Starting phenix.real_space_refine on Tue Feb 3 14:33:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vnm_65213/02_2026/9vnm_65213.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vnm_65213/02_2026/9vnm_65213.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vnm_65213/02_2026/9vnm_65213.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vnm_65213/02_2026/9vnm_65213.map" model { file = "/net/cci-nas-00/data/ceres_data/9vnm_65213/02_2026/9vnm_65213.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vnm_65213/02_2026/9vnm_65213.cif" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 2280 2.51 5 N 660 2.21 5 O 780 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3720 Number of models: 1 Model: "" Number of chains: 60 Chain: "G" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {'SFE': 2} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="GLY G 209 " pdbres="SFE G 210 " Not linked: pdbres="ASN G 215 " pdbres="SFE G 216 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SFE:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {'SFE': 2} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="GLY A 209 " pdbres="SFE A 210 " Not linked: pdbres="ASN A 215 " pdbres="SFE A 216 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SFE:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {'SFE': 2} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="GLY B 209 " pdbres="SFE B 210 " Not linked: pdbres="ASN B 215 " pdbres="SFE B 216 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SFE:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {'SFE': 2} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="GLY C 209 " pdbres="SFE C 210 " Not linked: pdbres="ASN C 215 " pdbres="SFE C 216 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SFE:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {'SFE': 2} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="GLY D 209 " pdbres="SFE D 210 " Not linked: pdbres="ASN D 215 " pdbres="SFE D 216 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SFE:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "E" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {'SFE': 2} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="GLY E 209 " pdbres="SFE E 210 " Not linked: pdbres="ASN E 215 " pdbres="SFE E 216 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SFE:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "F" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {'SFE': 2} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="GLY F 209 " pdbres="SFE F 210 " Not linked: pdbres="ASN F 215 " pdbres="SFE F 216 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SFE:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "H" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {'SFE': 2} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="GLY H 209 " pdbres="SFE H 210 " Not linked: pdbres="ASN H 215 " pdbres="SFE H 216 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SFE:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "I" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {'SFE': 2} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="GLY I 209 " pdbres="SFE I 210 " Not linked: pdbres="ASN I 215 " pdbres="SFE I 216 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SFE:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "J" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {'SFE': 2} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="GLY J 209 " pdbres="SFE J 210 " Not linked: pdbres="ASN J 215 " pdbres="SFE J 216 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SFE:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "Q" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {'SFE': 2} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="GLY Q 209 " pdbres="SFE Q 210 " Not linked: pdbres="ASN Q 215 " pdbres="SFE Q 216 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SFE:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "K" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {'SFE': 2} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="GLY K 209 " pdbres="SFE K 210 " Not linked: pdbres="ASN K 215 " pdbres="SFE K 216 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SFE:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "L" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {'SFE': 2} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="GLY L 209 " pdbres="SFE L 210 " Not linked: pdbres="ASN L 215 " pdbres="SFE L 216 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SFE:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "M" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {'SFE': 2} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="GLY M 209 " pdbres="SFE M 210 " Not linked: pdbres="ASN M 215 " pdbres="SFE M 216 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SFE:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "N" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {'SFE': 2} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="GLY N 209 " pdbres="SFE N 210 " Not linked: pdbres="ASN N 215 " pdbres="SFE N 216 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SFE:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "O" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {'SFE': 2} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="GLY O 209 " pdbres="SFE O 210 " Not linked: pdbres="ASN O 215 " pdbres="SFE O 216 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SFE:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "P" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {'SFE': 2} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="GLY P 209 " pdbres="SFE P 210 " Not linked: pdbres="ASN P 215 " pdbres="SFE P 216 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SFE:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "R" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {'SFE': 2} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="GLY R 209 " pdbres="SFE R 210 " Not linked: pdbres="ASN R 215 " pdbres="SFE R 216 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SFE:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "S" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {'SFE': 2} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="GLY S 209 " pdbres="SFE S 210 " Not linked: pdbres="ASN S 215 " pdbres="SFE S 216 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SFE:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "T" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {'SFE': 2} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="GLY T 209 " pdbres="SFE T 210 " Not linked: pdbres="ASN T 215 " pdbres="SFE T 216 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SFE:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "g" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {'SFE': 2} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="GLY g 209 " pdbres="SFE g 210 " Not linked: pdbres="ASN g 215 " pdbres="SFE g 216 