Starting phenix.real_space_refine on Fri Feb 6 23:29:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lts_63379/02_2026/9lts_63379.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lts_63379/02_2026/9lts_63379.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lts_63379/02_2026/9lts_63379.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lts_63379/02_2026/9lts_63379.map" model { file = "/net/cci-nas-00/data/ceres_data/9lts_63379/02_2026/9lts_63379.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lts_63379/02_2026/9lts_63379.cif" } resolution = 2.49 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.062 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 4 7.16 5 P 9 5.49 5 Mg 38 5.21 5 S 99 5.16 5 C 19955 2.51 5 N 3951 2.21 5 O 4407 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28463 Number of models: 1 Model: "" Number of chains: 78 Chain: "A" Number of atoms: 552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 552 Classifications: {'peptide': 76} Link IDs: {'TRANS': 75} Chain: "1" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "2" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 358 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "5" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "6" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 358 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "3" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "4" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 358 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "w" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "x" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 358 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "u" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "v" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 358 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "s" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "t" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 358 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "q" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "r" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 358 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "o" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "p" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 358 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "m" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "n" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 358 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "k" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "l" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 358 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "g" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "h" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 358 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "e" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "f" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 358 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "c" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "d" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 358 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "a" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "b" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 358 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "i" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "j" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 358 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "7" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "8" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 358 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "C" Number of atoms: 2785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2785 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 27, 'TRANS': 329} Chain: "H" Number of atoms: 2015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2015 Classifications: {'peptide': 255} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 236} Chain: "L" Number of atoms: 2172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2172 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 16, 'TRANS': 256} Chain: "M" Number of atoms: 2634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2634 Classifications: {'peptide': 325} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 310} Chain: "9" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "0" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 358 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'U10': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'U10:plan-8': 1, 'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 16 Chain: "1" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 238 Unusual residues: {'BCL': 1, 'SPN': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "2" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 152 Unusual residues: {'BCL': 1, 'SPN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "6" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'BCL': 1, 'SPN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "w" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'BCL': 1, 'SPN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "x" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "u" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'BCL': 1, 'SPN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "v" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'BCL': 1, 'SPN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "s" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'BCL': 1, 'SPN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "t" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'BCL': 1, 'SPN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "q" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'BCL': 1, 'SPN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "r" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'BCL': 1, 'SPN': 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: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 152 Unusual residues: {'BCL': 1, 'SPN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "m" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'BCL': 1, 'SPN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "n" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'BCL': 1, 'SPN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "k" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'BCL': 1, 'SPN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "l" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'BCL': 1, 'SPN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "g" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 169 Unusual residues: {'BCL': 1, 'MW9': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "h" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 152 Unusual residues: {'BCL': 1, 'SPN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "e" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'BCL': 1, 'SPN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "f" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'BCL': 1, 'SPN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "c" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 152 Unusual residues: {'BCL': 1, 'SPN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "d" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 152 Unusual residues: {'BCL': 1, 'SPN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: "i" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'BCL': 1, 'SPN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "j" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'BCL': 1, 'SPN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "7" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 152 Unusual residues: {'BCL': 1, 'SPN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "8" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 129 Unusual residues: {'HEM': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 212 Unusual residues: {'MW9': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "L" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 273 Unusual residues: {'BCL': 2, 'BPH': 1, 'U10': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'U10:plan-7': 2, 'U10:plan-8': 2, 'U10:plan-9': 2, 'U10:plan-10': 