Starting phenix.real_space_refine on Mon Jul 6 02:06:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xxf_33501/07_2026/7xxf_33501.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xxf_33501/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7xxf_33501/07_2026/7xxf_33501.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xxf_33501/07_2026/7xxf_33501.cif" model { file = "/net/cci-nas-00/data/ceres_data/7xxf_33501/07_2026/7xxf_33501.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xxf_33501/07_2026/7xxf_33501.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xxf_33501/07_2026/7xxf_33501.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xxf_33501/07_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 26 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: 10 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: 36 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: 6.37, per 1000 atoms: 0.21 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: 3.18 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: 0.67 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: 4.97 Time building geometry restraints manager: 3.99 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: 15668 35.51 - 71.03: 614 71.03 - 106.54: 74 106.54 - 142.05: 28 142.05 - 177.57: 15 Dihedral angle restraints: 16399 sinusoidal: 7814 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 16396 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.990 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: 0.040 Extract box with map and model: 0.600 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 27.260 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 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 : 19.243 177.566 10826 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/Z covalent geometry : bond 0.01926 / 0.90 (30386) covalent geometry : angle 1.76959 / 0.78 (41735) SS BOND : bond 0.00651 / 0.34 ( 1) SS BOND : angle 1.22048 / 0.71 ( 2) hydrogen bonds : bond 0.18522 / 12.61 ( 1492) hydrogen bonds : angle 5.83227 / 4.18 ( 4228) Misc. bond : bond 0.18645 / 12.74 ( 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 : 0.836 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: I 12 ARG cc_start: 0.6486 (mmp80) cc_final: 0.6145 (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: 0.6642 time to fit residues: 292.8909 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 : 1.112 ------------------------------------------------------------------------------- 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... 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 = 0.3587 r_free = 0.3587 target = 0.123125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.087532 restraints weight = 52507.724| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.82 r_work: 0.2764 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2627 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2627 r_free = 0.2627 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 = 0.2625 r_free = 0.2625 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.2625 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9071 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.324 30435 Z= 0.224 Angle : 0.796 15.863 41737 Z= 0.330 Chirality : 0.043 0.192 4238 Planarity : 0.005 0.070 4949 Dihedral : 20.858 176.345 5705 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.49 % Allowed : 7.35 % 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: 2.31 (0.12), residues: 1724 sheet: 0.38 (0.74), residues: 53 loop : -0.28 (0.19), residues: 1110 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 0.010 0.002 HIS Y 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.22 (30386) covalent geometry : angle 0.79635 / 0.33 (41735) SS BOND : bond 0.00674 / 0.35 ( 1) SS BOND : angle 0.91207 / 0.53 ( 2) hydrogen bonds : bond 0.05814 / 3.91 ( 1492) hydrogen bonds : angle 4.37531 / 3.12 ( 4228) Misc. bond : bond 0.07722 / 5.33 ( 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 378 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 318 time to evaluate : 1.065 Fit side-chains REVERT: L 82 ARG cc_start: 0.8847 (mtm110) cc_final: 0.8363 (mtm-85) REVERT: H 128 THR cc_start: 0.6830 (m) cc_final: 0.6509 (p) REVERT: H 166 LYS cc_start: 0.8582 (mtpt) cc_final: 0.8139 (mtpp) REVERT: H 185 LYS cc_start: 0.8906 (tptm) cc_final: 0.8474 (tmtm) REVERT: B 17 LYS cc_start: 0.8131 (mmmt) cc_final: 0.7923 (mmtm) REVERT: F 7 LEU cc_start: 0.8446 (mt) cc_final: 0.8243 (mm) REVERT: I 12 ARG cc_start: 0.6581 (mmp80) cc_final: 