Starting phenix.real_space_refine on Fri Mar 6 15:14:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xxf_33501/03_2026/7xxf_33501.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xxf_33501/03_2026/7xxf_33501.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xxf_33501/03_2026/7xxf_33501.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xxf_33501/03_2026/7xxf_33501.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xxf_33501/03_2026/7xxf_33501.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xxf_33501/03_2026/7xxf_33501.map" } resolution = 2.24 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= 0.007 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: 7 Type Number sf(0) Gaussians Fe 5 7.16 5 P 37 5.49 5 Mg 36 5.21 5 S 116 5.16 5 C 20373 2.51 5 N 4137 2.21 5 O 5122 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29826 Number of models: 1 Model: "" Number of chains: 120 Chain: "C" Number of atoms: 2655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2655 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 316} Chain: "L" Number of atoms: 2177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2177 Classifications: {'peptide': 274} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 258} Chain: "M" Number of atoms: 2550 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 320, 2543 Classifications: {'peptide': 320} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 300} Conformer: "B" Number of residues, atoms: 320, 2543 Classifications: {'peptide': 320} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 300} bond proxies already assigned to first conformer: 2637 Chain: "H" Number of atoms: 2000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2000 Classifications: {'peptide': 258} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 21, 'TRANS': 233} Chain: "A" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 384 Classifications: {'peptide': 45} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 42} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'FME:plan-2': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 396 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "D" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 384 Classifications: {'peptide': 45} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 42} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'FME:plan-2': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 396 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "F" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 384 Classifications: {'peptide': 45} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 42} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'FME:plan-2': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "G" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 396 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "I" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 394 Classifications: {'peptide': 46} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 43} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'FME:plan-2': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "J" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 396 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "K" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 384 Classifications: {'peptide': 45} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 42} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'FME:plan-2': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "N" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 396 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "O" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 389 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 396 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "Q" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 389 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 396 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "S" Number of atoms: 475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 475 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 396 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "U" Number of atoms: 443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 443 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "V" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 396 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "W" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 470 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "X" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 396 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "Y" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 384 Classifications: {'peptide': 45} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 42} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'FME:plan-2': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "Z" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 396 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "1" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 395 Classifications: {'peptide': 46} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 43} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'FME:plan-2': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "2" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 396 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "3" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 472 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 51} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "4" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 396 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "5" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 389 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "6" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 396 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "7" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 389 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "8" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 396 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "9" Number of atoms: 392 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 45, 384 Classifications: {'peptide': 45} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 42} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'FME:plan-2': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 45, 384 Classifications: {'peptide': 45} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 42} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'FME:plan-2': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 388 Chain: "0" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 396 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "a" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 177 Classifications: {'peptide': 22} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "b" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 177 Classifications: {'peptide': 22} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "c" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 177 Classifications: {'peptide': 22} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "d" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 177 Classifications: {'peptide': 22} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "e" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 177 Classifications: {'peptide': 22} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "f" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 177 Classifications: {'peptide': 22} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "g" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 177 Classifications: {'peptide': 22} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "h" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 177 Classifications: {'peptide': 22} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "i" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 177 Classifications: {'peptide': 22} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "j" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 177 Classifications: {'peptide': 22} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "k" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 177 Classifications: {'peptide': 22} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 296 Unusual residues: {'HEC': 4, 'PGV': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 539 Unusual residues: {'BCL': 2, 'BPH': 1, 'LMT': 2, 'PGV': 5, 'U10': 3} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 150 Planarities with less than four sites: {'U10:plan-6': 3, 'U10:plan-7': 3, 'U10:plan-8': 3, 'U10:plan-9': 3, 'U10:plan-10': 3, 'U10:plan-11': 3, 'PGV:plan-3': 5, 'U10:plan-2': 1, 'U10:plan-3': 1, 'U10:plan-4': 1, 'U10:plan-5': 1} Unresolved non-hydrogen planarities: 101 Chain: "M" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 514 Unusual residues: {' FE': 1, 'BCL': 2, 'BPH': 1, 'CDL': 2, 'I7D': 1, 'MQ9': 1, 'PEE': 1, 'PGV': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 134 Planarities with less than four sites: {'MQ9:plan-3': 1, 'MQ9:plan-4': 1, 'MQ9:plan-5': 1, 'MQ9:plan-6': 1, 'CDL:plan-4': 1, 'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 26 Chain: "H" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 144 Unusual residues: {'CDL': 1, 'PGV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 58 Planarities with less than four sites: {'PGV:plan-3': 2} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 169 Unusual residues: {'BCL': 1, 'CDL': 1, 'I7D': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 42 Chain: "B" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 144 Unusual residues: {'BCL': 1, 'I7D': 1, 'PGV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 111 Unusual residues: {'BCL': 1, 'I7D': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 105 Unusual residues: {'BCL': 1, 'PGV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 144 Unusual residues: {'BCL': 1, 'I7D': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "J" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'I7D': 1, 'PGV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 111 Unusual residues: {'BCL': 1, 'I7D': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 111 Unusual residues: {'BCL': 1, 'I7D': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 111 Unusual residues: {'BCL': 1, 'I7D': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 183 Unusual residues: {'BCL': 1, 'CDL': 1, 'I7D': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Chain: "U" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 111 Unusual residues: {'BCL': 1, 'I7D': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 111 Unusual residues: {'BCL': 1, 'I7D': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 146 Unusual residues: {'BCL': 1, 'I7D': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "2" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 138 Unusual residues: {'BCL': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Chain: "3" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 142 Unusual residues: {'BCL': 1, 