2, 'U10:plan-11': 2} Unresolved non-hydrogen planarities: 40 Chain: "M" Number of atoms: 475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 475 Unusual residues: {' FE': 1, 'BCL': 2, 'BPH': 2, 'MW9': 2, 'SPN': 1, 'U10': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "9" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 162 Unusual residues: {'BCL': 1, 'MW9': 1, 'SPN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "0" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'BCL': 1, 'SPN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.85, per 1000 atoms: 0.24 Number of scatterers: 28463 At special positions: 0 Unit cell: (145.5, 140.65, 138.71, 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 4 26.01 S 99 16.00 P 9 15.00 Mg 38 11.99 O 4407 8.00 N 3951 7.00 C 19955 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 10 " - pdb=" SG CYS A 59 " distance=2.03 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=41, symmetry=0 Number of additional bonds: simple=41, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.89 Conformation dependent library (CDL) restraints added in 852.5 milliseconds 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5448 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 9 sheets defined 70.3% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 7 through 33 removed outlier: 3.875A pdb=" N THR A 11 " --> pdb=" O ASP A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 58 removed outlier: 3.591A pdb=" N MET A 42 " --> pdb=" O GLN A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 79 removed outlier: 3.849A pdb=" N ARG A 77 " --> pdb=" O ALA A 73 " (cutoff:3.500A) Processing helix chain '1' and resid 3 through 10 removed outlier: 3.576A pdb=" N LYS 1 6 " --> pdb=" O LYS 1 3 " (cutoff:3.500A) Processing helix chain '1' and resid 12 through 37 removed outlier: 3.529A pdb=" N VAL 1 16 " --> pdb=" O ASP 1 12 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL 1 18 " --> pdb=" O ARG 1 14 " (cutoff:3.500A) Processing helix chain '1' and resid 42 through 50 Processing helix chain '2' and resid 14 through 45 removed outlier: 3.977A pdb=" N GLU 2 18 " --> pdb=" O GLU 2 14 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU 2 19 " --> pdb=" O GLN 2 15 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N HIS 2 20 " --> pdb=" O ALA 2 16 " (cutoff:3.500A) Processing helix chain '5' and resid 3 through 10 removed outlier: 3.680A pdb=" N LYS 5 6 " --> pdb=" O LYS 5 3 " (cutoff:3.500A) Processing helix chain '5' and resid 14 through 37 removed outlier: 3.517A pdb=" N HIS 5 32 " --> pdb=" O ALA 5 28 " (cutoff:3.500A) Processing helix chain '5' and resid 42 through 50 removed outlier: 3.632A pdb=" N ALA 5 48 " --> pdb=" O PHE 5 44 " (cutoff:3.500A) Processing helix chain '6' and resid 12 through 45 removed outlier: 3.567A pdb=" N LEU 6 29 " --> pdb=" O SER 6 25 " (cutoff:3.500A) Processing helix chain '3' and resid 3 through 10 removed outlier: 3.593A pdb=" N LYS 3 6 " --> pdb=" O LYS 3 3 " (cutoff:3.500A) Processing helix chain '3' and resid 12 through 37 removed outlier: 3.601A pdb=" N VAL 3 18 " --> pdb=" O ARG 3 14 " (cutoff:3.500A) Processing helix chain '3' and resid 42 through 51 removed outlier: 3.615A pdb=" N ALA 3 47 " --> pdb=" O TRP 3 43 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA 3 48 " --> pdb=" O PHE 3 44 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA 3 51 " --> pdb=" O ALA 3 47 " (cutoff:3.500A) Processing helix chain '4' and resid 12 through 45 removed outlier: 3.688A pdb=" N SER 4 25 " --> pdb=" O SER 4 21 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY 4 26 " --> pdb=" O VAL 4 22 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU 4 29 " --> pdb=" O SER 4 25 " (cutoff:3.500A) Processing helix chain 'w' and resid 3 through 10 removed outlier: 3.641A pdb=" N TRP w 8 " --> pdb=" O TYR w 5 " (cutoff:3.500A) Processing helix chain 'w' and resid 12 through 37 removed outlier: 3.697A pdb=" N PHE w 25 " --> pdb=" O GLY w 21 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU w 36 " --> pdb=" O HIS w 32 " (cutoff:3.500A) Processing helix chain 'w' and resid 42 through 50 removed outlier: 3.725A pdb=" N ALA w 48 " --> pdb=" O PHE w 44 " (cutoff:3.500A) Processing helix chain 'x' and resid 12 through 45 removed outlier: 3.516A pdb=" N VAL x 22 " --> pdb=" O GLU x 18 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU x 29 " --> pdb=" O SER x 25 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N PHE x 30 " --> pdb=" O GLY x 26 " (cutoff:3.500A) Processing helix chain 'u' and resid 3 through 10 removed outlier: 3.589A pdb=" N LYS u 6 " --> pdb=" O LYS u 3 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TRP u 8 " --> pdb=" O TYR u 5 " (cutoff:3.500A) Processing helix chain 'u' and resid 12 through 37 Processing helix chain 'u' and resid 42 through 50 removed outlier: 3.685A pdb=" N ALA u 48 " --> pdb=" O PHE u 44 " (cutoff:3.500A) Processing helix chain 'v' and resid 12 through 45 removed outlier: 3.576A pdb=" N GLY v 26 " --> pdb=" O VAL v 22 " (cutoff:3.500A) Processing helix chain 's' and resid 3 through 10 Processing helix chain 's' and resid 12 through 37 Processing helix chain 's' and resid 42 through 51 Processing helix chain 't' and resid 14 through 45 removed outlier: 3.642A pdb=" N SER t 25 " --> pdb=" O SER t 21 " (cutoff:3.500A) Processing helix chain 'q' and resid 3 through 8 removed outlier: 4.352A pdb=" N LYS q 6 " --> pdb=" O LYS q 3 " (cutoff:3.500A) Processing helix chain 'q' and resid 12 through 37 Processing helix chain 'q' and resid 42 through 50 removed outlier: 3.515A pdb=" N ALA q 47 " --> pdb=" O TRP q 43 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA q 48 " --> pdb=" O PHE q 44 " (cutoff:3.500A) Processing helix chain 'r' and resid 13 through 45 removed outlier: 4.388A pdb=" N GLU r 18 " --> pdb=" O GLU r 14 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU r 19 " --> pdb=" O GLN r 15 " (cutoff:3.500A) Processing helix chain 'o' and resid 3 through 7 removed outlier: 3.907A pdb=" N LYS o 6 " --> pdb=" O LYS o 3 " (cutoff:3.500A) Processing helix chain 'o' and resid 12 through 36 removed outlier: 4.046A pdb=" N VAL o 18 " --> pdb=" O ARG o 14 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ALA o 19 " --> pdb=" O ARG o 15 " (cutoff:3.500A) Processing helix chain 'o' and resid 42 through 49 removed outlier: 3.916A pdb=" N ALA o 47 " --> pdb=" O TRP o 43 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA o 48 " --> pdb=" O PHE o 44 " (cutoff:3.500A) Processing helix chain 'p' and resid 12 through 45 removed outlier: 3.738A pdb=" N SER p 21 " --> pdb=" O GLN p 17 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL p 22 " --> pdb=" O GLU p 18 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N TYR p 23 " --> pdb=" O LEU p 19 " (cutoff:3.500A) Processing helix chain 'm' and resid 3 through 10 Processing helix chain 'm' and resid 12 through 37 Processing helix chain 'm' and resid 42 through 51 removed outlier: 3.511A pdb=" N LEU m 46 " --> pdb=" O ASN m 42 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA m 47 " --> pdb=" O TRP m 43 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA m 48 " --> pdb=" O PHE m 44 " (cutoff:3.500A) Processing helix chain 'n' and resid 12 through 45 removed outlier: 3.774A pdb=" N LEU n 29 " --> pdb=" O SER n 25 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE n 30 " --> pdb=" O GLY n 26 " (cutoff:3.500A) Processing helix chain 'k' and resid 3 through 10 removed outlier: 3.516A pdb=" N LYS k 6 " --> pdb=" O LYS k 3 " (cutoff:3.500A) Processing helix chain 'k' and resid 12 through 37 removed outlier: 4.000A pdb=" N VAL k 18 " --> pdb=" O ARG k 14 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA k 19 " --> pdb=" O ARG k 15 " (cutoff:3.500A) Processing helix chain 'k' and resid 42 through 51 removed outlier: 3.625A pdb=" N ALA k 47 " --> pdb=" O TRP k 43 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA k 48 " --> pdb=" O PHE k 44 " (cutoff:3.500A) Processing helix chain 'l' and resid 12 through 45 removed outlier: 3.649A pdb=" N VAL l 22 " --> pdb=" O GLU l 18 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU l 29 " --> pdb=" O SER l 25 " (cutoff:3.500A) Processing helix chain 'g' and resid 3 through 10 Processing helix chain 'g' and resid 12 through 37 removed outlier: 3.650A pdb=" N VAL g 18 " --> pdb=" O ARG g 14 