0.5923 (mmm-85) REVERT: K 3 ARG cc_start: 0.7115 (OUTLIER) cc_final: 0.6602 (mtt90) REVERT: N 17 LYS cc_start: 0.7463 (mttm) cc_final: 0.7085 (mtpm) REVERT: O 3 ARG cc_start: 0.8022 (mtt-85) cc_final: 0.7788 (mtm-85) REVERT: R 18 GLU cc_start: 0.8037 (tt0) cc_final: 0.7737 (tt0) REVERT: Y 6 LEU cc_start: 0.8018 (mt) cc_final: 0.7803 (mm) REVERT: 1 12 ARG cc_start: 0.7479 (mpt90) cc_final: 0.6699 (mtm180) REVERT: 2 25 THR cc_start: 0.8326 (t) cc_final: 0.7941 (p) REVERT: 2 43 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7384 (mp10) REVERT: 3 3 ARG cc_start: 0.7326 (OUTLIER) cc_final: 0.7124 (mmm160) REVERT: 3 11 ARG cc_start: 0.7087 (mtt180) cc_final: 0.6846 (mtp-110) REVERT: 4 17 LYS cc_start: 0.7405 (OUTLIER) cc_final: 0.7007 (mtpt) REVERT: 8 23 PHE cc_start: 0.7331 (t80) cc_final: 0.6471 (m-80) REVERT: g 3 MET cc_start: 0.6201 (OUTLIER) cc_final: 0.5997 (ptm) REVERT: k 5 TRP cc_start: 0.6483 (OUTLIER) cc_final: 0.5232 (p90) outliers start: 60 outliers final: 32 residues processed: 348 average time/residue: 0.6431 time to fit residues: 264.4693 Evaluate side-chains 340 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 302 time to evaluate : 1.030 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 166 optimal weight: 0.9980 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: 0.8980 chunk 195 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3618 r_free = 0.3618 target = 0.125168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.090259 restraints weight = 54234.519| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.90 r_work: 0.2802 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2668 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2668 r_free = 0.2668 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2668 r_free = 0.2668 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (6 function evaluations) r_final: 0.2668 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9044 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.291 30435 Z= 0.128 Angle : 0.658 13.731 41737 Z= 0.267 Chirality : 0.037 0.186 4238 Planarity : 0.004 0.069 4949 Dihedral : 19.613 179.612 5703 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.12 % Allowed : 9.11 % 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: 2.14 (0.16), residues: 2887 helix: 2.50 (0.12), residues: 1732 sheet: 0.16 (0.72), residues: 53 loop : -0.29 (0.19), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG W 46 TYR 0.020 0.001 TYR M 193 PHE 0.016 0.001 PHE H 20 TRP 0.017 0.001 TRP U 2 HIS 0.006 0.001 HIS Y 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (30386) covalent geometry : angle 0.65836 / 0.27 (41735) SS BOND : bond 0.00363 / 0.19 ( 1) SS BOND : angle 0.70124 / 0.41 ( 2) hydrogen bonds : bond 0.04763 / 3.20 ( 1492) hydrogen bonds : angle 4.11703 / 2.93 ( 4228) Misc. bond : bond 0.06095 / 4.25 ( 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 383 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 332 time to evaluate : 0.957 Fit side-chains REVERT: C 68 ARG cc_start: 0.8448 (ttt-90) cc_final: 0.7984 (ttt90) REVERT: L 82 ARG cc_start: 0.8811 (mtm110) cc_final: 0.8429 (mtm-85) REVERT: M 182 HIS cc_start: 0.9346 (OUTLIER) cc_final: 0.9099 (p-80) REVERT: H 2 GLU cc_start: 0.7575 (mm-30) cc_final: 0.6977 (pm20) REVERT: H 128 THR cc_start: 0.6859 (m) cc_final: 0.6513 (p) REVERT: H 185 LYS cc_start: 0.8850 (tptm) cc_final: 0.8499 (tmtm) REVERT: B 17 LYS cc_start: 0.8139 (mmmt) cc_final: 0.7805 (mttm) REVERT: F 7 LEU cc_start: 0.8353 (mt) cc_final: 0.8150 (mm) REVERT: I 12 ARG cc_start: 0.6551 (mmp80) cc_final: 0.5907 (mmm-85) REVERT: K 3 ARG cc_start: 0.7046 (OUTLIER) cc_final: 0.6703 (mtt90) REVERT: N 18 GLU cc_start: 0.7643 (tp30) cc_final: 0.7295 (tt0) REVERT: O 3 ARG cc_start: 0.7963 (mtt-85) cc_final: 0.7518 (mtm-85) REVERT: O 15 VAL cc_start: 0.8971 (t) cc_final: 0.8701 (p) REVERT: P 43 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8346 (mp10) REVERT: Q 8 PHE cc_start: 0.8061 (m-80) cc_final: 0.7675 (m-80) REVERT: R 18 GLU cc_start: 0.8075 (tt0) cc_final: 0.7504 (tt0) REVERT: V 25 THR cc_start: 0.8593 (m) cc_final: 0.8167 (t) REVERT: Y 6 LEU cc_start: 0.8075 (mt) cc_final: 0.7855 (mm) REVERT: 1 4 MET cc_start: 0.7477 (OUTLIER) cc_final: 0.7037 (ttp) REVERT: 1 12 ARG cc_start: 0.7485 (mpt90) cc_final: 0.6765 (mtm180) REVERT: 2 18 GLU cc_start: 0.7923 (tp30) cc_final: 0.7685 (tp30) REVERT: 2 25 THR cc_start: 0.8388 (t) cc_final: 0.7973 (p) REVERT: 2 43 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7401 (mp10) REVERT: 3 3 ARG cc_start: 