'I7D': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "4" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 111 Unusual residues: {'BCL': 1, 'I7D': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "5" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 177 Unusual residues: {'BCL': 1, 'PGV': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PGV:plan-3': 2} Unresolved non-hydrogen planarities: 6 Chain: "6" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 243 Unusual residues: {'BCL': 1, 'CDL': 2, 'I7D': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 68 Chain: "7" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 129 Unusual residues: {'BCL': 1, 'U10': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "8" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 111 Unusual residues: {'BCL': 1, 'I7D': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "9" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "0" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 129 Unusual residues: {'BCL': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 37 Chain: "C" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 136 Classifications: {'water': 136} Link IDs: {None: 135} Chain: "L" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 65 Classifications: {'water': 65} Link IDs: {None: 64} Chain: "M" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Chain: "H" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "O" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "P" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "Q" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "R" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "S" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "T" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "U" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "V" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "W" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "X" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "Y" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "Z" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "1" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "2" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "3" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "4" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "5" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "6" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "7" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "8" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "9" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "0" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AVAL M 58 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BVAL M 58 " occ=0.50 residue: pdb=" N ALEU 9 6 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU 9 6 " occ=0.50 Time building chain proxies: 7.43, per 1000 atoms: 0.25 Number of scatterers: 29826 At special positions: 0 Unit cell: (133.66, 133.66, 142.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 5 26.01 S 116 16.00 P 37 15.00 Mg 36 11.99 O 5122 8.00 N 4137 7.00 C 20373 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS M 170 " - pdb=" SG CYS M 172 " distance=2.04 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=48, symmetry=0 Number of additional bonds: simple=48, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.80 Conformation dependent library (CDL) restraints added in 1.2 seconds 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5570 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 10 sheets defined 65.9% alpha, 2.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'C' and resid 2 through 27 Processing helix chain 'C' and resid 49 through 60 Processing helix chain 'C' and resid 75 through 80 Processing helix chain 'C' and resid 90 through 106 Processing helix chain 'C' and resid 109 through 114 removed outlier: 3.721A pdb=" N GLY C 112 " --> pdb=" O GLN C 109 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N CYS C 114 " --> pdb=" O CYS C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 145 removed outlier: 3.604A pdb=" N VAL C 129 " --> pdb=" O LYS C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 150 Processing helix chain 'C' and resid 158 through 164 removed outlier: 4.232A pdb=" N CYS C 162 " --> pdb=" O VAL C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 200 Processing helix chain 'C' and resid 208 through 214 removed outlier: 3.650A pdb=" N PHE C 212 " --> pdb=" O PRO C 208 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 253 removed outlier: 3.914A pdb=" N TRP C 240 " --> pdb=" O LYS C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 259 Processing helix chain 'C' and resid 273 through 292 removed outlier: 3.663A pdb=" N ARG C 283 " --> pdb=" O TRP C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 297 Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 315 through 321 removed outlier: 4.141A pdb=" N CYS C 319 " --> pdb=" O TRP C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 330 Processing helix chain 'C' and resid 336 through 340 Processing helix chain 'L' and resid 6 through 11 removed outlier: 3.999A pdb=" N LYS L 9 " --> pdb=" O PHE L 6 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 23 removed outlier: 4.258A pdb=" N LEU L 22 " --> pdb=" O GLY L 19 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE L 23 " --> pdb=" O GLY L 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 19 through 23' Processing helix chain 'L' and resid 32 through 57 Processing helix chain 'L' and resid 71 through 75 Processing helix chain 'L' and resid 80 through 83 Processing helix chain 'L' and resid 84 through 112 Processing helix chain 'L' and resid 116 through 134 removed outlier: 3.820A pdb=" N PHE L 124 " --> pdb=" O PHE L 120 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA L 125 " --> pdb=" O ALA L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 141 Processing helix chain 'L' and resid 142 through 146 Processing helix chain 'L' and resid 152 through 164 removed outlier: 3.590A pdb=" N ASP L 156 " --> pdb=" O LEU L 152 " (cutoff:3.500A) Processing helix chain 'L' and resid 165 through 166 No H-bonds generated for 'chain 'L' and resid 165 through 166' Processing helix chain 'L' and resid 167 through 170 Processing helix chain 'L' and resid 171 through 200 Processing helix chain 'L' and resid 209 through 222 removed outlier: 3.832A pdb=" N PHE L 217 " --> pdb=" O GLU L 213 " (cutoff:3.500A) Processing helix chain 'L' and resid 226 through 251 removed outlier: 3.529A pdb=" N HIS L 231 " --> pdb=" O THR L 227 " (cutoff:3.500A) Processing helix chain 'L' and resid 259 through 264 removed outlier: 3.794A pdb=" N TRP L 263 " --> pdb=" O GLY L 259 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N TRP L 264 " --> pdb=" O TRP L 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 259 through 264' Processing helix chain 'L' and resid 264 through 269 Processing helix chain 'M' and resid 37 through 44 removed outlier: 4.225A pdb=" N ILE M 43 " --> pdb=" O LEU M 39 " (cutoff:3.500A) Processing helix chain 'M' and resid 54 through 79 removed outlier: 3.509A pdb=" N VAL M 79 " --> pdb=" O MET M 75 " (cutoff:3.500A) Processing helix chain 'M' and resid 82 through 90 Processing helix chain 'M' and resid 99 through 103 Processing helix chain 'M' and resid 108 through 111 Processing helix chain 'M' and resid 112 through 140 Processing helix chain 'M' and resid 144 through 162 Processing helix chain 'M' and resid 162 through 169 Processing helix chain 'M' and resid 170 through 174 removed outlier: 3.557A pdb=" N GLU M 173 " --> pdb=" O CYS M 170 " (cutoff:3.500A) Processing helix chain 'M' and resid 179 through 193 Processing helix chain 'M' and resid 195 through 198 Processing helix chain 'M' and resid 199 through 226 Processing helix chain 'M' and resid 227 through 230 Processing helix chain 'M' and resid 233 through 240 Processing helix chain 'M' and resid 242 through 257 Processing helix chain 'M' and resid 263 through 287 removed outlier: 4.039A pdb=" N THR M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 301 Processing helix chain 'M' and resid 316 through 321 removed outlier: 4.045A pdb=" N LEU M 320 " --> pdb=" O ASP M 316 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA M 321 " --> pdb=" O PRO M 317 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 316 through 321' Processing helix chain 'H' and resid 11 through 36 Processing helix chain 'H' and resid 104 through 108 Processing helix chain 'H' and resid 110 through 114 Processing helix chain 'H' and resid 197 through 199 No H-bonds generated for 'chain 'H' and resid 197 through 199' Processing helix chain 'H' and resid 214 through 219 removed outlier: 3.903A pdb=" N LEU H 219 " --> pdb=" O GLY H 215 " (cutoff:3.500A) Processing helix chain 'H' and resid 231 through 244 Processing helix chain 'H' and resid 244 through 249 Processing helix chain 'H' and resid 250 through 255 removed outlier: 3.822A pdb=" N GLN H 254 " --> pdb=" O THR H 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 7 Processing helix chain 'A' and resid 9 through 35 Processing helix chain 'B' and resid 12 through 45 Processing helix chain 'D' and resid 1 through 7 Processing helix chain 'D' and resid 9 through 35 Processing helix chain 'E' and resid 12 through 45 Processing helix chain 'F' and resid 1 through 7 removed outlier: 3.827A pdb=" N TRP F 5 " --> pdb=" O TRP F 2 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 35 Processing helix chain 'G' and resid 12 through 45 Processing helix chain 'I' and resid 1 through 7 Processing helix chain 'I' and resid 9 through 35 Processing helix chain 'J' and resid 12 through 45 Processing helix chain 'K' and resid 2 through 7 Processing helix chain 'K' and resid 9 through 35 Processing helix chain 'N' and resid 12 through 45 Processing helix chain 'O' and resid 3 through 8 removed outlier: 3.661A pdb=" N LEU O 7 " --> pdb=" O ARG O 3 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 34 Processing helix chain 'P' and resid 12 through 45 Processing helix chain 'Q' and resid 3 through 8 removed outlier: 3.842A pdb=" N LEU Q 7 " --> pdb=" O ARG Q 3 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 34 Processing helix chain 'R' and resid 12 through 45 Processing helix chain 'S' and resid 1 through 7 Processing helix chain 'S' and resid 9 through 34 Processing helix chain 'T' and resid 12 through 45 removed outlier: 3.564A pdb=" N PHE T 19 " --> pdb=" O GLU T 15 " (cutoff:3.500A) Processing helix chain 'U' and resid 9 through 35 Processing helix chain 'V' and resid 12 through 45 removed outlier: 3.714A pdb=" N LYS V 17 " --> pdb=" O GLU V 13 " (cutoff:3.500A) Processing helix chain 'W' and resid 3 through 8 removed outlier: 3.509A pdb=" N LEU W 7 " --> pdb=" O ARG W 3 " (cutoff:3.500A) Processing helix chain 'W' and resid 9 through 35 Processing helix chain 'X' and resid 12 through 45 Processing helix chain 'Y' and resid 1 through 7 removed outlier: 3.513A pdb=" N MET Y 4 " --> pdb=" O FME Y 1 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TRP Y 5 " --> pdb=" O TRP Y 2 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 35 removed outlier: 3.543A pdb=" N