Starting phenix.real_space_refine on Tue Feb 3 13:56:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vnk_65211/02_2026/9vnk_65211.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vnk_65211/02_2026/9vnk_65211.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vnk_65211/02_2026/9vnk_65211.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vnk_65211/02_2026/9vnk_65211.map" model { file = "/net/cci-nas-00/data/ceres_data/9vnk_65211/02_2026/9vnk_65211.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vnk_65211/02_2026/9vnk_65211.cif" } resolution = 3.38 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= 0.001 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 2052 2.51 5 N 594 2.21 5 O 702 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: 3348 Number of models: 1 Model: "" Number of chains: 54 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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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 Time building chain proxies: 1.01, per 1000 atoms: 0.30 Number of scatterers: 3348 At special positions: 0 Unit cell: (89.64, 124.5, 31.54, 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 702 8.00 N 594 7.00 C 2052 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=108, symmetry=0 Number of additional bonds: simple=108, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.40 Conformation dependent library (CDL) restraints added in 58.2 milliseconds 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB SFE A 210 " pdb=" CB SFE L 210 " pdb=" CB SFE O 210 " pdb=" CB SFE B 210 " pdb=" CB SFE C 210 " pdb=" CB SFE N 210 " pdb=" CB SFE P 210 " pdb=" CB SFE E 210 " pdb=" CB SFE S 210 " pdb=" CB SFE o 210 " pdb=" CB SFE u 210 " pdb=" CB SFE U 210 " pdb=" CB SFE W 210 " pdb=" CB SFE s 210 " pdb=" CB SFE w 210 " pdb=" CB SFE a 210 " pdb=" CB SFE T 210 " pdb=" CB SFE p 210 " pdb=" CB SFE v 210 " pdb=" CB SFE V 210 " pdb=" CB SFE X 210 " pdb=" CB SFE t 210 " pdb=" CB SFE x 210 " pdb=" CB SFE b 210 " Number of C-beta restraints generated: 492 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 2 sheets defined 0.0% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 214 through 216 Processing sheet with id=AA2, first strand: chain 'F' and resid 214 through 216 8 hydrogen bonds defined for protein. 24 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: 0.34 Time building geometry restraints manager: 0.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.30: 702 1.30 - 1.39: 1066 1.39 - 1.47: 79 1.47 - 1.56: 1417 1.56 - 1.64: 30 Bond restraints: 3294 Sorted by residual: bond pdb=" N SFE f 216 " pdb=" CB SFE f 216 " ideal model delta sigma weight residual 1.454 1.645 -0.191 2.00e-02 2.50e+03 9.09e+01 bond pdb=" N SFE J 216 " pdb=" CB SFE J 216 " ideal model delta sigma weight residual 1.454 1.644 -0.190 2.00e-02 2.50e+03 9.04e+01 bond pdb=" N SFE e 216 " pdb=" CB SFE e 216 " ideal model delta sigma weight residual 1.454 1.644 -0.190 2.00e-02 2.50e+03 9.03e+01 bond pdb=" N SFE G 216 " pdb=" CB SFE G 216 " ideal model delta sigma weight residual 1.454 1.644 -0.190 2.00e-02 2.50e+03 9.02e+01 bond pdb=" N SFE l 216 " pdb=" CB SFE l 216 " ideal model delta sigma weight residual 1.454 1.644 -0.190 2.00e-02 2.50e+03 9.01e+01 ... (remaining 3289 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.79: 3918 6.79 - 13.58: 132 13.58 - 20.37: 42 20.37 - 27.16: 6 27.16 - 33.94: 6 Bond angle restraints: 4104 Sorted by residual: angle pdb=" C SFE t 210 " pdb=" CA SFE t 210 " pdb=" CB SFE t 210 " ideal model delta sigma weight residual 112.84 146.78 -33.94 3.00e+00 1.11e-01 1.28e+02 angle pdb=" C SFE p 210 " pdb=" CA SFE p 210 " pdb=" CB SFE p 210 " ideal model delta sigma weight residual 112.84 146.77 -33.93 3.00e+00 1.11e-01 1.28e+02 angle pdb=" C SFE L 210 " pdb=" CA SFE L 210 " pdb=" CB SFE L 210 " ideal model delta sigma weight residual 112.84 146.76 -33.92 3.00e+00 1.11e-01 1.28e+02 angle pdb=" C SFE N 210 " pdb=" CA SFE N 210 " pdb=" CB SFE N 210 " ideal model delta sigma weight residual 112.84 146.76 -33.92 3.00e+00 1.11e-01 1.28e+02 angle pdb=" C SFE s 210 " pdb=" CA SFE s 210 " pdb=" CB SFE s 210 " ideal model delta sigma weight residual 112.84 146.74 -33.90 3.00e+00 1.11e-01 1.28e+02 ... (remaining 4099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.80: 1032 22.80 - 45.60: 54 45.60 - 68.41: 54 68.41 - 91.21: 96 91.21 - 114.01: 12 Dihedral angle restraints: 1248 sinusoidal: 432 harmonic: 816 Sorted by residual: dihedral pdb=" N SFE y 210 " pdb=" C SFE y 210 " pdb=" CA SFE y 210 " pdb=" CB SFE y 210 " ideal model delta harmonic sigma weight residual 122.80 8.79 114.01 0 2.50e+00 1.60e-01 2.08e+03 dihedral pdb=" N SFE 1 210 " pdb=" C SFE 1 210 " pdb=" CA SFE 1 210 " pdb=" CB SFE 1 210 " ideal model delta harmonic sigma weight residual 122.80 8.79 114.01 0 2.50e+00 1.60e-01 2.08e+03 dihedral pdb=" N SFE Q 210 " pdb=" C SFE Q 210 " pdb=" CA SFE Q 210 " pdb=" CB SFE Q 210 " ideal model delta harmonic sigma weight residual 122.80 8.79 114.01 0 2.50e+00 1.60e-01 2.08e+03 ... (remaining 1245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 162 0.115 - 0.230: 48 0.230 - 0.344: 0 0.344 - 0.459: 36 0.459 - 0.573: 24 Chirality restraints: 270 Sorted by residual: chirality pdb=" CB SFE g 216 " pdb=" N SFE g 216 " pdb=" CA SFE g 216 " pdb=" CG SFE g 216 " both_signs ideal model delta sigma weight residual False -2.38 -2.95 0.57 2.00e-01 2.50e+01 8.21e+00 chirality pdb=" CB SFE h 216 " pdb=" N SFE h 216 " pdb=" CA SFE h 216 " pdb=" CG SFE h 216 " both_signs ideal model delta sigma weight residual False -2.38 -2.95 0.57 2.00e-01 2.50e+01 8.18e+00 chirality pdb=" CB SFE m 216 " pdb=" N SFE m 216 " pdb=" CA SFE m 216 " pdb=" CG SFE m 216 " both_signs ideal model delta sigma weight residual False -2.38 -2.95 0.57 2.00e-01 2.50e+01 8.17e+00 ... (remaining 267 not shown) Planarity restraints: 594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 213 " 0.019 2.00e-02 2.50e+03 3.84e-02 1.47e+01 pdb=" C ASN C 213 " -0.066 2.00e-02 2.50e+03 pdb=" O ASN C 213 " 0.025 2.00e-02 2.50e+03 pdb=" N ASP C 214 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN S 213 " -0.019 2.00e-02 2.50e+03 3.84e-02 1.47e+01 pdb=" C ASN S 213 " 0.066 2.00e-02 2.50e+03 pdb=" O ASN S 213 " -0.025 2.00e-02 2.50e+03 pdb=" N ASP S 214 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN W 213 " 0.019 2.00e-02 2.50e+03 3.83e-02 1.47e+01 pdb=" C ASN W 213 " -0.066 2.00e-02 2.50e+03 pdb=" O ASN W 213 " 0.025 2.00e-02 2.50e+03 pdb=" N ASP W 214 " 0.022 2.00e-02 2.50e+03 ... (remaining 591 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 370 2.66 - 3.22: 3407 3.22 - 3.78: 4725 3.78 - 4.34: 7138 4.34 - 4.90: 12663 Nonbonded interactions: 28303 Sorted by model distance: nonbonded pdb=" O SFE e 216 " pdb=" CB SFE e 216 " model vdw 2.104 2.776 nonbonded pdb=" O SFE G 216 " pdb=" CB SFE G 216 " model vdw 2.104 2.776 nonbonded pdb=" O SFE k 216 " pdb=" CB SFE k 216 " model vdw 2.104 2.776 nonbonded pdb=" O SFE J 216 " pdb=" CB SFE J 216 " model vdw 2.104 2.776 nonbonded pdb=" O SFE f 216 " pdb=" CB SFE f 216 " model vdw 2.104 2.776 ... (remaining 28298 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 '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: 9.840 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: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.070 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6721 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 : 0.025 0.191 3402 Z= 1.771 Angle : 3.356 33.944 4104 Z= 1.358 Chirality : 0.234 0.573 270 Planarity : 0.005 0.038 594 Dihedral : 21.409 81.131 756 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 190.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.81 % Favored : 85.19 % Rotamer: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Cbeta Deviations : 42.22 % 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: -6.19 (0.13), residues: 162 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.71 (0.10), residues: 162 Details of bonding type rmsd covalent geometry : bond 0.02086 ( 3294) covalent geometry : angle 3.35596 ( 4104) hydrogen bonds : bond 0.24489 ( 8) hydrogen bonds : angle 11.64376 ( 24) Misc. bond : bond 0.07581 ( 108) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.052 Fit side-chains revert: symmetry clash REVERT: O 213 ASN cc_start: 0.7212 (p0) cc_final: 0.6646 (p0) REVERT: Q 213 ASN cc_start: 0.7364 (p0) cc_final: 0.5685 (t0) REVERT: J 214 ASP cc_start: 0.6832 (p0) cc_final: 0.6474 (p0) REVERT: k 214 ASP cc_start: 0.6101 (p0) cc_final: 0.5800 (p0) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.0319 time to fit residues: 1.8414 Evaluate side-chains 33 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.088 ------------------------------------------------------------------------------- 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: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 213 ASN N 213 ASN o 213 ASN c 215 ASN q 213 ASN ** s 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 213 ASN v 213 ASN d 215 ASN r 213 ASN ** t 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 213 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.111174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.096449 restraints weight = 8095.623| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 3.13 r_work: 0.3825 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.7099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.071 0.281 3402 Z= 3.666 Angle : 7.945 44.966 4104 Z= 3.036 Chirality : 0.285 0.754 270 Planarity : 0.021 0.071 594 Dihedral : 32.436 89.485 432 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 100.55 Ramachandran Plot: Outliers : 3.09 % Allowed : 30.86 % Favored : 66.05 % Rotamer: Outliers : 22.84 % Allowed : 20.99 % Favored : 56.17 % Cbeta Deviations : 41.48 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.69 % Twisted Proline : 0.00 % Twisted General : 21.76 % 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: -6.84 (0.14), residues: 162 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.21 (0.11), residues: 162 Details of bonding type rmsd covalent geometry : bond 0.07252 ( 3294) covalent geometry : angle 7.94539 ( 4104) hydrogen bonds : bond 0.26959 ( 8) hydrogen bonds : angle 14.39053 ( 24) Misc. bond : bond 0.01227 ( 108) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 15 time to evaluate : 0.091 Fit side-chains REVERT: G 215 ASN cc_start: 0.8928 (OUTLIER) cc_final: 0.8669 (p0) REVERT: C 213 ASN cc_start: 0.7740 (m-40) cc_final: 0.7363 (p0) REVERT: N 213 ASN cc_start: 0.8752 (OUTLIER) cc_final: 0.8340 (p0) REVERT: N 215 ASN cc_start: 0.7986 (OUTLIER) cc_final: 0.7436 (p0) REVERT: P 215 ASN cc_start: 0.8817 (OUTLIER) cc_final: 0.8318 (p0) REVERT: s 215 ASN cc_start: 0.8078 (OUTLIER) cc_final: 0.7743 (p0) REVERT: w 215 ASN cc_start: 0.8651 (OUTLIER) cc_final: 0.8031 (p0) REVERT: p 215 ASN cc_start: 0.8406 (OUTLIER) cc_final: 0.8167 (p0) REVERT: X 214 ASP cc_start: 0.8371 (m-30) cc_final: 0.7810 (p0) outliers start: 37 outliers final: 22 residues processed: 52 average time/residue: 0.0309 time to fit residues: 2.3965 Evaluate side-chains 42 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 13 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 213 ASN Chi-restraints excluded: chain L residue 215 ASN Chi-restraints