name CB )) or resid 68 \ 4 through 685 or (resid 686 and (name N or name CA or name C or name O or name C \ B )) or resid 687 through 694 or (resid 695 and (name N or name CA or name C or \ name O or name CB )) or resid 696 through 700 or (resid 701 and (name N or name \ CA or name C or name O or name CB )) or resid 702 through 711 or (resid 712 and \ (name N or name CA or name C or name O or name CB )) or resid 713 through 733 or \ (resid 734 and (name N or name CA or name C or name O or name CB )) or resid 73 \ 5 through 747 or (resid 748 and (name N or name CA or name C or name O or name C \ B )) or resid 749 through 750 or (resid 751 through 752 and (name N or name CA o \ r name C or name O or name CB )) or resid 753 through 756 or (resid 757 and (nam \ e N or name CA or name C or name O or name CB )) or resid 758 through 777 or (re \ sid 778 and (name N or name CA or name C or name O or name CB )) or resid 779 th \ rough 813 or (resid 814 through 815 and (name N or name CA or name C or name O o \ r name CB )) or resid 901 through 903)) } ncs_group { reference = (chain 'E' and (resid 5 through 209 or (resid 1201 and (name N or name C1 or nam \ e C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name O11 or name O12 or name O13 or name O14 or name O21 or n \ ame O22 or name O31 or name O32 or name P or name C210 or name C211)))) selection = (chain 'F' and (resid 5 through 209 or (resid 1301 and (name N or name C1 or nam \ e C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name O11 or name O12 or name O13 or name O14 or name O21 or n \ ame O22 or name O31 or name O32 or name P or name C210 or name C211)))) selection = (chain 'G' and (resid 5 through 209 or (resid 1201 and (name N or name C1 or nam \ e C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name O11 or name O12 or name O13 or name O14 or name O21 or n \ ame O22 or name O31 or name O32 or name P or name C210 or name C211)))) selection = (chain 'H' and (resid 5 through 209 or (resid 1301 and (name N or name C1 or nam \ e C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name O11 or name O12 or name O13 or name O14 or name O21 or n \ ame O22 or name O31 or name O32 or name P or name C210 or name C211)))) } 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: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 3.610 Check model and map are aligned: 0.290 Set scattering table: 0.170 Process input model: 58.020 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.150 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: 0.000 Load rotamer database and sin/cos tables:16.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.117 18847 Z= 0.673 Angle : 1.401 11.389 25456 Z= 0.911 Chirality : 0.084 0.462 2811 Planarity : 0.014 0.189 3111 Dihedral : 16.038 105.783 6800 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.66 % Favored : 97.30 % Rotamer: Outliers : 2.54 % Allowed : 4.11 % Favored : 93.35 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 18.75 % 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: -0.72 (0.16), residues: 2293 helix: 0.48 (0.13), residues: 1359 sheet: -1.04 (0.38), residues: 170 loop : -2.03 (0.18), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.012 TRP C 602 HIS 0.022 0.007 HIS G 60 PHE 0.050 0.010 PHE D 810 TYR 0.062 0.010 TYR A 612 ARG 0.073 0.005 ARG A 416 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 338 time to evaluate : 2.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8129 (mm-30) REVERT: A 431 HIS cc_start: 0.8029 (m90) cc_final: 0.7200 (m90) REVERT: A 438 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8336 (mp) REVERT: A 588 SER cc_start: 0.9261 (OUTLIER) cc_final: 0.8931 (p) REVERT: A 657 ARG cc_start: 0.8233 (mtm110) cc_final: 0.7861 (ptt-90) REVERT: A 664 GLU cc_start: 0.8264 (mt-10) cc_final: 0.8051 (mt-10) REVERT: A 752 GLN cc_start: 0.8393 (mt0) cc_final: 0.8155 (mt0) REVERT: B 475 LEU cc_start: 0.8084 (tp) cc_final: 0.7785 (tp) REVERT: B 623 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8486 (mp0) REVERT: B 809 GLU cc_start: 0.6951 (mm-30) cc_final: 0.6724 (tt0) REVERT: C 423 GLU cc_start: 0.8572 (mp0) cc_final: 0.8361 (mp0) REVERT: C 445 LYS cc_start: 0.7002 (OUTLIER) cc_final: 0.6761 (pttm) REVERT: C 504 GLN cc_start: 0.7410 (pt0) cc_final: 0.7204 (pt0) REVERT: C 630 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7839 (pp20) REVERT: C 724 ASP cc_start: 0.7131 (t70) cc_final: 0.6798 (p0) REVERT: C 803 MET cc_start: 0.8911 (mtm) cc_final: 0.8635 (mtp) REVERT: D 397 LEU cc_start: 0.7723 (mm) cc_final: 0.7430 (mm) REVERT: D 657 ARG cc_start: 0.8377 (ptm-80) cc_final: 0.7922 (ppt170) REVERT: D 678 PHE cc_start: 0.7788 (m-10) cc_final: 0.7549 (m-10) REVERT: E 126 GLU cc_start: 0.7383 (mt-10) cc_final: 0.6983 (tt0) REVERT: E 127 PHE cc_start: 0.6478 (m-10) cc_final: 0.6270 (m-10) REVERT: E 129 ARG cc_start: 0.6285 (mtt-85) cc_final: 0.6080 (mmm160) REVERT: F 24 MET cc_start: 0.8390 (tpt) cc_final: 0.8092 (tpt) REVERT: F 59 THR cc_start: 0.7945 (p) cc_final: 0.7594 (t) REVERT: F 202 GLU cc_start: 0.8224 (tt0) cc_final: 0.7940 (pt0) REVERT: G 10 MET cc_start: 0.7000 (tpp) cc_final: 0.6737 (tpt) REVERT: G 41 ARG cc_start: 0.6390 (ttp80) cc_final: 0.5797 (ppp80) REVERT: G 127 PHE cc_start: 0.5442 (m-10) cc_final: 0.5001 (t80) REVERT: G 190 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8282 (tp30) REVERT: H 24 MET cc_start: 0.8657 (tpt) cc_final: 0.8449 (tpt) REVERT: H 81 ASP cc_start: 0.8182 (p0) cc_final: 0.7736 (t70) outliers start: 38 outliers final: 10 residues processed: 369 average time/residue: 1.4191 time to fit residues: 583.0478 Evaluate side-chains 258 residues out of total 1913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 244 time to evaluate : 2.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain C residue 445 LYS Chi-restraints excluded: chain C residue 502 LYS Chi-restraints excluded: chain C residue 630 GLU Chi-restraints excluded: chain C residue 631 SER Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 622 VAL Chi-restraints excluded: chain D residue 724 ASP Chi-restraints excluded: chain E residue 174 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 5.9990 chunk 172 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 116 optimal weight: 10.0000 chunk 92 optimal weight: 0.9980 chunk 178 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 108 optimal weight: 20.0000 chunk 133 optimal weight: 0.9980 chunk 207 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 ASN A 743 ASN B 710 GLN C 504 GLN E 204 HIS G 204 HIS H 160 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 18847 Z= 0.178 Angle : 0.535 10.335 25456 Z= 0.287 Chirality : 0.040 0.241 2811 Planarity : 0.005 0.090 3111 Dihedral : 12.027 86.177 2959 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 2.97 % Allowed : 11.72 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: 0.85 (0.17), residues: 2293 helix: 1.72 (0.14), residues: 1359 sheet: -1.16 (0.40), residues: 159 loop : -1.15 (0.20), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 762 HIS 0.003 0.001 HIS E 82 PHE 0.014 0.001 PHE A 542 TYR 0.015 0.001 TYR A 669 ARG 0.012 0.001 ARG C 688 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 290 time to evaluate : 1.997 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 417 TYR cc_start: 0.7268 (OUTLIER) cc_final: 0.6685 (m-80) REVERT: A 427 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8203 (mm-30) REVERT: A 431 HIS cc_start: 0.7906 (m90) cc_final: 0.7019 (m90) REVERT: A 437 ARG cc_start: 0.8382 (ppp80) cc_final: 0.8119 (ppp80) REVERT: A 510 VAL cc_start: 0.8619 (t) cc_final: 0.8358 (p) REVERT: A 630 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8327 (tp30) REVERT: B 431 HIS cc_start: 0.6341 (t-90) cc_final: 0.6086 (t-90) REVERT: B 623 GLU cc_start: 0.8795 (mt-10) cc_final: 0.8405 (mp0) REVERT: C 423 GLU cc_start: 0.8637 (mp0) cc_final: 0.8345 (mp0) REVERT: C 504 GLN cc_start: 0.7343 (pt0) cc_final: 0.7098 (pt0) REVERT: C 667 TRP cc_start: 0.7776 (t-100) cc_final: 0.7421 (t-100) REVERT: C 693 LYS cc_start: 0.6490 (tppt) cc_final: 0.6189 (mmmm) REVERT: C 699 LEU cc_start: 0.7815 (mp) cc_final: 0.7567 (mp) REVERT: C 743 ASN cc_start: 0.7255 (t0) cc_final: 0.6989 (t0) REVERT: C 762 TRP cc_start: 0.7842 (m100) cc_final: 0.7256 (m100) REVERT: C 768 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7211 (tm-30) REVERT: D 397 LEU cc_start: 0.7804 (mm) cc_final: 0.7555 (mm) REVERT: D 657 ARG cc_start: 0.8240 (ptm-80) cc_final: 0.7795 (ppt170) REVERT: D 704 MET cc_start: 0.8903 (tpp) cc_final: 0.8694 (tpt) REVERT: E 41 ARG cc_start: 0.6790 (ptm-80) cc_final: 0.6541 (ptm-80) REVERT: E 99 ARG cc_start: 0.6824 (mtm-85) cc_final: 0.6490 (tpp80) REVERT: E 126 GLU cc_start: 0.7326 (mt-10) cc_final: 0.7085 (tt0) REVERT: F 10 MET cc_start: 0.8505 (tpp) cc_final: 0.8277 (mmm) REVERT: F 37 ARG cc_start: 0.7013 (mmt-90) cc_final: 0.6631 (mmm-85) REVERT: F 79 LYS cc_start: 0.7558 (mptt) cc_final: 0.7235 (mppt) REVERT: F 202 GLU cc_start: 0.8297 (tt0) cc_final: 0.8012 (pt0) REVERT: G 41 ARG cc_start: 0.6502 (ttp80) cc_final: 0.5967 (ppp80) REVERT: G 79 LYS cc_start: 0.6434 (ttmm) cc_final: 0.6110 (mptt) REVERT: H 24 MET cc_start: 0.8533 (tpt) cc_final: 0.8265 (tpt) REVERT: H 59 THR cc_start: 0.7672 (p) cc_final: 0.7010 (t) REVERT: H 81 ASP cc_start: 0.8207 (p0) cc_final: 0.7785 (t70) outliers start: 46 outliers final: 21 residues processed: 316 average time/residue: 1.3878 time to fit residues: 489.6208 Evaluate side-chains 268 residues out of total 1913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 244 time to evaluate : 2.