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SFE:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "U" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {'SFE': 2} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="GLY U 209 " pdbres="SFE U 210 " Not linked: pdbres="ASN U 215 " pdbres="SFE U 216 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SFE:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "W" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {'SFE': 2} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="GLY W 209 " pdbres="SFE W 210 " Not linked: pdbres="ASN W 215 " pdbres="SFE W 216 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SFE:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "Y" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {'SFE': 2} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="GLY Y 209 " pdbres="SFE Y 210 " Not linked: pdbres="ASN Y 215 " pdbres="SFE Y 216 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SFE:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "a" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {'SFE': 2} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="GLY a 209 " pdbres="SFE a 210 " Not linked: pdbres="ASN a 215 " pdbres="SFE a 216 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SFE:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "c" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {'SFE': 2} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="GLY c 209 " pdbres="SFE c 210 " Not linked: pdbres="ASN c 215 " pdbres="SFE c 216 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SFE:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "e" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {'SFE': 2} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="GLY e 209 " pdbres="SFE e 210 " Not linked: pdbres="ASN e 215 " pdbres="SFE e 216 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SFE:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "i" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {'SFE': 2} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="GLY i 209 " pdbres="SFE i 210 " Not linked: pdbres="ASN i 215 " pdbres="SFE i 216 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SFE:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "k" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {'SFE': 2} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="GLY k 209 " pdbres="SFE k 210 " Not linked: pdbres="ASN k 215 " pdbres="SFE k 216 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SFE:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "m" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {'SFE': 2} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="GLY m 209 " pdbres="SFE m 210 " Not linked: pdbres="ASN m 215 " pdbres="SFE m 216 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SFE:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "0" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {'SFE': 2} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="GLY 0 209 " pdbres="SFE 0 210 " Not linked: pdbres="ASN 0 215 " pdbres="SFE 0 216 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SFE:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "o" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {'SFE': 2} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="GLY o 209 " pdbres="SFE o 210 " Not linked: pdbres="ASN o 215 " pdbres="SFE o 216 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SFE:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "q" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {'SFE': 2} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="GLY q 209 " pdbres="SFE q 210 " Not linked: pdbres="ASN q 215 " pdbres="SFE q 216 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SFE:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "s" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {'SFE': 2} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="GLY s 209 " pdbres="SFE s 210 " Not linked: pdbres="ASN s 215 " pdbres="SFE s 216 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SFE:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "u" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {'SFE': 2} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="GLY u 209 " pdbres="SFE u 210 " Not linked: pdbres="ASN u 215 " pdbres="SFE u 216 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SFE:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "w" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {'SFE': 2} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="GLY w 209 " pdbres="SFE w 210 " Not linked: pdbres="ASN w 215 " pdbres="SFE w 216 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SFE:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "y" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {'SFE': 2} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="GLY y 209 " pdbres="SFE y 210 " Not linked: pdbres="ASN y 215 " pdbres="SFE y 216 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SFE:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "2" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {'SFE': 2} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="GLY 2 209 " pdbres="SFE 2 210 " Not linked: pdbres="ASN 2 215 " pdbres="SFE 2 216 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SFE:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "4" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {'SFE': 2} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="GLY 4 209 " pdbres="SFE 4 210 " Not linked: pdbres="ASN 4 215 " pdbres="SFE 4 216 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SFE:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "6" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {'SFE': 2} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="GLY 6 209 " pdbres="SFE 6 210 " Not linked: pdbres="ASN 6 215 " pdbres="SFE 6 216 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SFE:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "h" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {'SFE': 2} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="GLY h 209 " pdbres="SFE h 210 " Not linked: pdbres="ASN h 215 " pdbres="SFE h 216 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SFE:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "V" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {'SFE': 2} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="GLY V 209 " pdbres="SFE V 210 " Not linked: pdbres="ASN V 215 " pdbres="SFE V 216 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SFE:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "X" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {'SFE': 2} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="GLY X 209 " pdbres="SFE X 210 " Not linked: pdbres="ASN X 215 " pdbres="SFE X 216 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SFE:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "Z" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {'SFE': 2} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="GLY Z 209 " pdbres="SFE Z 210 " Not linked: pdbres="ASN Z 215 " pdbres="SFE Z 216 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SFE:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "b" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {'SFE': 2} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="GLY b 209 " pdbres="SFE b 210 " Not linked: pdbres="ASN b 215 " pdbres="SFE b 216 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SFE:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "d" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {'SFE': 2} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="GLY d 209 " pdbres="SFE d 210 " Not linked: pdbres="ASN d 215 " pdbres="SFE d 216 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SFE:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "f" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {'SFE': 2} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="GLY f 209 " pdbres="SFE f 210 " Not linked: pdbres="ASN f 215 " pdbres="SFE f 216 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SFE:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "j" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {'SFE': 2} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="GLY j 209 " pdbres="SFE j 210 " Not linked: pdbres="ASN j 215 " pdbres="SFE j 216 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SFE:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "l" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {'SFE': 2} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="GLY l 209 " pdbres="SFE l 210 " Not linked: pdbres="ASN l 215 " pdbres="SFE l 216 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SFE:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "n" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {'SFE': 2} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="GLY n 209 " pdbres="SFE n 210 " Not linked: pdbres="ASN n 215 " pdbres="SFE n 216 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SFE:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "1" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {'SFE': 2} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="GLY 1 209 " pdbres="SFE 1 210 " Not linked: pdbres="ASN 1 215 " pdbres="SFE 1 216 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SFE:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "p" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {'SFE': 2} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="GLY p 209 " pdbres="SFE p 210 " Not linked: pdbres="ASN p 215 " pdbres="SFE p 216 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SFE:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "r" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {'SFE': 2} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="GLY r 209 " pdbres="SFE r 210 " Not linked: pdbres="ASN r 215 " pdbres="SFE r 216 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SFE:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "t" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {'SFE': 2} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="GLY t 209 " pdbres="SFE t 210 " Not linked: pdbres="ASN t 215 " pdbres="SFE t 216 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SFE:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "v" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {'SFE': 2} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="GLY v 209 " pdbres="SFE v 210 " Not linked: pdbres="ASN v 215 " pdbres="SFE v 216 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SFE:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "x" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {'SFE': 2} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="GLY x 209 " pdbres="SFE x 210 " Not linked: pdbres="ASN x 215 " pdbres="SFE x 216 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SFE:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "z" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {'SFE': 2} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="GLY z 209 " pdbres="SFE z 210 " Not linked: pdbres="ASN z 215 " pdbres="SFE z 216 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SFE:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "3" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {'SFE': 2} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="GLY 3 209 " pdbres="SFE 3 210 " Not linked: pdbres="ASN 3 215 " pdbres="SFE 3 216 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SFE:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "5" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {'SFE': 2} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="GLY 5 209 " pdbres="SFE 5 210 " Not linked: pdbres="ASN 5 215 " pdbres="SFE 5 216 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SFE:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "7" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Unusual residues: {'SFE': 2} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'TRANS': 6, None: 2} Not linked: pdbres="GLY 7 209 " pdbres="SFE 7 210 " Not linked: pdbres="ASN 7 215 " pdbres="SFE 7 216 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SFE:plan-2': 2} Unresolved non-hydrogen planarities: 2 Time building chain proxies: 0.67, per 1000 atoms: 0.18 Number of scatterers: 3720 At special positions: 0 Unit cell: (117.03, 109.56, 34.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 780 8.00 N 660 7.00 C 2280 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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=120, symmetry=0 Number of additional bonds: simple=120, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.43 Conformation dependent library (CDL) restraints added in 61.9 milliseconds 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB SFE B 210 " pdb=" CB SFE H 210 " pdb=" CB SFE I 210 " pdb=" CB SFE L 210 " pdb=" CB SFE R 210 " pdb=" CB SFE S 210 " pdb=" CB SFE W 210 " pdb=" CB SFE i 210 " pdb=" CB SFE k 210 " pdb=" CB SFE q 210 " pdb=" CB SFE 2 210 " pdb=" CB SFE 4 210 " pdb=" CB SFE X 210 " pdb=" CB SFE j 210 " pdb=" CB SFE l 210 " pdb=" CB SFE r 210 " pdb=" CB SFE 3 210 " pdb=" CB SFE 5 210 " Number of C-beta restraints generated: 564 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 5 sheets defined 0.0% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'G' and resid 215 through 216 removed outlier: 6.504A pdb=" N ASN G 215 " --> pdb=" O SFE g 216 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ASN g 215 " --> pdb=" O SFE h 216 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 215 through 216 removed outlier: 6.668A pdb=" N ASN A 215 " --> pdb=" O SFE U 216 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ASN U 215 " --> pdb=" O SFE V 216 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'D' and resid 213 through 214 Processing sheet with id=AA4, first strand: chain 'K' and resid 215 through 216 removed outlier: 6.653A pdb=" N ASN K 215 " --> pdb=" O SFE o 216 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ASN o 215 " --> pdb=" O SFE p 216 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'N' and resid 213 through 214 4 hydrogen bonds defined for protein. 