Starting phenix.real_space_refine on Thu Oct 22 18:21:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vnk_65211/10_2026/9vnk_65211.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vnk_65211/10_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_65211/10_2026/9vnk_65211.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vnk_65211/10_2026/9vnk_65211.map" model { file = "/net/cci-nas-00/data/ceres_data/9vnk_65211/10_2026/9vnk_65211.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vnk_65211/10_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-2.3rc1-6221/lib/python3.11/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: 1.25, per 1000 atoms: 0.37 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: 0.31 Conformation dependent library (CDL) restraints added in 83.1 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: 0.04 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: 0.28 Time building geometry restraints manager: 0.39 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 4.930 Find NCS groups from input model: 0.080 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: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 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/Z covalent geometry : bond 0.02086 / 1.16 ( 3294) covalent geometry : angle 3.35596 / 1.36 ( 4104) hydrogen bonds : bond 0.24489 / 13.97 ( 8) hydrogen bonds : angle 11.64376 / 4.72 ( 24) Misc. bond : bond 0.07581 / 4.39 ( 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 : 0.102 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: 0.0323 time to fit residues: 1.9582 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 : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.9990 overall best weight: 0.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 213 ASN ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 215 ASN M 213 ASN i 213 ASN ** U 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 215 ASN q 213 ASN j 213 ASN d 215 ASN r 213 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4963 r_free = 0.4963 target = 0.183475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4817 r_free = 0.4817 target = 0.171652 restraints weight = 6274.023| |-----------------------------------------------------------------------------| r_work (start): 0.4755 rms_B_bonded: 3.24 r_work: 0.4750 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.4661 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.4661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.162 3402 Z= 1.116 Angle : 8.143 53.329 4104 Z= 2.861 Chirality : 0.120 0.424 270 Planarity : 0.011 0.042 594 Dihedral : 29.871 88.381 432 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 94.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.52 % Favored : 81.48 % Rotamer: Outliers : 4.32 % Allowed : 12.35 % Favored : 83.33 % Cbeta Deviations : 40.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 10.42 % 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: -5.97 (0.14), residues: 162 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.55 (0.11), residues: 162 Details of bonding type rmsd/Z covalent geometry : bond 0.02187 / 1.13 ( 3294) covalent geometry : angle 8.14346 / 2.86 ( 4104) hydrogen bonds : bond 0.15695 / 8.91 ( 8) hydrogen bonds : angle 10.42254 / 4.01 ( 24) Misc. bond : bond 0.00664 / 0.39 ( 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 36 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.115 Fit side-chains REVERT: Q 213 ASN cc_start: 0.7575 (p0) cc_final: 0.5769 (t0) REVERT: J 214 ASP cc_start: 0.6608 (p0) cc_final: 0.6166 (p0) REVERT: k 214 ASP cc_start: 0.6565 (p0) cc_final: 0.6153 (p0) REVERT: l 214 ASP cc_start: 0.6346 (p0) cc_final: 0.5606 (p0) outliers start: 7 outliers final: 6 residues processed: 34 average time/residue: 0.0328 time to fit residues: 1.7303 Evaluate side-chains 33 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 215 ASN Chi-restraints excluded: chain U residue 214 ASP Chi-restraints excluded: chain a residue 214 ASP Chi-restraints excluded: chain V residue 214 ASP Chi-restraints excluded: chain d residue 215 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: [0] chunk 0 optimal weight: 0.9990 overall best weight: 0.