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 768 GLU Chi-restraints excluded: chain D residue 392 ILE Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 622 VAL Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 207 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 chunk 172 optimal weight: 7.9990 chunk 140 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 224 optimal weight: 3.9990 chunk 184 optimal weight: 6.9990 chunk 205 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 166 optimal weight: 9.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 HIS F 160 ASN H 132 HIS H 204 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 18847 Z= 0.332 Angle : 0.580 10.625 25456 Z= 0.309 Chirality : 0.042 0.214 2811 Planarity : 0.006 0.085 3111 Dihedral : 11.861 87.166 2941 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.78 % Allowed : 13.72 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: 0.59 (0.17), residues: 2293 helix: 1.47 (0.14), residues: 1346 sheet: -1.17 (0.35), residues: 199 loop : -1.12 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 762 HIS 0.005 0.001 HIS E 60 PHE 0.018 0.002 PHE C 604 TYR 0.015 0.002 TYR F 180 ARG 0.009 0.001 ARG A 739 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 248 time to evaluate : 1.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 HIS cc_start: 0.7918 (m90) cc_final: 0.7212 (m90) REVERT: A 510 VAL cc_start: 0.8443 (t) cc_final: 0.8154 (p) REVERT: A 630 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8358 (tp30) REVERT: A 657 ARG cc_start: 0.8575 (mtp-110) cc_final: 0.7865 (ptt-90) REVERT: B 492 MET cc_start: 0.6764 (ptm) cc_final: 0.6421 (ptp) REVERT: B 623 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8378 (mp0) REVERT: B 769 CYS cc_start: 0.6836 (t) cc_final: 0.6621 (m) REVERT: C 504 GLN cc_start: 0.7390 (pt0) cc_final: 0.7105 (pm20) REVERT: C 630 GLU cc_start: 0.8074 (pm20) cc_final: 0.7596 (pp20) REVERT: C 667 TRP cc_start: 0.7794 (t-100) cc_final: 0.7512 (t-100) REVERT: C 693 LYS cc_start: 0.6604 (tppt) cc_final: 0.6384 (mmmt) REVERT: C 699 LEU cc_start: 0.7826 (mp) cc_final: 0.7590 (mp) REVERT: C 743 ASN cc_start: 0.7238 (t0) cc_final: 0.6982 (t0) REVERT: D 657 ARG cc_start: 0.8328 (ptm-80) cc_final: 0.7834 (ppt170) REVERT: E 126 GLU cc_start: 0.7364 (mt-10) cc_final: 0.7078 (tt0) REVERT: F 79 LYS cc_start: 0.7425 (mptt) cc_final: 0.7078 (mppt) REVERT: F 202 GLU cc_start: 0.8203 (tt0) cc_final: 0.7965 (tt0) REVERT: G 79 LYS cc_start: 0.6666 (ttmm) cc_final: 0.6282 (mptt) REVERT: H 24 MET cc_start: 0.8595 (tpt) cc_final: 0.8279 (tpt) REVERT: H 81 ASP cc_start: 0.8262 (p0) cc_final: 0.7865 (t70) outliers start: 61 outliers final: 34 residues processed: 282 average time/residue: 1.3552 time to fit residues: 428.3860 Evaluate side-chains 262 residues out of total 1913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 227 time to evaluate : 2.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 722 ASN Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 768 GLU Chi-restraints excluded: chain D residue 392 ILE Chi-restraints excluded: chain D residue 459 MET Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 622 VAL Chi-restraints excluded: chain D residue 682 THR Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 78 LYS Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 174 SER Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 207 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 20.0000 chunk 155 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 139 optimal weight: 0.9990 chunk 208 optimal weight: 4.9990 chunk 220 optimal weight: 8.9990 chunk 108 optimal weight: 5.9990 chunk 197 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 407 ASN B 504 GLN ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 18847 Z= 0.360 Angle : 0.576 10.977 25456 Z= 0.309 Chirality : 0.042 0.225 2811 Planarity : 0.006 0.088 3111 Dihedral : 11.920 89.820 2941 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.67 % Allowed : 15.34 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: 0.44 (0.17), residues: 2293 helix: 1.32 (0.14), residues: 1346 sheet: -1.36 (0.35), residues: 201 loop : -1.07 (0.21), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 762 HIS 0.004 0.001 HIS H 60 PHE 0.034 0.002 PHE D 810 TYR 0.016 0.002 TYR H 200 ARG 0.007 0.001 ARG A 657 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 236 time to evaluate : 2.