excluded: chain Q residue 214 ASP Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain G residue 215 ASN Chi-restraints excluded: chain N residue 213 ASN Chi-restraints excluded: chain N residue 215 ASN Chi-restraints excluded: chain P residue 215 ASN Chi-restraints excluded: chain E residue 214 ASP Chi-restraints excluded: chain o residue 214 ASP Chi-restraints excluded: chain o residue 215 ASN Chi-restraints excluded: chain u residue 215 ASN Chi-restraints excluded: chain y residue 214 ASP Chi-restraints excluded: chain U residue 213 ASN Chi-restraints excluded: chain U residue 214 ASP Chi-restraints excluded: chain s residue 215 ASN Chi-restraints excluded: chain w residue 215 ASN Chi-restraints excluded: chain a residue 213 ASN Chi-restraints excluded: chain a residue 214 ASP Chi-restraints excluded: chain p residue 214 ASP Chi-restraints excluded: chain p residue 215 ASN Chi-restraints excluded: chain z residue 214 ASP Chi-restraints excluded: chain V residue 213 ASN Chi-restraints excluded: chain V residue 214 ASP Chi-restraints excluded: chain t residue 215 ASN Chi-restraints excluded: chain x residue 215 ASN Chi-restraints excluded: chain b residue 213 ASN Chi-restraints excluded: chain b 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: ** s 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 213 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 = 0.4087 r_free = 0.4087 target = 0.108757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.094249 restraints weight = 8082.636| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 2.99 r_work: 0.3893 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3797 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.7109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.071 0.290 3402 Z= 3.622 Angle : 7.919 47.703 4104 Z= 3.033 Chirality : 0.274 0.678 270 Planarity : 0.021 0.137 594 Dihedral : 32.502 89.898 432 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 99.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 38.27 % Favored : 61.73 % Rotamer: Outliers : 22.84 % Allowed : 29.01 % Favored : 48.15 % Cbeta Deviations : 41.85 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.93 % Twisted Proline : 0.00 % Twisted General : 20.60 % 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: -6.94 (0.15), residues: 162 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.29 (0.11), residues: 162 Details of bonding type rmsd covalent geometry : bond 0.07179 ( 3294) covalent geometry : angle 7.91912 ( 4104) hydrogen bonds : bond 0.27425 ( 8) hydrogen bonds : angle 15.02344 ( 24) Misc. bond : bond 0.01198 ( 108) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 12 time to evaluate : 0.087 Fit side-chains REVERT: G 215 ASN cc_start: 0.9013 (OUTLIER) cc_final: 0.8778 (p0) REVERT: N 213 ASN cc_start: 0.8856 (OUTLIER) cc_final: 0.7988 (p0) REVERT: N 215 ASN cc_start: 0.8224 (OUTLIER) cc_final: 0.7555 (p0) REVERT: P 215 ASN cc_start: 0.8870 (OUTLIER) cc_final: 0.8329 (p0) REVERT: s 215 ASN cc_start: 0.8284 (OUTLIER) cc_final: 0.7921 (p0) REVERT: w 215 ASN cc_start: 0.8783 (OUTLIER) cc_final: 0.8204 (p0) REVERT: p 215 ASN cc_start: 0.8506 (OUTLIER) cc_final: 0.8279 (p0) REVERT: l 214 ASP cc_start: 0.8482 (OUTLIER) cc_final: 0.7597 (p0) outliers start: 37 outliers final: 26 residues processed: 47 average time/residue: 0.0310 time to fit residues: 2.1945 Evaluate side-chains 46 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 12 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 215 ASN Chi-restraints excluded: chain Q residue 214 ASP Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain G residue 215 ASN Chi-restraints excluded: chain N residue 213 ASN Chi-restraints excluded: chain N residue 215 ASN Chi-restraints excluded: chain P residue 215 ASN Chi-restraints excluded: chain R residue 215 ASN Chi-restraints excluded: chain E residue 214 ASP Chi-restraints excluded: chain i residue 214 ASP Chi-restraints excluded: chain o residue 214 ASP Chi-restraints excluded: chain o residue 215 ASN Chi-restraints excluded: chain u residue 215 ASN Chi-restraints excluded: chain y residue 214 ASP Chi-restraints excluded: chain U residue 213 ASN Chi-restraints excluded: chain U residue 214 ASP Chi-restraints excluded: chain e residue 215 ASN Chi-restraints excluded: chain s residue 215 ASN Chi-restraints excluded: chain w residue 215 ASN Chi-restraints excluded: chain a residue 213 ASN Chi-restraints excluded: chain a residue 214 ASP Chi-restraints excluded: chain p residue 214 ASP Chi-restraints excluded: chain p residue 215 ASN Chi-restraints excluded: chain z residue 214 ASP Chi-restraints excluded: chain V residue 213 ASN Chi-restraints excluded: chain V residue 214 ASP Chi-restraints excluded: chain f residue 215 ASN Chi-restraints excluded: chain d residue 214 ASP Chi-restraints excluded: chain t residue 215 ASN Chi-restraints excluded: chain x residue 215 ASN Chi-restraints excluded: chain b residue 213 ASN Chi-restraints excluded: chain b residue 214 ASP Chi-restraints excluded: chain l 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: ** s 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 213 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 = 0.4148 r_free = 0.4148 target = 0.111977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.096514 restraints weight = 8081.800| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 3.17 r_work: 0.3893 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3799 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.7119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.071 0.290 3402 Z= 3.621 Angle : 7.919 47.702 4104 Z= 3.033 Chirality : 0.274 0.678 270 Planarity : 0.021 0.137 594 Dihedral : 32.498 89.891 432 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 99.