Starting phenix.real_space_refine on Fri Jun 27 17:01:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xxf_33501/06_2025/7xxf_33501.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xxf_33501/06_2025/7xxf_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7xxf_33501/06_2025/7xxf_33501.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xxf_33501/06_2025/7xxf_33501.map" model { file = "/net/cci-nas-00/data/ceres_data/7xxf_33501/06_2025/7xxf_33501.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xxf_33501/06_2025/7xxf_33501.cif" } resolution = 2.24 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 29826 Number of models: 1 Model: "" Number of chains: 120 Chain: "C" Number of atoms: 2655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2655 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 316} Chain: "L" Number of atoms: 2177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2177 Classifications: {'peptide': 274} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 258} Chain: "M" Number of atoms: 2550 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 320, 2543 Classifications: {'peptide': 320} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 300} Conformer: "B" Number of residues, atoms: 320, 2543 Classifications: {'peptide': 320} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 300} bond proxies already assigned to first conformer: 2637 Chain: "H" Number of atoms: 2000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2000 Classifications: {'peptide': 258} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 21, 'TRANS': 233} Chain: "A" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 384 Classifications: {'peptide': 45} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 42} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'FME:plan-2': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 396 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "D" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 384 Classifications: {'peptide': 45} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 42} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'FME:plan-2': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 396 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "F" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 384 Classifications: {'peptide': 45} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 42} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'FME:plan-2': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "G" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 396 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "I" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 394 Classifications: {'peptide': 46} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 43} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'FME:plan-2': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "J" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 396 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "K" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 384 Classifications: {'peptide': 45} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 42} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'FME:plan-2': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "N" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 396 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "O" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 389 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 396 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "Q" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 389 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 396 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "S" Number of atoms: 475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 475 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 396 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "U" Number of atoms: 443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 443 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "V" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 396 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "W" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 470 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "X" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 396 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "Y" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 384 Classifications: {'peptide': 45} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 42} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'FME:plan-2': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "Z" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 396 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "1" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 395 Classifications: {'peptide': 46} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 43} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'FME:plan-2': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "2" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 396 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "3" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 472 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 51} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "4" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 396 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "5" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 389 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "6" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 396 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "7" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 389 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "8" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 396 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "9" Number of atoms: 392 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 45, 384 Classifications: {'peptide': 45} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 42} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'FME:plan-2': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 45, 384 Classifications: {'peptide': 45} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 42} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'FME:plan-2': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 388 Chain: "0" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 396 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "a" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 177 Classifications: {'peptide': 22} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "b" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 177 Classifications: {'peptide': 22} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "c" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 177 Classifications: {'peptide': 22} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "d" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 177 Classifications: {'peptide': 22} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "e" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 177 Classifications: {'peptide': 22} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "f" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 177 Classifications: {'peptide': 22} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "g" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 177 Classifications: {'peptide': 22} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "h" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 177 Classifications: {'peptide': 22} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "i" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 177 Classifications: {'peptide': 22} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "j" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 177 Classifications: {'peptide': 22} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "k" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 177 Classifications: {'peptide': 22} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 296 Unusual residues: {'HEC': 4, 'PGV': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 539 Unusual residues: {'BCL': 2, 'BPH': 1, 'LMT': 2, 'PGV': 5, 'U10': 3} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 150 Planarities with less than four sites: {'PGV:plan-3': 5, 'U10:plan-2': 1, 'U10:plan-8': 3, 'U10:plan-9': 3, 'U10:plan-3': 1, 'U10:plan-4': 1, 'U10:plan-5': 1, 'U10:plan-6': 3, 'U10:plan-7': 3, 'U10:plan-10': 3, 'U10:plan-11': 3} 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: {'CDL:plan-4': 1, 'PGV:plan-3': 1, 'MQ9:plan-3': 1, 'MQ9:plan-6': 1, 'MQ9:plan-5': 1, 'MQ9:plan-4': 1} Unresolved non-hydrogen planarities: 26 Chain: "H" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 144 Unusual residues: {'CDL': 1, 'PGV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 58 Planarities with less than four sites: {'PGV:plan-3': 2} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 169 Unusual residues: {'BCL': 1, 'CDL': 1, 'I7D': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 42 Chain: "B" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 144 Unusual residues: {'BCL': 1, 'I7D': 1, 'PGV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 111 Unusual residues: {'BCL': 1, 'I7D': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 105 Unusual residues: {'BCL': 1, 'PGV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 144 Unusual residues: {'BCL': 1, 'I7D': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "J" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'I7D': 1, 'PGV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 111 Unusual residues: {'BCL': 1, 'I7D': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 111 Unusual residues: {'BCL': 1, 'I7D': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 111 Unusual residues: {'BCL': 1, 'I7D': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 183 Unusual residues: {'BCL': 1, 'CDL': 1, 'I7D': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Chain: "U" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 111 Unusual residues: {'BCL': 1, 'I7D': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 111 Unusual residues: {'BCL': 1, 'I7D': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 146 Unusual residues: {'BCL': 1, 'I7D': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "2" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 138 Unusual residues: {'BCL': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Chain: "3" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 142 Unusual residues: {'BCL': 1, 'I7D': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "4" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 111 Unusual residues: {'BCL': 1, 'I7D': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "5" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 177 Unusual residues: {'BCL': 1, 'PGV': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PGV:plan-3': 2} Unresolved non-hydrogen planarities: 6 Chain: "6" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 243 Unusual residues: {'BCL': 1, 'CDL': 2, 'I7D': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 68 Chain: "7" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 129 Unusual residues: {'BCL': 1, 'U10': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "8" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 111 Unusual residues: {'BCL': 1, 'I7D': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "9" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "0" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 129 Unusual residues: {'BCL': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 37 Chain: "C" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 136 Classifications: {'water': 136} Link IDs: {None: 135} Chain: "L" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 65 Classifications: {'water': 65} Link IDs: {None: 64} Chain: "M" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Chain: "H" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "O" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "P" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "Q" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "R" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "S" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "T" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "U" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "V" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "W" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "X" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "Y" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "Z" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "1" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "2" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "3" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "4" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "5" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "6" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "7" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "8" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "9" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "0" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AVAL M 58 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BVAL M 58 " occ=0.50 residue: pdb=" N ALEU 9 6 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU 9 6 " occ=0.50 Time building chain proxies: 18.55, per 1000 atoms: 0.62 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: 8.89 Conformation dependent library (CDL) restraints added in 3.5 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: 2.17 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: 8.64 Time building geometry restraints manager: 10.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.38: 10270 1.38 - 1.56: 19664 1.56 - 1.74: 74 1.74 - 1.93: 222 1.93 - 2.11: 156 Bond restraints: 30386 Sorted by residual: bond pdb=" CA7 CDL H 303 " pdb=" OA8 CDL H 303 " ideal model delta sigma weight residual 1.334 1.455 -0.121 1.10e-02 8.26e+03 1.22e+02 bond pdb=" CA7 CDL A 101 " pdb=" OA8 CDL A 101 " ideal model delta sigma weight residual 1.334 1.455 -0.121 1.10e-02 8.26e+03 1.21e+02 bond pdb=" CA7 CDL 0 101 " pdb=" OA8 CDL 0 101 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.10e-02 8.26e+03 1.19e+02 bond pdb=" CA7 CDL 6 101 " pdb=" OA8 CDL 6 101 " ideal model delta sigma weight residual 1.334 1.453 -0.119 1.10e-02 8.26e+03 1.18e+02 bond pdb=" CA7 CDL 6 104 " pdb=" OA8 CDL 6 104 " ideal model delta sigma weight residual 1.334 1.453 -0.119 1.10e-02 8.26e+03 1.17e+02 ... (remaining 30381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.77: 39279 3.77 - 7.54: 2039 7.54 - 11.31: 316 11.31 - 15.08: 87 15.08 - 18.85: 14 Bond angle restraints: 41735 Sorted by residual: angle pdb=" C1D BCL O 101 " pdb=" C2D BCL O 101 " pdb=" CMD BCL O 101 " ideal model delta sigma weight residual 125.57 139.35 -13.77 1.83e+00 2.99e-01 5.68e+01 angle pdb=" C1D BCL L 301 " pdb=" C2D BCL L 301 " pdb=" CMD BCL L 301 " ideal model delta sigma weight residual 125.57 139.24 -13.67 1.83e+00 2.99e-01 5.59e+01 angle pdb=" C1D BCL W 101 " pdb=" C2D BCL W 101 " pdb=" CMD BCL W 101 " ideal model delta sigma weight residual 125.57 139.16 -13.59 1.83e+00 2.99e-01 5.52e+01 angle pdb=" C1D BCL M 403 " pdb=" C2D BCL M 403 " pdb=" CMD BCL M 403 " ideal model delta sigma weight residual 125.57 139.15 -13.57 1.83e+00 2.99e-01 5.51e+01 angle pdb=" C1D BCL S 101 " pdb=" C2D BCL S 101 " pdb=" CMD BCL S 101 " ideal model delta sigma weight residual 125.57 139.08 -13.50 1.83e+00 2.99e-01 5.46e+01 ... (remaining 41730 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.51: 16176 35.51 - 71.03: 738 71.03 - 106.54: 100 106.54 - 142.05: 59 142.05 - 177.57: 23 Dihedral angle restraints: 17096 sinusoidal: 8511 harmonic: 8585 Sorted by residual: dihedral pdb=" C1 BCL Z 101 " pdb=" CGA BCL Z 101 " pdb=" O2A BCL Z 101 " pdb=" CBA BCL Z 101 " ideal model delta sinusoidal sigma weight residual 180.00 131.90 48.10 1 6.00e+00 2.78e-02 8.86e+01 dihedral pdb=" C1 BCL X 102 " pdb=" CGA BCL X 102 " pdb=" O2A BCL X 102 " pdb=" CBA BCL X 102 " ideal model delta sinusoidal sigma weight residual 180.00 137.16 42.84 1 6.00e+00 2.78e-02 7.11e+01 dihedral pdb=" CBD BCL L 301 " pdb=" CGD BCL L 301 " pdb=" O2D BCL L 301 " pdb=" CED BCL L 301 " ideal model delta sinusoidal sigma weight residual 180.00 146.92 33.08 1 5.00e+00 4.00e-02 6.23e+01 ... (remaining 17093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 3530 0.058 - 0.116: 547 0.116 - 0.174: 130 0.174 - 0.232: 12 0.232 - 0.290: 19 Chirality restraints: 4238 Sorted by residual: chirality pdb=" C05 PGV H 302 " pdb=" C04 PGV H 302 " pdb=" C06 PGV H 302 " pdb=" O05 PGV H 302 " both_signs ideal model delta sigma weight residual False 2.29 2.58 -0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" C05 PGV L 311 " pdb=" C04 PGV L 311 " pdb=" C06 PGV L 311 " pdb=" O05 PGV L 311 " both_signs ideal model delta sigma weight residual False 2.29 2.58 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" C05 PGV L 305 " pdb=" C04 PGV L 305 " pdb=" C06 PGV L 305 " pdb=" O05 PGV L 305 " both_signs ideal