0.7386 (mtm180) cc_final: 0.7175 (mmm160) REVERT: 3 11 ARG cc_start: 0.6922 (mtt180) cc_final: 0.6626 (mtm180) REVERT: 4 17 LYS cc_start: 0.7474 (OUTLIER) cc_final: 0.7017 (mtpt) REVERT: 8 18 GLU cc_start: 0.7851 (tt0) cc_final: 0.7463 (tt0) REVERT: 8 23 PHE cc_start: 0.7282 (t80) cc_final: 0.6481 (m-80) REVERT: 9 4 MET cc_start: 0.7847 (ptt) cc_final: 0.7549 (ptm) REVERT: g 3 MET cc_start: 0.6251 (OUTLIER) cc_final: 0.5809 (ptp) REVERT: k 5 TRP cc_start: 0.6356 (OUTLIER) cc_final: 0.5500 (p90) outliers start: 51 outliers final: 29 residues processed: 357 average time/residue: 0.6821 time to fit residues: 286.5174 Evaluate side-chains 344 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 307 time to evaluate : 1.065 ------------------------------------------------------------------------------- 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 262 PHE Chi-restraints excluded: chain M residue 287 THR Chi-restraints excluded: chain M residue 314 VAL Chi-restraints excluded: chain H residue 1 MET 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 P residue 43 GLN Chi-restraints excluded: chain R residue 43 GLN Chi-restraints excluded: chain Y residue 7 LEU Chi-restraints excluded: chain 1 residue 4 MET 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 3 MET Chi-restraints excluded: chain j residue 5 TRP Chi-restraints excluded: chain k residue 5 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 18 optimal weight: 0.7980 chunk 169 optimal weight: 0.9990 chunk 234 optimal weight: 4.9990 chunk 32 optimal weight: 0.0570 chunk 29 optimal weight: 2.9990 chunk 230 optimal weight: 6.9990 chunk 178 optimal weight: 0.9990 chunk 140 optimal weight: 0.0870 chunk 249 optimal weight: 5.9990 chunk 135 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3656 r_free = 0.3656 target = 0.127899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.096888 restraints weight = 44953.357| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.48 r_work: 0.2906 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2773 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2773 r_free = 0.2773 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2773 r_free = 0.2773 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2773 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8984 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.226 30435 Z= 0.107 Angle : 0.617 13.636 41737 Z= 0.246 Chirality : 0.036 0.193 4238 Planarity : 0.004 0.065 4949 Dihedral : 18.413 175.962 5698 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.08 % Allowed : 10.25 % Favored : 87.66 % 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: 2.38 (0.16), residues: 2887 helix: 2.61 (0.12), residues: 1775 sheet: 0.08 (0.73), residues: 53 loop : -0.13 (0.20), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG W 46 TYR 0.018 0.001 TYR M 193 PHE 0.013 0.001 PHE H 20 TRP 0.020 0.001 TRP U 2 HIS 0.004 0.001 HIS M 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (30386) covalent geometry : angle 0.61672 / 0.25 (41735) SS BOND : bond 0.00318 / 0.17 ( 1) SS BOND : angle 0.49344 / 0.29 ( 2) hydrogen bonds : bond 0.04048 / 2.72 ( 1492) hydrogen bonds : angle 3.90429 / 2.77 ( 4228) Misc. bond : bond 0.04637 / 3.13 ( 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 375 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 325 time to evaluate : 1.087 Fit side-chains REVERT: C 68 ARG cc_start: 0.8450 (ttt-90) cc_final: 0.8121 (ttt90) REVERT: L 82 ARG cc_start: 0.8728 (mtm110) cc_final: 0.8419 (mtm-85) REVERT: M 117 MET cc_start: 0.8843 (mtp) cc_final: 0.8606 (mtp) REVERT: M 182 HIS cc_start: 0.9293 (OUTLIER) cc_final: 0.8972 (p-80) REVERT: H 2 GLU cc_start: 0.7548 (mm-30) cc_final: 0.6980 (pm20) REVERT: H 128 THR cc_start: 0.6934 (OUTLIER) cc_final: 0.6553 (p) REVERT: H 185 LYS cc_start: 0.8843 (tptm) cc_final: 0.8450 (tmtm) REVERT: A 4 MET cc_start: 0.8237 (ptm) cc_final: 0.8016 (ppp) REVERT: B 17 LYS cc_start: 0.8095 (mmmt) cc_final: 0.7824 (mttm) REVERT: D 3 ARG cc_start: 0.7402 (mtm-85) cc_final: 0.7030 (mpt-90) REVERT: F 4 MET cc_start: 0.7794 (OUTLIER) cc_final: 0.7538 (tpp) REVERT: F 7 LEU cc_start: 0.8375 (mt) cc_final: 0.8172 (mm) REVERT: I 12 ARG cc_start: 0.6541 (mmp80) cc_final: 0.5950 (mmm-85) REVERT: K 3 ARG cc_start: 0.6961 (OUTLIER) cc_final: 0.6752 (mtt90) REVERT: N 18 GLU cc_start: 0.7513 (tp30) cc_final: 0.7209 (tt0) REVERT: O 3 ARG cc_start: 0.7889 (mtt-85) cc_final: 0.7557 (mtm-85) REVERT: O 15 VAL cc_start: 0.8949 (t) cc_final: 0.8648 (p) REVERT: O 45 HIS cc_start: 0.6336 (OUTLIER) cc_final: 