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 38.27 % Favored : 61.73 % Rotamer: Outliers : 21.60 % Allowed : 30.25 % Favored : 48.15 % Cbeta Deviations : 41.85 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.93 % Twisted Proline : 0.00 % Twisted General : 20.60 % 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: -6.94 (0.15), residues: 162 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.29 (0.11), residues: 162 Details of bonding type rmsd covalent geometry : bond 0.07179 ( 3294) covalent geometry : angle 7.91888 ( 4104) hydrogen bonds : bond 0.27427 ( 8) hydrogen bonds : angle 15.02345 ( 24) Misc. bond : bond 0.01190 ( 108) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 12 time to evaluate : 0.102 Fit side-chains REVERT: G 215 ASN cc_start: 0.9014 (OUTLIER) cc_final: 0.8780 (p0) REVERT: N 213 ASN cc_start: 0.8858 (OUTLIER) cc_final: 0.7990 (p0) REVERT: N 215 ASN cc_start: 0.8224 (OUTLIER) cc_final: 0.7558 (p0) REVERT: P 215 ASN cc_start: 0.8878 (OUTLIER) cc_final: 0.8340 (p0) REVERT: s 215 ASN cc_start: 0.8284 (OUTLIER) cc_final: 0.7922 (p0) REVERT: w 215 ASN cc_start: 0.8799 (OUTLIER) cc_final: 0.8220 (p0) REVERT: p 215 ASN cc_start: 0.8519 (OUTLIER) cc_final: 0.8291 (p0) REVERT: l 214 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.7571 (p0) outliers start: 35 outliers final: 27 residues processed: 45 average time/residue: 0.0320 time to fit residues: 2.1546 Evaluate side-chains 47 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 12 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 215 ASN Chi-restraints excluded: chain Q residue 214 ASP Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain G residue 215 ASN Chi-restraints excluded: chain N residue 213 ASN Chi-restraints excluded: chain N residue 215 ASN Chi-restraints excluded: chain P residue 215 ASN Chi-restraints excluded: chain R residue 215 ASN Chi-restraints excluded: chain E residue 214 ASP Chi-restraints excluded: chain i residue 214 ASP Chi-restraints excluded: chain o residue 214 ASP Chi-restraints excluded: chain o residue 215 ASN Chi-restraints excluded: chain u residue 215 ASN Chi-restraints excluded: chain y residue 214 ASP Chi-restraints excluded: chain U residue 213 ASN Chi-restraints excluded: chain U residue 214 ASP Chi-restraints excluded: chain e residue 215 ASN Chi-restraints excluded: chain s residue 215 ASN Chi-restraints excluded: chain w residue 215 ASN Chi-restraints excluded: chain a residue 213 ASN Chi-restraints excluded: chain a residue 214 ASP Chi-restraints excluded: chain p residue 214 ASP Chi-restraints excluded: chain p residue 215 ASN Chi-restraints excluded: chain z residue 214 ASP Chi-restraints excluded: chain V residue 213 ASN Chi-restraints excluded: chain V residue 214 ASP Chi-restraints excluded: chain f residue 215 ASN Chi-restraints excluded: chain d residue 214 ASP Chi-restraints excluded: chain t residue 215 ASN Chi-restraints excluded: chain x residue 215 ASN Chi-restraints excluded: chain 1 residue 215 ASN Chi-restraints excluded: chain b residue 213 ASN Chi-restraints excluded: chain b residue 214 ASP Chi-restraints excluded: chain l 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: ** s 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 213 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 = 0.4148 r_free = 0.4148 target = 0.111977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.096512 restraints weight = 8091.534| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 3.19 r_work: 0.3894 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3801 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.7119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.071 0.290 3402 Z= 3.621 Angle : 7.919 47.702 4104 Z= 3.033 Chirality : 0.274 0.678 270 Planarity : 0.021 0.137 594 Dihedral : 32.498 89.891 432 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 99.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 38.27 % Favored : 61.73 % Rotamer: Outliers : 21.60 % Allowed : 30.25 % Favored : 48.15 % Cbeta Deviations : 41.85 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.93 % Twisted Proline : 0.00 % Twisted General : 20.60 % 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: -6.94 (0.15), residues: 162 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.29 (0.11), residues: 162 Details of bonding type rmsd covalent geometry : bond 0.07179 ( 3294) covalent geometry : angle 7.91888 ( 4104) hydrogen bonds : bond 0.27427 ( 8) hydrogen bonds : angle 15.02345 ( 24) Misc. bond : bond 0.01190 ( 108) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 12 time to evaluate : 0.087 Fit side-chains REVERT: G 215 ASN cc_start: 0.9014 (OUTLIER) cc_final: 0.8779 (p0) REVERT: N 213 ASN cc_start: 0.8859 (OUTLIER) cc_final: 0.7989 (p0) REVERT: N 215 ASN cc_start: 0.8221 (OUTLIER) cc_final: 0.7556 (p0) REVERT: P 215 ASN cc_start: 0.8881 (OUTLIER) cc_final: 0.8341 (p0) REVERT: s 215 ASN cc_start: 0.8283 (OUTLIER) cc_final: 0.7921 (p0) REVERT: w 215 ASN cc_start: 0.8803 (OUTLIER) cc_final: 0.8224 (p0) REVERT: p 215 ASN cc_start: 0.8518 (OUTLIER) cc_final: 0.8290 (p0) REVERT: l 214 ASP cc_start: 0.8469 (OUTLIER) cc_final: 0.7572 (p0) outliers start: 35 outliers final: 27 residues processed: 45 average time/residue: 0.0305 time to fit residues: 2.0591 Evaluate side-chains 47 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 12 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 215 ASN Chi-restraints excluded: chain Q residue 214 ASP Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain G residue 215 ASN Chi-restraints excluded: chain N residue 213 ASN Chi-restraints excluded: chain N residue 215 ASN Chi-restraints excluded: chain P residue 215 ASN Chi-restraints excluded: chain R residue 215 ASN Chi-restraints excluded: chain E residue 214 ASP Chi-restraints excluded: chain i residue 214 ASP Chi-restraints excluded: chain o residue 214 ASP Chi-restraints excluded: chain o residue 215 ASN Chi-restraints excluded: chain u residue 215 ASN Chi-restraints excluded: chain y residue 214 ASP Chi-restraints excluded: chain U residue 213 ASN Chi-restraints excluded: chain U residue 214 ASP Chi-restraints excluded: chain e residue 215 ASN Chi-restraints excluded: chain s residue 215 ASN Chi-restraints excluded: chain w residue 215 ASN Chi-restraints excluded: chain a residue 213 ASN Chi-restraints excluded: chain a residue 214 ASP Chi-restraints excluded: chain p residue 214 ASP Chi-restraints excluded: chain p residue 215 ASN Chi-restraints excluded: chain z residue 214 ASP Chi-restraints excluded: chain V residue 213 ASN Chi-restraints excluded: chain V residue 214 ASP Chi-restraints excluded: chain f residue 215 ASN Chi-restraints excluded: chain d residue 214 ASP Chi-restraints excluded: chain t residue 215 ASN Chi-restraints excluded: chain x residue 215 ASN Chi-restraints excluded: chain 1 residue 215 ASN Chi-restraints excluded: chain b residue 213 ASN Chi-restraints excluded: chain b residue 214 ASP Chi-restraints excluded: chain l 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: 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: ** s 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 213 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 = 0.4148 r_free = 0.4148 target = 0.111977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.096473 restraints weight = 8131.619| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 3.15 r_work: 0.3893 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3799 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.7119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.071 0.290 3402 Z= 3.621 Angle : 7.919 47.702 4104 Z= 3.033 Chirality : 0.274 0.678 270 Planarity : 0.021 0.137 594 Dihedral : 32.498 89.891 432 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 99.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 38.27 % Favored : 61.73 % Rotamer: Outliers : 21.60 % Allowed : 30.25 % Favored : 48.15 % Cbeta Deviations : 41.85 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.93 % Twisted Proline : 0.00 % Twisted General : 20.60 % 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: -6.94 (0.15), residues: 162 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.29 (0.11), residues: 162 Details of bonding type rmsd covalent geometry : bond 0.07179 ( 3294) covalent geometry : angle 7.91888 ( 4104) hydrogen bonds : bond 0.27427 ( 8) hydrogen bonds : angle 15.02345 ( 24) Misc. bond : bond 0.01190 ( 108) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 12 time to evaluate : 0.071 Fit side-chains REVERT: G 215 ASN cc_start: 0.9014 (OUTLIER) cc_final: 0.8779 (p0) REVERT: N 213 ASN cc_start: 0.8859 (OUTLIER) cc_final: 0.7990 (p0) REVERT: N 215 ASN cc_start: 0.8220 (OUTLIER) cc_final: 0.7554 (p0) REVERT: P 215 ASN cc_start: 0.8878 (OUTLIER) cc_final: 0.8339 (p0) REVERT: s 215 ASN cc_start: 0.8281 (OUTLIER) cc_final: 0.7919 (p0) REVERT: w 215 ASN cc_start: 0.8799 (OUTLIER) cc_final: 0.8219 (p0) REVERT: p 215 ASN cc_start: 0.8519 (OUTLIER) cc_final: 0.8291 (p0) REVERT: l 214 ASP cc_start: 0.8469 (OUTLIER) cc_final: 0.7574 (p0) outliers start: 35 outliers final: 27 residues processed: 45 average time/residue: 0.0209 time to fit residues: 1.4764 Evaluate side-chains 47 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 12 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 215 ASN Chi-restraints excluded: chain Q residue 214 ASP Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain G residue 215 ASN Chi-restraints excluded: chain N residue 213 ASN Chi-restraints excluded: chain N residue 215 ASN Chi-restraints excluded: chain P residue 215 ASN Chi-restraints excluded: chain R residue 215 ASN Chi-restraints excluded: chain E residue 214 ASP Chi-restraints excluded: chain i residue 214 ASP Chi-restraints excluded: chain o residue 214 ASP Chi-restraints excluded: chain o residue 215 ASN Chi-restraints excluded: chain u residue 215 ASN Chi-restraints excluded: chain y residue 214 ASP Chi-restraints excluded: chain U residue 213 ASN Chi-restraints excluded: chain U residue 214 ASP Chi-restraints excluded: chain e residue 215 ASN Chi-restraints excluded: chain s residue 215 ASN Chi-restraints excluded: chain w residue 215 ASN Chi-restraints excluded: chain a residue 213 ASN Chi-restraints excluded: chain a residue 214 ASP Chi-restraints excluded: chain p residue 214 ASP Chi-restraints excluded: chain p residue 215 ASN Chi-restraints excluded: chain z residue 214 ASP Chi-restraints excluded: chain V residue 213 ASN Chi-restraints excluded: chain V residue 214 ASP Chi-restraints excluded: chain f residue 215 ASN Chi-restraints excluded: chain d residue 214 ASP Chi-restraints excluded: chain t residue 215 ASN Chi-restraints excluded: chain x residue 215 ASN Chi-restraints excluded: chain 1 residue 215 ASN Chi-restraints excluded: chain b residue 213 ASN Chi-restraints excluded: chain b residue 214 ASP Chi-restraints excluded: chain l 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: 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: ** s 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 213 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 = 0.4148 r_free = 0.4148 target = 0.111977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.096438 restraints weight = 8213.424| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 3.18 r_work: 0.3889 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3797 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.7119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.071 0.290 3402 Z= 3.621 Angle : 7.919 47.702 4104 Z= 3.033 Chirality : 0.274 0.678 270 Planarity : 0.021 0.137 594 Dihedral : 32.498 89.891 432 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 99.