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 215 ASN c 215 ASN d 215 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4872 r_free = 0.4872 target = 0.174842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4732 r_free = 0.4732 target = 0.161962 restraints weight = 5996.391| |-----------------------------------------------------------------------------| r_work (start): 0.4750 rms_B_bonded: 3.51 r_work: 0.4682 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.4682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.162 3402 Z= 1.116 Angle : 8.143 53.329 4104 Z= 2.861 Chirality : 0.120 0.424 270 Planarity : 0.011 0.042 594 Dihedral : 29.871 88.381 432 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 95.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.52 % Favored : 81.48 % Rotamer: Outliers : 3.09 % Allowed : 14.81 % Favored : 82.10 % Cbeta Deviations : 40.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 10.42 % 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: -5.97 (0.14), residues: 162 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.55 (0.11), residues: 162 Details of bonding type rmsd/Z covalent geometry : bond 0.02187 / 1.13 ( 3294) covalent geometry : angle 8.14346 / 2.86 ( 4104) hydrogen bonds : bond 0.15695 / 8.91 ( 8) hydrogen bonds : angle 10.42254 / 4.01 ( 24) Misc. bond : bond 0.00664 / 0.39 ( 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 32 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.068 Fit side-chains REVERT: Q 213 ASN cc_start: 0.7558 (p0) cc_final: 0.5721 (t0) REVERT: J 214 ASP cc_start: 0.6761 (p0) cc_final: 0.6274 (p0) REVERT: k 214 ASP cc_start: 0.6651 (p0) cc_final: 0.6194 (p0) REVERT: l 214 ASP cc_start: 0.6355 (p0) cc_final: 0.5700 (p0) outliers start: 5 outliers final: 4 residues processed: 30 average time/residue: 0.0219 time to fit residues: 1.0236 Evaluate side-chains 31 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 214 ASP Chi-restraints excluded: chain a residue 214 ASP Chi-restraints excluded: chain V residue 214 ASP Chi-restraints excluded: chain b residue 214 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.9980 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** c 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4873 r_free = 0.4873 target = 0.174878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4732 r_free = 0.4732 target = 0.162040 restraints weight = 5906.716| |-----------------------------------------------------------------------------| r_work (start): 0.4753 rms_B_bonded: 3.48 r_work: 0.4683 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.4683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.162 3402 Z= 1.116 Angle : 8.143 53.329 4104 Z= 2.861 Chirality : 0.120 0.424 270 Planarity : 0.011 0.042 594 Dihedral : 29.871 88.381 432 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 96.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.52 % Favored : 81.48 % Rotamer: Outliers : 2.47 % Allowed : 15.43 % Favored : 82.10 % Cbeta Deviations : 40.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 10.42 % 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: -5.97 (0.14), residues: 162 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.55 (0.11), residues: 162 Details of bonding type rmsd/Z covalent geometry : bond 0.02187 / 1.13 ( 3294) covalent geometry : angle 8.14346 / 2.86 ( 4104) hydrogen bonds : bond 0.15695 / 8.91 ( 8) hydrogen bonds : angle 10.42254 / 4.01 ( 24) Misc. bond : bond 0.00664 / 0.39 ( 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 31 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.093 Fit side-chains REVERT: Q 213 ASN cc_start: 0.7559 (p0) cc_final: 0.5724 (t0) REVERT: J 214 ASP cc_start: 0.6755 (p0) cc_final: 0.6269 (p0) REVERT: k 214 ASP cc_start: 0.6652 (p0) cc_final: 0.6196 (p0) REVERT: l 214 ASP cc_start: 0.6359 (p0) cc_final: 0.5699 (p0) outliers start: 4 outliers final: 4 residues processed: 29 average time/residue: 0.0303 time to fit residues: 1.3462 Evaluate side-chains 31 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 214 ASP Chi-restraints excluded: chain a residue 214 ASP Chi-restraints excluded: chain V residue 214 ASP Chi-restraints excluded: chain b residue 214 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.9980 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** c 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4873 r_free = 0.4873 target = 0.174878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4732 r_free = 0.4732 target = 0.162024 restraints weight = 5923.537| |-----------------------------------------------------------------------------| r_work (start): 0.4753 rms_B_bonded: 3.48 r_work: 0.4680 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.4680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.162 3402 Z= 1.116 Angle : 8.143 53.329 4104 Z= 2.861 Chirality : 0.120 0.424 270 Planarity : 0.011 0.042 594 Dihedral : 29.871 88.381 432 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 96.