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU g 36 " --> pdb=" O HIS g 32 " (cutoff:3.500A) Processing helix chain 'g' and resid 42 through 50 Processing helix chain 'h' and resid 12 through 45 removed outlier: 3.590A pdb=" N VAL h 22 " --> pdb=" O GLU h 18 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU h 29 " --> pdb=" O SER h 25 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE h 30 " --> pdb=" O GLY h 26 " (cutoff:3.500A) Processing helix chain 'e' and resid 3 through 10 removed outlier: 3.689A pdb=" N LYS e 6 " --> pdb=" O LYS e 3 " (cutoff:3.500A) Processing helix chain 'e' and resid 12 through 37 removed outlier: 3.613A pdb=" N PHE e 25 " --> pdb=" O GLY e 21 " (cutoff:3.500A) Processing helix chain 'e' and resid 42 through 50 Processing helix chain 'f' and resid 12 through 45 Processing helix chain 'c' and resid 3 through 10 removed outlier: 3.744A pdb=" N LYS c 6 " --> pdb=" O LYS c 3 " (cutoff:3.500A) Processing helix chain 'c' and resid 12 through 37 removed outlier: 3.678A pdb=" N VAL c 18 " --> pdb=" O ARG c 14 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER c 37 " --> pdb=" O LEU c 33 " (cutoff:3.500A) Processing helix chain 'c' and resid 42 through 50 removed outlier: 3.555A pdb=" N ALA c 48 " --> pdb=" O PHE c 44 " (cutoff:3.500A) Processing helix chain 'd' and resid 12 through 45 Processing helix chain 'a' and resid 3 through 10 removed outlier: 3.592A pdb=" N LYS a 6 " --> pdb=" O LYS a 3 " (cutoff:3.500A) Processing helix chain 'a' and resid 12 through 38 removed outlier: 3.581A pdb=" N VAL a 18 " --> pdb=" O ARG a 14 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR a 38 " --> pdb=" O VAL a 34 " (cutoff:3.500A) Processing helix chain 'a' and resid 42 through 50 removed outlier: 3.539A pdb=" N ALA a 47 " --> pdb=" O TRP a 43 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA a 48 " --> pdb=" O PHE a 44 " (cutoff:3.500A) Processing helix chain 'b' and resid 12 through 45 removed outlier: 3.592A pdb=" N SER b 25 " --> pdb=" O SER b 21 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY b 26 " --> pdb=" O VAL b 22 " (cutoff:3.500A) Processing helix chain 'i' and resid 3 through 10 Processing helix chain 'i' and resid 12 through 37 removed outlier: 3.521A pdb=" N VAL i 16 " --> pdb=" O ASP i 12 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL i 18 " --> pdb=" O ARG i 14 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE i 25 " --> pdb=" O GLY i 21 " (cutoff:3.500A) Processing helix chain 'i' and resid 42 through 50 removed outlier: 3.509A pdb=" N ALA i 47 " --> pdb=" O TRP i 43 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA i 48 " --> pdb=" O PHE i 44 " (cutoff:3.500A) Processing helix chain 'j' and resid 12 through 45 removed outlier: 3.676A pdb=" N LEU j 29 " --> pdb=" O SER j 25 " (cutoff:3.500A) Processing helix chain '7' and resid 3 through 10 removed outlier: 3.526A pdb=" N LYS 7 6 " --> pdb=" O LYS 7 3 " (cutoff:3.500A) Processing helix chain '7' and resid 12 through 37 removed outlier: 3.585A pdb=" N LEU 7 36 " --> pdb=" O HIS 7 32 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER 7 37 " --> pdb=" O LEU 7 33 " (cutoff:3.500A) Processing helix chain '7' and resid 42 through 51 removed outlier: 3.583A pdb=" N ALA 7 51 " --> pdb=" O ALA 7 47 " (cutoff:3.500A) Processing helix chain '8' and resid 12 through 45 removed outlier: 3.559A pdb=" N LEU 8 29 " --> pdb=" O SER 8 25 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL 8 36 " --> pdb=" O ALA 8 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 12 Processing helix chain 'C' and resid 18 through 40 removed outlier: 3.773A pdb=" N GLY C 29 " --> pdb=" O GLY C 25 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA C 30 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL C 31 " --> pdb=" O ALA C 27 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE C 32 " --> pdb=" O GLY C 28 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA C 33 " --> pdb=" O GLY C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 68 Processing helix chain 'C' and resid 73 through 79 Processing helix chain 'C' and resid 101 through 105 Processing helix chain 'C' and resid 108 through 117 Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 135 through 155 removed outlier: 3.709A pdb=" N ASN C 143 " --> pdb=" O LYS C 139 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN C 146 " --> pdb=" O ILE C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 160 Processing helix chain 'C' and resid 195 through 199 removed outlier: 3.898A pdb=" N VAL C 199 " --> pdb=" O TRP C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 263 Processing helix chain 'C' and resid 277 through 281 removed outlier: 3.802A pdb=" N HIS C 281 " --> pdb=" O PRO C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 302 removed outlier: 3.969A pdb=" N THR C 287 " --> pdb=" O PRO C 283 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER C 293 " --> pdb=" O MET C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 316 removed outlier: 3.762A pdb=" N LEU C 316 " --> pdb=" O PRO C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 333 Processing helix chain 'C' and resid 337 through 352 Processing helix chain 'C' and resid 358 through 362 Processing helix chain 'H' and resid 10 through 34 removed outlier: 3.549A pdb=" N ASN H 34 " --> pdb=" O LEU H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 108 Processing helix chain 'H' and resid 109 through 113 Processing helix chain 'H' and resid 135 through 137 No H-bonds generated for 'chain 'H' and resid 135 through 137' Processing helix chain 'H' and resid 185 through 188 removed outlier: 3.533A pdb=" N GLY H 188 " --> pdb=" O PRO H 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 185 through 188' 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 212 through 219 removed outlier: 4.467A pdb=" N LYS H 217 " --> pdb=" O LYS H 214 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL H 219 " --> pdb=" O PHE H 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 229 through 247 removed outlier: 3.665A pdb=" N GLY H 243 " --> pdb=" O TYR H 239 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N THR H 244 " --> pdb=" O TYR H 240 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU H 245 " --> pdb=" O ALA H 241 " (cutoff:3.500A) Processing helix chain 'H' and resid 248 through 253 removed outlier: 3.819A pdb=" N LEU H 252 " --> pdb=" O ASP H 248 " (cutoff:3.500A) Processing helix chain 'L' and resid 7 through 11 Processing helix chain 'L' and resid 33 through 58 removed outlier: 3.502A pdb=" N VAL L 37 " --> pdb=" O GLY L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 71 through 75 Processing helix chain 'L' and resid 84 through 113 removed outlier: 3.641A pdb=" N GLN L 88 " --> pdb=" O GLY L 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 116 through 134 removed outlier: 3.613A pdb=" N PHE L 120 " --> pdb=" O TYR L 116 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL L 124 " --> pdb=" O PHE L 120 " (cutoff:3.500A) removed outlier: 3.943A 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 removed outlier: 3.505A pdb=" N HIS L 145 " --> pdb=" O ALA L 142 " (cutoff:3.500A) Processing helix chain 'L' and resid 153 through 164 removed outlier: 3.586A pdb=" N TRP L 157 " --> pdb=" O SER L 153 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL L 158 " --> pdb=" O HIS L 154 " (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 Processing helix chain 'L' and resid 228 through 253 removed outlier: 3.613A pdb=" N ARG L 232 " --> pdb=" O LEU L 228 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER L 252 " --> pdb=" O CYS L 248 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY L 253 " --> pdb=" O ILE L 249 " (cutoff:3.500A) Processing helix chain 'L' and resid 260 through 263 Processing helix chain 'L' and resid 264 through 269 Processing helix chain 'M' and resid 26 through 31 removed outlier: 3.746A pdb=" N GLU M 29 " --> pdb=" O ASN M 26 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU M 30 " --> pdb=" O LEU M 27 " (cutoff:3.500A) Processing helix chain 'M' and resid 40 through 44 removed outlier: 3.562A pdb=" N TRP M 43 " --> pdb=" O LEU M 40 " (cutoff:3.500A) Processing helix chain 'M' and resid 55 through 80 removed outlier: 3.716A pdb=" N VAL M 80 " --> pdb=" O MET M 76 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 90 Processing helix chain 'M' and resid 100 