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 38.27 % Favored : 61.73 % Rotamer: Outliers : 21.60 % Allowed : 30.25 % Favored : 48.15 % Cbeta Deviations : 41.85 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.93 % Twisted Proline : 0.00 % Twisted General : 20.60 % 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: -6.94 (0.15), residues: 162 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.29 (0.11), residues: 162 Details of bonding type rmsd covalent geometry : bond 0.07179 ( 3294) covalent geometry : angle 7.91888 ( 4104) hydrogen bonds : bond 0.27427 ( 8) hydrogen bonds : angle 15.02345 ( 24) Misc. bond : bond 0.01190 ( 108) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 12 time to evaluate : 0.094 Fit side-chains REVERT: G 215 ASN cc_start: 0.9015 (OUTLIER) cc_final: 0.8780 (p0) REVERT: N 213 ASN cc_start: 0.8861 (OUTLIER) cc_final: 0.7990 (p0) REVERT: N 215 ASN cc_start: 0.8223 (OUTLIER) cc_final: 0.7557 (p0) REVERT: P 215 ASN cc_start: 0.8877 (OUTLIER) cc_final: 0.8339 (p0) REVERT: s 215 ASN cc_start: 0.8285 (OUTLIER) cc_final: 0.7922 (p0) REVERT: w 215 ASN cc_start: 0.8800 (OUTLIER) cc_final: 0.8220 (p0) REVERT: p 215 ASN cc_start: 0.8520 (OUTLIER) cc_final: 0.8291 (p0) REVERT: l 214 ASP cc_start: 0.8468 (OUTLIER) cc_final: 0.7573 (p0) outliers start: 35 outliers final: 27 residues processed: 45 average time/residue: 0.0324 time to fit residues: 2.1828 Evaluate side-chains 47 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 12 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 215 ASN Chi-restraints excluded: chain Q residue 214 ASP Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain G residue 215 ASN Chi-restraints excluded: chain N residue 213 ASN Chi-restraints excluded: chain N residue 215 ASN Chi-restraints excluded: chain P residue 215 ASN Chi-restraints excluded: chain R residue 215 ASN Chi-restraints excluded: chain E residue 214 ASP Chi-restraints excluded: chain i residue 214 ASP Chi-restraints excluded: chain o residue 214 ASP Chi-restraints excluded: chain o residue 215 ASN Chi-restraints excluded: chain u residue 215 ASN Chi-restraints excluded: chain y residue 214 ASP Chi-restraints excluded: chain U residue 213 ASN Chi-restraints excluded: chain U residue 214 ASP Chi-restraints excluded: chain e residue 215 ASN Chi-restraints excluded: chain s residue 215 ASN Chi-restraints excluded: chain w residue 215 ASN Chi-restraints excluded: chain a residue 213 ASN Chi-restraints excluded: chain a residue 214 ASP Chi-restraints excluded: chain p residue 214 ASP Chi-restraints excluded: chain p residue 215 ASN Chi-restraints excluded: chain z residue 214 ASP Chi-restraints excluded: chain V residue 213 ASN Chi-restraints excluded: chain V residue 214 ASP Chi-restraints excluded: chain f residue 215 ASN Chi-restraints excluded: chain d residue 214 ASP Chi-restraints excluded: chain t residue 215 ASN Chi-restraints excluded: chain x residue 215 ASN Chi-restraints excluded: chain 1 residue 215 ASN Chi-restraints excluded: chain b residue 213 ASN Chi-restraints excluded: chain b residue 214 ASP Chi-restraints excluded: chain l 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: ** s 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 213 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 = 0.4148 r_free = 0.4148 target = 0.111977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.096418 restraints weight = 8287.589| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 3.19 r_work: 0.3890 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3794 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.7119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.071 0.290 3402 Z= 3.621 Angle : 7.919 47.702 4104 Z= 3.033 Chirality : 0.274 0.678 270 Planarity : 0.021 0.137 594 Dihedral : 32.498 89.891 432 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 99.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 38.27 % Favored : 61.73 % Rotamer: Outliers : 21.60 % Allowed : 30.25 % Favored : 48.15 % Cbeta Deviations : 41.85 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.93 % Twisted Proline : 0.00 % Twisted General : 20.60 % 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: -6.94 (0.15), residues: 162 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.29 (0.11), residues: 162 Details of bonding type rmsd covalent geometry : bond 0.07179 ( 3294) covalent geometry : angle 7.91888 ( 4104) hydrogen bonds : bond 0.27427 ( 8) hydrogen bonds : angle 15.02345 ( 24) Misc. bond : bond 0.01190 ( 108) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 12 time to evaluate : 0.090 Fit side-chains REVERT: G 215 ASN cc_start: 0.9014 (OUTLIER) cc_final: 0.8780 (p0) REVERT: N 213 ASN cc_start: 0.8862 (OUTLIER) cc_final: 0.7993 (p0) REVERT: N 215 ASN cc_start: 0.8221 (OUTLIER) cc_final: 0.7556 (p0) REVERT: P 215 ASN cc_start: 0.8873 (OUTLIER) cc_final: 0.8335 (p0) REVERT: s 215 ASN cc_start: 0.8283 (OUTLIER) cc_final: 0.7919 (p0) REVERT: w 215 ASN cc_start: 0.8791 (OUTLIER) cc_final: 0.8210 (p0) REVERT: p 215 ASN cc_start: 0.8518 (OUTLIER) cc_final: 