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 431 HIS cc_start: 0.7917 (m90) cc_final: 0.7265 (m90) REVERT: A 510 VAL cc_start: 0.8415 (t) cc_final: 0.8117 (p) REVERT: A 630 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8350 (tp30) REVERT: A 657 ARG cc_start: 0.8553 (mtp-110) cc_final: 0.7872 (ptt-90) REVERT: B 492 MET cc_start: 0.6718 (OUTLIER) cc_final: 0.6426 (ptp) REVERT: B 623 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8410 (mp0) REVERT: C 504 GLN cc_start: 0.7376 (pt0) cc_final: 0.7091 (pm20) REVERT: C 667 TRP cc_start: 0.7828 (t-100) cc_final: 0.7520 (t-100) REVERT: C 693 LYS cc_start: 0.6680 (tppt) cc_final: 0.6363 (mmmt) REVERT: C 699 LEU cc_start: 0.7832 (mp) cc_final: 0.7598 (mp) REVERT: C 743 ASN cc_start: 0.7254 (t0) cc_final: 0.6987 (t0) REVERT: D 657 ARG cc_start: 0.8187 (ptm-80) cc_final: 0.7749 (ppt170) REVERT: E 95 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7792 (tp30) REVERT: E 126 GLU cc_start: 0.7368 (mt-10) cc_final: 0.7125 (tt0) REVERT: F 10 MET cc_start: 0.8481 (tpp) cc_final: 0.8252 (mmm) REVERT: F 79 LYS cc_start: 0.7298 (mptt) cc_final: 0.7001 (mppt) REVERT: F 202 GLU cc_start: 0.8192 (tt0) cc_final: 0.7926 (tt0) REVERT: G 79 LYS cc_start: 0.6733 (ttmm) cc_final: 0.6308 (mmtt) REVERT: H 24 MET cc_start: 0.8583 (tpt) cc_final: 0.8261 (tpt) REVERT: H 56 GLU cc_start: 0.6982 (pt0) cc_final: 0.6737 (pp20) REVERT: H 81 ASP cc_start: 0.8185 (p0) cc_final: 0.7905 (t70) outliers start: 59 outliers final: 33 residues processed: 270 average time/residue: 1.4345 time to fit residues: 433.3599 Evaluate side-chains 260 residues out of total 1913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 224 time to evaluate : 2.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 722 ASN Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 768 GLU Chi-restraints excluded: chain D residue 392 ILE Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 622 VAL Chi-restraints excluded: chain D residue 682 THR Chi-restraints excluded: chain D residue 687 ILE Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 78 LYS Chi-restraints excluded: chain G residue 174 SER Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 204 HIS Chi-restraints excluded: chain H residue 207 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 9.9990 chunk 125 optimal weight: 8.9990 chunk 3 optimal weight: 8.9990 chunk 164 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 chunk 188 optimal weight: 4.9990 chunk 152 optimal weight: 0.0020 chunk 0 optimal weight: 10.0000 chunk 112 optimal weight: 0.9990 chunk 197 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 overall best weight: 3.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 504 GLN ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 ASN H 206 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 18847 Z= 0.326 Angle : 0.559 10.725 25456 Z= 0.299 Chirality : 0.041 0.257 2811 Planarity : 0.006 0.087 3111 Dihedral : 11.551 89.584 2941 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.84 % Allowed : 15.67 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: 0.46 (0.17), residues: 2293 helix: 1.33 (0.14), residues: 1348 sheet: -1.30 (0.35), residues: 206 loop : -1.08 (0.21), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 762 HIS 0.004 0.001 HIS H 60 PHE 0.024 0.002 PHE D 810 TYR 0.017 0.002 TYR H 200 ARG 0.008 0.001 ARG G 6 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 230 time to evaluate : 2.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 431 HIS cc_start: 0.7920 (m90) cc_final: 0.7271 (m90) REVERT: A 510 VAL cc_start: 0.8413 (t) cc_final: 0.8119 (p) REVERT: A 630 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8359 (tp30) REVERT: A 657 ARG cc_start: 0.8568 (mtp-110) cc_final: 0.7872 (ptt-90) REVERT: B 492 MET cc_start: 0.6747 (OUTLIER) cc_final: 0.6518 (ptp) REVERT: B 623 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8334 (mm-30) REVERT: B 768 GLU cc_start: 0.6975 (mt-10) cc_final: 0.6367 (pp20) REVERT: C 693 LYS cc_start: 0.6798 (tppt) cc_final: 0.6436 (mmmt) REVERT: C 699 LEU cc_start: 0.7786 (mp) cc_final: 0.7559 (mp) REVERT: C 743 ASN cc_start: 0.7259 (t0) cc_final: 0.6973 (t0) REVERT: D 657 ARG cc_start: 0.8138 (ptm-80) cc_final: 0.7639 (ppt170) REVERT: E 95 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7791 (tp30) REVERT: F 79 LYS cc_start: 0.7168 (mptt) cc_final: 0.6882 (mppt) REVERT: F 202 GLU cc_start: 0.8188 (tt0) cc_final: 0.7918 (tt0) REVERT: G 79 LYS cc_start: 0.6844 (ttmm) cc_final: 0.6418 (mmtt) REVERT: H 24 MET cc_start: 0.8580 (tpt) cc_final: 0.8285 (tpt) REVERT: H 56 GLU cc_start: 0.7026 (pt0) cc_final: 0.6645 (pp20) outliers start: 62 outliers final: 41 residues processed: 267 average time/residue: 1.3458 time to fit residues: 402.5791 Evaluate side-chains 268 residues out of total 1913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 224 time to evaluate : 2.