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.52 % Favored : 81.48 % Rotamer: Outliers : 2.47 % Allowed : 15.43 % Favored : 82.10 % Cbeta Deviations : 40.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 10.42 % 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: -5.97 (0.14), residues: 162 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.55 (0.11), residues: 162 Details of bonding type rmsd/Z covalent geometry : bond 0.02187 / 1.13 ( 3294) covalent geometry : angle 8.14346 / 2.86 ( 4104) hydrogen bonds : bond 0.15695 / 8.91 ( 8) hydrogen bonds : angle 10.42254 / 4.01 ( 24) Misc. bond : bond 0.00664 / 0.39 ( 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 31 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.057 Fit side-chains REVERT: Q 213 ASN cc_start: 0.7517 (p0) cc_final: 0.5709 (t0) REVERT: J 214 ASP cc_start: 0.6754 (p0) cc_final: 0.6270 (p0) REVERT: k 214 ASP cc_start: 0.6655 (p0) cc_final: 0.6199 (p0) REVERT: l 214 ASP cc_start: 0.6361 (p0) cc_final: 0.5695 (p0) outliers start: 4 outliers final: 4 residues processed: 29 average time/residue: 0.0266 time to fit residues: 1.1824 Evaluate side-chains 31 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 214 ASP Chi-restraints excluded: chain a residue 214 ASP Chi-restraints excluded: chain V residue 214 ASP Chi-restraints excluded: chain b residue 214 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.9980 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** c 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4873 r_free = 0.4873 target = 0.174878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4733 r_free = 0.4733 target = 0.161961 restraints weight = 5953.867| |-----------------------------------------------------------------------------| r_work (start): 0.4748 rms_B_bonded: 3.51 r_work: 0.4683 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.4683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.162 3402 Z= 1.116 Angle : 8.143 53.329 4104 Z= 2.861 Chirality : 0.120 0.424 270 Planarity : 0.011 0.042 594 Dihedral : 29.871 88.381 432 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 96.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.52 % Favored : 81.48 % Rotamer: Outliers : 2.47 % Allowed : 15.43 % Favored : 82.10 % Cbeta Deviations : 40.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 10.42 % 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: -5.97 (0.14), residues: 162 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.55 (0.11), residues: 162 Details of bonding type rmsd/Z covalent geometry : bond 0.02187 / 1.13 ( 3294) covalent geometry : angle 8.14346 / 2.86 ( 4104) hydrogen bonds : bond 0.15695 / 8.91 ( 8) hydrogen bonds : angle 10.42254 / 4.01 ( 24) Misc. bond : bond 0.00664 / 0.39 ( 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 31 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.095 Fit side-chains REVERT: Q 213 ASN cc_start: 0.7541 (p0) cc_final: 0.5719 (t0) REVERT: J 214 ASP cc_start: 0.6722 (p0) cc_final: 0.6241 (p0) REVERT: k 214 ASP cc_start: 0.6636 (p0) cc_final: 0.6184 (p0) REVERT: l 214 ASP cc_start: 0.6350 (p0) cc_final: 0.5674 (p0) outliers start: 4 outliers final: 4 residues processed: 29 average time/residue: 0.0307 time to fit residues: 1.3693 Evaluate side-chains 31 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 214 ASP Chi-restraints excluded: chain a residue 214 ASP Chi-restraints excluded: chain V residue 214 ASP Chi-restraints excluded: chain b residue 214 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** c 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4873 r_free = 0.4873 target = 0.174878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4732 r_free = 0.4732 target = 0.161922 restraints weight = 6019.553| |-----------------------------------------------------------------------------| r_work (start): 0.4749 rms_B_bonded: 3.54 r_work: 0.4681 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.4681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.162 3402 Z= 1.116 Angle : 8.143 53.329 4104 Z= 2.861 Chirality : 0.120 0.424 270 Planarity : 0.011 0.042 594 Dihedral : 29.871 88.381 432 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 96.