model delta sigma weight residual False 2.29 2.58 -0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 4235 not shown) Planarity restraints: 4949 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C33 I7D N 101 " 0.131 2.00e-02 2.50e+03 2.24e-01 5.00e+02 pdb=" C35 I7D N 101 " -0.290 2.00e-02 2.50e+03 pdb=" C36 I7D N 101 " 0.287 2.00e-02 2.50e+03 pdb=" C37 I7D N 101 " -0.128 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL Z 101 " 0.301 3.00e-02 1.11e+03 2.40e-01 3.21e+02 pdb=" CBA BCL Z 101 " 0.190 3.00e-02 1.11e+03 pdb=" CGA BCL Z 101 " -0.072 3.00e-02 1.11e+03 pdb=" O1A BCL Z 101 " -0.024 3.00e-02 1.11e+03 pdb=" O2A BCL Z 101 " -0.396 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL X 102 " 0.277 3.00e-02 1.11e+03 2.20e-01 2.69e+02 pdb=" CBA BCL X 102 " 0.181 3.00e-02 1.11e+03 pdb=" CGA BCL X 102 " -0.065 3.00e-02 1.11e+03 pdb=" O1A BCL X 102 " -0.035 3.00e-02 1.11e+03 pdb=" O2A BCL X 102 " -0.357 3.00e-02 1.11e+03 ... (remaining 4946 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 360 2.59 - 3.17: 23701 3.17 - 3.75: 51653 3.75 - 4.32: 76372 4.32 - 4.90: 119088 Nonbonded interactions: 271174 Sorted by model distance: nonbonded pdb=" NE2 HIS C 148 " pdb="FE HEC C 404 " model vdw 2.014 3.080 nonbonded pdb=" OE2 GLU M 234 " pdb="FE FE M 401 " model vdw 2.037 2.260 nonbonded pdb=" NE2 HIS L 191 " pdb="FE FE M 401 " model vdw 2.055 2.340 nonbonded pdb=" SD MET C 134 " pdb="FE HEC C 402 " model vdw 2.075 3.360 nonbonded pdb=" OE1 GLU M 234 " pdb="FE FE M 401 " model vdw 2.078 2.260 ... (remaining 271169 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain '0' and resid 7 through 56) selection = (chain '2' and resid 7 through 56) selection = (chain '4' and resid 7 through 56) selection = (chain '6' and resid 7 through 56) selection = (chain '8' and resid 7 through 56) selection = (chain 'B' and resid 7 through 56) selection = (chain 'E' and resid 7 through 56) selection = (chain 'G' and resid 7 through 56) selection = (chain 'J' and resid 7 through 56) selection = (chain 'N' and resid 7 through 56) selection = (chain 'P' and resid 7 through 56) selection = (chain 'R' and resid 7 through 56) selection = (chain 'T' and resid 7 through 56) selection = (chain 'V' and resid 7 through 56) selection = (chain 'X' and resid 7 through 56) selection = (chain 'Z' and resid 7 through 56) } ncs_group { reference = (chain '1' and (resid 1 through 5 or resid 7 through 45)) selection = (chain '5' and (resid 1 through 5 or resid 7 through 44 or (resid 45 and (name N \ or name CA or name C or name O or name CB )))) selection = (chain '7' and (resid 1 through 5 or resid 7 through 44 or (resid 45 and (name N \ or name CA or name C or name O or name CB )))) selection = (chain '9' and (resid 1 through 5 or resid 7 through 45)) selection = (chain 'A' and (resid 1 through 5 or resid 7 through 45)) selection = (chain 'D' and (resid 1 through 5 or resid 7 through 45)) selection = (chain 'F' and (resid 1 through 5 or resid 7 through 45)) selection = (chain 'I' and (resid 1 through 5 or resid 7 through 44 or (resid 45 and (name N \ or name CA or name C or name O or name CB )))) selection = (chain 'K' and (resid 1 through 5 or resid 7 through 45)) selection = (chain 'O' and (resid 1 through 5 or resid 7 through 44 or (resid 45 and (name N \ or name CA or name C or name O or name CB )))) selection = (chain 'Q' and (resid 1 through 5 or resid 7 through 44 or (resid 45 and (name N \ or name CA or name C or name O or name CB )))) selection = (chain 'U' and (resid 1 through 5 or resid 7 through 44 or (resid 45 and (name N \ or name CA or name C or name O or name CB )))) selection = (chain 'Y' and (resid 1 through 5 or resid 7 through 45)) } ncs_group { reference = (chain '3' and resid 1 through 58) selection = (chain 'S' and (resid 1 through 45 or resid 50 through 58)) } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.970 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: 0.030 Extract box with map and model: 1.180 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 64.840 Find NCS groups from input model: 1.630 Set up NCS constraints: 0.180 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:13.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.021 0.281 30435 Z= 1.148 Angle : 1.770 18.845 41737 Z= 0.778 Chirality : 0.050 0.290 4238 Planarity : 0.017 0.240 4949 Dihedral : 21.325 177.566 11523 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 7.34 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.018 0.002 TRP C 315 HIS 0.007 0.001 HIS C 260 PHE 0.015 0.001 PHE M 8 TYR 0.021 0.001 TYR L 165 ARG 0.003 0.000 ARG M 132 Details of bonding type rmsd hydrogen bonds : bond 0.18522 ( 1492) hydrogen bonds : angle 5.83227 ( 4228) SS BOND : bond 0.00651 ( 1) SS BOND : angle 1.22048 ( 2) covalent geometry : bond 0.01926 (30386) covalent geometry : angle 1.76959 (41735) Misc. bond : bond 0.18645 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 353 time to evaluate : 2.692 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: 0.8373 (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: 1.4652 time to fit residues: 638.0507 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 : 3.027 ------------------------------------------------------------------------------- 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 243 optimal weight: 8.9990 chunk 218 optimal weight: 0.9990 chunk 121 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 147 optimal weight: 5.9990 chunk 116 optimal weight: 0.7980 chunk 225 optimal weight: 5.9990 chunk 87 optimal weight: 0.5980 chunk 137 optimal weight: 0.9980 chunk 168 optimal weight: 1.9990 chunk 261 optimal weight: 10.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 175 ASN 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 = 0.3636 r_free = 0.3636 target = 0.126566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.092351 restraints weight = 48357.239| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.78 r_work: 0.2850 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2717 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2715 r_free = 0.2715 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2715 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.285 30435 Z= 0.131 Angle : 0.686 14.543 41737 Z= 0.277 Chirality : 0.038 0.207 4238 Planarity : 0.004 0.065 4949 Dihedral : 21.929 179.796 6402 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.00 % Allowed : 7.39 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.16), residues: 2887 helix: 2.54 (0.12), residues: 1725 sheet: 0.40 (0.73), residues: 53 loop : -0.23 (0.19), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP U 2 HIS 0.006 0.001 HIS 6 38 PHE 0.015 0.002 PHE H 20 TYR 0.018 0.001 TYR M 193 ARG 0.005 0.000 ARG O 3 Details of bonding type rmsd hydrogen bonds : bond 0.04982 ( 1492) hydrogen bonds : angle 4.20269 ( 4228) SS BOND : bond 0.00392 ( 1) SS BOND : angle 0.76061 ( 2) covalent geometry : bond 0.00298 (30386) covalent geometry : angle 0.68551 (41735) Misc. bond : bond 0.06120 ( 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 383 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 335 time to evaluate : 3.894 Fit side-chains REVERT: C 68 ARG cc_start: 0.8390 (ttt-90) cc_final: 0.7937 (ttt90) REVERT: L 82 ARG cc_start: 0.8829 (mtm110) cc_final: 0.8415 (mtm-85) REVERT: H 128 THR cc_start: 0.6903 (m) cc_final: 0.6568 (p) REVERT: H 185 LYS cc_start: 0.8854 (tptm) cc_final: 0.8432 (tmtm) REVERT: B 17 LYS cc_start: 0.8126 (mmmt) cc_final: 0.7777 (mttm) REVERT: D 3 ARG cc_start: 0.7661 (mtm-85) cc_final: 0.7340 (mtt90) REVERT: I 12 ARG cc_start: 0.6549 (mmp80) cc_final: 0.5911 (mmm-85) REVERT: K 3 ARG cc_start: 0.7032 (OUTLIER) cc_final: 0.6608 (mtt90) REVERT: N 18 GLU cc_start: 0.7753 (tp30) cc_final: 0.7338 (tt0) REVERT: O 3 ARG cc_start: 0.7889 (mtt-85) cc_final: 0.7613 (mtm-85) REVERT: Q 8 PHE cc_start: 0.7924 (m-80) cc_final: 0.7671 (m-80) REVERT: R 18 GLU cc_start: 0.7984 (tt0) cc_final: 0.7596 (tt0) REVERT: V 25 THR cc_start: 0.8573 (m) cc_final: 0.8219 (t) REVERT: Y 3 ARG cc_start: 0.7512 (mtt90) cc_final: 0.7239 (mtt-85) REVERT: 1 12 ARG cc_start: 0.7507 (mpt90) cc_final: 0.6745 (mtm180) REVERT: 2 18 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7544 (tp30) REVERT: 2 25 THR cc_start: 0.8337 (t) cc_final: 0.7928 (p) REVERT: 2 43 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7408 (mp10) REVERT: 4 17 LYS cc_start: 0.7482 (OUTLIER) cc_final: 0.7036 (mtpt) REVERT: 8 18 GLU cc_start: 0.7844 (tt0) cc_final: 0.7373 (tt0) REVERT: 8 23 PHE cc_start: 0.7308 (t80) cc_final: 0.6504 (m-80) REVERT: 9 4 MET cc_start: 0.7722 (ptt) cc_final: 0.7431 (ptm) REVERT: g 3 MET cc_start: 0.6209 (OUTLIER) cc_final: 0.5818 (ptp) REVERT: k 5 TRP cc_start: 0.6350 (OUTLIER) cc_final: 0.5342 (p90) outliers start: 48 outliers final: 26 residues processed: 358 average time/residue: 1.5273 time to fit residues: 644.3060 Evaluate side-chains 334 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 302 time to evaluate : 2.