12 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: 0.40 Time building geometry restraints manager: 0.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1185 1.34 - 1.45: 795 1.45 - 1.56: 1656 1.56 - 1.67: 12 1.67 - 1.78: 12 Bond restraints: 3660 Sorted by residual: bond pdb=" N SFE r 210 " pdb=" CB SFE r 210 " ideal model delta sigma weight residual 1.454 1.784 -0.330 2.00e-02 2.50e+03 2.72e+02 bond pdb=" N SFE B 210 " pdb=" CB SFE B 210 " ideal model delta sigma weight residual 1.454 1.784 -0.330 2.00e-02 2.50e+03 2.72e+02 bond pdb=" N SFE W 210 " pdb=" CB SFE W 210 " ideal model delta sigma weight residual 1.454 1.784 -0.330 2.00e-02 2.50e+03 2.72e+02 bond pdb=" N SFE L 210 " pdb=" CB SFE L 210 " ideal model delta sigma weight residual 1.454 1.784 -0.330 2.00e-02 2.50e+03 2.72e+02 bond pdb=" N SFE X 210 " pdb=" CB SFE X 210 " ideal model delta sigma weight residual 1.454 1.784 -0.330 2.00e-02 2.50e+03 2.72e+02 ... (remaining 3655 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.89: 4390 8.89 - 17.79: 158 17.79 - 26.68: 6 26.68 - 35.57: 0 35.57 - 44.47: 6 Bond angle restraints: 4560 Sorted by residual: angle pdb=" C SFE H 210 " pdb=" CA SFE H 210 " pdb=" CB SFE H 210 " ideal model delta sigma weight residual 112.84 157.31 -44.47 3.00e+00 1.11e-01 2.20e+02 angle pdb=" C SFE j 210 " pdb=" CA SFE j 210 " pdb=" CB SFE j 210 " ideal model delta sigma weight residual 112.84 157.30 -44.46 3.00e+00 1.11e-01 2.20e+02 angle pdb=" C SFE R 210 " pdb=" CA SFE R 210 " pdb=" CB SFE R 210 " ideal model delta sigma weight residual 112.84 157.30 -44.46 3.00e+00 1.11e-01 2.20e+02 angle pdb=" C SFE i 210 " pdb=" CA SFE i 210 " pdb=" CB SFE i 210 " ideal model delta sigma weight residual 112.84 157.27 -44.43 3.00e+00 1.11e-01 2.19e+02 angle pdb=" C SFE 3 210 " pdb=" CA SFE 3 210 " pdb=" CB SFE 3 210 " ideal model delta sigma weight residual 112.84 157.27 -44.43 3.00e+00 1.11e-01 2.19e+02 ... (remaining 4555 not shown) Histogram of dihedral angle deviations from ideal: 0.10 - 23.70: 1134 23.70 - 47.31: 114 47.31 - 70.91: 30 70.91 - 94.52: 84 94.52 - 118.13: 42 Dihedral angle restraints: 1404 sinusoidal: 480 harmonic: 924 Sorted by residual: dihedral pdb=" N SFE 7 210 " pdb=" C SFE 7 210 " pdb=" CA SFE 7 210 " pdb=" CB SFE 7 210 " ideal model delta harmonic sigma weight residual 122.80 4.67 118.13 0 2.50e+00 1.60e-01 2.23e+03 dihedral pdb=" N SFE 6 210 " pdb=" C SFE 6 210 " pdb=" CA SFE 6 210 " pdb=" CB SFE 6 210 " ideal model delta harmonic sigma weight residual 122.80 4.69 118.11 0 2.50e+00 1.60e-01 2.23e+03 dihedral pdb=" N SFE J 210 " pdb=" C SFE J 210 " pdb=" CA SFE J 210 " pdb=" CB SFE J 210 " ideal model delta harmonic sigma weight residual 122.80 4.69 118.11 0 2.50e+00 1.60e-01 2.23e+03 ... (remaining 1401 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.122: 156 0.122 - 0.243: 84 0.243 - 0.364: 30 0.364 - 0.485: 12 0.485 - 0.606: 18 Chirality restraints: 300 Sorted by residual: chirality pdb=" CA ASN w 213 " pdb=" N ASN w 213 " pdb=" C ASN w 213 " pdb=" CB ASN w 213 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.17e+00 chirality pdb=" CA ASN O 213 " pdb=" N ASN O 213 " pdb=" C ASN O 213 " pdb=" CB ASN O 213 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.17e+00 chirality pdb=" CA ASN d 213 " pdb=" N ASN d 213 " pdb=" C ASN d 213 " pdb=" CB ASN d 213 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.61 2.00e-01 2.50e+01 9.16e+00 ... (remaining 297 not shown) Planarity restraints: 660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY y 211 " -0.019 2.00e-02 2.50e+03 3.95e-02 1.56e+01 pdb=" C GLY y 211 " 0.068 2.00e-02 2.50e+03 pdb=" O GLY y 211 " -0.025 2.00e-02 2.50e+03 pdb=" N GLY y 212 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY f 211 " -0.019 2.00e-02 2.50e+03 3.94e-02 1.55e+01 pdb=" C GLY f 211 " 0.068 2.00e-02 2.50e+03 pdb=" O GLY f 211 " -0.025 2.00e-02 2.50e+03 pdb=" N GLY f 212 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY z 211 " -0.019 2.00e-02 2.50e+03 3.94e-02 1.55e+01 pdb=" C GLY z 211 " 0.068 2.00e-02 2.50e+03 pdb=" O GLY z 211 " -0.025 2.00e-02 2.50e+03 pdb=" N GLY z 212 " -0.023 2.00e-02 2.50e+03 ... (remaining 657 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.30: 90 2.30 - 2.95: 2338 2.95 - 3.60: 4704 3.60 - 4.25: 8845 4.25 - 4.90: 15151 Nonbonded interactions: 31128 Sorted by model distance: nonbonded pdb=" N SFE B 210 " pdb=" O SFE B 210 " model vdw 1.653 3.120 nonbonded pdb=" N SFE W 210 " pdb=" O SFE W 210 " model vdw 1.653 3.120 nonbonded pdb=" N SFE X 210 " pdb=" O SFE X 210 " model vdw 1.653 3.120 nonbonded pdb=" N SFE r 210 " pdb=" O SFE r 210 " model vdw 1.653 3.120 nonbonded pdb=" N SFE L 210 " pdb=" O SFE L 210 " model vdw 1.653 3.120 ... (remaining 31123 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' selection = chain 'z' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.640 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6500 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 : 0.030 0.330 3780 Z= 2.075 Angle : 3.738 44.465 4560 Z= 1.566 Chirality : 0.212 0.606 300 Planarity : 0.010 0.039 660 Dihedral : 20.061 84.626 840 Min Nonbonded Distance : 1.653 Molprobity Statistics. All-atom Clashscore : 141.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.00 % Favored : 80.00 % Rotamer: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Cbeta Deviations : 44.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.59 (0.11), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.01 (0.09), residues: 180 Details of bonding type rmsd covalent geometry : bond 0.02537 ( 3660) covalent geometry : angle 3.73822 ( 4560) hydrogen bonds : bond 0.02078 ( 4) hydrogen bonds : angle 8.21012 ( 12) Misc. bond : bond 0.08854 ( 120) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.087 Fit side-chains REVERT: V 213 ASN cc_start: 0.5048 (m-40) cc_final: 0.4401 (m-40) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0307 time to fit residues: 1.0547 Evaluate side-chains 15 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 215 ASN c 215 ASN ** u 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 215 ASN d 215 ASN ** v 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 215 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.119660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.107150 restraints weight = 7063.254| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.43 r_work: 0.3503 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.067 0.304 3780 Z= 3.441 Angle : 10.041 59.217 4560 Z= 3.761 Chirality : 0.490 2.397 300 Planarity : 0.030 0.107 660 Dihedral : 33.041 89.964 480 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 50.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.00 % Favored : 80.00 % Rotamer: Outliers : 9.44 % Allowed : 11.67 % Favored : 78.89 % Cbeta Deviations : 42.