through 104 Processing helix chain 'M' and resid 109 through 112 Processing helix chain 'M' and resid 113 through 142 removed outlier: 3.869A pdb=" N ALA M 138 " --> pdb=" O THR M 134 " (cutoff:3.500A) Processing helix chain 'M' and resid 145 through 163 removed outlier: 3.614A pdb=" N ALA M 154 " --> pdb=" O ALA M 150 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU M 157 " --> pdb=" O ALA M 153 " (cutoff:3.500A) Processing helix chain 'M' and resid 163 through 170 Processing helix chain 'M' and resid 171 through 175 removed outlier: 3.614A pdb=" N GLU M 174 " --> pdb=" O SER M 171 " (cutoff:3.500A) Processing helix chain 'M' and resid 181 through 194 removed outlier: 3.625A pdb=" N TYR M 194 " --> pdb=" O PHE M 190 " (cutoff:3.500A) Processing helix chain 'M' and resid 196 through 199 Processing helix chain 'M' and resid 200 through 227 removed outlier: 3.524A pdb=" N VAL M 227 " --> pdb=" O THR M 223 " (cutoff:3.500A) Processing helix chain 'M' and resid 228 through 231 Processing helix chain 'M' and resid 234 through 241 Processing helix chain 'M' and resid 243 through 258 removed outlier: 3.705A pdb=" N TRP M 253 " --> pdb=" O ALA M 249 " (cutoff:3.500A) Processing helix chain 'M' and resid 264 through 287 removed outlier: 3.985A pdb=" N ARG M 268 " --> pdb=" O GLU M 264 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR M 277 " --> pdb=" O PHE M 273 " (cutoff:3.500A) Proline residue: M 278 - end of helix Processing helix chain 'M' and resid 294 through 302 Processing helix chain 'M' and resid 313 through 317 Processing helix chain 'M' and resid 319 through 325 Processing helix chain '9' and resid 3 through 10 Processing helix chain '9' and resid 12 through 37 removed outlier: 3.674A pdb=" N VAL 9 18 " --> pdb=" O ARG 9 14 " (cutoff:3.500A) Processing helix chain '9' and resid 42 through 51 removed outlier: 3.518A pdb=" N ALA 9 47 " --> pdb=" O TRP 9 43 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA 9 48 " --> pdb=" O PHE 9 44 " (cutoff:3.500A) Processing helix chain '0' and resid 12 through 45 Processing sheet with id=AA1, first strand: chain 'C' and resid 46 through 50 Processing sheet with id=AA2, first strand: chain 'H' and resid 61 through 64 Processing sheet with id=AA3, first strand: chain 'H' and resid 87 through 89 Processing sheet with id=AA4, first strand: chain 'H' and resid 131 through 133 removed outlier: 6.370A pdb=" N GLY H 162 " --> pdb=" O LEU H 183 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU H 183 " --> pdb=" O GLY H 162 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL H 164 " --> pdb=" O LEU H 181 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU H 181 " --> pdb=" O VAL H 164 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ASP H 166 " --> pdb=" O LEU H 179 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N LEU H 179 " --> pdb=" O ASP H 166 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N TRP H 168 " --> pdb=" O ARG H 177 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 131 through 133 removed outlier: 4.166A pdb=" N GLY H 162 " --> pdb=" O VAL H 153 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 141 through 145 removed outlier: 6.620A pdb=" N GLN M 12 " --> pdb=" O SER H 143 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 25 through 27 removed outlier: 4.017A pdb=" N PHE L 25 " --> pdb=" O VAL L 32 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'M' and resid 36 through 37 Processing sheet with id=AA9, first strand: chain 'M' and resid 95 through 96 1451 hydrogen bonds defined for protein. 4032 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.43 Time building geometry restraints manager: 3.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.36: 8353 1.36 - 1.55: 20704 1.55 - 1.74: 133 1.74 - 1.93: 186 1.93 - 2.12: 164 Bond restraints: 29540 Sorted by residual: bond pdb=" C8 MW9 H 301 " pdb=" C9 MW9 H 301 " ideal model delta sigma weight residual 1.548 1.310 0.238 2.00e-02 2.50e+03 1.42e+02 bond pdb=" C8 MW9 M 408 " pdb=" C9 MW9 M 408 " ideal model delta sigma weight residual 1.548 1.311 0.237 2.00e-02 2.50e+03 1.41e+02 bond pdb=" C8 MW9 H 302 " pdb=" C9 MW9 H 302 " ideal model delta sigma weight residual 1.548 1.314 0.234 2.00e-02 2.50e+03 1.37e+02 bond pdb=" C8 MW9 g 103 " pdb=" C9 MW9 g 103 " ideal model delta sigma weight residual 1.548 1.315 0.233 2.00e-02 2.50e+03 1.36e+02 bond pdb=" C8 MW9 9 101 " pdb=" C9 MW9 9 101 " ideal model delta sigma weight residual 1.548 1.316 0.232 2.00e-02 2.50e+03 1.34e+02 ... (remaining 29535 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.66: 38793 4.66 - 9.32: 1235 9.32 - 13.97: 357 13.97 - 18.63: 157 18.63 - 23.29: 14 Bond angle restraints: 40556 Sorted by residual: angle pdb=" N ASP C 187 " pdb=" CA ASP C 187 " pdb=" C ASP C 187 " ideal model delta sigma weight residual 112.75 132.08 -19.33 1.36e+00 5.41e-01 2.02e+02 angle pdb=" N ASP C 7 " pdb=" CA ASP C 7 " pdb=" C ASP C 7 " ideal model delta sigma weight residual 113.17 98.67 14.50 1.26e+00 6.30e-01 1.32e+02 angle pdb=" N GLN A 66 " pdb=" CA GLN A 66 " pdb=" C GLN A 66 " ideal model delta sigma weight residual 113.72 99.60 14.12 1.30e+00 5.92e-01 1.18e+02 angle pdb=" N ALA A 64 " pdb=" CA ALA A 64 " pdb=" C ALA A 64 " ideal model delta sigma weight residual 108.07 91.23 16.84 1.59e+00 3.96e-01 1.12e+02 angle pdb=" N TRP 6 47 " pdb=" CA TRP 6 47 " pdb=" C TRP 6 47 " ideal model delta sigma weight residual 109.95 95.15 14.80 1.44e+00 4.82e-01 1.06e+02 ... (remaining 40551 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 14795 35.97 - 71.93: 1192 71.93 - 107.90: 102 107.90 - 143.86: 38 143.86 - 179.83: 36 Dihedral angle restraints: 16163 sinusoidal: 7769 harmonic: 8394 Sorted by residual: dihedral pdb=" C1 BCL v 101 " pdb=" CGA BCL v 101 " pdb=" O2A BCL v 101 " pdb=" CBA BCL v 101 " ideal model delta sinusoidal sigma weight residual -180.00 -1.34 -178.66 1 6.00e+00 2.78e-02 5.33e+02 dihedral pdb=" C1 BCL d 101 " pdb=" CGA BCL d 101 " pdb=" O2A BCL d 101 " pdb=" CBA BCL d 101 " ideal model delta sinusoidal sigma weight residual -180.00 -24.00 -156.00 1 6.00e+00 2.78e-02 5.10e+02 dihedral pdb=" C1 BCL p 101 " pdb=" CGA BCL p 101 " pdb=" O2A BCL p 101 " pdb=" CBA BCL p 101 " ideal model delta sinusoidal sigma weight residual -180.00 -36.59 -143.41 1 6.00e+00 2.78e-02 4.81e+02 ... (remaining 16160 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.525: 3932 0.525 - 1.051: 11 1.051 - 1.576: 1 1.576 - 2.102: 0 2.102 - 2.627: 35 Chirality restraints: 3979 Sorted by residual: chirality pdb=" C22 SPN a 103 " pdb=" C21 SPN a 103 " pdb=" C23 SPN a 103 " pdb=" CM7 SPN a 103 " both_signs ideal model delta sigma weight residual False -2.58 0.05 -2.63 2.00e-01 2.50e+01 1.73e+02 chirality pdb=" C22 SPN 1 104 " pdb=" C21 SPN 1 104 " pdb=" C23 SPN 1 104 " pdb=" CM7 SPN 1 104 " both_signs ideal model delta sigma weight residual False -2.58 0.04 -2.62 2.00e-01 2.50e+01 1.71e+02 chirality pdb=" C22 SPN 0 102 " pdb=" C21 SPN 0 102 " pdb=" C23 SPN 0 102 " pdb=" CM7 SPN 0 102 " both_signs ideal model delta sigma weight residual False -2.58 0.03 -2.61 2.00e-01 2.50e+01 1.70e+02 ... (remaining 3976 not shown) Planarity restraints: 4873 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" NB HEM C 403 " -0.082 2.00e-02 2.50e+03 3.22e-01 2.33e+03 pdb=" C1B HEM C 403 " -0.076 2.00e-02 2.50e+03 pdb=" C2B HEM C 403 " 0.127 2.00e-02 2.50e+03 pdb=" C3B HEM C 403 " -0.107 2.00e-02 2.50e+03 pdb=" C4B HEM C 403 " 0.082 2.00e-02 2.50e+03 pdb=" CAB HEM C 403 " -0.572 2.00e-02 2.50e+03 pdb=" CHB HEM C 403 " -0.319 2.00e-02 2.50e+03 pdb=" CHC HEM C 403 " 0.404 2.00e-02 2.50e+03 pdb=" CMB HEM C 403 " 0.542 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL L 301 " -0.350 1.50e-02 4.44e+03 2.97e-01 1.95e+03 pdb=" C2 BCL L 301 " 0.518 1.50e-02 4.44e+03 pdb=" C3 BCL L 301 " 0.105 1.50e-02 4.44e+03 pdb=" C4 BCL L 301 " -0.144 1.50e-02 4.44e+03 pdb=" C5 BCL L 301 " -0.130 1.50e-02 4.44e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL m 101 " 0.347 1.50e-02 4.44e+03 2.92e-01 1.89e+03 pdb=" C2 BCL m 101 " -0.503 1.50e-02 4.44e+03 pdb=" C3 BCL m 101 " -0.108 1.50e-02 4.44e+03 pdb=" C4 BCL m 101 " 0.074 1.50e-02 4.44e+03 pdb=" C5 BCL m 101 " 0.190 1.50e-02 4.44e+03 ... (remaining 4870 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 376 2.67 - 3.23: 22816 3.23 - 3.78: 42561 3.78 - 4.34: 62574 4.34 - 4.90: 100431 Nonbonded interactions: 228758 Sorted by model