0.5909 (m170) REVERT: Q 8 PHE cc_start: 0.8035 (m-80) cc_final: 0.7646 (m-80) REVERT: R 18 GLU cc_start: 0.7977 (tt0) cc_final: 0.7594 (tt0) REVERT: V 25 THR cc_start: 0.8554 (m) cc_final: 0.8188 (t) REVERT: Y 6 LEU cc_start: 0.8084 (mt) cc_final: 0.7831 (mm) REVERT: 1 4 MET cc_start: 0.7452 (ptt) cc_final: 0.7015 (ttp) REVERT: 1 12 ARG cc_start: 0.7404 (mpt90) cc_final: 0.6897 (mtp180) REVERT: 2 25 THR cc_start: 0.8377 (t) cc_final: 0.7973 (p) REVERT: 3 11 ARG cc_start: 0.6810 (mtt180) cc_final: 0.6589 (mtp-110) REVERT: 4 17 LYS cc_start: 0.7438 (OUTLIER) cc_final: 0.7017 (mtpt) REVERT: 6 43 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.8547 (tt0) REVERT: 8 23 PHE cc_start: 0.7258 (t80) cc_final: 0.6526 (m-80) REVERT: 9 4 MET cc_start: 0.7729 (ptt) cc_final: 0.7442 (ptm) REVERT: g 3 MET cc_start: 0.6262 (ptm) cc_final: 0.5894 (ptp) REVERT: k 5 TRP cc_start: 0.6269 (OUTLIER) cc_final: 0.5815 (p-90) REVERT: k 6 MET cc_start: 0.5853 (OUTLIER) cc_final: 0.5334 (mtp) outliers start: 50 outliers final: 24 residues processed: 347 average time/residue: 0.6491 time to fit residues: 267.2115 Evaluate side-chains 332 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 299 time to evaluate : 1.136 ------------------------------------------------------------------------------- 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 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 6 residue 43 GLN 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 252 optimal weight: 0.8980 chunk 268 optimal weight: 2.9990 chunk 180 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 204 optimal weight: 3.9990 chunk 153 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 144 optimal weight: 0.3980 chunk 218 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3621 r_free = 0.3621 target = 0.125243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.090600 restraints weight = 52091.348| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 1.80 r_work: 0.2818 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2687 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2687 r_free = 0.2687 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2687 r_free = 0.2687 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2687 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9034 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.279 30435 Z= 0.132 Angle : 0.650 13.064 41737 Z= 0.264 Chirality : 0.038 0.193 4238 Planarity : 0.004 0.067 4949 Dihedral : 18.407 176.891 5694 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.17 % Allowed : 10.70 % 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: 2.32 (0.16), residues: 2887 helix: 2.54 (0.12), residues: 1780 sheet: 0.00 (0.72), residues: 53 loop : -0.14 (0.20), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG W 46 TYR 0.020 0.001 TYR M 193 PHE 0.018 0.002 PHE H 20 TRP 0.023 0.001 TRP I 2 HIS 0.007 0.001 HIS L 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (30386) covalent geometry : angle 0.65033 / 0.26 (41735) SS BOND : bond 0.00399 / 0.21 ( 1) SS BOND : angle 0.58971 / 0.34 ( 2) hydrogen bonds : bond 0.04520 / 3.03 ( 1492) hydrogen bonds : angle 3.98865 / 2.84 ( 4228) Misc. bond : bond 0.05977 / 4.11 ( 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 356 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 304 time to evaluate : 1.123 Fit side-chains REVERT: C 40 ARG cc_start: 0.8965 (OUTLIER) cc_final: 0.8269 (mtm180) REVERT: C 68 ARG cc_start: 0.8445 (ttt-90) cc_final: 0.8063 (ttt90) REVERT: M 182 HIS cc_start: 0.9398 (OUTLIER) cc_final: 0.9158 (p-80) REVERT: H 2 GLU cc_start: 0.7558 (mm-30) cc_final: 0.6959 (pm20) REVERT: H 128 THR cc_start: 0.6878 (OUTLIER) cc_final: 0.6483 (p) REVERT: H 185 LYS cc_start: 0.8853 (tptm) cc_final: 0.8536 (tmtm) REVERT: B 17 LYS cc_start: 0.8066 (mmmt) cc_final: 0.7811 (mttm) REVERT: F 4 MET cc_start: 0.7892 (OUTLIER) cc_final: 0.7638 (tpp) REVERT: F 7 LEU cc_start: 0.8355 (mt) cc_final: 0.8149 (mm) REVERT: F 12 ARG cc_start: 0.7978 (mtp180) cc_final: 0.7757 (mtp-110) REVERT: I 12 ARG cc_start: 0.6497 (mmp80) cc_final: 0.5889 (mmm-85) REVERT: K 3 ARG cc_start: 0.7083 (OUTLIER) cc_final: 0.6797 (mtt90) REVERT: N 18 GLU cc_start: 0.7548 (tp30) cc_final: 0.7252 (tt0) REVERT: O 3 ARG cc_start: 0.7915 (mtt-85) cc_final: 0.7612 (mtm-85) REVERT: O 45 HIS cc_start: 0.6386 (OUTLIER) cc_final: 0.5993 (m170) REVERT: Q 8 PHE cc_start: 0.8046 (m-80) cc_final: 0.7672 (m-80) REVERT: V 25 THR cc_start: 0.8570 (m) cc_final: 0.8152 (t) REVERT: 1 4 MET cc_start: 0.7490 (ptt) cc_final: 