THR Y 35 " --> pdb=" O ILE Y 31 " (cutoff:3.500A) Processing helix chain 'Z' and resid 12 through 45 removed outlier: 3.811A pdb=" N THR Z 25 " --> pdb=" O GLY Z 21 " (cutoff:3.500A) Processing helix chain '1' and resid 1 through 7 Processing helix chain '1' and resid 9 through 35 Processing helix chain '2' and resid 12 through 45 removed outlier: 3.613A pdb=" N LYS 2 17 " --> pdb=" O GLU 2 13 " (cutoff:3.500A) Processing helix chain '3' and resid 1 through 7 Processing helix chain '3' and resid 9 through 34 Processing helix chain '4' and resid 12 through 45 Processing helix chain '5' and resid 1 through 7 Processing helix chain '5' and resid 9 through 34 Processing helix chain '6' and resid 12 through 45 Processing helix chain '7' and resid 1 through 7 Processing helix chain '7' and resid 9 through 12 Processing helix chain '7' and resid 13 through 35 Processing helix chain '8' and resid 12 through 45 Processing helix chain '9' and resid 1 through 7 removed outlier: 3.569A pdb=" N MET 9 4 " --> pdb=" O FME 9 1 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TRP 9 5 " --> pdb=" O TRP 9 2 " (cutoff:3.500A) Processing helix chain '9' and resid 9 through 34 Processing helix chain '0' and resid 12 through 45 Processing helix chain 'a' and resid 2 through 21 Proline residue: a 12 - end of helix removed outlier: 3.748A pdb=" N ARG a 21 " --> pdb=" O VAL a 17 " (cutoff:3.500A) Processing helix chain 'b' and resid 2 through 22 Proline residue: b 12 - end of helix Processing helix chain 'c' and resid 2 through 20 removed outlier: 3.628A pdb=" N ILE c 8 " --> pdb=" O VAL c 4 " (cutoff:3.500A) Proline residue: c 12 - end of helix Processing helix chain 'd' and resid 2 through 21 removed outlier: 3.720A pdb=" N ILE d 8 " --> pdb=" O VAL d 4 " (cutoff:3.500A) Proline residue: d 12 - end of helix Processing helix chain 'e' and resid 2 through 19 Proline residue: e 12 - end of helix Processing helix chain 'f' and resid 2 through 22 Proline residue: f 12 - end of helix Processing helix chain 'g' and resid 2 through 22 removed outlier: 3.518A pdb=" N ILE g 8 " --> pdb=" O VAL g 4 " (cutoff:3.500A) Proline residue: g 12 - end of helix removed outlier: 4.138A pdb=" N GLN g 22 " --> pdb=" O LEU g 18 " (cutoff:3.500A) Processing helix chain 'h' and resid 2 through 21 removed outlier: 3.705A pdb=" N ILE h 8 " --> pdb=" O VAL h 4 " (cutoff:3.500A) Proline residue: h 12 - end of helix Processing helix chain 'i' and resid 2 through 20 removed outlier: 3.514A pdb=" N ILE i 8 " --> pdb=" O VAL i 4 " (cutoff:3.500A) Proline residue: i 12 - end of helix Processing helix chain 'j' and resid 2 through 21 removed outlier: 3.632A pdb=" N ILE j 8 " --> pdb=" O VAL j 4 " (cutoff:3.500A) Proline residue: j 12 - end of helix Processing helix chain 'k' and resid 2 through 20 removed outlier: 3.827A pdb=" N ILE k 8 " --> pdb=" O VAL k 4 " (cutoff:3.500A) Proline residue: k 12 - end of helix removed outlier: 3.584A pdb=" N VAL k 17 " --> pdb=" O ALA k 13 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 33 through 36 Processing sheet with id=AA2, first strand: chain 'L' and resid 26 through 27 Processing sheet with id=AA3, first strand: chain 'M' and resid 13 through 14 Processing sheet with id=AA4, first strand: chain 'M' and resid 35 through 36 Processing sheet with id=AA5, first strand: chain 'M' and resid 94 through 95 Processing sheet with id=AA6, first strand: chain 'H' and resid 42 through 43 Processing sheet with id=AA7, first strand: chain 'H' and resid 61 through 64 Processing sheet with id=AA8, first strand: chain 'H' and resid 87 through 89 Processing sheet with id=AA9, first strand: chain 'H' and resid 133 through 135 removed outlier: 5.688A pdb=" N ILE H 167 " --> pdb=" O LYS H 185 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N LYS H 185 " --> pdb=" O ILE H 167 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ASP H 173 " --> pdb=" O VAL H 179 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL H 179 " --> pdb=" O ASP H 173 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 133 through 135 removed outlier: 3.606A pdb=" N GLY H 165 " --> pdb=" O LEU H 156 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ASP H 155 " --> pdb=" O VAL H 208 " (cutoff:3.500A) 1494 hydrogen bonds defined for protein. 4228 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.16 Time building geometry restraints manager: 3.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.38: 10270 1.38 - 1.56: 19664 1.56 - 1.74: 74 1.74 - 1.93: 222 1.93 - 2.11: 156 Bond restraints: 30386 Sorted by residual: bond pdb=" CA7 CDL H 303 " pdb=" OA8 CDL H 303 " ideal model delta sigma weight residual 1.334 1.455 -0.121 1.10e-02 8.26e+03 1.22e+02 bond pdb=" CA7 CDL A 101 " pdb=" OA8 CDL A 101 " ideal model delta sigma weight residual 1.334 1.455 -0.121 1.10e-02 8.26e+03 1.21e+02 bond pdb=" CA7 CDL 0 101 " pdb=" OA8 CDL 0 101 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.10e-02 8.26e+03 1.19e+02 bond pdb=" CA7 CDL 6 101 " pdb=" OA8 CDL 6 101 " ideal model delta sigma weight residual 1.334 1.453 -0.119 1.10e-02 8.26e+03 1.18e+02 bond pdb=" CA7 CDL 6 104 " pdb=" OA8 CDL 6 104 " ideal model delta sigma weight residual 1.334 1.453 -0.119 1.10e-02 8.26e+03 1.17e+02 ... (remaining 30381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.77: 39279 3.77 - 7.54: 2039 7.54 - 11.31: 316 11.31 - 15.08: 87 15.08 - 18.85: 14 Bond angle restraints: 41735 Sorted by residual: angle pdb=" C1D BCL O 101 " pdb=" C2D BCL O 101 " pdb=" CMD BCL O 101 " ideal model delta sigma weight residual 125.57 139.35 -13.77 1.83e+00 2.99e-01 5.68e+01 angle pdb=" C1D BCL L 301 " pdb=" C2D BCL L 301 " pdb=" CMD BCL L 301 " ideal model delta sigma weight residual 125.57 139.24 -13.67 1.83e+00 2.99e-01 5.59e+01 angle pdb=" C1D BCL W 101 " pdb=" C2D BCL W 101 " pdb=" CMD BCL W 101 " ideal model delta sigma weight residual 125.57 139.16 -13.59 1.83e+00 2.99e-01 5.52e+01 angle pdb=" C1D BCL M 403 " pdb=" C2D BCL M 403 " pdb=" CMD BCL M 403 " ideal model delta sigma weight residual 125.57 139.15 -13.57 1.83e+00 2.99e-01 5.51e+01 angle pdb=" C1D BCL S 101 " pdb=" C2D BCL S 101 " pdb=" CMD BCL S 101 " ideal model delta sigma weight residual 125.57 139.08 -13.50 1.83e+00 2.99e-01 5.46e+01 ... (remaining 41730 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.51: 16176 35.51 - 71.03: 738 71.03 - 106.54: 100 106.54 - 142.05: 59 142.05 - 177.57: 23 Dihedral angle restraints: 17096 sinusoidal: 8511 harmonic: 8585 Sorted by residual: dihedral pdb=" C1 BCL Z 101 " pdb=" CGA BCL Z 101 " pdb=" O2A BCL Z 101 " pdb=" CBA BCL Z 101 " ideal model delta sinusoidal sigma weight residual 180.00 131.90 48.10 1 6.00e+00 2.78e-02 8.86e+01 dihedral pdb=" C1 BCL X 102 " pdb=" CGA BCL X 102 " pdb=" O2A BCL X 102 " pdb=" CBA BCL X 102 " ideal model delta sinusoidal sigma weight residual 180.00 137.16 42.84 1 6.00e+00 2.78e-02 7.11e+01 dihedral pdb=" CBD BCL L 301 " pdb=" CGD BCL L 301 " pdb=" O2D BCL L 301 " pdb=" CED BCL L 301 " ideal model delta sinusoidal sigma weight residual 180.00 146.92 33.08 1 5.00e+00 4.00e-02 6.23e+01 ... (remaining 17093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 3530 0.058 - 0.116: 547 0.116 - 0.174: 130 0.174 - 0.232: 12 0.232 - 0.290: 19 Chirality restraints: 4238 Sorted by residual: chirality pdb=" C05 PGV H 302 " pdb=" C04 PGV H 302 " pdb=" C06 PGV H 302 " pdb=" O05 PGV H 302 " both_signs ideal model delta sigma weight residual False 2.29 2.58 -0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" C05 PGV L 311 " pdb=" C04 PGV L 311 " pdb=" C06 PGV L 311 " pdb=" O05 PGV L 311 " both_signs ideal model delta sigma weight residual False 2.29 2.58 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" C05 PGV L 305 " pdb=" C04 PGV L 305 " pdb=" C06 PGV L 305 " pdb=" O05 PGV L 305 " both_signs ideal model delta sigma weight residual False 2.29 2.58 -0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 4235 not shown) Planarity restraints: 4949 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C33 I7D N 101 " 0.131 2.00e-02 2.50e+03 2.24e-01 5.00e+02 pdb=" C35 I7D N 101 " -0.290 2.00e-02 2.50e+03 pdb=" C36 I7D N 101 " 0.287 2.00e-02 2.50e+03 pdb=" C37 I7D N 101 " -0.128 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL Z 101 " 0.301 3.00e-02 1.11e+03 2.40e-01 3.21e+02 pdb=" CBA BCL Z 101 " 0.190 3.00e-02 1.11e+03 pdb=" CGA BCL Z 101 " -0.072 3.00e-02 1.11e+03 pdb=" O1A BCL Z 101 " -0.024 3.00e-02 1.11e+03 pdb=" O2A BCL Z 101 " -0.396 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL X 102 " 0.277 3.00e-02 1.11e+03 2.20e-01 2.69e+02 pdb=" CBA BCL X 102 " 0.181 3.00e-02 1.11e+03 pdb=" CGA BCL X 102 " -0.065 3.00e-02 1.11e+03 pdb=" O1A BCL X 102 " -0.035 3.00e-02 1.11e+03 pdb=" O2A BCL X 102 " -0.357 3.00e-02 1.11e+03 ... (remaining 4946 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 360 2.59 - 3.17: 23701 3.17 - 3.75: 51653 3.75 - 4.32: 76372 4.32 - 4.90: 119088 Nonbonded interactions: 271174 Sorted by model distance: nonbonded pdb=" NE2 HIS C 148 " pdb="FE HEC C 404 " model vdw 2.014 3.080 nonbonded pdb=" OE2 GLU M 234 " pdb="FE FE M 401 " model vdw 2.037 2.260 nonbonded pdb=" NE2 HIS L 191 " pdb="FE FE M 401 " model vdw 2.055 2.340 nonbonded pdb=" SD MET C 134 " pdb="FE HEC C 402 " model vdw 2.075 3.360 nonbonded pdb=" OE1 GLU M 234 " pdb="FE FE M 401 " model vdw 2.078 2.260 ... (remaining 271169 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' and resid 7 through 56) selection = (chain '2' and resid 7 through 56) selection = (chain '4' and resid 7 through 56) selection = (chain '6' and resid 7 through 56) selection = (chain '8' and resid 7 through 56) selection = (chain 'B' and resid 7 through 56) selection = (chain 'E' and resid 7 through 56) selection = (chain 'G' and resid 7 through 56) selection = (chain 'J' and resid 7 through 56) selection = (chain 'N' and resid 7 through 56) selection = (chain 'P' and resid 7 through 56) selection = (chain 'R' and resid 7 through 56) selection = (chain 'T' and resid 7 through 56) selection = (chain 'V' and resid 7 through 56) selection = (chain 'X' and resid 7 through 56) selection = (chain 'Z' and resid 7 through 56) } ncs_group { reference = (chain '1' and (resid 1 through 5 or resid 7 through 45)) selection = (chain '5' and (resid 1 through 5 or resid 7 through 44 or (resid 45 and (name N \ or name CA or name C or name O or name CB )))) selection = (chain '7' and (resid 1 through 5 or resid 7 through 44 or (resid 45 and (name N \ or name CA or name C or name O or name CB )))) selection = (chain '9' and (resid 1 through 5 or resid 7 through 45)) selection = (chain 'A' and (resid 1 through 5 or resid 7 through 45)) selection = (chain 'D' and (resid 1 through 5 or resid 7 through 45)) selection = (chain 'F' and (resid 1 through 5 or resid 7 through 45)) selection = (chain 'I' and (resid 1 through 5 or resid 7 through 44 or (resid 45 and (name N \ or name CA or name C or name O or name CB )))) selection = (chain 'K' and (resid 1 through 5 or resid 7 through 45)) selection = (chain 'O' and (resid 1 through 5 or resid 7 through 44 or (resid 45 and (name N \ or name CA or name C or name O or name CB )))) selection = (chain 'Q' and (resid 1 through 5 or resid 7 through 44 or (resid 45 and (name N \ or name CA or name C or name O or name CB )))) selection = (chain 'U' and (resid 1 through 5 or resid 7 through 44 or (resid 45 and (name N \ or name CA or name C or name O or name CB )))) selection = (chain 'Y' and (resid 1 through 5 or resid 7 through 45)) } ncs_group { reference = (chain '3' and resid 1 through 58) selection = (chain 'S' and (resid 1 through 45 or resid 50 through 58)) } ncs_group { reference = 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=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: 6.