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.52 % Favored : 81.48 % Rotamer: Outliers : 2.47 % Allowed : 15.43 % Favored : 82.10 % Cbeta Deviations : 40.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 10.42 % 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: -5.97 (0.14), residues: 162 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.55 (0.11), residues: 162 Details of bonding type rmsd/Z covalent geometry : bond 0.02187 / 1.13 ( 3294) covalent geometry : angle 8.14346 / 2.86 ( 4104) hydrogen bonds : bond 0.15695 / 8.91 ( 8) hydrogen bonds : angle 10.42254 / 4.01 ( 24) Misc. bond : bond 0.00664 / 0.39 ( 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 31 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.065 Fit side-chains REVERT: Q 213 ASN cc_start: 0.7544 (p0) cc_final: 0.5720 (t0) REVERT: J 214 ASP cc_start: 0.6729 (p0) cc_final: 0.6248 (p0) REVERT: k 214 ASP cc_start: 0.6638 (p0) cc_final: 0.6186 (p0) REVERT: l 214 ASP cc_start: 0.6353 (p0) cc_final: 0.5683 (p0) outliers start: 4 outliers final: 4 residues processed: 29 average time/residue: 0.0249 time to fit residues: 1.1408 Evaluate side-chains 31 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 214 ASP Chi-restraints excluded: chain a residue 214 ASP Chi-restraints excluded: chain V residue 214 ASP Chi-restraints excluded: chain b residue 214 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** c 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4873 r_free = 0.4873 target = 0.174878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.161895 restraints weight = 6088.934| |-----------------------------------------------------------------------------| r_work (start): 0.4749 rms_B_bonded: 3.55 r_work: 0.4680 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.4680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.162 3402 Z= 1.116 Angle : 8.143 53.329 4104 Z= 2.861 Chirality : 0.120 0.424 270 Planarity : 0.011 0.042 594 Dihedral : 29.871 88.381 432 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 96.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.52 % Favored : 81.48 % Rotamer: Outliers : 2.47 % Allowed : 15.43 % Favored : 82.10 % Cbeta Deviations : 40.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 10.42 % 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: -5.97 (0.14), residues: 162 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.55 (0.11), residues: 162 Details of bonding type rmsd/Z covalent geometry : bond 0.02187 / 1.13 ( 3294) covalent geometry : angle 8.14346 / 2.86 ( 4104) hydrogen bonds : bond 0.15695 / 8.91 ( 8) hydrogen bonds : angle 10.42254 / 4.01 ( 24) Misc. bond : bond 0.00664 / 0.39 ( 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 31 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.085 Fit side-chains REVERT: Q 213 ASN cc_start: 0.7558 (p0) cc_final: 0.5721 (t0) REVERT: J 214 ASP cc_start: 0.6759 (p0) cc_final: 0.6272 (p0) REVERT: k 214 ASP cc_start: 0.6652 (p0) cc_final: 0.6195 (p0) REVERT: l 214 ASP cc_start: 0.6359 (p0) cc_final: 0.5697 (p0) outliers start: 4 outliers final: 4 residues processed: 29 average time/residue: 0.0295 time to fit residues: 1.3563 Evaluate side-chains 31 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 214 ASP Chi-restraints excluded: chain a residue 214 ASP Chi-restraints excluded: chain V residue 214 ASP Chi-restraints excluded: chain b residue 214 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** c 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4873 r_free = 0.4873 target = 0.174878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.161889 restraints weight = 6085.129| |-----------------------------------------------------------------------------| r_work (start): 0.4749 rms_B_bonded: 3.55 r_work: 0.4677 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.4677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.162 3402 Z= 1.116 Angle : 8.143 53.329 4104 Z= 2.861 Chirality : 0.120 0.424 270 Planarity : 0.011 0.042 594 Dihedral : 29.871 88.381 432 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 96.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.52 % Favored : 81.48 % Rotamer: Outliers : 2.47 % Allowed : 15.43 % Favored : 82.10 % Cbeta Deviations : 40.