distance: nonbonded pdb=" OE2 GLU M 235 " pdb="FE FE M 401 " model vdw 2.109 2.260 nonbonded pdb=" O ASP t 13 " pdb=" OD1 ASP t 13 " model vdw 2.126 3.040 nonbonded pdb=" OG1 THR C 46 " pdb=" O GLU C 62 " model vdw 2.181 3.040 nonbonded pdb=" N TRP 6 47 " pdb=" O TRP 6 47 " model vdw 2.207 2.496 nonbonded pdb=" N ALA A 64 " pdb=" O ALA A 64 " model vdw 2.212 2.496 ... (remaining 228753 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 5 through 101) selection = chain '2' selection = chain '4' selection = chain '6' selection = chain '8' selection = chain 'b' selection = chain 'd' selection = (chain 'f' and resid 5 through 101) selection = (chain 'h' and resid 5 through 101) selection = (chain 'j' and resid 5 through 101) selection = (chain 'l' and resid 5 through 101) selection = (chain 'n' and resid 5 through 101) selection = (chain 'p' and resid 5 through 101) selection = (chain 'r' and resid 5 through 101) selection = (chain 't' and resid 5 through 101) selection = (chain 'v' and resid 5 through 101) selection = chain 'x' } ncs_group { reference = (chain '1' and resid 1 through 51) selection = (chain '3' and resid 1 through 51) selection = (chain '5' and resid 1 through 51) selection = (chain '7' and resid 1 through 51) selection = (chain '9' and resid 1 through 51) selection = (chain 'a' and resid 1 through 51) selection = (chain 'c' and resid 1 through 51) selection = (chain 'e' and resid 1 through 51) selection = (chain 'g' and resid 1 through 51) selection = (chain 'i' and resid 1 through 51) selection = (chain 'k' and resid 1 through 51) selection = (chain 'm' and resid 1 through 51) selection = (chain 'o' and resid 1 through 51) selection = (chain 'q' and resid 1 through 51) selection = (chain 's' and resid 1 through 51) selection = (chain 'u' and resid 1 through 51) selection = (chain 'w' and resid 1 through 51) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.500 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: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 26.420 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.070 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:10.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 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 : 0.028 0.599 29582 Z= 1.754 Angle : 2.163 23.288 40558 Z= 0.951 Chirality : 0.264 2.627 3979 Planarity : 0.028 0.331 4873 Dihedral : 25.145 179.830 10712 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.25 % Allowed : 8.20 % Favored : 91.55 % Cbeta Deviations : 0.37 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.15), residues: 2823 helix: 0.96 (0.12), residues: 1725 sheet: 0.31 (0.93), residues: 27 loop : -1.30 (0.17), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 2 45 TYR 0.030 0.002 TYR L 165 PHE 0.029 0.002 PHE 4 8 TRP 0.024 0.002 TRP C 9 HIS 0.012 0.001 HIS M 183 Details of bonding type rmsd covalent geometry : bond 0.02588 (29540) covalent geometry : angle 2.16313 (40556) SS BOND : bond 0.00021 ( 1) SS BOND : angle 0.88879 ( 2) hydrogen bonds : bond 0.21719 ( 1449) hydrogen bonds : angle 5.32642 ( 4032) Misc. bond : bond 0.31227 ( 41) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 372 time to evaluate : 1.029 Fit side-chains REVERT: o 3 LYS cc_start: 0.8549 (mttt) cc_final: 0.7639 (mmtt) REVERT: m 45 GLU cc_start: 0.7103 (mt-10) cc_final: 0.6866 (mm-30) REVERT: M 217 PHE cc_start: 0.9086 (OUTLIER) cc_final: 0.7631 (t80) REVERT: M 219 MET cc_start: 0.9166 (mtp) cc_final: 0.8878 (mtp) outliers start: 6 outliers final: 2 residues processed: 377 average time/residue: 0.7075 time to fit residues: 310.1936 Evaluate side-chains 299 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 296 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 234 ASP Chi-restraints excluded: chain M residue 217 PHE Chi-restraints excluded: chain M residue 321 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: s 40 HIS o 20 GLN o 40 HIS e 50 ASN c 50 ASN a 20 GLN 8 15 GLN C 100 ASN H 94 ASN H 128 HIS L 169 HIS L 212 ASN ** M 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.121358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.091691 restraints weight = 32864.994| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 1.25 r_work: 0.2880 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 29582 Z= 0.223 Angle : 0.946 17.683 40558 Z= 0.373 Chirality : 0.046 0.259 3979 Planarity : 0.005 0.062 4873 Dihedral : 26.300 179.995 5672 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.15 % Allowed : 10.06 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.15), residues: 2823 helix: 1.85 (0.12), residues: 1649 sheet: 0.03 (1.13), residues: 17 loop : -1.29 (0.17), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG 2 45 TYR 0.027 0.002 TYR L 165 PHE 0.026 0.002 PHE L 217 TRP 0.023 0.002 TRP C 9 HIS 0.013 0.002 HIS M 183 Details of bonding type rmsd covalent geometry : bond 0.00543 (29540) covalent geometry : angle 0.94551 (40556) SS BOND : bond 0.00175 ( 1) SS BOND : angle 0.75262 ( 2) hydrogen bonds : bond 0.09669 ( 1449) hydrogen bonds : angle 3.79626 ( 4032) Misc. bond : bond 0.01726 ( 41) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 295 time to evaluate : 1.230 Fit side-chains revert: symmetry clash REVERT: 1 3 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8116 (mttp) REVERT: 4 18 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7422 (tp30) REVERT: w 45 GLU cc_start: 0.7243 (mm-30) cc_final: 0.6966 (mm-30) REVERT: q 39 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7265 (tt0) REVERT: o 3 LYS cc_start: 0.8568 (mttt) cc_final: 0.7524 (mmtt) REVERT: o 35 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7496 (mp) REVERT: m 45 GLU cc_start: 0.7207 (mt-10) cc_final: 0.6905 (mm-30) REVERT: k 45 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7434 (mm-30) REVERT: j 18 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7450 (mm-30) REVERT: 7 3 LYS cc_start: 0.8726 (mttt) cc_final: 0.8421 (mttm) REVERT: C 115 ARG cc_start: 0.7377 (ttp-170) cc_final: 0.7158 (ttp-170) REVERT: L 13 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.8537 (ttt-90) REVERT: L 81 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8824 (mp) REVERT: L 83 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8355 (mm-30) REVERT: L 211 ASP cc_start: 0.8422 (OUTLIER) cc_final: 0.7907 (m-30) REVERT: L 217 PHE cc_start: 0.8897 (OUTLIER) cc_final: 0.8579 (t80) REVERT: M 217 PHE cc_start: 0.9018 (OUTLIER) cc_final: 0.6610 (t80) REVERT: M 219 MET cc_start: 0.8937 (mtp) cc_final: 0.8564 (mtp) REVERT: M 307 ASP cc_start: 0.8407 (OUTLIER) cc_final: 0.8080 (m-30) REVERT: 9 46 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8293 (mm) outliers start: 76 outliers final: 27 residues processed: 325 average time/residue: 0.7001 time to fit residues: 264.1580 Evaluate side-chains 325 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 285 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 3 LYS Chi-restraints excluded: chain 6 residue 14 GLU Chi-restraints excluded: chain 6 residue 27 LEU Chi-restraints excluded: chain 4 residue 18 GLU Chi-restraints excluded: chain u residue 34 VAL Chi-restraints excluded: chain v residue 43 ILE Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain q residue 37 SER Chi-restraints excluded: chain q residue 39 GLU Chi-restraints excluded: chain r residue 21 SER Chi-restraints excluded: chain r residue 43 ILE Chi-restraints excluded: chain o residue 35 LEU Chi-restraints excluded: chain m residue 2 SER Chi-restraints excluded: chain l residue 17 GLN Chi-restraints excluded: chain f residue 39 LEU Chi-restraints excluded: chain a residue 2 SER Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain j residue 18 GLU Chi-restraints excluded: chain j residue 39 LEU Chi-restraints excluded: chain 7 residue 2 SER Chi-restraints excluded: chain 7 residue 30 MET Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain H residue 77 GLU Chi-restraints excluded: chain H residue 146 THR Chi-restraints excluded: chain H residue 194 VAL Chi-restraints excluded: chain H residue 234 ASP Chi-restraints excluded: chain L residue 13 ARG Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain L residue 83 GLU Chi-restraints excluded: chain L residue 211 ASP Chi-restraints excluded: chain L residue 217 PHE Chi-restraints excluded: chain M residue 29 GLU Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 217 PHE Chi-restraints excluded: chain M residue 307 ASP Chi-restraints excluded: chain 9 residue 46 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 94 optimal weight: 1.9990 chunk 257 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 235 optimal weight: 0.6980 chunk 141 optimal weight: 8.9990 chunk 6 optimal weight: 20.0000 chunk 59 optimal weight: 5.9990 chunk 242 optimal weight: 1.9990 chunk 259 optimal weight: 4.