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 287 THR Chi-restraints excluded: chain M residue 314 VAL Chi-restraints excluded: chain H residue 236 ASP Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain O residue 6 LEU Chi-restraints excluded: chain 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 2 residue 18 GLU 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 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 109 optimal weight: 9.9990 chunk 244 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 163 optimal weight: 4.9990 chunk 238 optimal weight: 1.9990 chunk 247 optimal weight: 0.4980 chunk 108 optimal weight: 1.9990 chunk 204 optimal weight: 0.0070 chunk 197 optimal weight: 5.9990 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 43 GLN 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 = 0.3648 r_free = 0.3648 target = 0.127351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.091978 restraints weight = 62707.027| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.08 r_work: 0.2820 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2689 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2689 r_free = 0.2689 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2689 r_free = 0.2689 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2689 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.238 30435 Z= 0.114 Angle : 0.631 13.450 41737 Z= 0.253 Chirality : 0.037 0.201 4238 Planarity : 0.004 0.065 4949 Dihedral : 20.330 179.464 6393 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.12 % Allowed : 9.03 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.16), residues: 2887 helix: 2.56 (0.12), residues: 1775 sheet: 0.27 (0.72), residues: 53 loop : -0.10 (0.20), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP U 2 HIS 0.006 0.001 HIS Y 29 PHE 0.014 0.001 PHE H 20 TYR 0.018 0.001 TYR M 193 ARG 0.008 0.000 ARG W 46 Details of bonding type rmsd hydrogen bonds : bond 0.04423 ( 1492) hydrogen bonds : angle 3.97935 ( 4228) SS BOND : bond 0.00380 ( 1) SS BOND : angle 0.64331 ( 2) covalent geometry : bond 0.00256 (30386) covalent geometry : angle 0.63093 (41735) Misc. bond : bond 0.05027 ( 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 382 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 331 time to evaluate : 2.795 Fit side-chains REVERT: C 68 ARG cc_start: 0.8445 (ttt-90) cc_final: 0.8007 (ttt90) REVERT: L 82 ARG cc_start: 0.8780 (mtm110) cc_final: 0.8425 (mtm-85) REVERT: M 182 HIS cc_start: 0.9222 (OUTLIER) cc_final: 0.8985 (p-80) REVERT: H 2 GLU cc_start: 0.7679 (mm-30) cc_final: 0.6830 (pm20) REVERT: H 104 ASN cc_start: 0.8668 (t0) cc_final: 0.8466 (t160) REVERT: H 166 LYS cc_start: 0.8529 (mtpt) cc_final: 0.8139 (mtpp) REVERT: H 185 LYS cc_start: 0.8842 (tptm) cc_final: 0.8462 (tmtm) REVERT: B 17 LYS cc_start: 0.8163 (mmmt) cc_final: 0.7865 (mttm) REVERT: D 3 ARG cc_start: 0.7694 (mtm-85) cc_final: 0.7008 (mpt-90) REVERT: F 4 MET cc_start: 0.7817 (OUTLIER) cc_final: 0.7580 (tpp) REVERT: F 12 ARG cc_start: 0.8169 (mmm-85) cc_final: 0.7962 (mmm-85) REVERT: I 12 ARG cc_start: 0.6525 (mmp80) cc_final: 0.5870 (mmm-85) REVERT: K 3 ARG cc_start: 0.7007 (OUTLIER) cc_final: 0.6698 (mtt90) REVERT: K 42 ASP cc_start: 0.8770 (m-30) cc_final: 0.8496 (m-30) REVERT: N 18 GLU cc_start: 0.7697 (tp30) cc_final: 0.7354 (tt0) REVERT: O 3 ARG cc_start: 0.7932 (mtt-85) cc_final: 0.7616 (mtm-85) REVERT: O 12 ARG cc_start: 0.7981 (mtt-85) cc_final: 0.7251 (mtt-85) REVERT: O 15 VAL cc_start: 0.8968 (t) cc_final: 0.8679 (p) REVERT: Q 8 PHE cc_start: 0.7889 (m-80) cc_final: 0.7554 (m-80) REVERT: R 13 GLU cc_start: 0.7517 (mt-10) cc_final: 0.6977 (mp0) REVERT: R 18 GLU cc_start: 0.8095 (tt0) cc_final: 0.7722 (tt0) REVERT: V 25 THR cc_start: 0.8536 (m) cc_final: 0.8143 (t) REVERT: Y 3 ARG cc_start: 0.7552 (mtt90) cc_final: 0.7340 (mtt-85) REVERT: 1 4 MET cc_start: 0.7637 (ptt) cc_final: 0.7119 (mtp) REVERT: 1 12 ARG cc_start: 0.7511 (mpt90) cc_final: 0.6780 (mtm180) REVERT: 2 25 THR cc_start: 0.8380 (t) cc_final: 0.7961 (p) REVERT: 4 17 LYS cc_start: 0.7432 (OUTLIER) cc_final: 0.7025 (mtpt) REVERT: 6 43 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8626 (tt0) REVERT: 8 18 GLU cc_start: 0.7898 (tt0) cc_final: 0.7428 (tt0) REVERT: 8 23 PHE cc_start: 0.7304 (t80) cc_final: 0.6502 (m-80) REVERT: 9 4 MET cc_start: 0.7814 (ptt) cc_final: 0.7513 (ptm) REVERT: k 5 TRP cc_start: 0.6289 (OUTLIER) cc_final: 0.5715 (p-90) REVERT: k 6 MET cc_start: 0.5763 (OUTLIER) cc_final: 0.5203 (mtp) outliers start: 51 outliers final: 24 residues processed: 358 average time/residue: 1.4371 time to fit residues: 605.0270 Evaluate side-chains 336 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 305 time to evaluate : 3.117 ------------------------------------------------------------------------------- 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 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 R residue 43 GLN Chi-restraints excluded: chain W residue 34 SER 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 a residue 5 TRP Chi-restraints excluded: chain c residue 5 TRP Chi-restraints excluded: chain d residue 5 TRP Chi-restraints excluded: chain e residue 5 TRP Chi-restraints excluded: chain f residue 5 TRP Chi-restraints excluded: chain g residue 5 TRP Chi-restraints excluded: chain g residue 6 MET Chi-restraints excluded: chain j residue 5 TRP Chi-restraints excluded: chain k residue 5 TRP Chi-restraints excluded: chain k residue 6 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 249 optimal weight: 1.9990 chunk 228 optimal weight: 1.9990 chunk 232 optimal weight: 2.9990 chunk 201 optimal weight: 9.9990 chunk 139 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 chunk 224 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 186 optimal weight: 0.3980 chunk 197 optimal weight: 5.9990 chunk 33 optimal weight: 0.3980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 43 GLN 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 = 0.3617 r_free = 0.3617 target = 0.125166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.092380 restraints weight = 45984.334| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.40 r_work: 0.2842 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2709 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2709 r_free = 0.2709 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2709 r_free = 0.2709 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2709 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.302 30435 Z= 0.144 Angle : 0.673 13.286 41737 Z= 0.273 Chirality : 0.038 0.193 4238 Planarity : 0.004 0.067 4949 Dihedral : 20.115 176.487 6391 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.41 % Allowed : 9.97 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.16), residues: 2887 helix: 2.52 (0.12), residues: 1774 sheet: 0.20 (0.72), residues: 53 loop : -0.12 (0.20), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP U 2 HIS 0.007 0.001 HIS Y 29 PHE 0.019 0.002 PHE H 20 TYR 0.020 0.001 TYR M 193 ARG 0.005 0.000 ARG W 46 Details of bonding type rmsd hydrogen bonds : bond 0.04750 ( 1492) hydrogen bonds : angle 4.05252 ( 4228) SS BOND : bond 0.00415 ( 1) SS BOND : angle 0.66901 ( 2) covalent geometry : bond 0.00334 (30386) covalent geometry : angle 0.67265 (41735) Misc. bond : bond 0.06349 ( 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 367 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 309 time to evaluate : 3.733 Fit side-chains REVERT: C 68 ARG cc_start: 0.8437 (ttt-90) cc_final: 0.7977 (ttt90) REVERT: H 2 GLU cc_start: 0.7612 (mm-30) cc_final: 0.6969 (pm20) REVERT: H 128 THR cc_start: 0.6938 (OUTLIER) cc_final: 0.6560 (p) REVERT: H 185 LYS cc_start: 0.8884 (tptm) cc_final: 0.8497 (tmtm) REVERT: B 17 LYS cc_start: 0.8155 (mmmt) cc_final: 0.7875 (mttm) REVERT: F 4 MET cc_start: 0.7857 (OUTLIER) cc_final: 0.7612 (tpp) REVERT: F 12 ARG cc_start: 0.8095 (mmm-85) cc_final: 0.7874 (mmm-85) REVERT: I 12 ARG cc_start: 0.6486 (mmp80) cc_final: 0.5861 (mmm-85) REVERT: K 3 ARG cc_start: 0.7029 (OUTLIER) cc_final: 0.6699 (mtt90) REVERT: N 18 GLU cc_start: 0.7666 (tp30) cc_final: 0.7351 (tt0) REVERT: O 3 ARG cc_start: 0.7936 (mtt-85) cc_final: 0.7710 (mtm-85) REVERT: O 12 ARG cc_start: 0.7970 (mtt-85) cc_final: 0.7364 (mtt-85) REVERT: O 45 HIS cc_start: 0.6386 (OUTLIER) cc_final: 0.5967 (m170) REVERT: P 43 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.8156 (mp10) REVERT: Q 8 PHE cc_start: 0.7839 (m-80) cc_final: 0.7563 (m-80) REVERT: R 13 GLU cc_start: 0.7405 (mt-10) cc_final: 0.6907 (mp0) REVERT: V 25 THR cc_start: 0.8555 (m) cc_final: 0.8173 (t) REVERT: Y 3 ARG cc_start: 0.7584 (mtt90) cc_final: 0.7380 (mtt-85) REVERT: 1 4 MET cc_start: 0.7452 (ptt) cc_final: 0.7084 (ttp) REVERT: 1 12 ARG cc_start: 0.7437 (mpt90) cc_final: 0.6943 (mtp180) REVERT: 2 25 THR cc_start: 0.8391 (t) cc_final: 0.7989 (p) REVERT: 4 17 LYS cc_start: 0.7424 (OUTLIER) cc_final: 0.7028 (mtpt) REVERT: 8 23 PHE cc_start: 0.7273 (t80) cc_final: 0.6528 (m-80) REVERT: 9 4 MET cc_start: 0.7831 (ptt) cc_final: 0.7530 (ptm) REVERT: k 5 TRP cc_start: 0.6409 (OUTLIER) cc_final: 0.5465 (p90) REVERT: k 6 MET cc_start: 0.5806 (OUTLIER) cc_final: 0.5259 (mtp) outliers start: 58 outliers final: 32 residues processed: 340 average time/residue: 1.4752 time to fit residues: 592.9323 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 : 3.168 ------------------------------------------------------------------------------- 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 134 VAL Chi-restraints excluded: chain L residue 166 LEU Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 262 PHE Chi-restraints excluded: chain M residue 287 THR Chi-restraints excluded: chain M residue 314 VAL Chi-restraints excluded: chain H residue 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 6 LEU Chi-restraints excluded: chain O residue 45 HIS Chi-restraints excluded: chain P residue 8 ILE Chi-restraints excluded: chain P residue 43 GLN Chi-restraints excluded: chain R residue 43 GLN Chi-restraints excluded: chain U residue 13 ILE Chi-restraints excluded: chain Y residue 7 LEU Chi-restraints excluded: chain Y residue 42 ASP Chi-restraints excluded: chain 2 residue 17 LYS 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 5 residue 34 SER 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 221 optimal weight: 0.6980 chunk 246 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 217 optimal weight: 5.9990 chunk 204 optimal weight: 0.0040 chunk 45 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 268 optimal weight: 0.9980 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 43 GLN 8 43 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.126974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.092409 restraints weight = 51532.939| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 1.81 r_work: 0.2834 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2703 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2703 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.235 30435 Z= 0.110 Angle : 0.619 13.037 41737 Z= 0.248 Chirality : 0.036 0.191 4238 Planarity : 0.004 0.067 4949 Dihedral : 19.257 176.163 6391 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.17 % Allowed : 10.01 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.16), residues: 2887 helix: 2.59 (0.12), residues: 1781 sheet: 0.18 (0.73), residues: 53 loop : -0.13 (0.20), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP I 2 HIS 0.004 0.001 HIS Y 29 PHE 0.015 0.001 PHE Z 19 TYR 0.019 0.001 TYR M 193 ARG 0.004 0.000 ARG W 46 Details of bonding type rmsd hydrogen bonds : bond 0.04153 ( 1492) hydrogen bonds : angle 3.92314 ( 4228) SS BOND : bond 0.00357 ( 1) SS BOND : angle 0.58537 ( 2) covalent geometry : bond 0.00249 (30386) covalent geometry : angle 0.61883 (41735) Misc. bond : bond 0.05068 ( 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 363 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 311 time to evaluate : 3.193 Fit side-chains REVERT: C 68 ARG cc_start: 0.8449 (ttt-90) cc_final: 0.8088 (ttt90) REVERT: M 85 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8674 (mm-30) REVERT: M 182 HIS cc_start: 0.9254 (OUTLIER) cc_final: 0.8975 (p-80) REVERT: H 128 THR cc_start: 0.6884 (OUTLIER) cc_final: 0.6483 (p) REVERT: H 166 LYS cc_start: 0.8530 (mtpt) cc_final: 0.8259 (mtpp) REVERT: H 185 LYS cc_start: 0.8873 (tptm) cc_final: 0.8579 (tmtm) REVERT: A 4 MET cc_start: 0.8293 (ptm) cc_final: 0.8085 (ppp) REVERT: B 17 LYS cc_start: 0.8164 (mmmt) cc_final: 0.7906 (mttm) REVERT: F 4 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.7617 (tpp) REVERT: F 12 ARG cc_start: 0.8074 (mmm-85) cc_final: 0.7721 (mtp180) REVERT: G 24 ILE cc_start: 0.8506 (mm) cc_final: 0.8296 (OUTLIER) REVERT: I 12 ARG cc_start: 0.6513 (mmp80) cc_final: 0.5854 (mmm-85) REVERT: K 3 ARG cc_start: 0.6992 (OUTLIER) cc_final: 0.6748 (mtt90) REVERT: N 18 GLU cc_start: 0.7639 (tp30) cc_final: 0.7341 (tt0) REVERT: O 3 ARG cc_start: 0.7865 (mtt-85) cc_final: 0.7594 (mtm-85) REVERT: O 12 ARG cc_start: 0.7888 (mtt-85) cc_final: 0.7171 (mtt-85) REVERT: O 15 VAL cc_start: 0.8947 (t) cc_final: 0.8648 (p) REVERT: P 43 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8404 (mp10) REVERT: Q 8 PHE cc_start: 0.7843 (m-80) cc_final: 0.7517 (m-80) REVERT: R 13 GLU cc_start: 0.7390 (mt-10) cc_final: 0.6897 (mp0) REVERT: V 25 THR cc_start: 0.8544 (m) cc_final: 0.8170 (t) REVERT: 1 12 ARG cc_start: 0.7437 (mpt90) cc_final: 0.6901 (mtp180) REVERT: 2 17 LYS cc_start: 0.7667 (OUTLIER) cc_final: 0.7264 (mttm) REVERT: 2 18 GLU cc_start: 0.7818 (tp30) cc_final: 0.7551 (tp30) REVERT: 2 25 THR cc_start: 0.8372 (t) cc_final: 0.7944 (p) REVERT: 3 11 ARG cc_start: 0.6956 (mtp180) cc_final: 0.6583 (mtm180) REVERT: 4 17 LYS cc_start: 0.7396 (OUTLIER) cc_final: 0.6991 (mtpt) REVERT: 8 23 PHE cc_start: 0.7276 (t80) cc_final: 0.6522 (m-80) REVERT: 9 4 MET cc_start: 0.7822 (ptt) cc_final: 0.7508 (ptm) REVERT: g 3 MET cc_start: 0.6312 (OUTLIER) cc_final: 0.5884 (ptp) REVERT: k 5 TRP cc_start: 0.6313 (OUTLIER) cc_final: 0.5762 (p-90) REVERT: k 6 MET cc_start: 0.5592 (OUTLIER) cc_final: 0.5054 (mtp) REVERT: k 9 LEU cc_start: 0.5869 (OUTLIER) cc_final: 0.5345 (tp) outliers start: 52 outliers final: 32 residues processed: 341 average time/residue: 1.4005 time to fit residues: 564.0172 Evaluate side-chains 338 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 296 time to evaluate : 2.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 62 ILE Chi-restraints excluded: chain L residue 134 VAL Chi-restraints excluded: chain L residue 166 LEU Chi-restraints excluded: chain M residue 182 HIS Chi-restraints excluded: chain M residue 287 THR Chi-restraints excluded: chain M residue 314 VAL Chi-restraints excluded: chain H residue 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 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 U residue 4 MET Chi-restraints excluded: chain U residue 13 ILE Chi-restraints excluded: chain W residue 34 SER Chi-restraints excluded: chain Y residue 7 LEU Chi-restraints excluded: chain Y residue 42 ASP Chi-restraints excluded: chain 2 residue 17 LYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 95 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 chunk 287 optimal weight: 4.9990 chunk 233 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 153 optimal weight: 0.2980 chunk 173 optimal weight: 1.9990 chunk 166 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 248 optimal weight: 1.9990 chunk 260 optimal weight: 0.6980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 43 GLN 8 43 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.125540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.089925 restraints weight = 61196.320| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.04 r_work: 0.2776 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2644 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2644 r_free = 0.2644 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2644 r_free = 0.2644 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2644 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.278 30435 Z= 0.128 Angle : 0.644 12.990 41737 Z= 0.261 Chirality : 0.037 0.188 4238 Planarity : 0.004 0.066 4949 Dihedral : 19.101 176.934 6391 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.21 % Allowed : 10.62 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.16), residues: 2887 helix: 2.60 (0.12), residues: 1768 sheet: 0.21 (0.73), residues: 53 loop : -0.08 (0.20), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP I 2 HIS 0.006 0.001 HIS C 148 PHE 0.017 0.001 PHE H 20 TYR 0.019 0.001 TYR M 193 ARG 0.008 0.000 ARG W 46 Details of bonding type rmsd hydrogen bonds : bond 0.04444 ( 1492) hydrogen bonds : angle 3.97221 ( 4228) SS BOND : bond 0.00366 ( 1) SS BOND : angle 0.62542 ( 2) covalent geometry : bond 0.00295 (30386) covalent geometry : angle 0.64402 (41735) Misc. bond : bond 0.06036 ( 