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 10.42 % 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: -5.97 (0.14), residues: 162 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.55 (0.11), residues: 162 Details of bonding type rmsd/Z covalent geometry : bond 0.02187 / 1.13 ( 3294) covalent geometry : angle 8.14346 / 2.86 ( 4104) hydrogen bonds : bond 0.15695 / 8.91 ( 8) hydrogen bonds : angle 10.42254 / 4.01 ( 24) Misc. bond : bond 0.00664 / 0.39 ( 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 31 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.089 Fit side-chains REVERT: Q 213 ASN cc_start: 0.7550 (p0) cc_final: 0.5722 (t0) REVERT: J 214 ASP cc_start: 0.6766 (p0) cc_final: 0.6277 (p0) REVERT: k 214 ASP cc_start: 0.6655 (p0) cc_final: 0.6198 (p0) REVERT: l 214 ASP cc_start: 0.6365 (p0) cc_final: 0.5705 (p0) outliers start: 4 outliers final: 4 residues processed: 29 average time/residue: 0.0303 time to fit residues: 1.3753 Evaluate side-chains 31 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 214 ASP Chi-restraints excluded: chain a residue 214 ASP Chi-restraints excluded: chain V residue 214 ASP Chi-restraints excluded: chain b residue 214 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** c 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4873 r_free = 0.4873 target = 0.174878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4734 r_free = 0.4734 target = 0.161948 restraints weight = 5936.851| |-----------------------------------------------------------------------------| r_work (start): 0.4751 rms_B_bonded: 3.50 r_work: 0.4681 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.4681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.162 3402 Z= 1.116 Angle : 8.143 53.329 4104 Z= 2.861 Chirality : 0.120 0.424 270 Planarity : 0.011 0.042 594 Dihedral : 29.871 88.381 432 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 96.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.52 % Favored : 81.48 % Rotamer: Outliers : 2.47 % Allowed : 15.43 % Favored : 82.10 % Cbeta Deviations : 40.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 10.42 % 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: -5.97 (0.14), residues: 162 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.55 (0.11), residues: 162 Details of bonding type rmsd/Z covalent geometry : bond 0.02187 / 1.13 ( 3294) covalent geometry : angle 8.14346 / 2.86 ( 4104) hydrogen bonds : bond 0.15695 / 8.91 ( 8) hydrogen bonds : angle 10.42254 / 4.01 ( 24) Misc. bond : bond 0.00664 / 0.39 ( 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 31 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.093 Fit side-chains REVERT: Q 213 ASN cc_start: 0.7532 (p0) cc_final: 0.5718 (t0) REVERT: J 214 ASP cc_start: 0.6727 (p0) cc_final: 0.6247 (p0) REVERT: k 214 ASP cc_start: 0.6643 (p0) cc_final: 0.6191 (p0) REVERT: l 214 ASP cc_start: 0.6357 (p0) cc_final: 0.5682 (p0) outliers start: 4 outliers final: 4 residues processed: 29 average time/residue: 0.0326 time to fit residues: 1.4689 Evaluate side-chains 31 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 214 ASP Chi-restraints excluded: chain a residue 214 ASP Chi-restraints excluded: chain V residue 214 ASP Chi-restraints excluded: chain b residue 214 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.9990 overall best weight: 0.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** c 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4873 r_free = 0.4873 target = 0.174878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.161869 restraints weight = 6111.971| |-----------------------------------------------------------------------------| r_work (start): 0.4748 rms_B_bonded: 3.56 r_work: 0.4678 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.4678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.162 3402 Z= 1.116 Angle : 8.143 53.329 4104 Z= 2.861 Chirality : 0.120 0.424 270 Planarity : 0.011 0.042 594 Dihedral : 29.871 88.381 432 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 96.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.52 % Favored : 81.48 % Rotamer: Outliers : 2.47 % Allowed : 15.43 % Favored : 82.10 % Cbeta Deviations : 40.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 10.42 % 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: -5.97 (0.14), residues: 162 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.55 (0.11), residues: 162 Details of bonding type rmsd/Z covalent geometry : bond 0.02187 / 1.13 ( 3294) covalent geometry : angle 8.14346 / 2.86 ( 4104) hydrogen bonds : bond 0.15695 / 8.91 ( 8) hydrogen bonds : angle 10.42254 / 4.01 ( 24) Misc. bond : bond 0.00664 / 0.39 ( 108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 603.58 seconds wall clock time: 11 minutes 7.90 seconds (667.90 seconds total)