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 26.450 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.090 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:6.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 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 : 0.021 0.281 30435 Z= 1.148 Angle : 1.770 18.845 41737 Z= 0.778 Chirality : 0.050 0.290 4238 Planarity : 0.017 0.240 4949 Dihedral : 21.325 177.566 11523 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.31 % Allowed : 3.88 % Favored : 94.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % 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: 1.59 (0.15), residues: 2887 helix: 1.81 (0.12), residues: 1789 sheet: 0.30 (0.70), residues: 58 loop : -0.18 (0.20), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 132 TYR 0.021 0.001 TYR L 165 PHE 0.015 0.001 PHE M 8 TRP 0.018 0.002 TRP C 315 HIS 0.007 0.001 HIS C 260 Details of bonding type rmsd covalent geometry : bond 0.01926 (30386) covalent geometry : angle 1.76959 (41735) SS BOND : bond 0.00651 ( 1) SS BOND : angle 1.22048 ( 2) hydrogen bonds : bond 0.18522 ( 1492) hydrogen bonds : angle 5.83227 ( 4228) Misc. bond : bond 0.18645 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 353 time to evaluate : 0.867 Fit side-chains REVERT: L 82 ARG cc_start: 0.8662 (mtm110) cc_final: 0.8351 (mtm-85) REVERT: H 185 LYS cc_start: 0.8837 (tptm) cc_final: 0.8547 (tmtm) REVERT: B 17 LYS cc_start: 0.8113 (mmmt) cc_final: 0.7752 (mttm) REVERT: F 7 LEU cc_start: 0.8531 (mt) cc_final: 0.8322 (mm) REVERT: I 12 ARG cc_start: 0.6486 (mmp80) cc_final: 0.6144 (mmm160) REVERT: K 3 ARG cc_start: 0.7087 (OUTLIER) cc_final: 0.6708 (mtt90) REVERT: Y 3 ARG cc_start: 0.7317 (mtt90) cc_final: 0.7103 (mtt-85) REVERT: 1 5 TRP cc_start: 0.8374 (m100) cc_final: 0.8148 (m100) REVERT: 1 12 ARG cc_start: 0.7295 (mpt90) cc_final: 0.6850 (mtm180) REVERT: 2 25 THR cc_start: 0.8517 (t) cc_final: 0.8268 (p) REVERT: 4 17 LYS cc_start: 0.7514 (OUTLIER) cc_final: 0.7080 (mtmm) REVERT: 8 18 GLU cc_start: 0.8019 (tt0) cc_final: 0.7568 (tt0) REVERT: 8 23 PHE cc_start: 0.7360 (t80) cc_final: 0.7153 (t80) REVERT: 9 4 MET cc_start: 0.7461 (ptt) cc_final: 0.7085 (ptm) REVERT: k 5 TRP cc_start: 0.6254 (OUTLIER) cc_final: 0.5375 (p90) outliers start: 31 outliers final: 19 residues processed: 371 average time/residue: 0.7041 time to fit residues: 305.4274 Evaluate side-chains 329 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 307 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 166 LEU Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain M residue 262 PHE Chi-restraints excluded: chain M residue 287 THR Chi-restraints excluded: chain M residue 314 VAL Chi-restraints excluded: chain H residue 236 ASP Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain O residue 45 HIS Chi-restraints excluded: chain W residue 9 ASP Chi-restraints excluded: chain Y residue 42 ASP Chi-restraints excluded: chain 4 residue 17 LYS Chi-restraints excluded: chain 4 residue 22 ILE Chi-restraints excluded: chain a residue 5 TRP Chi-restraints excluded: chain c residue 5 TRP Chi-restraints excluded: chain d residue 5 TRP Chi-restraints excluded: chain e residue 5 TRP Chi-restraints excluded: chain f residue 5 TRP Chi-restraints excluded: chain g residue 5 TRP Chi-restraints excluded: chain j residue 5 TRP Chi-restraints excluded: chain k residue 5 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 181 GLN H 69 GLN H 104 ASN H 229 GLN V 43 GLN W 45 HIS Z 20 HIS Z 43 GLN 8 43 GLN 0 43 GLN c 22 GLN g 22 GLN h 22 GLN k 22 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.122899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.087946 restraints weight = 52546.694| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.79 r_work: 0.2763 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2629 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2629 r_free = 0.2629 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2627 r_free = 0.2627 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2627 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.323 30435 Z= 0.225 Angle : 0.803 15.715 41737 Z= 0.331 Chirality : 0.043 0.194 4238 Planarity : 0.005 0.070 4949 Dihedral : 22.745 179.762 6402 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.57 % Allowed : 7.27 % Favored : 90.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % 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: 1.96 (0.16), residues: 2887 helix: 2.32 (0.12), residues: 1723 sheet: 0.38 (0.74), residues: 53 loop : -0.28 (0.19), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 3 TYR 0.024 0.002 TYR L 165 PHE 0.024 0.002 PHE H 20 TRP 0.020 0.002 TRP U 2 HIS 0.011 0.002 HIS Y 29 Details of bonding type rmsd covalent geometry : bond 0.00536 (30386) covalent geometry : angle 0.80347 (41735) SS BOND : bond 0.00669 ( 1) SS BOND : angle 0.93582 ( 2) hydrogen bonds : bond 0.05797 ( 1492) hydrogen bonds : angle 4.36627 ( 4228) Misc. bond : bond 0.07657 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 319 time to evaluate : 1.004 Fit side-chains REVERT: L 82 ARG cc_start: 0.8849 (mtm110) cc_final: 0.8365 (mtm-85) REVERT: H 128 THR cc_start: 0.6828 (m) cc_final: 0.6504 (p) REVERT: H 166 LYS cc_start: 0.8575 (mtpt) cc_final: 0.8133 (mtpp) REVERT: H 185 LYS cc_start: 0.8905 (tptm) cc_final: 0.8473 (tmtm) REVERT: B 17 LYS cc_start: 0.8131 (mmmt) cc_final: 0.7925 (mmtm) REVERT: F 7 LEU cc_start: 0.8444 (mt) cc_final: 0.8231 (mm) REVERT: I 12 ARG cc_start: 0.6595 (mmp80) cc_final: 0.5942 (mmm-85) REVERT: K 3 ARG cc_start: 0.7117 (OUTLIER) cc_final: 0.6613 (mtt90) REVERT: N 17 LYS cc_start: 0.7453 (mttm) cc_final: 0.7110 (mtpm) REVERT: O 3 ARG cc_start: 0.8019 (mtt-85) cc_final: 0.7784 (mtm-85) REVERT: P 43 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8110 (mp10) REVERT: R 18 GLU cc_start: 0.8033 (tt0) cc_final: 0.7733 (tt0) REVERT: Y 6 LEU cc_start: 0.8024 (mt) cc_final: 0.7809 (mm) REVERT: 1 12 ARG cc_start: 0.7506 (mpt90) cc_final: 0.6769 (mtm180) REVERT: 2 25 THR cc_start: 0.8323 (t) cc_final: 0.7940 (p) REVERT: 2 43 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.7382 (mp10) REVERT: 3 3 ARG cc_start: 0.7352 (OUTLIER) cc_final: 0.7149 (mmm160) REVERT: 3 11 ARG cc_start: 0.7082 (mtt180) cc_final: 0.6830 (mtp-110) REVERT: 4 17 LYS cc_start: 0.7391 (OUTLIER) cc_final: 0.6996 (mtpt) REVERT: 8 18 GLU cc_start: 0.7937 (tt0) cc_final: 0.7524 (tt0) REVERT: 8 23 PHE cc_start: 0.7331 (t80) cc_final: 0.6470 (m-80) REVERT: 9 4 MET cc_start: 0.7845 (ptt) cc_final: 0.7541 (ptm) REVERT: g 3 MET cc_start: 0.6208 (OUTLIER) cc_final: 0.6004 (ptm) REVERT: k 5 TRP cc_start: 0.6482 (OUTLIER) cc_final: 0.5221 (p90) REVERT: k 6 MET cc_start: 0.5729 (OUTLIER) cc_final: 0.5382 (mtm) outliers start: 62 outliers final: 32 residues processed: 349 average time/residue: 0.6564 time to fit residues: 269.0633 Evaluate side-chains 343 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 303 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 62 ILE Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 166 LEU Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain M residue 262 PHE Chi-restraints excluded: chain M residue 287 THR Chi-restraints excluded: chain M residue 314 VAL Chi-restraints excluded: chain H residue 236 ASP Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain O residue 6 LEU Chi-restraints excluded: chain O residue 45 HIS Chi-restraints excluded: chain P residue 43 GLN Chi-restraints excluded: chain R residue 43 GLN Chi-restraints excluded: chain U residue 13 ILE Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain Y residue 7 LEU Chi-restraints excluded: chain Y residue 42 ASP Chi-restraints excluded: chain 2 residue 32 VAL Chi-restraints excluded: chain 2 residue 43 GLN Chi-restraints excluded: chain 3 residue 3 ARG Chi-restraints excluded: chain 4 residue 17 LYS Chi-restraints excluded: chain 4 residue 22 ILE Chi-restraints excluded: chain 6 residue 31 THR Chi-restraints excluded: chain 6 residue 35 ILE Chi-restraints excluded: chain 8 residue 26 SER Chi-restraints excluded: chain a residue 5 TRP Chi-restraints excluded: chain c residue 5 TRP Chi-restraints excluded: chain d residue 5 TRP Chi-restraints excluded: chain e residue 5 TRP Chi-restraints excluded: chain f residue 5 TRP Chi-restraints excluded: chain g residue 3 MET Chi-restraints excluded: chain g residue 5 TRP Chi-restraints excluded: chain g residue 6 MET Chi-restraints excluded: chain i residue 3 MET Chi-restraints excluded: chain j residue 5 TRP Chi-restraints excluded: chain k residue 5 TRP Chi-restraints excluded: chain k residue 6 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 166 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 218 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 241 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 184 optimal weight: 0.5980 chunk 195 optimal weight: 0.0040 chunk 14 optimal weight: 0.9990 overall best weight: 0.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 175 ASN H 104 ASN V 43 GLN Z 43 GLN 8 43 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.125982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.090760 restraints weight = 54380.875| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.93 r_work: 0.2817 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2686 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2686 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.269 30435 Z= 0.122 Angle : 0.653 13.840 41737 Z= 0.264 Chirality : 0.037 0.267 4238 Planarity : 0.004 0.068 4949 Dihedral : 20.968 177.902 6400 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.00 % Allowed : 9.23 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % 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: 2.17 (0.16), residues: 2887 helix: 2.53 (0.12), residues: 1732 sheet: 0.18 (0.72), residues: 53 loop : -0.29 (0.19), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG W 46 TYR 0.019 0.001 TYR M 193 PHE 0.015 0.001 PHE H 20 TRP 0.017 0.001 TRP U 2 HIS 0.005 0.001 HIS Y 29 Details of bonding type rmsd covalent geometry : bond 0.00276 (30386) covalent geometry : angle 0.65252 (41735) SS BOND : bond 0.00440 ( 1) SS BOND : angle 0.66545 ( 2) hydrogen bonds : bond 0.04599 ( 1492) hydrogen bonds : angle 4.07623 ( 4228) Misc. bond : bond 0.05632 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 329 time to evaluate : 1.069 Fit side-chains REVERT: C 68 ARG cc_start: 0.8437 (ttt-90) cc_final: 0.7999 (ttt90) REVERT: L 82 ARG cc_start: 0.8802 (mtm110) cc_final: 0.8430 (mtm-85) REVERT: M 182 HIS cc_start: 0.9283 (OUTLIER) cc_final: 0.9075 (p-80) REVERT: H 2 GLU cc_start: 0.7700 (mm-30) cc_final: 0.6937 (pm20) REVERT: H 185 LYS cc_start: 0.8864 (tptm) cc_final: 0.8510 (tmtm) REVERT: B 17 LYS cc_start: 0.8157 (mmmt) cc_final: 0.7830 (mttm) REVERT: F 7 LEU cc_start: 0.8339 (mt) cc_final: 0.8126 (mm) REVERT: I 12 ARG cc_start: 0.6552 (mmp80) cc_final: 0.5910 (mmm-85) REVERT: K 3 ARG cc_start: 0.7023 (OUTLIER) cc_final: 0.6665 (mtt90) REVERT: N 18 GLU cc_start: 0.7621 (tp30) cc_final: 0.7274 (tt0) REVERT: O 3 ARG cc_start: 0.7979 (mtt-85) cc_final: 0.7537 (mtm-85) REVERT: O 15 VAL cc_start: 0.8957 (t) cc_final: 0.8681 (p) REVERT: Q 8 PHE cc_start: 0.8031 (m-80) cc_final: 0.7636 (m-80) REVERT: R 13 GLU cc_start: 0.6408 (tp30) cc_final: 0.6048 (tp30) REVERT: R 17 LYS cc_start: 0.7572 (mmmm) cc_final: 0.7318 (mttp) REVERT: R 18 GLU cc_start: 0.8050 (tt0) cc_final: 0.7468 (tt0) REVERT: V 25 THR cc_start: 0.8575 (m) cc_final: 0.8160 (t) REVERT: Y 6 LEU cc_start: 0.8075 (mt) cc_final: 0.7857 (mm) REVERT: 1 4 MET cc_start: 0.7562 (ptt) cc_final: 0.7091 (ttp) REVERT: 1 12 ARG cc_start: 0.7500 (mpt90) cc_final: 0.6790 (mtm180) REVERT: 2 18 GLU cc_start: 0.7921 (tp30) cc_final: 0.7637 (tp30) REVERT: 2 25 THR cc_start: 0.8393 (t) cc_final: 0.7970 (p) REVERT: 2 43 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7365 (mp10) REVERT: 3 3 ARG cc_start: 0.7384 (mtm180) cc_final: 0.7162 (mmm160) REVERT: 3 11 ARG cc_start: 0.6867 (mtt180) cc_final: 0.6575 (mtm180) REVERT: 4 17 LYS cc_start: 0.7485 (OUTLIER) cc_final: 0.7034 (mtpt) REVERT: 8 18 GLU cc_start: 0.7905 (tt0) cc_final: 0.7404 (tt0) REVERT: 8 23 PHE cc_start: 0.7289 (t80) cc_final: 0.6479 (m-80) REVERT: 9 4 MET cc_start: 0.7827 (ptt) cc_final: 0.7537 (ptm) REVERT: g 3 MET cc_start: 0.6224 (OUTLIER) cc_final: 0.5770 (ptp) REVERT: k 5 TRP cc_start: 0.6366 (OUTLIER) cc_final: 0.5757 (p-90) REVERT: k 6 MET cc_start: 0.5532 (OUTLIER) cc_final: 0.5231 (mtm) outliers start: 48 outliers final: 27 residues processed: 353 average time/residue: 0.7233 time to fit residues: 299.6625 Evaluate side-chains 339 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 305 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 62 ILE Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 166 LEU Chi-restraints excluded: chain M residue 182 HIS Chi-restraints excluded: chain M residue 287 THR Chi-restraints excluded: chain M residue 314 VAL Chi-restraints excluded: chain H residue 236 ASP Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain O residue 6 LEU Chi-restraints excluded: chain P residue 8 ILE Chi-restraints excluded: chain R residue 43 GLN Chi-restraints excluded: chain Y residue 7 LEU Chi-restraints excluded: chain Y residue 36 ASP Chi-restraints excluded: chain 2 residue 43 GLN Chi-restraints excluded: chain 4 residue 17 LYS Chi-restraints excluded: chain 4 residue 22 ILE Chi-restraints excluded: chain 4 residue 24 ILE Chi-restraints excluded: chain 6 residue 35 ILE Chi-restraints excluded: chain a residue 5 TRP Chi-restraints excluded: chain c residue 5 TRP Chi-restraints excluded: chain d residue 5 TRP Chi-restraints excluded: chain e residue 5 TRP Chi-restraints excluded: chain f residue 5 TRP Chi-restraints excluded: chain g residue 3 MET Chi-restraints excluded: chain g residue 5 TRP Chi-restraints excluded: chain g residue 6 MET Chi-restraints excluded: chain i residue 3 MET Chi-restraints excluded: chain j residue 5 TRP Chi-restraints excluded: chain k residue 5 TRP Chi-restraints excluded: chain k residue 6 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 18 optimal weight: 1.9990 chunk 169 optimal weight: 0.8980 chunk 234 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 230 optimal weight: 5.9990 chunk 178 optimal weight: 3.9990 chunk 140 optimal weight: 0.0020 chunk 249 optimal weight: 0.9990 chunk 135 optimal weight: 0.0370 chunk 118 optimal weight: 3.9990 overall best weight: 0.7870 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 104 ASN Z 43 GLN 8 43 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.126318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.093749 restraints weight = 44852.776| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.44 r_work: 0.2881 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2749 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2749 r_free = 0.2749 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2749 r_free = 0.2749 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2749 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.244 30435 Z= 0.116 Angle : 0.637 13.388 41737 Z= 0.255 Chirality : 0.037 0.201 4238 Planarity : 0.004 0.065 4949 Dihedral : 19.838 176.280 6393 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.25 % Allowed : 10.21 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % 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: 2.33 (0.16), residues: 2887 helix: 2.55 (0.12), residues: 1781 sheet: 0.01 (0.72), residues: 53 loop : -0.14 (0.20), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG W 46 TYR 0.018 0.001 TYR M 193 PHE 0.015 0.001 PHE H 20 TRP 0.017 0.001 TRP U 2 HIS 0.005 0.001 HIS L 154 Details of bonding type rmsd covalent geometry : bond 0.00264 (30386) covalent geometry : angle 0.63737 (41735) SS BOND : bond 0.00353 ( 1) SS BOND : angle 0.57748 ( 2) hydrogen bonds : bond 0.04289 ( 1492) hydrogen bonds : angle 3.95846 ( 4228) Misc. bond : bond 0.05165 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 315 time to evaluate : 1.023 Fit side-chains REVERT: C 68 ARG cc_start: 0.8403 (ttt-90) cc_final: 0.7964 (ttt90) REVERT: L 82 ARG cc_start: 0.8734 (mtm110) cc_final: 0.8398 (mtm-85) REVERT: M 117 MET cc_start: 0.8870 (mtp) cc_final: 0.8625 (mtp) REVERT: M 182 HIS cc_start: 0.9394 (OUTLIER) cc_final: 0.9094 (p-80) REVERT: H 2 GLU cc_start: 0.7582 (mm-30) cc_final: 0.6896 (pm20) REVERT: H 128 THR cc_start: 0.6916 (OUTLIER) cc_final: 0.6537 (p) REVERT: H 166 LYS cc_start: 0.8479 (mtpt) cc_final: 0.8226 (mtpp) REVERT: H 185 LYS cc_start: 0.8824 (tptm) cc_final: 0.8430 (tmtm) REVERT: A 4 MET cc_start: 0.8284 (ptm) cc_final: 0.8017 (ppp) REVERT: B 17 LYS cc_start: 0.8065 (mmmt) cc_final: 0.7796 (mttm) REVERT: F 4 MET cc_start: 0.7807 (OUTLIER) cc_final: 0.7561 (tpp) REVERT: F 7 LEU cc_start: 0.8354 (mt) cc_final: 0.8147 (mm) REVERT: I 12 ARG cc_start: 0.6488 (mmp80) cc_final: 0.5891 (mmm-85) REVERT: K 3 ARG cc_start: 0.6988 (OUTLIER) cc_final: 0.6736 (mtt90) REVERT: N 18 GLU cc_start: 0.7520 (tp30) cc_final: 0.7221 (tt0) REVERT: O 3 ARG cc_start: 0.7892 (mtt-85) cc_final: 0.7650 (mtm-85) REVERT: O 45 HIS cc_start: 0.6361 (OUTLIER) cc_final: 0.5931 (m170) REVERT: Q 8 PHE cc_start: 0.8036 (m-80) cc_final: 0.7675 (m-80) REVERT: R 18 GLU cc_start: 0.7994 (tt0) cc_final: 0.7726 (tt0) REVERT: V 25 THR cc_start: 0.8540 (m) cc_final: 0.8164 (t) REVERT: Y 6 LEU cc_start: 0.8074 (mt) cc_final: 0.7824 (mm) REVERT: 1 4 MET cc_start: 0.7425 (ptt) cc_final: 0.7043 (ttp) REVERT: 1 12 ARG cc_start: 0.7398 (mpt90) cc_final: 0.6890 (mtp180) REVERT: 2 25 THR cc_start: 0.8379 (t) cc_final: 0.7963 (p) REVERT: 4 17 LYS cc_start: 0.7482 (OUTLIER) cc_final: 0.7050 (mtpt) REVERT: 8 18 GLU cc_start: 0.7822 (tt0) cc_final: 0.7336 (tt0) REVERT: 8 23 PHE cc_start: 0.7227 (t80) cc_final: 0.6492 (m-80) REVERT: 9 4 MET cc_start: 0.7758 (ptt) cc_final: 0.7467 (ptm) REVERT: k 5 TRP cc_start: 0.6363 (OUTLIER) cc_final: 0.5521 (p90) outliers start: 54 outliers final: 26 residues processed: 341 average time/residue: 0.6972 time to fit residues: 279.7905 Evaluate side-chains 330 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 297 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain L residue 62 ILE Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 166 LEU Chi-restraints excluded: chain M residue 182 HIS Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 287 THR Chi-restraints excluded: chain M residue 314 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain H residue 236 ASP Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain O residue 45 HIS Chi-restraints excluded: chain R residue 43 GLN Chi-restraints excluded: chain U residue 13 ILE Chi-restraints excluded: chain Y residue 7 LEU Chi-restraints excluded: chain Y residue 42 ASP Chi-restraints excluded: chain 4 residue 17 LYS Chi-restraints excluded: chain 4 residue 22 ILE Chi-restraints excluded: chain 4 residue 24 ILE Chi-restraints excluded: chain 6 residue 35 ILE Chi-restraints excluded: chain 0 residue 24 ILE Chi-restraints excluded: chain a residue 5 TRP Chi-restraints excluded: chain c residue 5 TRP Chi-restraints excluded: chain d residue 5 TRP Chi-restraints excluded: chain e residue 5 TRP Chi-restraints excluded: chain f residue 5 TRP Chi-restraints excluded: chain g residue 5 TRP Chi-restraints excluded: chain g residue 6 MET Chi-restraints excluded: chain j residue 5 TRP Chi-restraints excluded: chain k residue 5 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 252 optimal weight: 5.9990 chunk 268 optimal weight: 0.8980 chunk 180 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 chunk 204 optimal weight: 0.7980 chunk 153 optimal weight: 0.9990 chunk 50 optimal weight: 7.9990 chunk 144 optimal weight: 1.9990 chunk 218 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 43 GLN 8 43 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.126427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.092061 restraints weight = 52200.875| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.82 r_work: 0.2846 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2714 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2714 r_free = 0.2714 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2714 r_free = 0.2714 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2714 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.251 30435 Z= 0.116 Angle : 0.629 13.061 41737 Z= 0.253 Chirality : 0.037 0.190 4238 Planarity : 0.004 0.067 4949 Dihedral : 19.395 176.452 6391 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.08 % Allowed : 10.78 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % 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: 2.35 (0.16), residues: 2887 helix: 2.58 (0.12), residues: 1781 sheet: -0.04 (0.72), residues: 53 loop : -0.14 (0.20), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG W 46 TYR 0.019 0.001 TYR M 193 PHE 0.015 0.001 PHE H 20 TRP 0.023 0.001 TRP I 2 HIS 0.005 0.001 HIS Y 29 Details of bonding type rmsd covalent geometry : bond 0.00262 (30386) covalent geometry : angle 0.62855 (41735) SS BOND : bond 0.00361 ( 1) SS BOND : angle 0.58967 ( 2) hydrogen bonds : bond 0.04252 ( 1492) hydrogen bonds : angle 3.93534 ( 4228) Misc. bond : bond 0.05412 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 314 time to evaluate : 1.069 Fit side-chains REVERT: C 40 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.7903 (mtm110) REVERT: C 68 ARG cc_start: 0.8441 (ttt-90) cc_final: 0.8072 (ttt90) REVERT: M 182 HIS cc_start: 0.9359 (OUTLIER) cc_final: 0.9077 (p-80) REVERT: H 2 GLU cc_start: 0.7593 (mm-30) cc_final: 0.6892 (pm20) REVERT: H 128 THR cc_start: 0.6844 (OUTLIER) cc_final: 0.6448 (p) REVERT: H 185 LYS cc_start: 0.8861 (tptm) cc_final: 0.8545 (tmtm) REVERT: A 4 MET cc_start: 0.8269 (ptm) cc_final: 0.8007 (ppp) REVERT: B 15 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7636 (mt-10) REVERT: B 17 LYS cc_start: 0.8051 (mmmt) cc_final: 0.7801 (mttm) REVERT: D 4 MET cc_start: 0.8337 (tpt) cc_final: 0.8065 (tpp) REVERT: F 4 MET cc_start: 0.7854 (OUTLIER) cc_final: 0.7650 (tpp) REVERT: F 7 LEU cc_start: 0.8353 (mt) cc_final: 0.8128 (mm) REVERT: F 12 ARG cc_start: 0.7800 (mtp180) cc_final: 0.7479 (mtp-110) REVERT: I 12 ARG cc_start: 0.6464 (mmp80) cc_final: 0.5863 (mmm-85) REVERT: K 3 ARG cc_start: 0.7028 (OUTLIER) cc_final: 0.6792 (mtt90) REVERT: N 18 GLU cc_start: 0.7520 (tp30) cc_final: 0.7256 (tt0) REVERT: O 3 ARG cc_start: 0.7902 (mtt-85) cc_final: 0.7609 (mtm-85) REVERT: O 45 HIS cc_start: 0.6405 (OUTLIER) cc_final: 0.5974 (m170) REVERT: Q 8 PHE cc_start: 0.8029 (m-80) cc_final: 0.7658 (m-80) REVERT: R 17 LYS cc_start: 0.7441 (mttp) cc_final: 0.6968 (mmtp) REVERT: V 25 THR cc_start: 0.8561 (m) cc_final: 0.8160 (t) REVERT: W 4 MET cc_start: 0.7314 (tpt) cc_final: 0.7055 (mmm) REVERT: Y 6 LEU cc_start: 0.8038 (mt) cc_final: 0.7759 (mm) REVERT: 1 4 MET cc_start: 0.7550 (ptt) cc_final: 0.7151 (mtp) REVERT: 1 12 ARG cc_start: 0.7417 (mpt90) cc_final: 0.6899 (mtp180) REVERT: 2 18 GLU cc_start: 0.7809 (tp30) cc_final: 0.7590 (tp30) REVERT: 2 25 THR cc_start: 0.8357 (t) cc_final: 0.7941 (p) REVERT: 3 11 ARG cc_start: 0.6984 (mtm180) cc_final: 0.6778 (mtp-110) REVERT: 4 17 LYS cc_start: 0.7396 (OUTLIER) cc_final: 0.6990 (mtpt) REVERT: 8 23 PHE cc_start: 0.7279 (t80) cc_final: 0.6511 (m-80) REVERT: 9 4 MET cc_start: 0.7762 (ptt) cc_final: 0.7462 (ptm) REVERT: g 3 MET cc_start: 0.6322 (ptm) cc_final: 0.5923 (ptp) REVERT: k 5 TRP cc_start: 0.6316 (OUTLIER) cc_final: 0.5515 (p90) outliers start: 50 outliers final: 30 residues processed: 343 average time/residue: 0.7127 time to fit residues: 287.1975 Evaluate side-chains 337 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 299 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain L residue 62 ILE Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 166 LEU Chi-restraints excluded: chain M residue 182 HIS Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 262 PHE Chi-restraints excluded: chain M residue 287 THR Chi-restraints excluded: chain M residue 314 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain H residue 236 ASP Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain O residue 45 HIS Chi-restraints excluded: chain P residue 8 ILE Chi-restraints excluded: chain R residue 43 GLN Chi-restraints excluded: chain U residue 13 ILE Chi-restraints excluded: chain W residue 34 SER Chi-restraints excluded: chain X residue 8 ILE Chi-restraints excluded: chain Y residue 7 LEU Chi-restraints excluded: chain Y residue 42 ASP Chi-restraints excluded: chain 4 residue 17 LYS Chi-restraints excluded: chain 4 residue 22 ILE Chi-restraints excluded: chain 4 residue 24 ILE Chi-restraints excluded: chain 6 residue 35 ILE Chi-restraints excluded: chain 0 residue 24 ILE Chi-restraints excluded: chain a residue 5 TRP Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain c residue 5 TRP Chi-restraints excluded: chain d residue 5 TRP Chi-restraints excluded: chain e residue 5 TRP Chi-restraints excluded: chain f residue 5 TRP Chi-restraints excluded: chain g residue 5 TRP Chi-restraints excluded: chain j residue 5 TRP Chi-restraints excluded: chain k residue 5 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 275 optimal weight: 5.9990 chunk 257 optimal weight: 0.8980 chunk 63 optimal weight: 7.9990 chunk 178 optimal weight: 0.9990 chunk 149 optimal weight: 8.9990 chunk 5 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 107 optimal weight: 0.0050 chunk 240 optimal weight: 0.8980 chunk 215 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 104 ASN Z 43 GLN 8 43 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.127045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.092290 restraints weight = 56623.254| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 1.92 r_work: 0.2842 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2709 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2709 r_free = 0.2709 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2709 r_free = 0.2709 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2709 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.239 30435 Z= 0.108 Angle : 0.616 12.872 41737 Z= 0.246 Chirality : 0.036 0.189 4238 Planarity : 0.004 0.066 4949 Dihedral : 19.038 176.114 6391 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.21 % Allowed : 10.95 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % 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: 2.39 (0.16), residues: 2887 helix: 2.62 (0.12), residues: 1781 sheet: -0.02 (0.72), residues: 53 loop : -0.14 (0.20), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG W 46 TYR 0.019 0.001 TYR M 193 PHE 0.014 0.001 PHE H 20 TRP 0.028 0.001 TRP I 2 HIS 0.005 0.001 HIS C 148 Details of bonding type rmsd covalent geometry : bond 0.00243 (30386) covalent geometry : angle 0.61618 (41735) SS BOND : bond 0.00341 ( 1) SS BOND : angle 0.57427 ( 2) hydrogen bonds : bond 0.04085 ( 1492) hydrogen bonds : angle 3.89500 ( 4228) Misc. bond : bond 0.05231 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 306 time to evaluate : 1.019 Fit side-chains REVERT: C 40 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.7785 (mtm110) REVERT: C 68 ARG cc_start: 0.8459 (ttt-90) cc_final: 0.8111 (ttt90) REVERT: L 203 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.7686 (tptt) REVERT: M 85 GLU cc_start: 0.8891 (mm-30) cc_final: 0.8659 (mm-30) REVERT: M 182 HIS cc_start: 0.9342 (OUTLIER) cc_final: 0.8992 (p-80) REVERT: H 128 THR cc_start: 0.6882 (OUTLIER) cc_final: 0.6470 (p) REVERT: H 185 LYS cc_start: 0.8863 (tptm) cc_final: 0.8552 (tmtm) REVERT: B 15 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7647 (mt-10) REVERT: B 17 LYS cc_start: 0.8047 (mmmt) cc_final: 0.7797 (mttm) REVERT: D 3 ARG cc_start: 0.7478 (mtm-85) cc_final: 0.7137 (mpt-90) REVERT: D 4 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.8014 (tpp) REVERT: F 4 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7666 (tpp) REVERT: F 7 LEU cc_start: 0.8452 (mt) cc_final: 0.8235 (mm) REVERT: F 12 ARG cc_start: 0.7817 (mtp180) cc_final: 0.7462 (mtp-110) REVERT: I 12 ARG cc_start: 0.6521 (mmp80) cc_final: 0.5914 (mmm-85) REVERT: K 3 ARG cc_start: 0.6997 (OUTLIER) cc_final: 0.6773 (mtt90) REVERT: N 18 GLU cc_start: 0.7500 (tp30) cc_final: 0.7262 (tt0) REVERT: O 3 ARG cc_start: 0.7890 (mtt-85) cc_final: 0.7589 (mtm-85) REVERT: P 43 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.8372 (mp10) REVERT: Q 8 PHE cc_start: 0.8035 (m-80) cc_final: 0.7634 (m-80) REVERT: S 4 MET cc_start: 0.7564 (ptm) cc_final: 0.7341 (ptm) REVERT: V 25 THR cc_start: 0.8559 (m) cc_final: 0.8162 (t) REVERT: 1 4 MET cc_start: 0.7394 (ptt) cc_final: 0.7042 (mtp) REVERT: 1 12 ARG cc_start: 0.7430 (mpt90) cc_final: 0.6656 (mtm-85) REVERT: 2 25 THR cc_start: 0.8366 (t) cc_final: 0.7955 (p) REVERT: 4 17 LYS cc_start: 0.7405 (OUTLIER) cc_final: 0.7003 (mtpt) REVERT: 8 23 PHE cc_start: 0.7313 (t80) cc_final: 0.6544 (m-80) REVERT: 9 4 MET cc_start: 0.7789 (ptt) cc_final: 0.7484 (ptm) REVERT: g 3 MET cc_start: 0.6314 (ptm) cc_final: 0.5896 (ptp) REVERT: k 5 TRP cc_start: 0.6303 (OUTLIER) cc_final: 0.5714 (p-90) REVERT: k 9 LEU cc_start: 0.5826 (OUTLIER) cc_final: 0.5236 (tp) outliers start: 53 outliers final: 30 residues processed: 334 average time/residue: 0.7219 time to fit residues: 283.0143 Evaluate side-chains 336 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 295 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain L residue 62 ILE Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 166 LEU Chi-restraints excluded: chain L residue 203 LYS Chi-restraints excluded: chain M residue 182 HIS Chi-restraints excluded: chain M residue 262 PHE Chi-restraints excluded: chain M residue 287 THR Chi-restraints excluded: chain M residue 314 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain H residue 236 ASP Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain P residue 8 ILE Chi-restraints excluded: chain P residue 43 GLN Chi-restraints excluded: chain R residue 43 GLN Chi-restraints excluded: chain U residue 13 ILE Chi-restraints excluded: chain W residue 34 SER Chi-restraints excluded: chain Y residue 42 ASP Chi-restraints excluded: chain 4 residue 17 LYS Chi-restraints excluded: chain 4 residue 22 ILE Chi-restraints excluded: chain 4 residue 24 ILE Chi-restraints excluded: chain 6 residue 35 ILE Chi-restraints excluded: chain 6 residue 43 GLN Chi-restraints excluded: chain 8 residue 26 SER Chi-restraints excluded: chain 0 residue 24 ILE Chi-restraints excluded: chain a residue 3 MET Chi-restraints excluded: chain a residue 5 TRP Chi-restraints excluded: chain c residue 5 TRP Chi-restraints excluded: chain d residue 5 TRP Chi-restraints excluded: chain e residue 5 TRP Chi-restraints excluded: chain f residue 5 TRP Chi-restraints excluded: chain g residue 5 TRP Chi-restraints excluded: chain i residue 3 MET Chi-restraints excluded: chain j residue 5 TRP Chi-restraints excluded: chain k residue 5 TRP Chi-restraints excluded: chain k residue 9 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 5 optimal weight: 0.9990 chunk 261 optimal weight: 0.0980 chunk 75 optimal weight: 10.0000 chunk 129 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 269 optimal weight: 1.9990 chunk 190 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 137 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 278 optimal weight: 8.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.127370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.095397 restraints weight = 49867.479| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.62 r_work: 0.2877 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2744 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2744 r_free = 0.2744 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2744 r_free = 0.2744 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2744 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.230 30435 Z= 0.108 Angle : 0.613 12.656 41737 Z= 0.245 Chirality : 0.036 0.187 4238 Planarity : 0.004 0.066 4949 Dihedral : 18.500 175.775 6391 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.17 % Allowed : 11.03 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % 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: 2.49 (0.16), residues: 2887 helix: 2.69 (0.12), residues: 1775 sheet: 0.03 (0.74), residues: 53 loop : -0.09 (0.20), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 5 11 TYR 0.019 0.001 TYR M 193 PHE 0.014 0.001 PHE H 20 TRP 0.030 0.001 TRP U 2 HIS 0.005 0.001 HIS C 148 Details of bonding type rmsd covalent geometry : bond 0.00245 (30386) covalent geometry : angle 0.61293 (41735) SS BOND : bond 0.00317 ( 1) SS BOND : angle 0.57688 ( 2) hydrogen bonds : bond 0.04024 ( 1492) hydrogen bonds : angle 3.86113 ( 4228) Misc. bond : bond 0.05143 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 303 time to evaluate : 1.052 Fit side-chains REVERT: C 40 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.7649 (mtm180) REVERT: C 68 ARG cc_start: 0.8452 (ttt-90) cc_final: 0.8110 (ttt90) REVERT: L 82 ARG cc_start: 0.8721 (mtp180) cc_final: 0.8330 (mpp80) REVERT: L 203 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.7693 (tptt) REVERT: M 85 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8623 (mm-30) REVERT: M 182 HIS cc_start: 0.9344 (OUTLIER) cc_final: 0.9054 (p-80) REVERT: H 128 THR cc_start: 0.6838 (OUTLIER) cc_final: 0.6458 (p) REVERT: H 185 LYS cc_start: 0.8867 (tptm) cc_final: 0.8550 (tmtm) REVERT: B 17 LYS cc_start: 0.8054 (mmmt) cc_final: 0.7829 (mttm) REVERT: D 3 ARG cc_start: 0.7458 (mtm-85) cc_final: 0.6982 (mpt-90) REVERT: D 4 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.8073 (tpp) REVERT: F 4 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.7635 (tpp) REVERT: F 7 LEU cc_start: 0.8543 (mt) cc_final: 0.8315 (mm) REVERT: I 12 ARG cc_start: 0.6493 (mmp80) cc_final: 0.5897 (mmm-85) REVERT: K 3 ARG cc_start: 0.6994 (OUTLIER) cc_final: 0.6780 (mtt90) REVERT: N 18 GLU cc_start: 0.7501 (tp30) cc_final: 0.7292 (tt0) REVERT: P 43 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.8337 (mp10) REVERT: Q 8 PHE cc_start: 0.8049 (m-80) cc_final: 0.7651 (m-80) REVERT: R 43 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.8691 (tt0) REVERT: V 25 THR cc_start: 0.8555 (m) cc_final: 0.8181 (t) REVERT: 1 12 ARG cc_start: 0.7371 (mpt90) cc_final: 0.6601 (mtm-85) REVERT: 2 25 THR cc_start: 0.8359 (t) cc_final: 0.7951 (p) REVERT: 3 2 TRP cc_start: 0.7609 (p-90) cc_final: 0.7390 (p-90) REVERT: 4 17 LYS cc_start: 0.7373 (tptp) cc_final: 0.6982 (mtpt) REVERT: 8 18 GLU cc_start: 0.7772 (tt0) cc_final: 0.7444 (tt0) REVERT: 8 23 PHE cc_start: 0.7307 (t80) cc_final: 0.6565 (m-80) REVERT: 9 4 MET cc_start: 0.7769 (ptt) cc_final: 0.7464 (ptm) REVERT: g 3 MET cc_start: 0.6307 (OUTLIER) cc_final: 0.5889 (ptp) REVERT: k 5 TRP cc_start: 0.6247 (OUTLIER) cc_final: 0.5473 (p90) REVERT: k 6 MET cc_start: 0.5303 (OUTLIER) cc_final: 0.5048 (mtp) REVERT: k 9 LEU cc_start: 0.5862 (OUTLIER) cc_final: 0.5279 (tp) outliers start: 52 outliers final: 31 residues processed: 331 average time/residue: 0.7294 time to fit residues: 283.6832 Evaluate side-chains 334 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 290 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain L residue 62 ILE Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 166 LEU Chi-restraints excluded: chain L residue 203 LYS Chi-restraints excluded: chain M residue 182 HIS Chi-restraints excluded: chain M residue 262 PHE Chi-restraints excluded: chain M residue 287 THR Chi-restraints excluded: chain M residue 314 VAL Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain H residue 236 ASP Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain O residue 45 HIS Chi-restraints excluded: chain P residue 8 ILE Chi-restraints excluded: chain P residue 43 GLN Chi-restraints excluded: chain R residue 43 GLN Chi-restraints excluded: chain U residue 13 ILE Chi-restraints excluded: chain W residue 34 SER Chi-restraints excluded: chain Y residue 42 ASP Chi-restraints excluded: chain 4 residue 22 ILE Chi-restraints excluded: chain 4 residue 24 ILE Chi-restraints excluded: chain 6 residue 35 ILE Chi-restraints excluded: chain 6 residue 43 GLN Chi-restraints excluded: chain 0 residue 24 ILE Chi-restraints excluded: chain a residue 3 MET Chi-restraints excluded: chain a residue 5 TRP Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain c residue 5 TRP Chi-restraints excluded: chain d residue 5 TRP Chi-restraints excluded: chain e residue 5 TRP Chi-restraints excluded: chain e residue 6 MET Chi-restraints excluded: chain f residue 5 TRP Chi-restraints excluded: chain g residue 3 MET Chi-restraints excluded: chain g residue 5 TRP Chi-restraints excluded: chain j residue 5 TRP Chi-restraints excluded: chain k residue 5 TRP Chi-restraints excluded: chain k residue 6 MET Chi-restraints excluded: chain k residue 9 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 253 optimal weight: 5.9990 chunk 211 optimal weight: 6.9990 chunk 166 optimal weight: 1.9990 chunk 156 optimal weight: 0.7980 chunk 195 optimal weight: 3.9990 chunk 226 optimal weight: 7.9990 chunk 259 optimal weight: 7.9990 chunk 265 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 52 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 6 GLN H 104 ASN E 43 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.123942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.089367 restraints weight = 51501.275| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.78 r_work: 0.2789 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2655 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2655 r_free = 0.2655 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2655 r_free = 0.2655 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2655 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.349 30435 Z= 0.182 Angle : 0.727 14.341 41737 Z= 0.296 Chirality : 0.041 0.204 4238 Planarity : 0.004 0.065 4949 Dihedral : 19.278 179.440 6387 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.17 % Allowed : 11.40 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % 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: 2.08 (0.16), residues: 2887 helix: 2.45 (0.12), residues: 1733 sheet: 0.04 (0.72), residues: 53 loop : -0.30 (0.19), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 3 TYR 0.024 0.002 TYR L 165 PHE 0.021 0.002 PHE H 20 TRP 0.033 0.002 TRP U 2 HIS 0.010 0.002 HIS C 148 Details of bonding type rmsd covalent geometry : bond 0.00428 (30386) covalent geometry : angle 0.72691 (41735) SS BOND : bond 0.00553 ( 1) SS BOND : angle 0.69074 ( 2) hydrogen bonds : bond 0.05076 ( 1492) hydrogen bonds : angle 4.14174 ( 4228) Misc. bond : bond 0.07678 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 299 time to evaluate : 0.941 Fit side-chains REVERT: C 40 ARG cc_start: 0.9056 (OUTLIER) cc_final: 0.8494 (mtm110) REVERT: C 68 ARG cc_start: 0.8436 (ttt-90) cc_final: 0.7914 (ttt90) REVERT: L 82 ARG cc_start: 0.8761 (mtp180) cc_final: 0.8461 (mpp80) REVERT: H 128 THR cc_start: 0.6745 (OUTLIER) cc_final: 0.6325 (p) REVERT: H 185 LYS cc_start: 0.8871 (tptm) cc_final: 0.8609 (tmtm) REVERT: B 17 LYS cc_start: 0.8073 (mmmt) cc_final: 0.7837 (mttm) REVERT: D 3 ARG cc_start: 0.7626 (mtm-85) cc_final: 0.7259 (mpt-90) REVERT: D 4 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.8030 (tpp) REVERT: F 4 MET cc_start: 0.7907 (OUTLIER) cc_final: 0.7681 (tpp) REVERT: F 7 LEU cc_start: 0.8392 (mt) cc_final: 0.8170 (mm) REVERT: I 12 ARG cc_start: 0.6527 (mmp80) cc_final: 0.5903 (mmm-85) REVERT: K 3 ARG cc_start: 0.7131 (OUTLIER) cc_final: 0.6773 (mtt90) REVERT: N 18 GLU cc_start: 0.7627 (tp30) cc_final: 0.7367 (tt0) REVERT: O 3 ARG cc_start: 0.8014 (mtt-85) cc_final: 0.7438 (mtm-85) REVERT: Q 8 PHE cc_start: 0.8082 (m-80) cc_final: 0.7757 (m-80) REVERT: R 18 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7564 (tt0) REVERT: 1 12 ARG cc_start: 0.7385 (mpt90) cc_final: 0.6896 (mtp180) REVERT: 2 25 THR cc_start: 0.8365 (t) cc_final: 0.7973 (p) REVERT: 3 2 TRP cc_start: 0.7692 (p-90) cc_final: 0.7455 (p-90) REVERT: 4 17 LYS cc_start: 0.7339 (OUTLIER) cc_final: 0.6984 (mtpt) REVERT: 8 18 GLU cc_start: 0.7851 (tt0) cc_final: 0.7506 (tt0) REVERT: 8 23 PHE cc_start: 0.7272 (t80) cc_final: 0.6515 (m-80) REVERT: g 3 MET cc_start: 0.6214 (OUTLIER) cc_final: 0.5754 (ptp) REVERT: k 5 TRP cc_start: 0.6355 (OUTLIER) cc_final: 0.5252 (p90) REVERT: k 6 MET cc_start: 0.5188 (OUTLIER) cc_final: 0.4871 (mtt) REVERT: k 9 LEU cc_start: 0.5834 (OUTLIER) cc_final: 0.5286 (tp) outliers start: 52 outliers final: 28 residues processed: 330 average time/residue: 0.7367 time to fit residues: 285.0131 Evaluate side-chains 328 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 289 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 62 ILE Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 166 LEU Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 262 PHE Chi-restraints excluded: chain M residue 287 THR Chi-restraints excluded: chain M residue 314 VAL Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain H residue 236 ASP Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain P residue 8 ILE Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain R residue 43 GLN Chi-restraints excluded: chain U residue 13 ILE Chi-restraints excluded: chain W residue 34 SER Chi-restraints excluded: chain X residue 52 THR Chi-restraints excluded: chain 4 residue 17 LYS Chi-restraints excluded: chain 4 residue 22 ILE Chi-restraints excluded: chain 4 residue 24 ILE Chi-restraints excluded: chain 8 residue 26 SER Chi-restraints excluded: chain 0 residue 24 ILE Chi-restraints excluded: chain a residue 5 TRP Chi-restraints excluded: chain c residue 5 TRP Chi-restraints excluded: chain d residue 5 TRP Chi-restraints excluded: chain e residue 5 TRP Chi-restraints excluded: chain f residue 5 TRP Chi-restraints excluded: chain g residue 3 MET Chi-restraints excluded: chain g residue 5 TRP Chi-restraints excluded: chain i residue 3 MET Chi-restraints excluded: chain j residue 5 TRP Chi-restraints excluded: chain k residue 5 TRP Chi-restraints excluded: chain k residue 6 MET Chi-restraints excluded: chain k residue 9 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 64 optimal weight: 4.9990 chunk 284 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 112 optimal weight: 0.9990 chunk 186 optimal weight: 10.0000 chunk 115 optimal weight: 4.9990 chunk 157 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 104 ASN E 43 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.124245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.089169 restraints weight = 56053.755| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.00 r_work: 0.2765 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2631 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2631 r_free = 0.2631 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2631 r_free = 0.2631 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2631 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.317 30435 Z= 0.162 Angle : 0.704 14.786 41737 Z= 0.285 Chirality : 0.040 0.191 4238 Planarity : 0.004 0.066 4949 Dihedral : 19.213 179.298 6387 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.00 % Allowed : 11.64 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % 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: 2.05 (0.16), residues: 2887 helix: 2.43 (0.12), residues: 1732 sheet: 0.12 (0.73), residues: 53 loop : -0.33 (0.19), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG O 3 TYR 0.022 0.002 TYR L 165 PHE 0.020 0.002 PHE H 20 TRP 0.037 0.002 TRP I 2 HIS 0.008 0.002 HIS C 148 Details of bonding type rmsd covalent geometry : bond 0.00380 (30386) covalent geometry : angle 0.70381 (41735) SS BOND : bond 0.00471 ( 1) SS BOND : angle 0.64983 ( 2) hydrogen bonds : bond 0.04840 ( 1492) hydrogen bonds : angle 4.10756 ( 4228) Misc. bond : bond 0.07025 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 292 time to evaluate : 1.061 Fit side-chains REVERT: C 40 ARG cc_start: 0.9021 (OUTLIER) cc_final: 0.8465 (mtm180) REVERT: C 68 ARG cc_start: 0.8444 (ttt-90) cc_final: 0.7954 (ttt90) REVERT: L 82 ARG cc_start: 0.8762 (mtp180) cc_final: 0.8433 (mtm-85) REVERT: H 128 THR cc_start: 0.6771 (OUTLIER) cc_final: 