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 357 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 304 time to evaluate : 3.015 Fit side-chains REVERT: C 68 ARG cc_start: 0.8422 (ttt-90) cc_final: 0.7928 (ttt90) REVERT: H 128 THR cc_start: 0.6811 (OUTLIER) cc_final: 0.6412 (p) REVERT: H 185 LYS cc_start: 0.8872 (tptm) cc_final: 0.8569 (tmtm) REVERT: A 4 MET cc_start: 0.8320 (ptm) cc_final: 0.8060 (ppp) REVERT: B 17 LYS cc_start: 0.8031 (mmmt) cc_final: 0.7775 (mttm) REVERT: F 7 LEU cc_start: 0.8185 (mm) cc_final: 0.7787 (mm) REVERT: F 12 ARG cc_start: 0.8025 (mmm-85) cc_final: 0.7738 (mtp180) REVERT: I 12 ARG cc_start: 0.6505 (mmp80) cc_final: 0.5840 (mmm-85) REVERT: K 3 ARG cc_start: 0.7028 (OUTLIER) cc_final: 0.6759 (mtt90) REVERT: N 18 GLU cc_start: 0.7682 (tp30) cc_final: 0.7336 (tt0) REVERT: O 3 ARG cc_start: 0.7885 (mtt-85) cc_final: 0.7581 (mtm-85) REVERT: O 12 ARG cc_start: 0.8024 (mtt-85) cc_final: 0.7380 (mtt-85) REVERT: P 43 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.8255 (mp10) REVERT: Q 4 MET cc_start: 0.7846 (ptt) cc_final: 0.7333 (ppp) REVERT: Q 8 PHE cc_start: 0.7867 (m-80) cc_final: 0.7512 (m-80) REVERT: R 13 GLU cc_start: 0.7450 (mt-10) cc_final: 0.6906 (mp0) REVERT: V 25 THR cc_start: 0.8527 (m) cc_final: 0.8109 (t) REVERT: 1 12 ARG cc_start: 0.7427 (mpt90) cc_final: 0.6885 (mtp180) REVERT: 2 17 LYS cc_start: 0.7661 (OUTLIER) cc_final: 0.7411 (mtmm) REVERT: 2 25 THR cc_start: 0.8345 (t) cc_final: 0.7929 (p) REVERT: 3 11 ARG cc_start: 0.6962 (mtp180) cc_final: 0.6579 (mtm180) REVERT: 4 17 LYS cc_start: 0.7374 (OUTLIER) cc_final: 0.6969 (mtpt) REVERT: 8 23 PHE cc_start: 0.7243 (t80) cc_final: 0.6477 (m-80) REVERT: 9 4 MET cc_start: 0.7871 (ptt) cc_final: 0.7536 (ptm) REVERT: g 3 MET cc_start: 0.6266 (OUTLIER) cc_final: 0.5759 (ptp) REVERT: h 6 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.7614 (mtm) REVERT: k 5 TRP cc_start: 0.6380 (OUTLIER) cc_final: 0.5483 (p90) REVERT: k 6 MET cc_start: 0.5442 (OUTLIER) cc_final: 0.5008 (mtp) REVERT: k 9 LEU cc_start: 0.5845 (OUTLIER) cc_final: 0.5236 (tp) outliers start: 53 outliers final: 36 residues processed: 332 average time/residue: 1.5274 time to fit residues: 600.3109 Evaluate side-chains 340 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 294 time to evaluate : 2.810 ------------------------------------------------------------------------------- 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 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 194 VAL Chi-restraints excluded: chain H residue 236 ASP Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain O residue 45 HIS Chi-restraints excluded: chain P residue 8 ILE Chi-restraints excluded: chain P residue 43 GLN Chi-restraints excluded: chain R residue 43 GLN Chi-restraints excluded: chain U residue 13 ILE Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain W residue 34 SER Chi-restraints excluded: chain X residue 8 ILE Chi-restraints excluded: chain Y residue 3 ARG Chi-restraints excluded: chain Y residue 42 ASP Chi-restraints excluded: chain 2 residue 17 LYS 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 3 MET Chi-restraints excluded: chain a residue 5 TRP Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain c residue 5 TRP Chi-restraints excluded: chain d residue 5 TRP Chi-restraints excluded: chain e residue 5 TRP Chi-restraints excluded: chain e residue 6 MET Chi-restraints excluded: chain f residue 5 TRP Chi-restraints excluded: chain g residue 3 MET Chi-restraints excluded: chain g residue 5 TRP Chi-restraints excluded: chain h 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 161 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 168 optimal weight: 4.9990 chunk 235 optimal weight: 3.9990 chunk 221 optimal weight: 4.9990 chunk 279 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 8.9990 chunk 134 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 233 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 43 GLN Z 43 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.125002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.092699 restraints weight = 40619.160| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.16 r_work: 0.2857 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2723 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2723 r_free = 0.2723 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2723 r_free = 0.2723 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2723 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.295 30435 Z= 0.140 Angle : 0.661 13.441 41737 Z= 0.269 Chirality : 0.038 0.191 4238 Planarity : 0.004 0.067 4949 Dihedral : 19.084 178.012 6391 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.29 % Allowed : 10.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.16), residues: 2887 helix: 2.62 (0.12), residues: 1726 sheet: 0.17 (0.73), residues: 53 loop : -0.24 (0.19), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP U 2 HIS 0.007 0.001 HIS Y 29 PHE 0.018 0.002 PHE H 20 TYR 0.019 0.001 TYR M 193 ARG 0.006 0.000 ARG W 46 Details of bonding type rmsd hydrogen bonds : bond 0.04581 ( 1492) hydrogen bonds : angle 4.01627 ( 4228) SS BOND : bond 0.00431 ( 1) SS BOND : angle 0.62368 ( 2) covalent geometry : bond 0.00325 (30386) covalent geometry : angle 0.66093 (41735) Misc. bond : bond 0.06309 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 300 time to evaluate : 4.348 Fit side-chains REVERT: C 68 ARG cc_start: 0.8421 (ttt-90) cc_final: 0.7948 (ttt90) REVERT: M 182 HIS cc_start: 0.9401 (OUTLIER) cc_final: 0.9181 (p-80) REVERT: H 128 THR cc_start: 0.6867 (OUTLIER) cc_final: 0.6471 (p) REVERT: H 166 LYS cc_start: 0.8528 (mtpt) cc_final: 0.8169 (mtpp) REVERT: H 185 LYS cc_start: 0.8864 (tptm) cc_final: 0.8549 (tmtm) REVERT: A 4 MET cc_start: 0.8234 (ptm) cc_final: 0.7990 (ppp) REVERT: B 17 LYS cc_start: 0.8035 (mmmt) cc_final: 0.7798 (mttm) REVERT: F 7 LEU cc_start: 0.8291 (mm) cc_final: 0.7901 (mm) REVERT: F 12 ARG cc_start: 0.8075 (mmm-85) cc_final: 0.7671 (mtp180) REVERT: I 12 ARG cc_start: 0.6479 (mmp80) cc_final: 0.5864 (mmm-85) REVERT: K 3 ARG cc_start: 0.7040 (OUTLIER) cc_final: 0.6751 (mtt90) REVERT: N 18 GLU cc_start: 0.7607 (tp30) cc_final: 0.7307 (tt0) REVERT: O 12 ARG cc_start: 0.7931 (mtt-85) cc_final: 0.7300 (mtt-85) REVERT: P 43 GLN cc_start: 0.8612 (OUTLIER) cc_final: 0.8183 (mp10) REVERT: Q 8 PHE cc_start: 0.7959 (m-80) cc_final: 0.7629 (m-80) REVERT: R 13 GLU cc_start: 0.7374 (mt-10) cc_final: 0.6898 (mp0) REVERT: V 25 THR cc_start: 0.8545 (m) cc_final: 0.8166 (t) REVERT: 1 4 MET cc_start: 0.7523 (ptt) cc_final: 0.7281 (ptm) REVERT: 1 12 ARG cc_start: 0.7392 (mpt90) cc_final: 0.6896 (mtp180) REVERT: 2 25 THR cc_start: 0.8387 (t) cc_final: 0.7973 (p) REVERT: 3 11 ARG cc_start: 0.6934 (mtp180) cc_final: 0.6548 (mtm180) REVERT: 4 17 LYS cc_start: 0.7288 (OUTLIER) cc_final: 0.6960 (mtpt) REVERT: 8 23 PHE cc_start: 0.7221 (t80) cc_final: 0.6530 (m-80) REVERT: 9 4 MET cc_start: 0.7784 (ptt) cc_final: 0.7467 (ptm) REVERT: g 3 MET cc_start: 0.6351 (OUTLIER) cc_final: 0.5884 (ptp) REVERT: h 6 MET cc_start: 0.8029 (mtp) cc_final: 0.7801 (mtm) REVERT: k 5 TRP cc_start: 0.6412 (OUTLIER) cc_final: 0.5529 (p90) REVERT: k 6 MET cc_start: 0.5604 (OUTLIER) cc_final: 0.5168 (mtp) REVERT: k 9 LEU cc_start: 0.5951 (OUTLIER) cc_final: 0.5453 (tp) outliers start: 55 outliers final: 36 residues processed: 330 average time/residue: 1.8081 time to fit residues: 704.1686 Evaluate side-chains 340 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 295 time to evaluate : 2.799 ------------------------------------------------------------------------------- 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 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 62 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain H residue 194 VAL Chi-restraints excluded: chain H residue 236 ASP Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain O residue 45 HIS Chi-restraints excluded: chain P residue 8 ILE Chi-restraints excluded: chain P residue 43 GLN Chi-restraints excluded: chain R residue 43 GLN Chi-restraints excluded: chain U residue 13 ILE Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain W residue 34 SER Chi-restraints excluded: chain Y residue 42 ASP Chi-restraints excluded: chain 4 residue 17 LYS Chi-restraints excluded: chain 4 residue 22 ILE Chi-restraints excluded: chain 4 residue 24 ILE Chi-restraints excluded: chain 6 residue 35 ILE Chi-restraints excluded: chain 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 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 271 optimal weight: 3.9990 chunk 206 optimal weight: 0.0570 chunk 137 optimal weight: 3.9990 chunk 133 