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: q 20 GLN p 20 HIS g 50 ASN c 50 ASN i 50 ASN C 226 GLN 9 50 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.125262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.093818 restraints weight = 32849.710| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.27 r_work: 0.2963 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 29582 Z= 0.144 Angle : 0.742 15.315 40558 Z= 0.291 Chirality : 0.038 0.179 3979 Planarity : 0.004 0.056 4873 Dihedral : 24.136 179.974 5670 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.19 % Allowed : 11.80 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.15), residues: 2823 helix: 2.52 (0.12), residues: 1633 sheet: -0.04 (0.88), residues: 27 loop : -1.16 (0.16), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG g 14 TYR 0.018 0.001 TYR L 165 PHE 0.019 0.001 PHE 5 25 TRP 0.013 0.001 TRP C 285 HIS 0.013 0.001 HIS M 183 Details of bonding type rmsd covalent geometry : bond 0.00327 (29540) covalent geometry : angle 0.74185 (40556) SS BOND : bond 0.00175 ( 1) SS BOND : angle 0.53715 ( 2) hydrogen bonds : bond 0.07136 ( 1449) hydrogen bonds : angle 3.43564 ( 4032) Misc. bond : bond 0.01136 ( 41) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 297 time to evaluate : 0.996 Fit side-chains REVERT: 1 3 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8084 (mttp) REVERT: 6 14 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7357 (mt-10) REVERT: w 15 ARG cc_start: 0.7162 (mtt180) cc_final: 0.6346 (mtm180) REVERT: w 45 GLU cc_start: 0.7392 (mm-30) cc_final: 0.7122 (mm-30) REVERT: q 39 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.7026 (tt0) REVERT: o 3 LYS cc_start: 0.8546 (mttt) cc_final: 0.7606 (mtpt) REVERT: o 15 ARG cc_start: 0.6562 (mtp180) cc_final: 0.6307 (mtp-110) REVERT: o 35 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7311 (mp) REVERT: m 45 GLU cc_start: 0.7125 (mt-10) cc_final: 0.6843 (mm-30) REVERT: n 11 LEU cc_start: 0.8233 (tt) cc_final: 0.7981 (tt) REVERT: k 45 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7295 (mm-30) REVERT: k 46 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7744 (mp) REVERT: 7 1 MET cc_start: 0.7714 (ttt) cc_final: 0.7476 (ttm) REVERT: 7 3 LYS cc_start: 0.8725 (mttt) cc_final: 0.8403 (mttp) REVERT: L 13 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.8525 (ttt-90) REVERT: L 211 ASP cc_start: 0.8285 (OUTLIER) cc_final: 0.7770 (m-30) REVERT: L 217 PHE cc_start: 0.8730 (OUTLIER) cc_final: 0.8427 (t80) REVERT: M 215 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8354 (tp) REVERT: M 217 PHE cc_start: 0.8857 (OUTLIER) cc_final: 0.6090 (t80) REVERT: M 219 MET cc_start: 0.8778 (mtp) cc_final: 0.8404 (mtp) REVERT: M 307 ASP cc_start: 0.8372 (OUTLIER) cc_final: 0.8040 (m-30) outliers start: 53 outliers final: 20 residues processed: 315 average time/residue: 0.7328 time to fit residues: 267.8287 Evaluate side-chains 316 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 285 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 3 LYS Chi-restraints excluded: chain 6 residue 14 GLU Chi-restraints excluded: chain 3 residue 30 MET Chi-restraints excluded: chain w residue 10 ILE Chi-restraints excluded: chain x residue 43 ILE Chi-restraints excluded: chain v residue 43 ILE Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain q residue 37 SER Chi-restraints excluded: chain q residue 39 GLU Chi-restraints excluded: chain r residue 43 ILE Chi-restraints excluded: chain o residue 35 LEU Chi-restraints excluded: chain m residue 2 SER Chi-restraints excluded: chain k residue 46 LEU Chi-restraints excluded: chain l residue 17 GLN Chi-restraints excluded: chain 7 residue 2 SER Chi-restraints excluded: chain 7 residue 30 MET Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain H residue 77 GLU Chi-restraints excluded: chain H residue 146 THR Chi-restraints excluded: chain H residue 234 ASP Chi-restraints excluded: chain L residue 13 ARG Chi-restraints excluded: chain L residue 211 ASP Chi-restraints excluded: chain L residue 217 PHE Chi-restraints excluded: chain M residue 6 ASN Chi-restraints excluded: chain M residue 29 GLU Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 217 PHE Chi-restraints excluded: chain M residue 307 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 13 optimal weight: 10.0000 chunk 196 optimal weight: 7.9990 chunk 213 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 246 optimal weight: 0.0470 chunk 220 optimal weight: 3.9990 chunk 261 optimal weight: 5.9990 chunk 265 optimal weight: 7.9990 chunk 164 optimal weight: 3.9990 chunk 268 optimal weight: 3.9990 overall best weight: 2.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: w 50 ASN q 20 GLN g 50 ASN c 50 ASN i 50 ASN H 128 HIS 9 50 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.123420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.093568 restraints weight = 32640.276| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.26 r_work: 0.2911 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 29582 Z= 0.160 Angle : 0.787 15.708 40558 Z= 0.306 Chirality : 0.040 0.201 3979 Planarity : 0.004 0.061 4873 Dihedral : 23.584 179.973 5670 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.65 % Allowed : 11.88 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.15), residues: 2823 helix: 2.60 (0.12), residues: 1651 sheet: -0.33 (0.83), residues: 27 loop : -1.16 (0.16), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 115 TYR 0.019 0.002 TYR L 165 PHE 0.020 0.002 PHE 5 25 TRP 0.015 0.002 TRP p 47 HIS 0.012 0.001 HIS M 183 Details of bonding type rmsd covalent geometry : bond 0.00366 (29540) covalent geometry : angle 0.78704 (40556) SS BOND : bond 0.00122 ( 1) SS BOND : angle 0.36643 ( 2) hydrogen bonds : bond 0.07845 ( 1449) hydrogen bonds : angle 3.46597 ( 4032) Misc. bond : bond 0.01702 ( 41) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 288 time to evaluate : 1.034 Fit side-chains revert: symmetry clash REVERT: A 9 THR cc_start: 0.5995 (OUTLIER) cc_final: 0.5566 (m) REVERT: 1 3 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8089 (mttp) REVERT: w 45 GLU cc_start: 0.7462 (mm-30) cc_final: 0.7137 (mm-30) REVERT: q 39 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.6981 (tt0) REVERT: o 3 LYS cc_start: 0.8594 (mttt) cc_final: 0.7544 (mmtt) REVERT: o 35 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7440 (mp) REVERT: m 1 MET cc_start: 0.6525 (ptm) cc_final: 0.6178 (ptp) REVERT: j 18 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7325 (mm-30) REVERT: L 13 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.8566 (ttt-90) REVERT: L 83 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8263 (mm-30) REVERT: L 211 ASP cc_start: 0.8365 (OUTLIER) cc_final: 0.7881 (m-30) REVERT: L 217 PHE cc_start: 0.8820 (OUTLIER) cc_final: 0.8403 (t80) REVERT: M 215 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8398 (tp) REVERT: M 217 PHE cc_start: 0.8931 (OUTLIER) cc_final: 0.6608 (t80) REVERT: M 219 MET cc_start: 0.8854 (mtp) cc_final: 0.8421 (mtp) REVERT: M 307 ASP cc_start: 0.8405 (OUTLIER) cc_final: 0.8163 (m-30) outliers start: 64 outliers final: 26 residues processed: 314 average time/residue: 0.7212 time to fit residues: 262.2420 Evaluate side-chains 322 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 284 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain 1 residue 3 LYS Chi-restraints excluded: chain 6 residue 25 SER Chi-restraints excluded: chain 3 residue 30 MET Chi-restraints excluded: chain 4 residue 7 SER Chi-restraints excluded: chain w residue 10 ILE Chi-restraints excluded: chain x residue 43 ILE Chi-restraints excluded: chain v residue 43 ILE Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain q residue 37 SER Chi-restraints excluded: chain q residue 39 GLU Chi-restraints excluded: chain r residue 43 ILE Chi-restraints excluded: chain o residue 35 LEU Chi-restraints excluded: chain p residue 7 SER