0.6323 (p) REVERT: H 185 LYS cc_start: 0.8871 (tptm) cc_final: 0.8554 (tmtm) REVERT: B 17 LYS cc_start: 0.8046 (mmmt) cc_final: 0.7794 (mttm) REVERT: D 3 ARG cc_start: 0.7656 (mtm-85) cc_final: 0.7307 (mpt-90) REVERT: D 4 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.8125 (tpp) REVERT: F 4 MET cc_start: 0.7952 (OUTLIER) cc_final: 0.7710 (tpp) REVERT: F 7 LEU cc_start: 0.8371 (mt) cc_final: 0.8155 (mm) REVERT: I 12 ARG cc_start: 0.6548 (mmp80) cc_final: 0.5908 (mmm-85) REVERT: K 3 ARG cc_start: 0.7118 (OUTLIER) cc_final: 0.6756 (mtt90) REVERT: N 18 GLU cc_start: 0.7621 (tp30) cc_final: 0.7359 (tt0) REVERT: O 3 ARG cc_start: 0.7972 (mtt-85) cc_final: 0.7247 (mtm-85) REVERT: P 43 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.8169 (mp10) REVERT: Q 8 PHE cc_start: 0.8068 (m-80) cc_final: 0.7765 (m-80) REVERT: R 18 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7420 (tt0) REVERT: W 4 MET cc_start: 0.7306 (tpt) cc_final: 0.7019 (mmm) REVERT: 1 4 MET cc_start: 0.7605 (ptt) cc_final: 0.7039 (ttp) REVERT: 1 12 ARG cc_start: 0.7409 (mpt90) cc_final: 0.6884 (mtp180) REVERT: 2 25 THR cc_start: 0.8336 (t) cc_final: 0.7951 (p) REVERT: 3 2 TRP cc_start: 0.7686 (p-90) cc_final: 0.7442 (p-90) REVERT: 4 17 LYS cc_start: 0.7330 (OUTLIER) cc_final: 0.6981 (mtpt) REVERT: 8 18 GLU cc_start: 0.7836 (tt0) cc_final: 0.7508 (tt0) REVERT: 8 23 PHE cc_start: 0.7298 (t80) cc_final: 0.6515 (m-80) REVERT: 9 4 MET cc_start: 0.7927 (ptt) cc_final: 0.7607 (ptm) REVERT: f 18 LEU cc_start: 0.6862 (OUTLIER) cc_final: 0.6648 (mt) REVERT: g 3 MET cc_start: 0.6171 (OUTLIER) cc_final: 0.5717 (ptp) REVERT: k 5 TRP cc_start: 0.6404 (OUTLIER) cc_final: 0.5407 (p90) REVERT: k 6 MET cc_start: 0.4970 (OUTLIER) cc_final: 0.4699 (mtp) REVERT: k 9 LEU cc_start: 0.5815 (OUTLIER) cc_final: 0.5236 (tp) outliers start: 48 outliers final: 29 residues processed: 319 average time/residue: 0.7235 time to fit residues: 269.6380 Evaluate side-chains 329 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 287 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 62 ILE Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 166 LEU Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 262 PHE Chi-restraints excluded: chain M residue 287 THR Chi-restraints excluded: chain M residue 314 VAL Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain H residue 236 ASP Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain P residue 8 ILE Chi-restraints excluded: chain P residue 43 GLN Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain R residue 43 GLN Chi-restraints excluded: chain U residue 13 ILE Chi-restraints excluded: chain X residue 52 THR Chi-restraints excluded: chain Y residue 36 ASP Chi-restraints excluded: chain Y residue 42 ASP Chi-restraints excluded: chain 4 residue 17 LYS Chi-restraints excluded: chain 4 residue 22 ILE Chi-restraints excluded: chain 4 residue 24 ILE Chi-restraints excluded: chain 6 residue 43 GLN Chi-restraints excluded: chain 8 residue 26 SER Chi-restraints excluded: chain 0 residue 24 ILE Chi-restraints excluded: chain a residue 5 TRP Chi-restraints excluded: chain c residue 5 TRP Chi-restraints excluded: chain d residue 5 TRP Chi-restraints excluded: chain e residue 5 TRP Chi-restraints excluded: chain e residue 6 MET Chi-restraints excluded: chain f residue 5 TRP Chi-restraints excluded: chain f residue 18 LEU Chi-restraints excluded: chain g residue 3 MET Chi-restraints excluded: chain g residue 5 TRP Chi-restraints excluded: chain j residue 5 TRP Chi-restraints excluded: chain k residue 5 TRP Chi-restraints excluded: chain k residue 6 MET Chi-restraints excluded: chain k residue 9 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 86 optimal weight: 0.7980 chunk 115 optimal weight: 0.2980 chunk 57 optimal weight: 6.9990 chunk 44 optimal weight: 0.6980 chunk 6 optimal weight: 6.9990 chunk 186 optimal weight: 0.0030 chunk 259 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 274 optimal weight: 9.9990 chunk 168 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 6 GLN H 104 ASN E 43 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.126715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.091505 restraints weight = 59827.625| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.04 r_work: 0.2818 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2684 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2684 r_free = 0.2684 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2684 r_free = 0.2684 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2684 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.260 30435 Z= 0.116 Angle : 0.641 14.724 41737 Z= 0.255 Chirality : 0.037 0.190 4238 Planarity : 0.004 0.064 4949 Dihedral : 18.563 179.455 6387 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.72 % Allowed : 11.93 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % 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: 2.23 (0.16), residues: 2887 helix: 2.60 (0.12), residues: 1733 sheet: 0.18 (0.73), residues: 52 loop : -0.31 (0.19), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG O 3 TYR 0.020 0.001 TYR M 193 PHE 0.015 0.001 PHE Z 19 TRP 0.037 0.001 TRP U 2 HIS 0.006 0.001 HIS C 148 Details of bonding type rmsd covalent geometry : bond 0.00263 (30386) covalent geometry : angle 0.64059 (41735) SS BOND : bond 0.00342 ( 1) SS BOND : angle 0.59760 ( 2) hydrogen bonds : bond 0.04198 ( 1492) hydrogen bonds : angle 3.96329 ( 4228) Misc. bond : bond 0.06089 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 295 time to evaluate : 1.080 Fit side-chains REVERT: C 68 ARG cc_start: 0.8447 (ttt-90) cc_final: 0.8075 (ttt90) REVERT: L 82 ARG cc_start: 0.8740 (mtp180) cc_final: 0.8488 (mpp80) REVERT: M 85 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8649 (mm-30) REVERT: H 128 THR cc_start: 0.6789 (OUTLIER) cc_final: 0.6332 (p) REVERT: H 185 LYS cc_start: 0.8854 (tptm) cc_final: 0.8523 (tmtm) REVERT: B 17 LYS cc_start: 0.8060 (mmmt) cc_final: 0.7817 (mttm) REVERT: D 3 ARG cc_start: 0.7650 (mtm-85) cc_final: 0.7286 (mpt-90) REVERT: D 4 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.8074 (tpp) REVERT: F 7 LEU cc_start: 0.8336 (mt) cc_final: 0.8122 (mm) REVERT: I 12 ARG cc_start: 0.6552 (mmp80) cc_final: 0.5935 (mmm-85) REVERT: K 3 ARG cc_start: 0.6978 (OUTLIER) cc_final: 0.6717 (mtt90) REVERT: N 18 GLU cc_start: 0.7620 (tp30) cc_final: 0.7359 (tt0) REVERT: O 3 ARG cc_start: 0.7945 (mtt-85) cc_final: 0.7255 (mtm-85) REVERT: P 43 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.8264 (mp10) REVERT: Q 8 PHE cc_start: 0.8006 (m-80) cc_final: 0.7717 (m-80) REVERT: R 18 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7441 (tt0) REVERT: V 25 THR cc_start: 0.8586 (m) cc_final: 0.8154 (t) REVERT: W 4 MET cc_start: 0.7309 (tpt) cc_final: 0.7066 (mmm) REVERT: 1 12 ARG cc_start: 0.7390 (mpt90) cc_final: 0.6577 (mtm-85) REVERT: 2 25 THR cc_start: 0.8376 (t) cc_final: 0.7984 (p) REVERT: 3 2 TRP cc_start: 0.7617 (p-90) cc_final: 0.7348 (p-90) REVERT: 4 17 LYS cc_start: 0.7342 (tptp) cc_final: 0.6986 (mtpt) REVERT: 8 18 GLU cc_start: 0.7802 (tt0) cc_final: 0.7481 (tt0) REVERT: 8 23 PHE cc_start: 0.7316 (t80) cc_final: 0.6548 (m-80) REVERT: 9 4 MET cc_start: 0.7836 (ptt) cc_final: 0.7521 (ptm) REVERT: f 18 LEU cc_start: 0.6846 (OUTLIER) cc_final: 0.6631 (mt) REVERT: g 3 MET cc_start: 0.6284 (OUTLIER) cc_final: 0.5799 (ptp) REVERT: k 5 TRP cc_start: 0.6226 (OUTLIER) cc_final: 0.5838 (p-90) REVERT: k 6 MET cc_start: 0.4961 (OUTLIER) cc_final: 0.4635 (mtp) REVERT: k 9 LEU cc_start: 0.5883 (OUTLIER) cc_final: 0.5352 (tp) outliers start: 41 outliers final: 28 residues processed: 318 average time/residue: 0.7354 time to fit residues: 273.0556 Evaluate side-chains 327 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 289 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 62 ILE Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 166 LEU Chi-restraints excluded: chain M residue 262 PHE Chi-restraints excluded: chain M residue 287 THR Chi-restraints excluded: chain M residue 314 VAL Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain H residue 236 ASP Chi-restraints excluded: chain D residue 4 MET Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain P residue 8 ILE Chi-restraints excluded: chain P residue 43 GLN Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain R residue 43 GLN Chi-restraints excluded: chain U residue 13 ILE Chi-restraints excluded: chain X residue 8 ILE Chi-restraints excluded: chain X residue 52 THR Chi-restraints excluded: chain Y residue 42 ASP Chi-restraints excluded: chain 4 residue 22 ILE Chi-restraints excluded: chain 4 residue 24 ILE Chi-restraints excluded: chain 6 residue 43 GLN Chi-restraints excluded: chain 8 residue 26 SER Chi-restraints excluded: chain 0 residue 24 ILE Chi-restraints excluded: chain a residue 5 TRP Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain c residue 5 TRP Chi-restraints excluded: chain d residue 5 TRP Chi-restraints excluded: chain e residue 5 TRP Chi-restraints excluded: chain f residue 5 TRP Chi-restraints excluded: chain f residue 18 LEU Chi-restraints excluded: chain g residue 3 MET Chi-restraints excluded: chain g residue 5 TRP Chi-restraints excluded: chain j residue 5 TRP Chi-restraints excluded: chain k residue 5 TRP Chi-restraints excluded: chain k residue 6 MET Chi-restraints excluded: chain k residue 9 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 69 optimal weight: 0.0970 chunk 235 optimal weight: 0.9980 chunk 285 optimal weight: 0.7980 chunk 202 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 200 optimal weight: 0.7980 chunk 98 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 256 optimal weight: 1.9990 chunk 240 optimal weight: 0.6980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 6 GLN E 43 GLN Z 43 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.127296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.092623 restraints weight = 56238.832| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.90 r_work: 0.2849 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2718 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2718 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.239 30435 Z= 0.110 Angle : 0.627 15.622 41737 Z= 0.249 Chirality : 0.036 0.186 4238 Planarity : 0.004 0.064 4949 Dihedral : 18.114 177.913 6387 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.67 % Allowed : 12.13 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % 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: 2.43 (0.16), residues: 2887 helix: 2.64 (0.12), residues: 1775 sheet: 0.18 (0.73), residues: 52 loop : -0.11 (0.20), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG O 3 TYR 0.019 0.001 TYR M 193 PHE 0.016 0.001 PHE Z 19 TRP 0.040 0.001 TRP I 2 HIS 0.005 0.001 HIS C 148 Details of bonding type rmsd covalent geometry : bond 0.00250 (30386) covalent geometry : angle 0.62653 (41735) SS BOND : bond 0.00315 ( 1) SS BOND : angle 0.55585 ( 2) hydrogen bonds : bond 0.04022 ( 1492) hydrogen bonds : angle 3.88416 ( 4228) Misc. bond : bond 0.05699 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16092.53 seconds wall clock time: 273 minutes 12.00 seconds (16392.00 seconds total)