optimal weight: 0.8980 chunk 200 optimal weight: 0.7980 chunk 214 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 260 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 6 GLN E 43 GLN Z 43 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.127049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.093648 restraints weight = 42861.637| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 1.39 r_work: 0.2904 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2775 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2775 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.252 30435 Z= 0.110 Angle : 0.619 12.864 41737 Z= 0.247 Chirality : 0.036 0.191 4238 Planarity : 0.004 0.066 4949 Dihedral : 18.526 177.254 6391 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.00 % Allowed : 11.27 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.16), residues: 2887 helix: 2.72 (0.12), residues: 1727 sheet: 0.21 (0.74), residues: 53 loop : -0.22 (0.19), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP U 2 HIS 0.005 0.001 HIS C 148 PHE 0.014 0.001 PHE H 20 TYR 0.019 0.001 TYR M 193 ARG 0.008 0.000 ARG O 3 Details of bonding type rmsd hydrogen bonds : bond 0.04067 ( 1492) hydrogen bonds : angle 3.91020 ( 4228) SS BOND : bond 0.00400 ( 1) SS BOND : angle 0.57344 ( 2) covalent geometry : bond 0.00249 (30386) covalent geometry : angle 0.61876 (41735) Misc. bond : bond 0.05551 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 303 time to evaluate : 3.346 Fit side-chains REVERT: C 68 ARG cc_start: 0.8428 (ttt-90) cc_final: 0.8079 (ttt90) REVERT: M 85 GLU cc_start: 0.8794 (mm-30) cc_final: 0.8554 (mm-30) REVERT: M 182 HIS cc_start: 0.9316 (OUTLIER) cc_final: 0.8948 (p-80) REVERT: H 128 THR cc_start: 0.6907 (OUTLIER) cc_final: 0.6507 (p) REVERT: H 166 LYS cc_start: 0.8487 (mtpt) cc_final: 0.8205 (mmmm) REVERT: H 185 LYS cc_start: 0.8838 (tptm) cc_final: 0.8522 (tmtm) REVERT: B 17 LYS cc_start: 0.8026 (mmmt) cc_final: 0.7804 (mttm) REVERT: F 7 LEU cc_start: 0.8151 (mm) cc_final: 0.7851 (mm) REVERT: F 12 ARG cc_start: 0.8007 (mmm-85) cc_final: 0.7715 (mtp180) REVERT: I 12 ARG cc_start: 0.6443 (mmp80) cc_final: 0.5831 (mmm-85) REVERT: K 3 ARG cc_start: 0.6990 (OUTLIER) cc_final: 0.6684 (mtt90) REVERT: N 18 GLU cc_start: 0.7504 (tp30) cc_final: 0.7295 (tt0) REVERT: O 3 ARG cc_start: 0.7900 (mtt-85) cc_final: 0.7599 (mtm-85) REVERT: O 12 ARG cc_start: 0.7833 (mtt-85) cc_final: 0.7098 (mtt-85) REVERT: O 15 VAL cc_start: 0.8958 (t) cc_final: 0.8661 (p) REVERT: P 43 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.8273 (mp10) REVERT: Q 8 PHE cc_start: 0.7888 (m-80) cc_final: 0.7588 (m-80) REVERT: R 13 GLU cc_start: 0.7358 (mt-10) cc_final: 0.6882 (mp0) REVERT: V 25 THR cc_start: 0.8541 (m) cc_final: 0.8190 (t) REVERT: 1 4 MET cc_start: 0.7519 (ptt) cc_final: 0.7000 (ttp) REVERT: 1 12 ARG cc_start: 0.7337 (mpt90) cc_final: 0.6567 (mtm-85) REVERT: 2 17 LYS cc_start: 0.7641 (OUTLIER) cc_final: 0.7374 (mttm) REVERT: 2 25 THR cc_start: 0.8365 (t) cc_final: 0.7940 (p) REVERT: 3 11 ARG cc_start: 0.6805 (mtp180) cc_final: 0.6552 (mtm180) REVERT: 4 17 LYS cc_start: 0.7277 (tptp) cc_final: 0.6968 (mtpt) REVERT: 8 23 PHE cc_start: 0.7225 (t80) cc_final: 0.6528 (m-80) REVERT: 9 4 MET cc_start: 0.7754 (ptt) cc_final: 0.7442 (ptm) REVERT: g 3 MET cc_start: 0.6382 (OUTLIER) cc_final: 0.5952 (ptp) REVERT: h 6 MET cc_start: 0.8001 (mtp) cc_final: 0.7771 (mtm) REVERT: k 5 TRP cc_start: 0.6245 (OUTLIER) cc_final: 0.5777 (p-90) REVERT: k 6 MET cc_start: 0.5640 (OUTLIER) cc_final: 0.5152 (mtp) REVERT: k 9 LEU cc_start: 0.5950 (OUTLIER) cc_final: 0.5527 (tp) outliers start: 48 outliers final: 31 residues processed: 329 average time/residue: 1.4799 time to fit residues: 574.1185 Evaluate side-chains 332 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 292 time to evaluate : 2.917 ------------------------------------------------------------------------------- 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 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 G residue 24 ILE Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain P residue 8 ILE Chi-restraints excluded: chain P residue 18 GLU Chi-restraints excluded: chain P residue 43 GLN Chi-restraints excluded: chain R residue 43 GLN Chi-restraints excluded: chain U residue 13 ILE Chi-restraints excluded: chain W residue 34 SER Chi-restraints excluded: chain Y residue 42 ASP Chi-restraints excluded: chain 2 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 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 i residue 3 MET Chi-restraints excluded: chain j residue 5 TRP Chi-restraints excluded: chain k residue 5 TRP Chi-restraints excluded: chain k residue 6 MET Chi-restraints excluded: chain k residue 9 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 19 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 chunk 234 optimal weight: 7.9990 chunk 40 optimal weight: 0.9980 chunk 199 optimal weight: 0.9990 chunk 178 optimal weight: 0.9990 chunk 190 optimal weight: 1.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 6 GLN E 43 GLN Z 43 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.126114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.092821 restraints weight = 42801.805| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.32 r_work: 0.2881 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2747 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2747 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.272 30435 Z= 0.121 Angle : 0.639 13.933 41737 Z= 0.256 Chirality : 0.037 0.190 4238 Planarity : 0.004 0.066 4949 Dihedral : 18.478 177.423 6387 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.96 % Allowed : 11.36 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.16), residues: 2887 helix: 2.61 (0.12), residues: 1775 sheet: 0.21 (0.73), residues: 53 loop : -0.08 (0.20), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP U 2 HIS 0.007 0.001 HIS C 148 PHE 0.016 0.001 PHE H 20 TYR 0.019 0.001 TYR M 193 ARG 0.007 0.000 ARG O 3 Details of bonding type rmsd hydrogen bonds : bond 0.04272 ( 1492) hydrogen bonds : angle 3.94155 ( 4228) SS BOND : bond 0.00400 ( 1) SS BOND : angle 0.59900 ( 2) covalent geometry : bond 0.00275 (30386) covalent geometry : angle 0.63910 (41735) Misc. bond : bond 0.06091 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 297 time to evaluate : 2.712 Fit side-chains REVERT: C 68 ARG cc_start: 0.8424 (ttt-90) cc_final: 0.8051 (ttt90) REVERT: M 85 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8546 (mm-30) REVERT: M 182 HIS cc_start: 0.9356 (OUTLIER) cc_final: 0.9052 (p-80) REVERT: H 128 THR cc_start: 0.6873 (OUTLIER) cc_final: 0.6472 (p) REVERT: H 166 LYS cc_start: 0.8521 (mtpt) cc_final: 0.8241 (mmmm) REVERT: H 185 LYS cc_start: 0.8856 (tptm) cc_final: 0.8544 (tmtm) REVERT: B 17 LYS cc_start: 0.8027 (mmmt) cc_final: 0.7814 (mttm) REVERT: F 7 LEU cc_start: 0.8075 (mm) cc_final: 0.7796 (mm) REVERT: F 12 ARG cc_start: 0.7981 (mmm-85) cc_final: 0.7619 (mtp-110) REVERT: I 12 ARG cc_start: 0.6436 (mmp80) cc_final: 0.5826 (mmm-85) REVERT: K 3 ARG cc_start: 0.7000 (OUTLIER) cc_final: 0.6689 (mtt90) REVERT: N 17 LYS cc_start: 0.7474 (mptt) cc_final: 0.7262 (mmtm) REVERT: O 3 ARG cc_start: 0.7929 (mtt-85) cc_final: 0.7513 (mtm-85) REVERT: O 12 ARG cc_start: 0.7940 (mtt-85) cc_final: 0.7278 (mtt-85) REVERT: P 43 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.8192 (mp10) REVERT: Q 8 PHE cc_start: 0.7905 (m-80) cc_final: 0.7594 (m-80) REVERT: R 13 GLU cc_start: 0.7423 (mt-10) cc_final: 0.6949 (mp0) REVERT: V 25 THR cc_start: 0.8545 (m) cc_final: 0.8181 (t) REVERT: W 4 MET cc_start: 0.7129 (tpt) cc_final: 0.6863 (mmm) REVERT: 1 4 MET cc_start: 0.7459 (ptt) cc_final: 0.7258 (ptm) REVERT: 1 12 ARG cc_start: 0.7324 (mpt90) cc_final: 0.6546 (mtm-85) REVERT: 2 17 LYS cc_start: 0.7590 (OUTLIER) cc_final: 0.7295 (mttm) REVERT: 2 25 THR cc_start: 0.8359 (t) cc_final: 0.7932 (p) REVERT: 3 2 TRP cc_start: 0.7647 (p-90) cc_final: 0.7434 (p-90) REVERT: 3 11 ARG cc_start: 0.6803 (mtp180) cc_final: 0.6555 (mtm180) REVERT: 4 17 LYS cc_start: 0.7317 (tptp) cc_final: 0.6985 (mtpt) REVERT: 8 23 PHE cc_start: 0.7206 (t80) cc_final: 0.6514 (m-80) REVERT: 9 4 MET cc_start: 0.7762 (ptt) cc_final: 0.7447 (ptm) REVERT: g 3 MET cc_start: 0.6367 (OUTLIER) cc_final: 0.5944 (ptp) REVERT: h 6 MET cc_start: 0.8011 (mtp) cc_final: 0.7788 (mtm) REVERT: k 5 TRP cc_start: 0.6318 (OUTLIER) cc_final: 0.5761 (p-90) REVERT: k 6 MET cc_start: 0.5625 (OUTLIER) cc_final: 0.5182 (mtp) REVERT: k 9 LEU cc_start: 0.5963 (OUTLIER) cc_final: 0.5539 (tp) outliers start: 47 outliers final: 34 residues processed: 326 average time/residue: 1.4134 