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 12.50 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.43 (0.12), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.90 (0.09), residues: 180 Details of bonding type rmsd covalent geometry : bond 0.06853 ( 3660) covalent geometry : angle 10.04080 ( 4560) hydrogen bonds : bond 0.08043 ( 4) hydrogen bonds : angle 7.53386 ( 12) Misc. bond : bond 0.01115 ( 120) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 30 time to evaluate : 0.054 Fit side-chains REVERT: x 214 ASP cc_start: 0.6998 (OUTLIER) cc_final: 0.6127 (p0) outliers start: 17 outliers final: 13 residues processed: 42 average time/residue: 0.0217 time to fit residues: 1.3813 Evaluate side-chains 38 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 24 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 213 ASN Chi-restraints excluded: chain H residue 213 ASN Chi-restraints excluded: chain J residue 215 ASN Chi-restraints excluded: chain T residue 214 ASP Chi-restraints excluded: chain T residue 215 ASN Chi-restraints excluded: chain g residue 213 ASN Chi-restraints excluded: chain a residue 213 ASN Chi-restraints excluded: chain m residue 215 ASN Chi-restraints excluded: chain 6 residue 214 ASP Chi-restraints excluded: chain V residue 215 ASN Chi-restraints excluded: chain n residue 215 ASN Chi-restraints excluded: chain r residue 214 ASP Chi-restraints excluded: chain x residue 214 ASP Chi-restraints excluded: chain 7 residue 214 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** u 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.118691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.106283 restraints weight = 6970.206| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.44 r_work: 0.3483 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.067 0.304 3780 Z= 3.441 Angle : 10.041 59.217 4560 Z= 3.761 Chirality : 0.490 2.397 300 Planarity : 0.030 0.107 660 Dihedral : 33.041 89.964 480 Min Nonbonded Distance : 1.584 Molprobity Statistics. All-atom Clashscore : 51.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.00 % Favored : 80.00 % Rotamer: Outliers : 7.78 % Allowed : 19.44 % Favored : 72.78 % Cbeta Deviations : 42.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 12.50 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.43 (0.12), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.90 (0.09), residues: 180 Details of bonding type rmsd covalent geometry : bond 0.06853 ( 3660) covalent geometry : angle 10.04080 ( 4560) hydrogen bonds : bond 0.08043 ( 4) hydrogen bonds : angle 7.53386 ( 12) Misc. bond : bond 0.01115 ( 120) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 24 time to evaluate : 0.102 Fit side-chains REVERT: x 214 ASP cc_start: 0.6961 (OUTLIER) cc_final: 0.6095 (p0) outliers start: 14 outliers final: 13 residues processed: 33 average time/residue: 0.0366 time to fit residues: 1.8712 Evaluate side-chains 38 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 24 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 213 ASN Chi-restraints excluded: chain H residue 213 ASN Chi-restraints excluded: chain J residue 215 ASN Chi-restraints excluded: chain T residue 214 ASP Chi-restraints excluded: chain T residue 215 ASN Chi-restraints excluded: chain g residue 213 ASN Chi-restraints excluded: chain a residue 213 ASN Chi-restraints excluded: chain m residue 215 ASN Chi-restraints excluded: chain 6 residue 214 ASP Chi-restraints excluded: chain V residue 215 ASN Chi-restraints excluded: chain n residue 215 ASN Chi-restraints excluded: chain r residue 214 ASP Chi-restraints excluded: chain x residue 214 ASP Chi-restraints excluded: chain 7 residue 214 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** u 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.118691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.106328 restraints weight = 6876.784| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.42 r_work: 0.3484 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.067 0.304 3780 Z= 3.440 Angle : 10.041 59.216 4560 Z= 3.761 Chirality : 0.490 2.397 300 Planarity : 0.030 0.107 660 Dihedral : 33.040 89.962 480 Min Nonbonded Distance : 1.584 Molprobity Statistics. All-atom Clashscore : 51.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.00 % Favored : 80.00 % Rotamer: Outliers : 7.78 % Allowed : 19.44 % Favored : 72.78 % Cbeta Deviations : 42.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 12.50 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.43 (0.12), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.90 (0.09), residues: 180 Details of bonding type rmsd covalent geometry : bond 0.06853 ( 3660) covalent geometry : angle 10.04057 ( 4560) hydrogen bonds : bond 0.08043 ( 4) hydrogen bonds : angle 7.53383 ( 12) Misc. bond : bond 0.01115 ( 120) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 24 time to evaluate : 0.101 Fit side-chains REVERT: x 214 ASP cc_start: 0.6965 (OUTLIER) cc_final: 0.6100 (p0) outliers start: 14 outliers final: 13 residues processed: 33 average time/residue: 0.0347 time to fit residues: 1.7951 Evaluate side-chains 38 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 24 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 213 ASN Chi-restraints excluded: chain H residue 213 ASN Chi-restraints excluded: chain J residue 215 ASN Chi-restraints excluded: chain T residue 214 ASP Chi-restraints excluded: chain T residue 215 ASN Chi-restraints excluded: chain g residue 213 ASN Chi-restraints excluded: chain a residue 213 ASN Chi-restraints excluded: chain m residue 215 ASN Chi-restraints excluded: chain 6 residue 214 ASP Chi-restraints excluded: chain V residue 215 ASN Chi-restraints excluded: chain n residue 215 ASN Chi-restraints excluded: chain r residue 214 ASP Chi-restraints excluded: chain x residue 214 ASP Chi-restraints excluded: chain 7 residue 214 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** u 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.118691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.106308 restraints weight = 6920.806| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.43 r_work: 0.3483 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.067 0.304 3780 Z= 3.440 Angle : 10.041 59.216 4560 Z= 3.761 Chirality : 0.490 2.397 300 Planarity : 0.030 0.107 660 Dihedral : 33.040 89.961 480 Min Nonbonded Distance : 1.584 Molprobity Statistics. All-atom Clashscore : 51.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.00 % Favored : 80.00 % Rotamer: Outliers : 7.78 % Allowed : 19.44 % Favored : 72.78 % Cbeta Deviations : 42.