0.8289 (p0) REVERT: l 214 ASP cc_start: 0.8471 (OUTLIER) cc_final: 0.7577 (p0) outliers start: 35 outliers final: 27 residues processed: 45 average time/residue: 0.0307 time to fit residues: 2.0928 Evaluate side-chains 47 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 12 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 215 ASN Chi-restraints excluded: chain Q residue 214 ASP Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain G residue 215 ASN Chi-restraints excluded: chain N residue 213 ASN Chi-restraints excluded: chain N residue 215 ASN Chi-restraints excluded: chain P residue 215 ASN Chi-restraints excluded: chain R residue 215 ASN Chi-restraints excluded: chain E residue 214 ASP Chi-restraints excluded: chain i residue 214 ASP Chi-restraints excluded: chain o residue 214 ASP Chi-restraints excluded: chain o residue 215 ASN Chi-restraints excluded: chain u residue 215 ASN Chi-restraints excluded: chain y residue 214 ASP Chi-restraints excluded: chain U residue 213 ASN Chi-restraints excluded: chain U residue 214 ASP Chi-restraints excluded: chain e residue 215 ASN Chi-restraints excluded: chain s residue 215 ASN Chi-restraints excluded: chain w residue 215 ASN Chi-restraints excluded: chain a residue 213 ASN Chi-restraints excluded: chain a residue 214 ASP Chi-restraints excluded: chain p residue 214 ASP Chi-restraints excluded: chain p residue 215 ASN Chi-restraints excluded: chain z residue 214 ASP Chi-restraints excluded: chain V residue 213 ASN Chi-restraints excluded: chain V residue 214 ASP Chi-restraints excluded: chain f residue 215 ASN Chi-restraints excluded: chain d residue 214 ASP Chi-restraints excluded: chain t residue 215 ASN Chi-restraints excluded: chain x residue 215 ASN Chi-restraints excluded: chain 1 residue 215 ASN Chi-restraints excluded: chain b residue 213 ASN Chi-restraints excluded: chain b residue 214 ASP Chi-restraints excluded: chain l 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: 4.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** s 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 213 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 = 0.4148 r_free = 0.4148 target = 0.111977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.096390 restraints weight = 8311.593| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 3.19 r_work: 0.3889 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3794 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.7119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.071 0.290 3402 Z= 3.621 Angle : 7.919 47.702 4104 Z= 3.033 Chirality : 0.274 0.678 270 Planarity : 0.021 0.137 594 Dihedral : 32.498 89.891 432 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 99.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 38.27 % Favored : 61.73 % Rotamer: Outliers : 21.60 % Allowed : 30.25 % Favored : 48.15 % Cbeta Deviations : 41.85 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.93 % Twisted Proline : 0.00 % Twisted General : 20.60 % 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: -6.94 (0.15), residues: 162 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.29 (0.11), residues: 162 Details of bonding type rmsd covalent geometry : bond 0.07179 ( 3294) covalent geometry : angle 7.91888 ( 4104) hydrogen bonds : bond 0.27427 ( 8) hydrogen bonds : angle 15.02345 ( 24) Misc. bond : bond 0.01190 ( 108) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 12 time to evaluate : 0.092 Fit side-chains REVERT: G 215 ASN cc_start: 0.9015 (OUTLIER) cc_final: 0.8781 (p0) REVERT: N 213 ASN cc_start: 0.8865 (OUTLIER) cc_final: 0.7995 (p0) REVERT: N 215 ASN cc_start: 0.8218 (OUTLIER) cc_final: 0.7553 (p0) REVERT: P 215 ASN cc_start: 0.8875 (OUTLIER) cc_final: 0.8336 (p0) REVERT: s 215 ASN cc_start: 0.8279 (OUTLIER) cc_final: 0.7918 (p0) REVERT: w 215 ASN cc_start: 0.8795 (OUTLIER) cc_final: 0.8215 (p0) REVERT: p 215 ASN cc_start: 0.8516 (OUTLIER) cc_final: 0.8287 (p0) REVERT: l 214 ASP cc_start: 0.8471 (OUTLIER) cc_final: 0.7576 (p0) outliers start: 35 outliers final: 27 residues processed: 45 average time/residue: 0.0314 time to fit residues: 2.1250 Evaluate side-chains 47 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 12 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 215 ASN Chi-restraints excluded: chain Q residue 214 ASP Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain G residue 215 ASN Chi-restraints excluded: chain N residue 213 ASN Chi-restraints excluded: chain N residue 215 ASN Chi-restraints excluded: chain P residue 215 ASN Chi-restraints excluded: chain R residue 215 ASN Chi-restraints excluded: chain E residue 214 ASP Chi-restraints excluded: chain i residue 214 ASP Chi-restraints excluded: chain o residue 214 ASP Chi-restraints excluded: chain o residue 215 ASN Chi-restraints excluded: chain u residue 215 ASN Chi-restraints excluded: chain y residue 214 ASP Chi-restraints excluded: chain U residue 213 ASN Chi-restraints excluded: chain U residue 214 ASP Chi-restraints excluded: chain e residue 215 ASN Chi-restraints excluded: chain s residue 215 ASN Chi-restraints excluded: chain w residue 215 ASN Chi-restraints excluded: chain a residue 213 ASN Chi-restraints excluded: chain a residue 214 ASP Chi-restraints excluded: chain p residue 214 ASP Chi-restraints excluded: chain p residue 215 ASN Chi-restraints excluded: chain z residue 214 ASP Chi-restraints excluded: chain V residue 213 ASN Chi-restraints excluded: chain V residue 214 ASP Chi-restraints excluded: chain f residue 215 ASN Chi-restraints excluded: chain d residue 214 ASP Chi-restraints excluded: chain t residue 215 ASN Chi-restraints excluded: chain x residue 215 ASN Chi-restraints excluded: chain 1 residue 215 ASN Chi-restraints excluded: chain b residue 213 ASN Chi-restraints excluded: chain b residue 214 ASP Chi-restraints excluded: chain l 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: 4.