time to fit residues: 543.2194 Evaluate side-chains 337 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 294 time to evaluate : 3.078 ------------------------------------------------------------------------------- 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 216 PHE Chi-restraints excluded: chain M residue 287 THR Chi-restraints excluded: chain M residue 314 VAL Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain H residue 194 VAL Chi-restraints excluded: chain H residue 236 ASP Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain P residue 8 ILE Chi-restraints excluded: chain P residue 43 GLN Chi-restraints excluded: chain R residue 43 GLN Chi-restraints excluded: chain U residue 13 ILE Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain W residue 34 SER Chi-restraints excluded: chain Y residue 42 ASP Chi-restraints excluded: chain 2 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 49 optimal weight: 1.9990 chunk 11 optimal weight: 20.0000 chunk 232 optimal weight: 5.9990 chunk 204 optimal weight: 0.7980 chunk 231 optimal weight: 1.9990 chunk 186 optimal weight: 30.0000 chunk 285 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 245 optimal weight: 0.9990 chunk 73 optimal weight: 7.9990 chunk 199 optimal weight: 0.6980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 6 GLN E 43 GLN Z 43 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.126095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.094489 restraints weight = 39980.580| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.24 r_work: 0.2877 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2744 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2744 r_free = 0.2744 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2744 r_free = 0.2744 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2744 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.1858 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= 0.123 Angle : 0.646 13.493 41737 Z= 0.259 Chirality : 0.037 0.191 4238 Planarity : 0.004 0.067 4949 Dihedral : 18.427 177.987 6387 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.88 % Allowed : 11.48 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.16), residues: 2887 helix: 2.66 (0.12), residues: 1727 sheet: 0.28 (0.74), residues: 53 loop : -0.22 (0.19), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP U 2 HIS 0.008 0.001 HIS C 148 PHE 0.017 0.001 PHE Z 19 TYR 0.019 0.001 TYR M 193 ARG 0.009 0.000 ARG W 46 Details of bonding type rmsd hydrogen bonds : bond 0.04326 ( 1492) hydrogen bonds : angle 3.96769 ( 4228) SS BOND : bond 0.00410 ( 1) SS BOND : angle 0.59332 ( 2) covalent geometry : bond 0.00282 (30386) covalent geometry : angle 0.64584 (41735) Misc. bond : bond 0.06283 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5774 Ramachandran restraints generated. 2887 Oldfield, 0 Emsley, 2887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 295 time to evaluate : 2.734 Fit side-chains REVERT: C 68 ARG cc_start: 0.8429 (ttt-90) cc_final: 0.8053 (ttt90) REVERT: M 85 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8542 (mm-30) REVERT: M 182 HIS cc_start: 0.9369 (OUTLIER) cc_final: 0.9122 (p-80) REVERT: H 128 THR cc_start: 0.6853 (OUTLIER) cc_final: 0.6445 (p) REVERT: H 166 LYS cc_start: 0.8549 (mtpt) cc_final: 0.8257 (mmmm) REVERT: H 185 LYS cc_start: 0.8853 (tptm) cc_final: 0.8542 (tmtm) REVERT: B 17 LYS cc_start: 0.8006 (mmmt) cc_final: 0.7806 (mttm) REVERT: F 7 LEU cc_start: 0.8106 (mm) cc_final: 0.7838 (mm) REVERT: F 12 ARG cc_start: 0.8043 (mmm-85) cc_final: 0.7679 (mtp-110) REVERT: I 12 ARG cc_start: 0.6452 (mmp80) cc_final: 0.5847 (mmm-85) REVERT: K 3 ARG cc_start: 0.6995 (OUTLIER) cc_final: 0.6669 (mtt90) REVERT: N 17 LYS cc_start: 0.7520 (mptt) cc_final: 0.7297 (mmtm) REVERT: O 3 ARG cc_start: 0.7905 (mtt-85) cc_final: 0.7440 (mtm-85) REVERT: O 12 ARG cc_start: 0.7937 (mtt-85) cc_final: 0.7278 (mtt-85) REVERT: P 43 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8206 (mp10) REVERT: Q 8 PHE cc_start: 0.7929 (m-80) cc_final: 0.7648 (m-80) REVERT: R 13 GLU cc_start: 0.7396 (mt-10) cc_final: 0.6939 (mp0) REVERT: V 25 THR cc_start: 0.8552 (m) cc_final: 0.8189 (t) REVERT: 1 4 MET cc_start: 0.7396 (ptt) cc_final: 0.7171 (ptm) REVERT: 1 12 ARG cc_start: 0.7323 (mpt90) cc_final: 0.6556 (mtm-85) REVERT: 2 17 LYS cc_start: 0.7637 (OUTLIER) cc_final: 0.7276 (mttm) REVERT: 2 25 THR cc_start: 0.8373 (t) cc_final: 0.7962 (p) REVERT: 3 2 TRP cc_start: 0.7662 (p-90) cc_final: 0.7445 (p-90) REVERT: 3 11 ARG cc_start: 0.6839 (mtp180) cc_final: 0.6579 (mtm180) REVERT: 4 17 LYS cc_start: 0.7293 (tptp) cc_final: 0.6981 (mtpt) REVERT: 8 23 PHE cc_start: 0.7201 (t80) cc_final: 0.6521 (m-80) REVERT: 9 4 MET cc_start: 0.7763 (ptt) cc_final: 0.7447 (ptm) REVERT: g 3 MET cc_start: 0.6391 (OUTLIER) cc_final: 0.5895 (ptp) REVERT: h 6 MET cc_start: 0.8015 (mtp) cc_final: 0.7794 (mtm) REVERT: k 5 TRP cc_start: 0.6324 (OUTLIER) cc_final: 0.5545 (p90) REVERT: k 6 MET cc_start: 0.5614 (OUTLIER) cc_final: 0.5262 (mtp) REVERT: k 9 LEU cc_start: 0.5940 (OUTLIER) cc_final: 0.5469 (tp) outliers start: 45 outliers final: 36 residues processed: 322 average time/residue: 1.4487 time to fit residues: 550.2332 Evaluate side-chains 334 residues out of total 2452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 289 time to evaluate : 6.084 ------------------------------------------------------------------------------- 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 216 PHE Chi-restraints excluded: chain M residue 287 THR Chi-restraints excluded: chain M residue 314 VAL Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain H residue 194 VAL Chi-restraints excluded: chain H residue 236 ASP Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain K residue 3 ARG 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 43 GLN Chi-restraints excluded: chain U residue 13 ILE Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain W residue 34 SER Chi-restraints excluded: chain Y residue 7 LEU Chi-restraints excluded: chain Y residue 42 ASP Chi-restraints excluded: chain 2 residue 17 LYS Chi-restraints excluded: chain 4 residue 22 ILE Chi-restraints excluded: chain 4 residue 24 ILE Chi-restraints excluded: chain 6 residue 43 GLN Chi-restraints excluded: chain 0 residue 24 ILE Chi-restraints excluded: chain a residue 3 MET Chi-restraints excluded: chain a residue 5 TRP Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain c residue 5 TRP Chi-restraints excluded: chain d residue 5 TRP Chi-restraints excluded: chain e residue 5 TRP Chi-restraints excluded: chain f residue 5 TRP Chi-restraints excluded: chain g residue 3 MET Chi-restraints excluded: chain g residue 5 TRP Chi-restraints excluded: chain i residue 3 MET Chi-restraints excluded: chain j residue 5 TRP Chi-restraints excluded: chain k residue 5 TRP Chi-restraints excluded: chain k residue 6 MET Chi-restraints excluded: chain k residue 9 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 193 optimal weight: 1.9990 chunk 201 optimal weight: 8.9990 chunk 120 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 183 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 287 optimal weight: 8.9990 chunk 78 optimal weight: 1.9990 chunk 158 optimal weight: 5.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 6 GLN E 43 GLN Z 43 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.125331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.092959 restraints weight = 44119.059| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.41 r_work: 0.2847 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2713 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2713 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.297 30435 Z= 0.136 Angle : 0.667 13.647 41737 Z= 0.269 Chirality : 0.038 0.192 4238 Planarity : 0.004 0.066 4949 Dihedral : 18.549 178.846 6387 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.00 % Allowed : 11.40 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.16), residues: 2887 helix: 2.61 (0.12), residues: 1726 sheet: 0.23 (0.73), residues: 53 loop : -0.23 (0.19), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP I 2 HIS 0.009 0.001 HIS C 148 PHE 0.018 0.002 PHE H 20 TYR 0.019 0.001 TYR M 193 ARG 0.008 0.000 ARG W 46 Details of bonding type rmsd hydrogen bonds : bond 0.04527 ( 1492) hydrogen bonds : angle 4.01891 ( 4228) SS BOND : bond 0.00416 ( 1) SS BOND : angle 0.62112 ( 2) covalent geometry : bond 0.00315 (30386) covalent geometry : angle 0.66748 (41735) Misc. bond : bond 0.06754 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 32163.36 seconds wall clock time: 553 minutes 5.82 seconds (33185.82 seconds total)