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 722 ASN Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 768 GLU Chi-restraints excluded: chain C residue 781 SER Chi-restraints excluded: chain D residue 392 ILE Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain D residue 459 MET Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 622 VAL Chi-restraints excluded: chain D residue 682 THR Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 132 HIS Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 78 LYS Chi-restraints excluded: chain G residue 174 SER Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 204 HIS Chi-restraints excluded: chain H residue 207 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 7.9990 chunk 198 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 129 optimal weight: 6.9990 chunk 54 optimal weight: 0.6980 chunk 220 optimal weight: 8.9990 chunk 183 optimal weight: 9.9990 chunk 102 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 115 optimal weight: 9.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 504 GLN ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 HIS F 160 ASN H 206 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 18847 Z= 0.321 Angle : 0.562 11.735 25456 Z= 0.299 Chirality : 0.041 0.269 2811 Planarity : 0.006 0.087 3111 Dihedral : 11.407 85.043 2940 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 4.05 % Allowed : 16.21 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.17), residues: 2293 helix: 1.39 (0.14), residues: 1334 sheet: -1.38 (0.35), residues: 201 loop : -0.99 (0.21), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 762 HIS 0.004 0.001 HIS H 60 PHE 0.024 0.002 PHE D 810 TYR 0.019 0.002 TYR H 200 ARG 0.007 0.001 ARG G 6 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 232 time to evaluate : 2.097 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 431 HIS cc_start: 0.7908 (m90) cc_final: 0.7262 (m90) REVERT: A 510 VAL cc_start: 0.8402 (t) cc_final: 0.8111 (p) REVERT: A 630 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8356 (tp30) REVERT: A 657 ARG cc_start: 0.8593 (mtp-110) cc_final: 0.7943 (ptt-90) REVERT: B 492 MET cc_start: 0.6882 (OUTLIER) cc_final: 0.6649 (ptp) REVERT: B 623 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8322 (mm-30) REVERT: B 768 GLU cc_start: 0.7010 (mt-10) cc_final: 0.6724 (pp20) REVERT: C 667 TRP cc_start: 0.7792 (t-100) cc_final: 0.7448 (t-100) REVERT: C 699 LEU cc_start: 0.7797 (mp) cc_final: 0.7555 (mp) REVERT: C 743 ASN cc_start: 0.7268 (t0) cc_final: 0.6974 (t0) REVERT: D 657 ARG cc_start: 0.8124 (ptm-80) cc_final: 0.7625 (ppt170) REVERT: E 95 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7849 (tp30) REVERT: E 205 GLN cc_start: 0.6815 (tt0) cc_final: 0.6537 (tm-30) REVERT: F 10 MET cc_start: 0.8617 (mmm) cc_final: 0.8263 (tpt) REVERT: F 79 LYS cc_start: 0.7108 (mptt) cc_final: 0.6829 (mppt) REVERT: F 202 GLU cc_start: 0.8195 (tt0) cc_final: 0.7926 (tt0) REVERT: G 58 MET cc_start: 0.7204 (tpt) cc_final: 0.6846 (mmm) REVERT: G 79 LYS cc_start: 0.6985 (ttmm) cc_final: 0.6578 (mptp) REVERT: H 24 MET cc_start: 0.8575 (tpt) cc_final: 0.8289 (tpt) REVERT: H 56 GLU cc_start: 0.7075 (pt0) cc_final: 0.6760 (pp20) outliers start: 66 outliers final: 45 residues processed: 272 average time/residue: 1.3975 time to fit residues: 424.4173 Evaluate side-chains 275 residues out of total 1913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 227 time to evaluate : 1.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 724 ASP Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 722 ASN Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 485 ILE Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 752 GLN Chi-restraints excluded: chain C residue 768 GLU Chi-restraints excluded: chain C residue 781 SER Chi-restraints excluded: chain D residue 392 ILE Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain D residue 459 MET Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 622 VAL Chi-restraints excluded: chain D residue 682 THR Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 78 LYS Chi-restraints excluded: chain G residue 174 SER Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 133 SER Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 125 optimal weight: 9.9990 chunk 161 optimal weight: 7.9990 chunk 124 optimal weight: 0.7980 chunk 185 optimal weight: 0.8980 chunk 123 optimal weight: 0.7980 chunk 219 optimal weight: 0.6980 chunk 137 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 504 GLN ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 HIS E 204 HIS F 160 ASN G 204 HIS H 206 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18847 Z= 0.160 Angle : 0.482 11.398 25456 Z= 0.258 Chirality : 0.038 0.196 2811 Planarity : 0.005 0.087 3111 Dihedral : 10.514 89.429 2940 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.65 % Allowed : 18.15 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: 0.85 (0.18), residues: 2293 helix: 1.71 (0.14), residues: 1338 sheet: -1.38 (0.36), residues: 185 loop : -0.95 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 762 HIS 0.002 0.001 HIS H 132 PHE 0.020 0.001 PHE D 810 TYR 0.019 0.001 TYR A 669 ARG 0.007 0.000 ARG F 6 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 236 time to evaluate : 2.