0.7040 (ttp) REVERT: 1 12 ARG cc_start: 0.7424 (mpt90) cc_final: 0.6910 (mtp180) REVERT: 2 18 GLU cc_start: 0.7798 (tp30) cc_final: 0.7589 (tp30) REVERT: 2 25 THR cc_start: 0.8374 (t) cc_final: 0.7973 (p) REVERT: 3 11 ARG cc_start: 0.6813 (mtt180) cc_final: 0.6574 (mtp-110) REVERT: 4 17 LYS cc_start: 0.7419 (OUTLIER) cc_final: 0.7015 (mtpt) REVERT: 8 18 GLU cc_start: 0.7784 (tt0) cc_final: 0.7440 (tt0) REVERT: 8 23 PHE cc_start: 0.7280 (t80) cc_final: 0.6522 (m-80) REVERT: 9 4 MET cc_start: 0.7782 (ptt) cc_final: 0.7478 (ptm) REVERT: h 6 MET cc_start: 0.7925 (mtp) cc_final: 0.7706 (mtm) REVERT: k 5 TRP cc_start: 0.6366 (OUTLIER) cc_final: 0.5459 (p90) REVERT: k 6 MET cc_start: 0.5751 (OUTLIER) cc_final: 0.5334 (mtp) outliers start: 52 outliers final: 31 residues processed: 331 average time/residue: 0.7138 time to fit residues: 278.7294 Evaluate side-chains 338 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 298 time to evaluate : 1.111 ------------------------------------------------------------------------------- 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 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 7 LEU 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 275 optimal weight: 0.9990 chunk 257 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 178 optimal weight: 0.9990 chunk 149 optimal weight: 8.9990 chunk 5 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 107 optimal weight: 0.0170 chunk 240 optimal weight: 0.7980 chunk 215 optimal weight: 0.0980 chunk 38 optimal weight: 2.9990 overall best weight: 0.5822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 104 ASN Z 43 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.127386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.093209 restraints weight = 56958.172| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.84 r_work: 0.2847 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- 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 = 0.22 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 = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2714 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9012 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.234 30435 Z= 0.105 Angle : 0.607 12.813 41737 Z= 0.243 Chirality : 0.036 0.191 4238 Planarity : 0.004 0.064 4949 Dihedral : 17.762 176.258 5694 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.04 % Allowed : 10.87 % Favored : 87.09 % 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: 2.45 (0.16), residues: 2887 helix: 2.67 (0.12), residues: 1769 sheet: 0.02 (0.73), residues: 53 loop : -0.08 (0.20), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG W 46 TYR 0.019 0.001 TYR M 193 PHE 0.013 0.001 PHE H 20 TRP 0.025 0.001 TRP I 2 HIS 0.004 0.001 HIS C 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.10 (30386) covalent geometry : angle 0.60653 / 0.24 (41735) SS BOND : bond 0.00315 / 0.17 ( 1) SS BOND : angle 0.51405 / 0.30 ( 2) hydrogen bonds : bond 0.04009 / 2.69 ( 1492) hydrogen bonds : angle 3.87849 / 2.75 ( 4228) Misc. bond : bond 0.04913 / 3.31 ( 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 363 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 314 time to evaluate : 1.157 Fit side-chains REVERT: C 68 ARG cc_start: 0.8481 (ttt-90) cc_final: 0.8146 (ttt90) REVERT: M 182 HIS cc_start: 0.9309 (OUTLIER) cc_final: 0.9009 (p-80) REVERT: H 2 GLU cc_start: 0.7610 (mm-30) cc_final: 0.6946 (pm20) REVERT: H 128 THR cc_start: 0.6866 (OUTLIER) cc_final: 0.6465 (p) REVERT: H 185 LYS cc_start: 0.8876 (tptm) cc_final: 0.8567 (tmtm) REVERT: B 17 LYS cc_start: 0.8037 (mmmt) cc_final: 0.7806 (mttm) REVERT: D 3 ARG cc_start: 0.7432 (mtm-85) cc_final: 0.7041 (mpt-90) REVERT: D 4 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.7982 (tpp) REVERT: F 4 MET cc_start: 0.7916 (OUTLIER) cc_final: 0.7687 (tpp) REVERT: I 12 ARG cc_start: 0.6534 (mmp80) cc_final: 0.5926 (mmm-85) REVERT: K 3 ARG cc_start: 0.7038 (OUTLIER) cc_final: 0.6801 (mtt90) REVERT: N 18 GLU cc_start: 0.7642 (tp30) cc_final: 0.7377 (tt0) REVERT: O 15 VAL cc_start: 0.8977 (t) cc_final: 0.8692 (p) REVERT: P 43 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.8343 (mp10) REVERT: Q 8 PHE cc_start: 0.8040 (m-80) cc_final: 0.7645 (m-80) REVERT: S 4 MET cc_start: 0.7558 (ptm) cc_final: 0.7345 (ptm) REVERT: V 25 THR cc_start: 0.8570 (m) cc_final: 0.8166 (t) REVERT: W 4 MET cc_start: 0.7319 (tpt) cc_final: 0.6981 (mmm) REVERT: Y 6 LEU cc_start: 0.8070 (mt) cc_final: 0.7795 (mm) REVERT: 1 12 ARG cc_start: 0.7425 (mpt90) cc_final: 0.6632 (mtm-85) REVERT: 2 24 ILE cc_start: 0.8266 (mm) cc_final: 0.7807 (mm) REVERT: 2 25 THR cc_start: 0.8396 (t) cc_final: 0.7987 (p) REVERT: 3 11 ARG cc_start: 0.6886 (mtt180) cc_final: 0.6666 (mtm180) REVERT: 4 17 LYS cc_start: 0.7419 (OUTLIER) cc_final: 0.7027 (mtpt) REVERT: 8 18 GLU cc_start: 0.7805 (tt0) cc_final: 0.7464 (tt0) REVERT: 8 23 PHE cc_start: 0.7321 (t80) cc_final: 0.6556 (m-80) REVERT: 9 4 MET cc_start: 0.7812 (ptt) cc_final: 0.7506 (ptm) REVERT: g 3 MET cc_start: 0.6297 (OUTLIER) cc_final: 0.5889 (ptp) REVERT: k 5 TRP cc_start: 0.6267 (OUTLIER) cc_final: 0.5821 (p-90) REVERT: k 6 MET cc_start: 0.5618 (OUTLIER) cc_final: 0.5010 (mtp) REVERT: k 9 LEU cc_start: 0.5869 (OUTLIER) cc_final: 0.5296 (tp) outliers start: 49 outliers final: 26 residues processed: 339 average time/residue: 0.6893 time to fit residues: 276.3100 Evaluate side-chains 331 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 294 time to evaluate : 1.048 ------------------------------------------------------------------------------- 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 287 THR Chi-restraints excluded: chain M residue 314 VAL Chi-restraints excluded: chain H residue 1 MET 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 43 GLN Chi-restraints excluded: chain R residue 43 GLN Chi-restraints excluded: chain U residue 13 ILE 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 3 MET 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 Chi-restraints excluded: chain k residue 6 MET 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: 0.7980 chunk 261 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 269 optimal weight: 4.9990 chunk 190 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 137 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 278 optimal weight: 8.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3626 r_free = 0.3626 target = 0.125596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.091210 restraints weight = 49740.143| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 1.80 r_work: 0.2832 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2699 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2699 r_free = 0.2699 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2699 r_free = 0.2699 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2699 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9023 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.273 30435 Z= 0.130 Angle : 0.644 12.819 41737 Z= 0.260 Chirality : 0.037 0.189 4238 Planarity : 0.004 0.064 4949 Dihedral : 17.804 177.194 5694 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.08 % Allowed : 11.11 % 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: 2.33 (0.16), residues: 2887 helix: 2.67 (0.12), residues: 1726 sheet: 0.02 (0.73), residues: 53 loop : -0.21 (0.19), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG O 3 TYR 0.020 0.001 TYR M 193 PHE 0.018 0.001 PHE H 20 TRP 0.027 0.001 TRP U 2 HIS 0.007 0.001 HIS C 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (30386) covalent geometry : angle 0.64386 / 0.26 (41735) SS BOND : bond 0.00395 / 0.21 ( 1) SS BOND : angle 0.58321 / 0.34 ( 2) hydrogen bonds : bond 0.04398 / 2.95 ( 1492) hydrogen bonds : angle 3.95862 / 2.81 ( 4228) Misc. bond : bond 0.05983 / 4.07 ( 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 347 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 297 time to evaluate : 1.138 Fit side-chains REVERT: C 68 ARG cc_start: 0.8442 (ttt-90) cc_final: 0.7977 (ttt90) REVERT: L 82 ARG cc_start: 0.8726 (mtp180) cc_final: 0.8501 (mpp80) REVERT: M 182 HIS cc_start: 0.9390 (OUTLIER) cc_final: 0.9138 (p-80) REVERT: H 2 GLU cc_start: 0.7569 (mm-30) cc_final: 0.6945 (pm20) REVERT: H 128 THR cc_start: 0.6852 (OUTLIER) cc_final: 0.6449 (p) REVERT: H 185 LYS cc_start: 0.8860 (tptm) cc_final: 0.8536 (tmtm) REVERT: B 17 LYS cc_start: 0.7988 (mmmt) cc_final: 0.7754 (mttm) REVERT: D 4 MET cc_start: 0.8295 (tpt) cc_final: 0.8051 (tpp) REVERT: F 4 MET cc_start: 0.7883 (OUTLIER) cc_final: 0.7667 (tpp) REVERT: I 12 ARG cc_start: 0.6474 (mmp80) cc_final: 0.5860 (mmm-85) REVERT: K 3 ARG cc_start: 0.7043 (OUTLIER) cc_final: 0.6771 (mtt90) REVERT: N 18 GLU cc_start: 0.7618 (tp30) cc_final: 0.7329 (tt0) REVERT: P 43 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8179 (mp10) REVERT: Q 8 PHE cc_start: 0.8038 (m-80) cc_final: 0.7594 (m-80) REVERT: R 18 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7769 (tt0) REVERT: S 4 MET cc_start: 0.7547 (ptm) cc_final: 0.7337 (ptm) REVERT: V 25 THR cc_start: 0.8559 (m) cc_final: 0.8147 (t) REVERT: 1 4 MET cc_start: 0.7705 (ptt) cc_final: 0.7146 (ttp) REVERT: 1 12 ARG cc_start: 0.7375 (mpt90) cc_final: 0.6581 (mtm-85) REVERT: 2 24 ILE cc_start: 0.8257 (mm) cc_final: 0.7796 (mm) REVERT: 2 25 THR cc_start: 0.8350 (t) cc_final: 0.7936 (p) REVERT: 3 2 TRP cc_start: 0.7598 (p-90) cc_final: 0.7394 (p-90) REVERT: 3 11 ARG cc_start: 0.6806 (mtt180) cc_final: 0.6577 (mtm180) REVERT: 4 17 LYS cc_start: 0.7388 (OUTLIER) cc_final: 0.6972 (mtpt) REVERT: 8 18 GLU cc_start: 0.7762 (tt0) cc_final: 0.7412 (tt0) REVERT: 8 23 PHE cc_start: 0.7262 (t80) cc_final: 0.6510 (m-80) REVERT: 9 4 MET cc_start: 0.7767 (ptt) cc_final: 0.7457 (ptm) REVERT: g 3 MET cc_start: 0.6304 (OUTLIER) cc_final: 0.5809 (ptp) REVERT: k 5 TRP cc_start: 0.6350 (OUTLIER) cc_final: 0.5494 (p90) REVERT: k 6 MET cc_start: 0.5671 (OUTLIER) cc_final: 0.5157 (mtp) REVERT: k 9 LEU cc_start: 0.5869 (OUTLIER) cc_final: 0.5303 (tp) outliers start: 50 outliers final: 34 residues processed: 323 average time/residue: 0.7180 time to fit residues: 273.0097 Evaluate side-chains 336 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 291 time to evaluate : 1.059 ------------------------------------------------------------------------------- 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 262 PHE Chi-restraints excluded: chain M residue 287 THR Chi-restraints excluded: chain M residue 314 VAL Chi-restraints excluded: chain H residue 1 MET 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 7 LEU 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 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 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 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 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: 1.9990 chunk 211 optimal weight: 8.9990 chunk 166 optimal weight: 0.5980 chunk 156 optimal weight: 2.9990 chunk 195 optimal weight: 3.9990 chunk 226 optimal weight: 0.8980 chunk 259 optimal weight: 7.9990 chunk 265 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 52 optimal weight: 7.9990 chunk 16 optimal weight: 8.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 6 GLN H 104 ASN E 43 GLN Z 43 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.125800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.091364 restraints weight = 51918.061| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.78 r_work: 0.2834 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2702 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2702 r_free = 0.2702 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2702 r_free = 0.2702 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2702 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9024 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.270 30435 Z= 0.122 Angle : 0.640 12.838 41737 Z= 0.256 Chirality : 0.037 0.189 4238 Planarity : 0.004 0.065 4949 Dihedral : 17.647 177.864 5694 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.12 % Allowed : 11.15 % Favored : 86.72 % 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: 2.32 (0.16), residues: 2887 helix: 2.66 (0.12), residues: 1726 sheet: 0.03 (0.73), residues: 53 loop : -0.22 (0.19), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG O 3 TYR 0.019 0.001 TYR M 193 PHE 0.017 0.001 PHE H 20 TRP 0.035 0.001 TRP U 2 HIS 0.006 0.001 HIS C 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (30386) covalent geometry : angle 0.63973 / 0.26 (41735) SS BOND : bond 0.00376 / 0.20 ( 1) SS BOND : angle 0.57805 / 0.33 ( 2) hydrogen bonds : bond 0.04314 / 2.89 ( 1492) hydrogen bonds : angle 3.95395 / 2.81 ( 4228) Misc. bond : bond 0.05957 / 4.04 ( 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 347 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 296 time to evaluate : 1.102 Fit side-chains REVERT: C 68 ARG cc_start: 0.8451 (ttt-90) cc_final: 0.8077 (ttt90) REVERT: L 82 ARG cc_start: 0.8723 (mtp180) cc_final: 0.8351 (mpp80) REVERT: M 182 HIS cc_start: 0.9367 (OUTLIER) cc_final: 0.9068 (p-80) REVERT: H 2 GLU cc_start: 0.7579 (mm-30) cc_final: 0.6931 (pm20) REVERT: H 128 THR cc_start: 0.6844 (OUTLIER) cc_final: 0.6433 (p) REVERT: H 166 LYS cc_start: 0.8511 (mtpt) cc_final: 0.8251 (mmtm) REVERT: H 185 LYS cc_start: 0.8857 (tptm) cc_final: 0.8529 (tmtm) REVERT: B 17 LYS cc_start: 0.8011 (mmmt) cc_final: 0.7777 (mttm) REVERT: D 3 ARG cc_start: 0.7570 (mtm-85) cc_final: 0.7207 (mpt-90) REVERT: D 4 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.8071 (tpp) REVERT: F 4 MET cc_start: 0.7883 (OUTLIER) cc_final: 0.7681 (tpp) REVERT: I 12 ARG cc_start: 0.6481 (mmp80) cc_final: 0.5848 (mmm-85) REVERT: K 3 ARG cc_start: 0.7029 (OUTLIER) cc_final: 0.6760 (mtt90) REVERT: N 18 GLU cc_start: 0.7619 (tp30) cc_final: 0.7315 (tt0) REVERT: O 3 ARG cc_start: 0.7954 (mtt-85) cc_final: 0.7327 (mtm-85) REVERT: P 43 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.8233 (mp10) REVERT: Q 8 PHE cc_start: 0.7967 (m-80) cc_final: 0.7555 (m-80) REVERT: R 18 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7389 (tt0) REVERT: S 4 MET cc_start: 0.7523 (ptm) cc_final: 0.7317 (ptm) REVERT: V 25 THR cc_start: 0.8565 (m) cc_final: 0.8148 (t) REVERT: 1 4 MET cc_start: 0.7654 (ptt) cc_final: 0.7061 (ttp) REVERT: 1 12 ARG cc_start: 0.7358 (mpt90) cc_final: 0.6571 (mtm-85) REVERT: 2 24 ILE cc_start: 0.8268 (mm) cc_final: 0.7798 (mm) REVERT: 2 25 THR cc_start: 0.8370 (t) cc_final: 0.7962 (p) REVERT: 3 2 TRP cc_start: 0.7603 (p-90) cc_final: 0.7347 (p-90) REVERT: 3 11 ARG cc_start: 0.6874 (mtt180) cc_final: 0.6661 (mtm180) REVERT: 4 17 LYS cc_start: 0.7316 (tptp) cc_final: 0.6953 (mtpt) REVERT: 8 23 PHE cc_start: 0.7262 (t80) cc_final: 0.6517 (m-80) REVERT: 9 4 MET cc_start: 0.7793 (ptt) cc_final: 0.7481 (ptm) REVERT: g 3 MET cc_start: 0.6305 (OUTLIER) cc_final: 0.5808 (ptp) REVERT: k 5 TRP cc_start: 0.6291 (OUTLIER) cc_final: 0.5494 (p90) REVERT: k 6 MET cc_start: 0.5654 (OUTLIER) cc_final: 0.5153 (mtp) REVERT: k 9 LEU cc_start: 0.5911 (OUTLIER) cc_final: 0.5347 (tp) outliers start: 51 outliers final: 36 residues processed: 322 average time/residue: 0.6996 time to fit residues: 265.8693 Evaluate side-chains 335 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 288 time to evaluate : 1.025 ------------------------------------------------------------------------------- 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 262 PHE Chi-restraints excluded: chain M residue 287 THR Chi-restraints excluded: chain M residue 314 VAL Chi-restraints excluded: chain H residue 1 MET 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 D residue 7 LEU 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 18 GLU 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 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 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 Chi-restraints excluded: chain k residue 9 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 63.4509 > 50: distance: 52 - 56: 19.860 distance: 56 - 57: 38.314 distance: 57 - 58: 13.829 distance: 57 - 60: 19.469 distance: 58 - 59: 10.436 distance: 58 - 63: 28.800 distance: 60 - 61: 27.313 distance: 60 - 62: 17.757 distance: 63 - 64: 55.947 distance: 64 - 65: 39.514 distance: 65 - 66: 48.953 distance: 65 - 67: 42.258 distance: 67 - 68: 22.100 distance: 69 - 70: 12.246 distance: 69 - 76: 39.662 distance: 71 - 72: 7.221 distance: 72 - 73: 5.088 distance: 73 - 74: 39.188 distance: 74 - 75: 45.449 distance: 76 - 77: 17.984 distance: 76 - 82: 29.641 distance: 77 - 78: 46.112 distance: 77 - 80: 30.448 distance: 78 - 79: 41.166 distance: 78 - 83: 39.284 distance: 80 - 81: 7.115 distance: 81 - 82: 13.935 distance: 83 - 84: 43.048 distance: 83 - 184: 17.791 distance: 84 - 85: 15.688 distance: 84 - 87: 28.534 distance: 85 - 86: 10.321 distance: 85 - 94: 13.868 distance: 86 - 181: 26.049 distance: 87 - 88: 17.253 distance: 88 - 89: 23.838 distance: 88 - 90: 25.056 distance: 89 - 91: 4.180 distance: 90 - 92: 11.231 distance: 91 - 93: 41.221 distance: 92 - 93: 10.347 distance: 94 - 95: 9.514 distance: 95 - 96: 26.448 distance: 95 - 98: 25.983 distance: 96 - 97: 26.895 distance: 96 - 104: 26.171 distance: 98 - 99: 6.739 distance: 99 - 100: 24.686 distance: 99 - 101: 44.939 distance: 100 - 102: 31.538 distance: 101 - 103: 28.474 distance: 102 - 103: 17.761 distance: 104 - 105: 40.891 distance: 105 - 106: 3.004 distance: 105 - 108: 38.892 distance: 106 - 107: 36.505 distance: 107 - 140: 25.736 distance: 108 - 109: 4.908 distance: 109 - 110: 15.957 distance: 109 - 111: 23.098 distance: 113 - 114: 22.979 distance: 113 - 116: 14.217 distance: 114 - 115: 6.664 distance: 114 - 124: 24.741 distance: 115 - 144: 29.360 distance: 116 - 117: 25.635 distance: 124 - 125: 36.283 distance: 125 - 126: 6.346 distance: 125 - 128: 43.806 distance: 126 - 127: 11.539 distance: 126 - 132: 9.346 distance: 128 - 129: 15.504 distance: 129 - 130: 39.616 distance: 132 - 133: 6.584 distance: 133 - 134: 37.783 distance: 133 - 136: 36.423 distance: 134 - 135: 29.495 distance: 134 - 140: 7.448 distance: 135 - 159: 29.312 distance: 136 - 137: 19.339 distance: 137 - 138: 21.459 distance: 137 - 139: 9.556