Chi-restraints excluded: chain m residue 2 SER Chi-restraints excluded: chain l residue 17 GLN Chi-restraints excluded: chain h residue 39 LEU Chi-restraints excluded: chain j residue 18 GLU Chi-restraints excluded: chain 7 residue 2 SER Chi-restraints excluded: chain 7 residue 30 MET Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain H residue 77 GLU Chi-restraints excluded: chain H residue 146 THR Chi-restraints excluded: chain H residue 234 ASP Chi-restraints excluded: chain L residue 13 ARG Chi-restraints excluded: chain L residue 83 GLU Chi-restraints excluded: chain L residue 211 ASP Chi-restraints excluded: chain L residue 217 PHE Chi-restraints excluded: chain M residue 6 ASN Chi-restraints excluded: chain M residue 29 GLU Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 217 PHE Chi-restraints excluded: chain M residue 307 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 151 optimal weight: 10.0000 chunk 90 optimal weight: 0.9990 chunk 137 optimal weight: 0.6980 chunk 208 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 186 optimal weight: 0.9980 chunk 146 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: q 20 GLN o 40 HIS g 50 ASN c 50 ASN i 50 ASN H 128 HIS ** L 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 50 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.128457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.097271 restraints weight = 32747.126| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.28 r_work: 0.3015 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 29582 Z= 0.115 Angle : 0.663 14.542 40558 Z= 0.256 Chirality : 0.036 0.148 3979 Planarity : 0.004 0.055 4873 Dihedral : 22.203 180.000 5670 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.11 % Allowed : 12.42 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.15), residues: 2823 helix: 3.03 (0.12), residues: 1627 sheet: -0.33 (0.81), residues: 27 loop : -1.01 (0.16), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 5 14 TYR 0.013 0.001 TYR L 165 PHE 0.018 0.001 PHE M 158 TRP 0.020 0.001 TRP p 47 HIS 0.009 0.001 HIS M 183 Details of bonding type rmsd covalent geometry : bond 0.00249 (29540) covalent geometry : angle 0.66268 (40556) SS BOND : bond 0.00076 ( 1) SS BOND : angle 0.36715 ( 2) hydrogen bonds : bond 0.05815 ( 1449) hydrogen bonds : angle 3.23026 ( 4032) Misc. bond : bond 0.00908 ( 41) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 290 time to evaluate : 1.020 Fit side-chains REVERT: A 24 MET cc_start: 0.8094 (ttt) cc_final: 0.7820 (ttt) REVERT: w 45 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7168 (mm-30) REVERT: o 3 LYS cc_start: 0.8581 (mttt) cc_final: 0.7408 (mmtt) REVERT: o 15 ARG cc_start: 0.7173 (mtp85) cc_final: 0.6611 (mtp-110) REVERT: o 35 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7279 (mp) REVERT: m 1 MET cc_start: 0.6243 (ptm) cc_final: 0.5951 (ptp) REVERT: k 46 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7715 (mp) REVERT: e 15 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.6213 (mtm110) REVERT: c 15 ARG cc_start: 0.7098 (mtp180) cc_final: 0.5625 (mmp-170) REVERT: C 36 LEU cc_start: 0.6584 (mt) cc_final: 0.6353 (mt) REVERT: L 156 ASP cc_start: 0.8943 (m-30) cc_final: 0.8725 (m-30) REVERT: L 217 PHE cc_start: 0.8619 (OUTLIER) cc_final: 0.8335 (t80) REVERT: M 215 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8297 (tp) REVERT: M 219 MET cc_start: 0.8707 (mtp) cc_final: 0.8306 (mtp) REVERT: M 273 PHE cc_start: 0.8946 (OUTLIER) cc_final: 0.7336 (t80) REVERT: M 307 ASP cc_start: 0.8354 (OUTLIER) cc_final: 0.8114 (m-30) outliers start: 51 outliers final: 21 residues processed: 317 average time/residue: 0.7179 time to fit residues: 263.8975 Evaluate side-chains 301 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 273 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 39 GLU Chi-restraints excluded: chain 6 residue 25 SER Chi-restraints excluded: chain w residue 10 ILE Chi-restraints excluded: chain x residue 43 ILE Chi-restraints excluded: chain v residue 43 ILE Chi-restraints excluded: chain q residue 37 SER Chi-restraints excluded: chain o residue 35 LEU Chi-restraints excluded: chain m residue 2 SER Chi-restraints excluded: chain k residue 46 LEU Chi-restraints excluded: chain l residue 17 GLN Chi-restraints excluded: chain g residue 3 LYS Chi-restraints excluded: chain e residue 15 ARG Chi-restraints excluded: chain b residue 18 GLU Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain H residue 77 GLU Chi-restraints excluded: chain H residue 146 THR Chi-restraints excluded: chain H residue 234 ASP Chi-restraints excluded: chain L residue 217 PHE Chi-restraints excluded: chain M residue 6 ASN Chi-restraints excluded: chain M residue 29 GLU Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 273 PHE Chi-restraints excluded: chain M residue 307 ASP Chi-restraints excluded: chain 0 residue 13 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 83 optimal weight: 6.9990 chunk 69 optimal weight: 8.9990 chunk 109 optimal weight: 0.9990 chunk 179 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 138 optimal weight: 7.9990 chunk 122 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 247 optimal weight: 0.0070 overall best weight: 1.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: q 20 GLN g 50 ASN c 50 ASN i 50 ASN H 128 HIS ** L 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 50 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.127448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.095927 restraints weight = 32705.635| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 1.28 r_work: 0.2994 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 29582 Z= 0.122 Angle : 0.674 14.418 40558 Z= 0.261 Chirality : 0.036 0.165 3979 Planarity : 0.004 0.058 4873 Dihedral : 21.830 179.991 5668 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.78 % Allowed : 13.37 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.15), residues: 2823 helix: 3.12 (0.12), residues: 1621 sheet: -0.41 (0.80), residues: 27 loop : -0.96 (0.16), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG a 15 TYR 0.015 0.001 TYR L 165 PHE 0.023 0.001 PHE o 23 TRP 0.022 0.001 TRP p 47 HIS 0.011 0.001 HIS M 183 Details of bonding type rmsd covalent geometry : bond 0.00267 (29540) covalent geometry : angle 0.67428 (40556) SS BOND : bond 0.00078 ( 1) SS BOND : angle 0.29052 ( 2) hydrogen bonds : bond 0.06125 ( 1449) hydrogen bonds : angle 3.22774 ( 4032) Misc. bond : bond 0.01106 ( 41) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 277 time to evaluate : 1.022 Fit side-chains REVERT: w 45 GLU cc_start: 0.7437 (mm-30) cc_final: 0.7130 (mm-30) REVERT: q 20 GLN cc_start: 0.7959 (OUTLIER) cc_final: 0.7626 (tt0) REVERT: o 3 LYS cc_start: 0.8594 (mttt) cc_final: 0.7448 (mmtt) REVERT: o 26 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7866 (mt) REVERT: o 35 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7269 (mp) REVERT: m 1 MET cc_start: 0.6181 (ptm) cc_final: 0.5876 (ptp) REVERT: k 46 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7715 (mp) REVERT: e 15 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.6301 (mtm110) REVERT: c 15 ARG cc_start: 0.7108 (mtp180) cc_final: 0.5618 (mmp-170) REVERT: L 217 PHE cc_start: 0.8678 (OUTLIER) cc_final: 0.8396 (t80) REVERT: M 215 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8315 (tp) REVERT: M 219 MET cc_start: 0.8758 (mtp) cc_final: 0.8344 (mtp) REVERT: M 273 PHE cc_start: 0.8956 (OUTLIER) cc_final: 0.7316 (t80) REVERT: M 307 ASP cc_start: 0.8335 (OUTLIER) cc_final: 0.8081 (m-30) outliers start: 43 outliers final: 25 residues processed: 300 average time/residue: 0.7520 time to fit residues: 261.4300 Evaluate side-chains 308 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 274 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 39 GLU Chi-restraints excluded: chain 3 residue 30 MET Chi-restraints excluded: chain w residue 10 ILE Chi-restraints excluded: chain x residue 43 ILE Chi-restraints excluded: chain v residue 25 SER Chi-restraints excluded: chain v residue 43 ILE Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain q residue 20 GLN Chi-restraints excluded: chain q residue 37 SER Chi-restraints excluded: chain o residue 26 LEU Chi-restraints excluded: chain o residue 35 LEU Chi-restraints excluded: chain m residue 2 SER Chi-restraints excluded: chain n residue 27 LEU Chi-restraints