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 417 TYR cc_start: 0.7463 (OUTLIER) cc_final: 0.6658 (m-80) REVERT: A 427 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8275 (mm-30) REVERT: A 431 HIS cc_start: 0.7953 (m90) cc_final: 0.7125 (m90) REVERT: A 510 VAL cc_start: 0.8430 (t) cc_final: 0.8159 (p) REVERT: A 657 ARG cc_start: 0.8538 (mtp-110) cc_final: 0.7911 (ptt-90) REVERT: B 623 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8291 (mm-30) REVERT: B 768 GLU cc_start: 0.6961 (mt-10) cc_final: 0.6759 (pp20) REVERT: C 667 TRP cc_start: 0.7767 (t-100) cc_final: 0.7410 (t-100) REVERT: C 699 LEU cc_start: 0.7669 (mp) cc_final: 0.7436 (mp) REVERT: D 657 ARG cc_start: 0.8016 (ptm-80) cc_final: 0.7508 (ppt170) REVERT: E 95 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7755 (tp30) REVERT: E 99 ARG cc_start: 0.6923 (mtm-85) cc_final: 0.6674 (tpp80) REVERT: E 205 GLN cc_start: 0.6793 (tt0) cc_final: 0.6520 (tm-30) REVERT: F 10 MET cc_start: 0.8576 (mmm) cc_final: 0.8217 (tpt) REVERT: F 79 LYS cc_start: 0.6975 (mptt) cc_final: 0.6738 (mppt) REVERT: F 202 GLU cc_start: 0.8186 (tt0) cc_final: 0.7912 (tt0) REVERT: G 79 LYS cc_start: 0.6663 (ttmm) cc_final: 0.6283 (mmtt) REVERT: H 24 MET cc_start: 0.8481 (tpt) cc_final: 0.8151 (tpt) REVERT: H 56 GLU cc_start: 0.7096 (pt0) cc_final: 0.6759 (pp20) outliers start: 39 outliers final: 25 residues processed: 262 average time/residue: 1.4721 time to fit residues: 429.4379 Evaluate side-chains 252 residues out of total 1913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 226 time to evaluate : 2.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 722 ASN Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 485 ILE Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 768 GLU Chi-restraints excluded: chain D residue 392 ILE Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 622 VAL Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 78 LYS Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 0.0370 chunk 87 optimal weight: 10.0000 chunk 131 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 43 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 139 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 108 optimal weight: 0.0570 chunk 20 optimal weight: 2.9990 chunk 172 optimal weight: 6.9990 overall best weight: 1.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 504 GLN ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 743 ASN ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 ASN H 206 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18847 Z= 0.213 Angle : 0.508 11.644 25456 Z= 0.268 Chirality : 0.038 0.165 2811 Planarity : 0.005 0.087 3111 Dihedral : 10.471 88.825 2939 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.70 % Allowed : 18.48 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: 0.84 (0.18), residues: 2293 helix: 1.70 (0.14), residues: 1338 sheet: -1.37 (0.36), residues: 185 loop : -0.96 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 456 HIS 0.005 0.001 HIS G 204 PHE 0.020 0.001 PHE D 810 TYR 0.019 0.001 TYR H 200 ARG 0.011 0.001 ARG D 449 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 229 time to evaluate : 1.958 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 417 TYR cc_start: 0.7468 (OUTLIER) cc_final: 0.6610 (m-80) REVERT: A 427 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8214 (mm-30) REVERT: A 431 HIS cc_start: 0.7929 (m90) cc_final: 0.7110 (m90) REVERT: A 510 VAL cc_start: 0.8403 (t) cc_final: 0.8122 (p) REVERT: A 657 ARG cc_start: 0.8530 (mtp-110) cc_final: 0.7890 (ptt-90) REVERT: B 427 GLU cc_start: 0.6834 (tp30) cc_final: 0.6415 (mp0) REVERT: B 623 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8341 (mm-30) REVERT: B 768 GLU cc_start: 0.6988 (mt-10) cc_final: 0.6772 (pp20) REVERT: C 667 TRP cc_start: 0.7773 (t-100) cc_final: 0.7422 (t-100) REVERT: C 699 LEU cc_start: 0.7663 (mp) cc_final: 0.7443 (mp) REVERT: D 657 ARG cc_start: 0.8074 (ptm-80) cc_final: 0.7596 (ppt170) REVERT: E 95 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7749 (tp30) REVERT: E 99 ARG cc_start: 0.6947 (mtm-85) cc_final: 0.6692 (tpp80) REVERT: E 205 GLN cc_start: 0.6756 (tt0) cc_final: 0.6481 (tm-30) REVERT: F 79 LYS cc_start: 0.6966 (OUTLIER) cc_final: 0.6731 (mppt) REVERT: F 202 GLU cc_start: 0.8189 (tt0) cc_final: 0.7914 (tt0) REVERT: G 58 MET cc_start: 0.7190 (tpt) cc_final: 0.6815 (mmm) REVERT: G 79 LYS cc_start: 0.6726 (ttmm) cc_final: 0.6354 (mmtt) REVERT: H 24 MET cc_start: 0.8528 (tpt) cc_final: 0.8196 (tpt) REVERT: H 56 GLU cc_start: 0.7096 (pt0) cc_final: 0.6757 (pp20) outliers start: 40 outliers final: 29 residues processed: 251 average time/residue: 1.4802 time to fit residues: 413.9751 Evaluate side-chains 255 residues out of total 1913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 223 time to evaluate : 2.