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 12.50 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.43 (0.12), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.90 (0.09), residues: 180 Details of bonding type rmsd covalent geometry : bond 0.06853 ( 3660) covalent geometry : angle 10.04050 ( 4560) hydrogen bonds : bond 0.08043 ( 4) hydrogen bonds : angle 7.53383 ( 12) Misc. bond : bond 0.01114 ( 120) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 24 time to evaluate : 0.127 Fit side-chains REVERT: x 214 ASP cc_start: 0.6960 (OUTLIER) cc_final: 0.6096 (p0) outliers start: 14 outliers final: 13 residues processed: 33 average time/residue: 0.0367 time to fit residues: 1.9178 Evaluate side-chains 38 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 24 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 213 ASN Chi-restraints excluded: chain H residue 213 ASN Chi-restraints excluded: chain J residue 215 ASN Chi-restraints excluded: chain T residue 214 ASP Chi-restraints excluded: chain T residue 215 ASN Chi-restraints excluded: chain g residue 213 ASN Chi-restraints excluded: chain a residue 213 ASN Chi-restraints excluded: chain m residue 215 ASN Chi-restraints excluded: chain 6 residue 214 ASP Chi-restraints excluded: chain V residue 215 ASN Chi-restraints excluded: chain n residue 215 ASN Chi-restraints excluded: chain r residue 214 ASP Chi-restraints excluded: chain x residue 214 ASP Chi-restraints excluded: chain 7 residue 214 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 6.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 213 ASN I 215 ASN ** M 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 213 ASN ** s 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 215 ASN Z 213 ASN ** t 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 215 ASN 7 215 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.086419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.075524 restraints weight = 8795.725| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.33 r_work: 0.3004 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.6203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.062 0.218 3780 Z= 3.180 Angle : 9.000 49.217 4560 Z= 3.426 Chirality : 0.289 0.778 300 Planarity : 0.021 0.058 660 Dihedral : 32.140 89.615 480 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 80.67 Ramachandran Plot: Outliers : 3.33 % Allowed : 33.89 % Favored : 62.78 % Rotamer: Outliers : 22.78 % Allowed : 18.89 % Favored : 58.33 % Cbeta Deviations : 42.33 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.42 % Twisted Proline : 0.00 % Twisted General : 17.50 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.91 (0.12), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.26 (0.09), residues: 180 Details of bonding type rmsd covalent geometry : bond 0.06314 ( 3660) covalent geometry : angle 8.99958 ( 4560) hydrogen bonds : bond 0.15999 ( 4) hydrogen bonds : angle 10.86434 ( 12) Misc. bond : bond 0.00895 ( 120) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 32 time to evaluate : 0.102 Fit side-chains REVERT: F 213 ASN cc_start: 0.8615 (OUTLIER) cc_final: 0.8398 (p0) REVERT: P 214 ASP cc_start: 0.7899 (p0) cc_final: 0.7178 (p0) REVERT: S 215 ASN cc_start: 0.8960 (OUTLIER) cc_final: 0.8618 (p0) REVERT: e 214 ASP cc_start: 0.8664 (p0) cc_final: 0.8462 (p0) REVERT: w 214 ASP cc_start: 0.7307 (OUTLIER) cc_final: 0.6588 (p0) REVERT: y 214 ASP cc_start: 0.8091 (p0) cc_final: 0.7324 (p0) REVERT: y 215 ASN cc_start: 0.8772 (p0) cc_final: 0.8533 (p0) REVERT: h 213 ASN cc_start: 0.8664 (OUTLIER) cc_final: 0.8404 (m-40) REVERT: x 214 ASP cc_start: 0.7479 (OUTLIER) cc_final: 0.6727 (p0) outliers start: 41 outliers final: 27 residues processed: 67 average time/residue: 0.0345 time to fit residues: 3.4271 Evaluate side-chains 56 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 24 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain F residue 213 ASN Chi-restraints excluded: chain H residue 213 ASN Chi-restraints excluded: chain I residue 214 ASP Chi-restraints excluded: chain J residue 215 ASN Chi-restraints excluded: chain L residue 214 ASP Chi-restraints excluded: chain O residue 214 ASP Chi-restraints excluded: chain S residue 215 ASN Chi-restraints excluded: chain T residue 214 ASP Chi-restraints excluded: chain T residue 215 ASN Chi-restraints excluded: chain W residue 214 ASP Chi-restraints excluded: chain a residue 213 ASN Chi-restraints excluded: chain e residue 213 ASN Chi-restraints excluded: chain i residue 213 ASN Chi-restraints excluded: chain m residue 215 ASN Chi-restraints excluded: chain q residue 214 ASP Chi-restraints excluded: chain w residue 214 ASP Chi-restraints excluded: chain 2 residue 213 ASN Chi-restraints excluded: chain 4 residue 215 ASN Chi-restraints excluded: chain 6 residue 214 ASP Chi-restraints excluded: chain h residue 213 ASN Chi-restraints excluded: chain V residue 215 ASN Chi-restraints excluded: chain X residue 214 ASP Chi-restraints excluded: chain b residue 213 ASN Chi-restraints excluded: chain f residue 213 ASN Chi-restraints excluded: chain l residue 214 ASP Chi-restraints excluded: chain n residue 215 ASN Chi-restraints excluded: chain r residue 214 ASP Chi-restraints excluded: chain x residue 214 ASP Chi-restraints excluded: chain 3 residue 213 ASN Chi-restraints excluded: chain 5 residue 215 ASN Chi-restraints excluded: chain 7 residue 214 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 3.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 215 ASN ** t 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 215 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.085596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.074759 restraints weight = 9000.742| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.27 r_work: 0.2995 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.6319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.062 0.218 3780 Z= 3.179 Angle : 8.999 49.215 4560 Z= 3.425 Chirality : 0.289 0.778 300 Planarity : 0.021 0.058 660 Dihedral : 32.140 89.629 480 Min Nonbonded Distance : 1.597 Molprobity Statistics. All-atom Clashscore : 82.91 Ramachandran Plot: Outliers : 3.33 % Allowed : 33.89 % Favored : 62.78 % Rotamer: Outliers : 18.89 % Allowed : 27.22 % Favored : 53.89 % Cbeta Deviations : 42.33 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.42 % Twisted Proline : 0.00 % Twisted General : 17.50 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.91 (0.12), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.26 (0.09), residues: 180 Details of bonding type rmsd covalent geometry : bond 0.06313 ( 3660) covalent geometry : angle 8.99878 ( 4560) hydrogen bonds : bond 0.16001 ( 4) hydrogen bonds : angle 10.86394 ( 12) Misc. bond : bond 0.00892 ( 120) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 24 time to evaluate : 0.108 Fit side-chains REVERT: F 213 ASN cc_start: 0.8625 (OUTLIER) cc_final: 0.8410 (p0) REVERT: P 214 ASP cc_start: 0.7761 (p0) cc_final: 0.7181 (p0) REVERT: S 215 ASN cc_start: 0.8965 (OUTLIER) cc_final: 0.8634 (p0) REVERT: e 214 ASP cc_start: 0.8677 (p0) cc_final: 0.8466 (p0) REVERT: w 214 ASP cc_start: 0.7584 (OUTLIER) cc_final: 0.6576 (p0) REVERT: y 214 ASP cc_start: 0.8154 (p0) cc_final: 0.7365 (p0) REVERT: y 215 ASN cc_start: 0.8753 (p0) cc_final: 0.8525 (p0) REVERT: h 213 ASN cc_start: 0.8679 (OUTLIER) cc_final: 0.8418 (m-40) REVERT: x 214 ASP cc_start: 0.7613 (OUTLIER) cc_final: 0.6726 (p0) outliers start: 34 outliers final: 27 residues processed: 52 average time/residue: 0.0261 time to fit residues: 2.0930 Evaluate side-chains 56 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 24 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain F residue 213 ASN Chi-restraints excluded: chain H residue 213 ASN Chi-restraints excluded: chain I residue 214 ASP Chi-restraints excluded: chain J residue 215 ASN Chi-restraints excluded: chain L residue 214 ASP Chi-restraints excluded: chain O residue 214 ASP Chi-restraints excluded: chain S residue 215 ASN Chi-restraints excluded: chain T residue 214 ASP Chi-restraints excluded: chain T residue 215 ASN Chi-restraints excluded: chain W residue 214 ASP Chi-restraints excluded: chain a residue 213 ASN Chi-restraints excluded: chain e residue 213 ASN Chi-restraints excluded: chain i residue 213 ASN Chi-restraints excluded: chain m residue 215 ASN Chi-restraints excluded: chain q residue 214 ASP Chi-restraints excluded: chain w residue 214 ASP Chi-restraints excluded: chain 2 residue 213 ASN Chi-restraints excluded: chain 4 residue 215 ASN Chi-restraints excluded: chain 6 residue 214 ASP Chi-restraints excluded: chain h residue 213 ASN Chi-restraints excluded: chain V residue 215 ASN Chi-restraints excluded: chain X residue 214 ASP Chi-restraints excluded: chain b residue 213 ASN Chi-restraints excluded: chain f residue 213 ASN Chi-restraints excluded: chain l residue 214 ASP Chi-restraints excluded: chain n residue 215 ASN Chi-restraints excluded: chain r residue 214 ASP Chi-restraints excluded: chain x residue 214 ASP Chi-restraints excluded: chain 3 residue 213 ASN Chi-restraints excluded: chain 5 residue 215 ASN Chi-restraints excluded: chain 7 residue 214 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 215 ASN ** t 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 215 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.085563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.074763 restraints weight = 8920.882| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.25 r_work: 0.2996 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.6322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.062 0.218 3780 Z= 3.179 Angle : 8.999 49.215 4560 Z= 3.425 Chirality : 0.289 0.778 300 Planarity : 0.021 0.058 660 Dihedral : 32.140 89.629 480 Min Nonbonded Distance : 1.597 Molprobity Statistics. All-atom Clashscore : 82.75 Ramachandran Plot: Outliers : 3.33 % Allowed : 33.89 % Favored : 62.78 % Rotamer: Outliers : 18.89 % Allowed : 27.78 % Favored : 53.33 % Cbeta Deviations : 42.33 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.42 % Twisted Proline : 0.00 % Twisted General : 17.50 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.91 (0.12), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.26 (0.09), residues: 180 Details of bonding type rmsd covalent geometry : bond 0.06313 ( 3660) covalent geometry : angle 8.99878 ( 4560) hydrogen bonds : bond 0.16001 ( 4) hydrogen bonds : angle 10.86394 ( 12) Misc. bond : bond 0.00892 ( 120) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 24 time to evaluate : 0.099 Fit side-chains REVERT: F 213 ASN cc_start: 0.8624 (OUTLIER) cc_final: 0.8408 (p0) REVERT: P 214 ASP cc_start: 0.7759 (p0) cc_final: 0.7181 (p0) REVERT: S 215 ASN cc_start: 0.8964 (OUTLIER) cc_final: 0.8634 (p0) REVERT: e 214 ASP cc_start: 0.8676 (p0) cc_final: 0.8464 (p0) REVERT: w 214 ASP cc_start: 0.7579 (OUTLIER) cc_final: 0.6572 (p0) REVERT: y 214 ASP cc_start: 0.8151 (p0) cc_final: 0.7362 (p0) REVERT: y 215 ASN cc_start: 0.8751 (p0) cc_final: 0.8522 (p0) REVERT: h 213 ASN cc_start: 0.8678 (OUTLIER) cc_final: 0.8417 (m-40) REVERT: x 214 ASP cc_start: 0.7608 (OUTLIER) cc_final: 0.6723 (p0) outliers start: 34 outliers final: 27 residues processed: 52 average time/residue: 0.0332 time to fit residues: 2.6031 Evaluate side-chains 56 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 24 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain F residue 213 ASN Chi-restraints excluded: chain H residue 213 ASN Chi-restraints excluded: chain I residue 214 ASP Chi-restraints excluded: chain J residue 215 ASN Chi-restraints excluded: chain L residue 214 ASP Chi-restraints excluded: chain O residue 214 ASP Chi-restraints excluded: chain S residue 215 ASN Chi-restraints excluded: chain T residue 214 ASP Chi-restraints excluded: chain T residue 215 ASN Chi-restraints excluded: chain W residue 214 ASP Chi-restraints excluded: chain a residue 213 ASN Chi-restraints excluded: chain e residue 213 ASN Chi-restraints excluded: chain i residue 213 ASN Chi-restraints excluded: chain m residue 215 ASN Chi-restraints excluded: chain q residue 214 ASP Chi-restraints excluded: chain w residue 214 ASP Chi-restraints excluded: chain 2 residue 213 ASN Chi-restraints excluded: chain 4 residue 215 ASN Chi-restraints excluded: chain 6 residue 214 ASP Chi-restraints excluded: chain h residue 213 ASN Chi-restraints excluded: chain V residue 215 ASN Chi-restraints excluded: chain X residue 214 ASP Chi-restraints excluded: chain b residue 213 ASN Chi-restraints excluded: chain f residue 213 ASN Chi-restraints excluded: chain l residue 214 ASP Chi-restraints excluded: chain n residue 215 ASN Chi-restraints excluded: chain r residue 214 ASP Chi-restraints excluded: chain x residue 214 ASP Chi-restraints excluded: chain 3 residue 213 ASN Chi-restraints excluded: chain 5 residue 215 ASN Chi-restraints excluded: chain 7 residue 214 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 215 ASN ** t 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 215 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.085537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.074759 restraints weight = 8849.687| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.25 r_work: 0.2995 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.6322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.062 0.218 3780 Z= 3.179 Angle : 8.999 49.215 4560 Z= 3.425 Chirality : 0.289 0.778 300 Planarity : 0.021 0.058 660 Dihedral : 32.140 89.629 480 Min Nonbonded Distance : 1.597 Molprobity Statistics. All-atom Clashscore : 82.75 Ramachandran Plot: Outliers : 3.33 % Allowed : 33.89 % Favored : 62.78 % Rotamer: Outliers : 18.89 % Allowed : 27.78 % Favored : 53.33 % Cbeta Deviations : 42.33 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.42 % Twisted Proline : 0.00 % Twisted General : 17.50 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.91 (0.12), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.26 (0.09), residues: 180 Details of bonding type rmsd covalent geometry : bond 0.06313 ( 3660) covalent geometry : angle 8.99878 ( 4560) hydrogen bonds : bond 0.16001 ( 4) hydrogen bonds : angle 10.86394 ( 12) Misc. bond : bond 0.00892 ( 120) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 24 time to evaluate : 0.103 Fit side-chains REVERT: F 213 ASN cc_start: 0.8624 (OUTLIER) cc_final: 0.8408 (p0) REVERT: P 214 ASP cc_start: 0.7762 (p0) cc_final: 0.7182 (p0) REVERT: S 215 ASN cc_start: 0.8963 (OUTLIER) cc_final: 0.8633 (p0) REVERT: e 214 ASP cc_start: 0.8678 (p0) cc_final: 0.8466 (p0) REVERT: w 214 ASP cc_start: 0.7582 (OUTLIER) cc_final: 0.6574 (p0) REVERT: y 214 ASP cc_start: 0.8156 (p0) cc_final: 0.7365 (p0) REVERT: y 215 ASN cc_start: 0.8751 (p0) cc_final: 