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** s 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 213 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 = 0.4148 r_free = 0.4148 target = 0.111977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.096510 restraints weight = 8094.303| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 3.19 r_work: 0.3893 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3800 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.7119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.071 0.290 3402 Z= 3.621 Angle : 7.919 47.702 4104 Z= 3.033 Chirality : 0.274 0.678 270 Planarity : 0.021 0.137 594 Dihedral : 32.498 89.891 432 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 99.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 38.27 % Favored : 61.73 % Rotamer: Outliers : 21.60 % Allowed : 30.25 % Favored : 48.15 % Cbeta Deviations : 41.85 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.93 % Twisted Proline : 0.00 % Twisted General : 20.60 % 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: -6.94 (0.15), residues: 162 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.29 (0.11), residues: 162 Details of bonding type rmsd covalent geometry : bond 0.07179 ( 3294) covalent geometry : angle 7.91888 ( 4104) hydrogen bonds : bond 0.27427 ( 8) hydrogen bonds : angle 15.02345 ( 24) Misc. bond : bond 0.01190 ( 108) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 12 time to evaluate : 0.091 Fit side-chains REVERT: G 215 ASN cc_start: 0.9014 (OUTLIER) cc_final: 0.8779 (p0) REVERT: N 213 ASN cc_start: 0.8857 (OUTLIER) cc_final: 0.7989 (p0) REVERT: N 215 ASN cc_start: 0.8225 (OUTLIER) cc_final: 0.7559 (p0) REVERT: P 215 ASN cc_start: 0.8879 (OUTLIER) cc_final: 0.8341 (p0) REVERT: s 215 ASN cc_start: 0.8286 (OUTLIER) cc_final: 0.7923 (p0) REVERT: w 215 ASN cc_start: 0.8800 (OUTLIER) cc_final: 0.8221 (p0) REVERT: p 215 ASN cc_start: 0.8519 (OUTLIER) cc_final: 0.8290 (p0) REVERT: l 214 ASP cc_start: 0.8466 (OUTLIER) cc_final: 0.7569 (p0) outliers start: 35 outliers final: 27 residues processed: 45 average time/residue: 0.0317 time to fit residues: 2.1482 Evaluate side-chains 47 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 12 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 215 ASN Chi-restraints excluded: chain Q residue 214 ASP Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain G residue 215 ASN Chi-restraints excluded: chain N residue 213 ASN Chi-restraints excluded: chain N residue 215 ASN Chi-restraints excluded: chain P residue 215 ASN Chi-restraints excluded: chain R residue 215 ASN Chi-restraints excluded: chain E residue 214 ASP Chi-restraints excluded: chain i residue 214 ASP Chi-restraints excluded: chain o residue 214 ASP Chi-restraints excluded: chain o residue 215 ASN Chi-restraints excluded: chain u residue 215 ASN Chi-restraints excluded: chain y residue 214 ASP Chi-restraints excluded: chain U residue 213 ASN Chi-restraints excluded: chain U residue 214 ASP Chi-restraints excluded: chain e residue 215 ASN Chi-restraints excluded: chain s residue 215 ASN Chi-restraints excluded: chain w residue 215 ASN Chi-restraints excluded: chain a residue 213 ASN Chi-restraints excluded: chain a residue 214 ASP Chi-restraints excluded: chain p residue 214 ASP Chi-restraints excluded: chain p residue 215 ASN Chi-restraints excluded: chain z residue 214 ASP Chi-restraints excluded: chain V residue 213 ASN Chi-restraints excluded: chain V residue 214 ASP Chi-restraints excluded: chain f residue 215 ASN Chi-restraints excluded: chain d residue 214 ASP Chi-restraints excluded: chain t residue 215 ASN Chi-restraints excluded: chain x residue 215 ASN Chi-restraints excluded: chain 1 residue 215 ASN Chi-restraints excluded: chain b residue 213 ASN Chi-restraints excluded: chain b residue 214 ASP Chi-restraints excluded: chain l 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: ** s 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 213 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 = 0.4148 r_free = 0.4148 target = 0.111977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.096360 restraints weight = 8354.626| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 3.21 r_work: 0.3890 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3796 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.7119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.071 0.290 3402 Z= 3.621 Angle : 7.919 47.702 4104 Z= 3.033 Chirality : 0.274 0.678 270 Planarity : 0.021 0.137 594 Dihedral : 32.498 89.891 432 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 99.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 38.27 % Favored : 61.73 % Rotamer: Outliers : 21.60 % Allowed : 30.25 % Favored : 48.15 % Cbeta Deviations : 41.85 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.93 % Twisted Proline : 0.00 % Twisted General : 20.60 % 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: -6.94 (0.15), residues: 162 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.29 (0.11), residues: 162 Details of bonding type rmsd covalent geometry : bond 0.07179 ( 3294) covalent geometry : angle 7.91888 ( 4104) hydrogen bonds : bond 0.27427 ( 8) hydrogen bonds : angle 15.02345 ( 24) Misc. bond : bond 0.01190 ( 108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 763.61 seconds wall clock time: 13 minutes 54.30 seconds (834.30 seconds total)