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 722 ASN Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 485 ILE Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 768 GLU Chi-restraints excluded: chain D residue 392 ILE Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain D residue 459 MET Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 622 VAL Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 132 HIS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 10 MET Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 78 LYS Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 8.9990 chunk 210 optimal weight: 7.9990 chunk 192 optimal weight: 5.9990 chunk 204 optimal weight: 20.0000 chunk 123 optimal weight: 4.9990 chunk 89 optimal weight: 9.9990 chunk 160 optimal weight: 9.9990 chunk 62 optimal weight: 0.9990 chunk 185 optimal weight: 0.9980 chunk 193 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 504 GLN ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 ASN H 206 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 18847 Z= 0.307 Angle : 0.552 11.883 25456 Z= 0.293 Chirality : 0.040 0.175 2811 Planarity : 0.005 0.086 3111 Dihedral : 10.866 84.406 2939 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.86 % Allowed : 18.37 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: 2293 helix: 1.55 (0.14), residues: 1332 sheet: -1.44 (0.36), residues: 185 loop : -0.95 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 456 HIS 0.004 0.001 HIS E 60 PHE 0.022 0.002 PHE D 810 TYR 0.023 0.002 TYR H 200 ARG 0.010 0.001 ARG D 449 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 227 time to evaluate : 2.128 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 417 TYR cc_start: 0.7483 (OUTLIER) cc_final: 0.6623 (m-80) REVERT: A 427 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8164 (mm-30) REVERT: A 431 HIS cc_start: 0.7942 (m90) cc_final: 0.7151 (m90) REVERT: A 510 VAL cc_start: 0.8397 (t) cc_final: 0.8111 (p) REVERT: A 657 ARG cc_start: 0.8600 (mtp-110) cc_final: 0.7961 (ptt-90) REVERT: B 623 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8361 (mm-30) REVERT: B 768 GLU cc_start: 0.7030 (mt-10) cc_final: 0.6691 (pp20) REVERT: C 667 TRP cc_start: 0.7719 (t-100) cc_final: 0.7361 (t-100) REVERT: C 699 LEU cc_start: 0.7729 (mp) cc_final: 0.7500 (mp) REVERT: C 743 ASN cc_start: 0.7284 (t0) cc_final: 0.7075 (t0) REVERT: D 657 ARG cc_start: 0.8147 (ptm-80) cc_final: 0.7661 (ppt170) REVERT: E 95 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7848 (tp30) REVERT: E 205 GLN cc_start: 0.6806 (tt0) cc_final: 0.6528 (tm-30) REVERT: F 79 LYS cc_start: 0.7089 (OUTLIER) cc_final: 0.6822 (mppt) REVERT: F 202 GLU cc_start: 0.8180 (tt0) cc_final: 0.7911 (tt0) REVERT: G 58 MET cc_start: 0.7158 (tpt) cc_final: 0.6809 (mmm) REVERT: G 79 LYS cc_start: 0.6987 (ttmm) cc_final: 0.6596 (mmtt) REVERT: H 24 MET cc_start: 0.8527 (tpt) cc_final: 0.8232 (tpt) REVERT: H 56 GLU cc_start: 0.7017 (pt0) cc_final: 0.6605 (pp20) outliers start: 43 outliers final: 35 residues processed: 253 average time/residue: 1.4357 time to fit residues: 407.9987 Evaluate side-chains 262 residues out of total 1913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 224 time to evaluate : 2.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 722 ASN Chi-restraints excluded: chain C residue 485 ILE Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 768 GLU Chi-restraints excluded: chain D residue 392 ILE Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain D residue 459 MET Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 622 VAL Chi-restraints excluded: chain D residue 682 THR Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 132 HIS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain G residue 10 MET Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 78 LYS Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 133 SER Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 8.9990 chunk 132 optimal weight: 2.9990 chunk 102 optimal weight: 7.9990 chunk 150 optimal weight: 3.9990 chunk 227 optimal weight: 3.9990 chunk 209 optimal weight: 0.9980 chunk 180 optimal weight: 9.9990 chunk 18 optimal weight: 0.3980 chunk 139 optimal weight: 0.5980 chunk 110 optimal weight: 0.0470 chunk 143 optimal weight: 0.9990 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 504 GLN ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 HIS E 204 HIS F 160 ASN G 204 HIS H 206 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 18847 Z= 0.137 Angle : 0.477 12.303 25456 Z= 0.253 Chirality : 0.037 0.132 2811 Planarity : 0.005 0.086 3111 Dihedral : 9.995 89.384 2939 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.38 % Allowed : 19.02 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: 0.98 (0.18), residues: 2293 helix: 1.83 (0.14), residues: 1336 sheet: -1.42 (0.36), residues: 185 loop : -0.90 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 762 HIS 0.003 0.001 HIS E 204 PHE 0.018 0.001 PHE D 810 TYR 0.020 0.001 TYR H 200 ARG 0.009 0.001 ARG D 449 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4586 Ramachandran restraints generated. 