0.8523 (p0) REVERT: h 213 ASN cc_start: 0.8678 (OUTLIER) cc_final: 0.8417 (m-40) REVERT: x 214 ASP cc_start: 0.7614 (OUTLIER) cc_final: 0.6728 (p0) outliers start: 34 outliers final: 27 residues processed: 52 average time/residue: 0.0377 time to fit residues: 2.9158 Evaluate side-chains 56 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 24 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain F residue 213 ASN Chi-restraints excluded: chain H residue 213 ASN Chi-restraints excluded: chain I residue 214 ASP Chi-restraints excluded: chain J residue 215 ASN Chi-restraints excluded: chain L residue 214 ASP Chi-restraints excluded: chain O residue 214 ASP Chi-restraints excluded: chain S residue 215 ASN Chi-restraints excluded: chain T residue 214 ASP Chi-restraints excluded: chain T residue 215 ASN Chi-restraints excluded: chain W residue 214 ASP Chi-restraints excluded: chain a residue 213 ASN Chi-restraints excluded: chain e residue 213 ASN Chi-restraints excluded: chain i residue 213 ASN Chi-restraints excluded: chain m residue 215 ASN Chi-restraints excluded: chain q residue 214 ASP Chi-restraints excluded: chain w residue 214 ASP Chi-restraints excluded: chain 2 residue 213 ASN Chi-restraints excluded: chain 4 residue 215 ASN Chi-restraints excluded: chain 6 residue 214 ASP Chi-restraints excluded: chain h residue 213 ASN Chi-restraints excluded: chain V residue 215 ASN Chi-restraints excluded: chain X residue 214 ASP Chi-restraints excluded: chain b residue 213 ASN Chi-restraints excluded: chain f residue 213 ASN Chi-restraints excluded: chain l residue 214 ASP Chi-restraints excluded: chain n residue 215 ASN Chi-restraints excluded: chain r residue 214 ASP Chi-restraints excluded: chain x residue 214 ASP Chi-restraints excluded: chain 3 residue 213 ASN Chi-restraints excluded: chain 5 residue 215 ASN Chi-restraints excluded: chain 7 residue 214 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 215 ASN ** t 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 215 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.085529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.074724 restraints weight = 8947.566| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.26 r_work: 0.2995 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.6322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.062 0.218 3780 Z= 3.179 Angle : 8.999 49.215 4560 Z= 3.425 Chirality : 0.289 0.778 300 Planarity : 0.021 0.058 660 Dihedral : 32.140 89.629 480 Min Nonbonded Distance : 1.597 Molprobity Statistics. All-atom Clashscore : 82.59 Ramachandran Plot: Outliers : 3.33 % Allowed : 33.89 % Favored : 62.78 % Rotamer: Outliers : 18.89 % Allowed : 27.78 % Favored : 53.33 % Cbeta Deviations : 42.33 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.42 % Twisted Proline : 0.00 % Twisted General : 17.50 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.91 (0.12), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.26 (0.09), residues: 180 Details of bonding type rmsd covalent geometry : bond 0.06313 ( 3660) covalent geometry : angle 8.99878 ( 4560) hydrogen bonds : bond 0.16001 ( 4) hydrogen bonds : angle 10.86394 ( 12) Misc. bond : bond 0.00892 ( 120) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 24 time to evaluate : 0.060 Fit side-chains REVERT: F 213 ASN cc_start: 0.8625 (OUTLIER) cc_final: 0.8409 (p0) REVERT: P 214 ASP cc_start: 0.7762 (p0) cc_final: 0.7183 (p0) REVERT: S 215 ASN cc_start: 0.8964 (OUTLIER) cc_final: 0.8634 (p0) REVERT: e 214 ASP cc_start: 0.8679 (p0) cc_final: 0.8467 (p0) REVERT: w 214 ASP cc_start: 0.7583 (OUTLIER) cc_final: 0.6573 (p0) REVERT: y 214 ASP cc_start: 0.8156 (p0) cc_final: 0.7366 (p0) REVERT: y 215 ASN cc_start: 0.8749 (p0) cc_final: 0.8522 (p0) REVERT: h 213 ASN cc_start: 0.8679 (OUTLIER) cc_final: 0.8418 (m-40) REVERT: x 214 ASP cc_start: 0.7615 (OUTLIER) cc_final: 0.6728 (p0) outliers start: 34 outliers final: 27 residues processed: 52 average time/residue: 0.0287 time to fit residues: 2.2238 Evaluate side-chains 56 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 24 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain F residue 213 ASN Chi-restraints excluded: chain H residue 213 ASN Chi-restraints excluded: chain I residue 214 ASP Chi-restraints excluded: chain J residue 215 ASN Chi-restraints excluded: chain L residue 214 ASP Chi-restraints excluded: chain O residue 214 ASP Chi-restraints excluded: chain S residue 215 ASN Chi-restraints excluded: chain T residue 214 ASP Chi-restraints excluded: chain T residue 215 ASN Chi-restraints excluded: chain W residue 214 ASP Chi-restraints excluded: chain a residue 213 ASN Chi-restraints excluded: chain e residue 213 ASN Chi-restraints excluded: chain i residue 213 ASN Chi-restraints excluded: chain m residue 215 ASN Chi-restraints excluded: chain q residue 214 ASP Chi-restraints excluded: chain w residue 214 ASP Chi-restraints excluded: chain 2 residue 213 ASN Chi-restraints excluded: chain 4 residue 215 ASN Chi-restraints excluded: chain 6 residue 214 ASP Chi-restraints excluded: chain h residue 213 ASN Chi-restraints excluded: chain V residue 215 ASN Chi-restraints excluded: chain X residue 214 ASP Chi-restraints excluded: chain b residue 213 ASN Chi-restraints excluded: chain f residue 213 ASN Chi-restraints excluded: chain l residue 214 ASP Chi-restraints excluded: chain n residue 215 ASN Chi-restraints excluded: chain r residue 214 ASP Chi-restraints excluded: chain x residue 214 ASP Chi-restraints excluded: chain 3 residue 213 ASN Chi-restraints excluded: chain 5 residue 215 ASN Chi-restraints excluded: chain 7 residue 214 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 215 ASN ** t 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 215 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.085509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.074751 restraints weight = 8780.322| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.24 r_work: 0.2998 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.6322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.062 0.218 3780 Z= 3.179 Angle : 8.999 49.215 4560 Z= 3.425 Chirality : 0.289 0.778 300 Planarity : 0.021 0.058 660 Dihedral : 32.140 89.629 480 Min Nonbonded Distance : 1.597 Molprobity Statistics. All-atom Clashscore : 82.75 Ramachandran Plot: Outliers : 3.33 % Allowed : 33.89 % Favored : 62.78 % Rotamer: Outliers : 18.89 % Allowed : 27.78 % Favored : 53.33 % Cbeta Deviations : 42.33 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.42 % Twisted Proline : 0.00 % Twisted General : 17.50 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.91 (0.12), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.26 (0.09), residues: 180 Details of bonding type rmsd covalent geometry : bond 0.06313 ( 3660) covalent geometry : angle 8.99878 ( 4560) hydrogen bonds : bond 0.16001 ( 4) hydrogen bonds : angle 10.86394 ( 12) Misc. bond : bond 0.00892 ( 120) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 669.78 seconds wall clock time: 12 minutes 12.62 seconds (732.62 seconds total)