2293 Oldfield, 0 Emsley, 2293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 237 time to evaluate : 2.103 Fit side-chains revert: symmetry clash REVERT: A 410 GLN cc_start: 0.6685 (OUTLIER) cc_final: 0.6352 (tm-30) REVERT: A 412 GLU cc_start: 0.6812 (tm-30) cc_final: 0.6567 (mp0) REVERT: A 417 TYR cc_start: 0.7446 (OUTLIER) cc_final: 0.6827 (m-80) REVERT: A 427 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8142 (mm-30) REVERT: A 431 HIS cc_start: 0.7964 (m90) cc_final: 0.7084 (m90) REVERT: A 510 VAL cc_start: 0.8423 (t) cc_final: 0.8153 (p) REVERT: A 657 ARG cc_start: 0.8476 (mtp-110) cc_final: 0.7833 (ptt-90) REVERT: A 724 ASP cc_start: 0.8718 (t0) cc_final: 0.8496 (p0) REVERT: B 623 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8355 (mm-30) REVERT: B 768 GLU cc_start: 0.7063 (mt-10) cc_final: 0.6811 (pp20) REVERT: C 667 TRP cc_start: 0.7857 (t-100) cc_final: 0.7518 (t-100) REVERT: C 699 LEU cc_start: 0.7678 (mp) cc_final: 0.7460 (mp) REVERT: C 743 ASN cc_start: 0.7232 (t0) cc_final: 0.7030 (t0) REVERT: C 769 CYS cc_start: 0.5636 (m) cc_final: 0.5354 (p) REVERT: D 657 ARG cc_start: 0.7933 (ptm-80) cc_final: 0.7392 (ppt170) REVERT: E 31 ASP cc_start: 0.7442 (m-30) cc_final: 0.7207 (m-30) REVERT: E 68 CYS cc_start: 0.8304 (m) cc_final: 0.7580 (t) REVERT: E 95 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7690 (tp30) REVERT: E 99 ARG cc_start: 0.6981 (mtm-85) cc_final: 0.6762 (tpp80) REVERT: E 205 GLN cc_start: 0.6784 (tt0) cc_final: 0.6511 (tm-30) REVERT: F 10 MET cc_start: 0.8586 (mmm) cc_final: 0.8316 (tpt) REVERT: F 202 GLU cc_start: 0.8211 (tt0) cc_final: 0.7931 (tt0) REVERT: G 58 MET cc_start: 0.7224 (tpt) cc_final: 0.6866 (mmm) REVERT: G 79 LYS cc_start: 0.6685 (ttmm) cc_final: 0.6312 (mmtt) REVERT: H 24 MET cc_start: 0.8487 (tpt) cc_final: 0.8186 (tpt) REVERT: H 56 GLU cc_start: 0.7129 (pt0) cc_final: 0.6763 (pp20) REVERT: H 76 VAL cc_start: 0.7282 (t) cc_final: 0.7067 (p) outliers start: 34 outliers final: 24 residues processed: 260 average time/residue: 1.3938 time to fit residues: 405.0812 Evaluate side-chains 255 residues out of total 1913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 229 time to evaluate : 2.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain C residue 485 ILE Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 588 SER Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain D residue 392 ILE Chi-restraints excluded: chain D residue 459 MET Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 622 VAL Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 160 ASN Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 78 LYS Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 133 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 166 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 181 optimal weight: 9.9990 chunk 75 optimal weight: 0.9980 chunk 186 optimal weight: 7.9990 chunk 22 optimal weight: 8.9990 chunk 33 optimal weight: 7.9990 chunk 159 optimal weight: 1.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 504 GLN ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 ASN H 206 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.157578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.113380 restraints weight = 76407.402| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 4.14 r_work: 0.2879 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2781 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2781 r_free = 0.2781 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2781 r_free = 0.2781 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2781 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 18847 Z= 0.324 Angle : 0.562 12.635 25456 Z= 0.295 Chirality : 0.040 0.184 2811 Planarity : 0.006 0.086 3111 Dihedral : 10.487 88.262 2939 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.43 % Allowed : 18.96 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: 0.75 (0.18), residues: 2293 helix: 1.61 (0.14), residues: 1336 sheet: -1.45 (0.36), residues: 185 loop : -0.94 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 762 HIS 0.014 0.001 HIS E 204 PHE 0.021 0.002 PHE D 810 TYR 0.028 0.002 TYR H 200 ARG 0.010 0.001 ARG D 449 =============================================================================== Job complete usr+sys time: 7078.66 seconds wall clock time: 126 minutes 58.04 seconds (7618.04 seconds total)