excluded: chain k residue 46 LEU Chi-restraints excluded: chain l residue 17 GLN Chi-restraints excluded: chain e residue 15 ARG Chi-restraints excluded: chain b residue 18 GLU Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain H residue 77 GLU Chi-restraints excluded: chain H residue 146 THR Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 234 ASP Chi-restraints excluded: chain L residue 167 HIS Chi-restraints excluded: chain L residue 217 PHE Chi-restraints excluded: chain M residue 6 ASN Chi-restraints excluded: chain M residue 29 GLU Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 273 PHE Chi-restraints excluded: chain M residue 307 ASP Chi-restraints excluded: chain 0 residue 13 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 63 optimal weight: 2.9990 chunk 260 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 51 optimal weight: 20.0000 chunk 4 optimal weight: 0.9990 chunk 202 optimal weight: 10.0000 chunk 85 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 247 optimal weight: 0.9990 chunk 176 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 40 HIS g 50 ASN c 50 ASN H 128 HIS L 167 HIS 9 50 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.123574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.091979 restraints weight = 32577.505| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 1.26 r_work: 0.2935 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 29582 Z= 0.163 Angle : 0.772 17.841 40558 Z= 0.302 Chirality : 0.040 0.203 3979 Planarity : 0.004 0.060 4873 Dihedral : 22.231 179.965 5668 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.28 % Allowed : 12.92 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.15), residues: 2823 helix: 2.84 (0.12), residues: 1651 sheet: -0.54 (0.81), residues: 27 loop : -1.02 (0.17), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG o 15 TYR 0.020 0.002 TYR L 165 PHE 0.023 0.002 PHE o 23 TRP 0.026 0.002 TRP p 47 HIS 0.012 0.001 HIS M 183 Details of bonding type rmsd covalent geometry : bond 0.00381 (29540) covalent geometry : angle 0.77219 (40556) SS BOND : bond 0.00083 ( 1) SS BOND : angle 0.29043 ( 2) hydrogen bonds : bond 0.07722 ( 1449) hydrogen bonds : angle 3.39955 ( 4032) Misc. bond : bond 0.01542 ( 41) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 279 time to evaluate : 0.951 Fit side-chains REVERT: A 9 THR cc_start: 0.5693 (OUTLIER) cc_final: 0.5400 (m) REVERT: A 24 MET cc_start: 0.8141 (ttt) cc_final: 0.7814 (ttt) REVERT: 6 14 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7437 (mt-10) REVERT: w 15 ARG cc_start: 0.7165 (mtt180) cc_final: 0.6427 (mtm180) REVERT: w 45 GLU cc_start: 0.7421 (mm-30) cc_final: 0.7072 (mm-30) REVERT: q 20 GLN cc_start: 0.7845 (tt0) cc_final: 0.7337 (tt0) REVERT: q 30 MET cc_start: 0.7803 (OUTLIER) cc_final: 0.7562 (tmm) REVERT: q 39 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6942 (tt0) REVERT: o 3 LYS cc_start: 0.8602 (mttt) cc_final: 0.7646 (mtpt) REVERT: o 35 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7431 (mp) REVERT: m 1 MET cc_start: 0.6360 (ptm) cc_final: 0.6029 (ptp) REVERT: k 46 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7727 (mp) REVERT: 7 1 MET cc_start: 0.7745 (ttt) cc_final: 0.7481 (ttm) REVERT: L 83 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8262 (mm-30) REVERT: L 211 ASP cc_start: 0.8302 (OUTLIER) cc_final: 0.7791 (m-30) REVERT: L 217 PHE cc_start: 0.8794 (OUTLIER) cc_final: 0.8365 (t80) REVERT: M 215 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8383 (tp) REVERT: M 217 PHE cc_start: 0.8864 (OUTLIER) cc_final: 0.6354 (t80) REVERT: M 219 MET cc_start: 0.8828 (mtp) cc_final: 0.8469 (mtp) REVERT: M 273 PHE cc_start: 0.8971 (OUTLIER) cc_final: 0.7315 (t80) REVERT: M 307 ASP cc_start: 0.8342 (OUTLIER) cc_final: 0.8092 (m-30) outliers start: 55 outliers final: 24 residues processed: 302 average time/residue: 0.7746 time to fit residues: 270.1766 Evaluate side-chains 315 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 278 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain 6 residue 14 GLU Chi-restraints excluded: chain 6 residue 25 SER Chi-restraints excluded: chain w residue 10 ILE Chi-restraints excluded: chain x residue 25 SER Chi-restraints excluded: chain x residue 43 ILE Chi-restraints excluded: chain v residue 43 ILE Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain q residue 30 MET Chi-restraints excluded: chain q residue 37 SER Chi-restraints excluded: chain q residue 39 GLU Chi-restraints excluded: chain o residue 35 LEU Chi-restraints excluded: chain m residue 2 SER Chi-restraints excluded: chain k residue 46 LEU Chi-restraints excluded: chain l residue 17 GLN Chi-restraints excluded: chain e residue 15 ARG Chi-restraints excluded: chain f residue 39 LEU Chi-restraints excluded: chain b residue 18 GLU Chi-restraints excluded: chain 7 residue 2 SER Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain H residue 77 GLU Chi-restraints excluded: chain H residue 146 THR Chi-restraints excluded: chain H residue 234 ASP Chi-restraints excluded: chain L residue 83 GLU Chi-restraints excluded: chain L residue 203 LYS Chi-restraints excluded: chain L residue 211 ASP Chi-restraints excluded: chain L residue 217 PHE Chi-restraints excluded: chain M residue 6 ASN Chi-restraints excluded: chain M residue 29 GLU Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 217 PHE Chi-restraints excluded: chain M residue 273 PHE Chi-restraints excluded: chain M residue 307 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 165 optimal weight: 4.9990 chunk 255 optimal weight: 4.9990 chunk 267 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 147 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 194 optimal weight: 8.9990 chunk 211 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 50 ASN c 50 ASN L 167 HIS 9 50 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.122388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.090819 restraints weight = 32731.964| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 1.28 r_work: 0.2917 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 29582 Z= 0.176 Angle : 0.807 18.435 40558 Z= 0.316 Chirality : 0.041 0.237 3979 Planarity : 0.004 0.060 4873 Dihedral : 22.542 179.934 5668 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.19 % Allowed : 13.21 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.15), residues: 2823 helix: 2.68 (0.12), residues: 1650 sheet: -0.53 (1.02), residues: 17 loop : -1.07 (0.17), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 1 14 TYR 0.021 0.002 TYR L 165 PHE 0.023 0.002 PHE o 23 TRP 0.030 0.002 TRP p 47 HIS 0.012 0.001 HIS M 183 Details of bonding type rmsd covalent geometry : bond 0.00416 (29540) covalent geometry : angle 0.80699 (40556) SS BOND : bond 0.00087 ( 1) SS BOND : angle 0.36539 ( 2) hydrogen bonds : bond 0.08261 ( 1449) hydrogen bonds : angle 3.48340 ( 4032) Misc. bond : bond 0.01698 ( 41) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 282 time to evaluate : 0.972 Fit side-chains revert: symmetry clash REVERT: A 9 THR cc_start: 0.5711 (OUTLIER) cc_final: 0.5437 (m) REVERT: A 24 MET cc_start: 0.8153 (ttt) cc_final: 0.7838 (ttt) REVERT: 6 14 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7496 (mt-10) REVERT: w 45 GLU cc_start: 0.7430 (mm-30) cc_final: 0.7079 (mm-30) REVERT: q 30 MET cc_start: 0.7795 (OUTLIER) cc_final: 0.7563 (tmm) REVERT: q 39 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.6993 (tt0) REVERT: q 50 ASN cc_start: 0.6578 (t0) cc_final: 0.6376 (m-40) REVERT: o 3 LYS cc_start: 0.8617 (mttt) cc_final: 0.7723 (mtpt) REVERT: o 15 ARG cc_start: 0.7001 (mtp85) cc_final: 0.6780 (mtp-110) REVERT: o 35 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7432 (mp) REVERT: m 1 MET cc_start: 0.6482 (ptm) cc_final: 0.6132 (ptp) REVERT: k 46 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7731 (mp) REVERT: 7 46 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7746 (tp) REVERT: L 21 ASP cc_start: 0.8221 (p0) cc_final: 0.8012 (p0) REVERT: L 211 ASP cc_start: 0.8394 (OUTLIER) cc_final: 0.7903 (m-30) REVERT: L 217 PHE cc_start: 0.8820 (OUTLIER) cc_final: 0.8349 (t80) REVERT: M 215 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8385 (tp) REVERT: M 217 PHE cc_start: 0.8909 (OUTLIER) cc_final: 0.6479 (t80) REVERT: M 219 MET cc_start: 0.8842 (mtp) cc_final: 0.8484 (mtp) REVERT: M 307 ASP cc_start: 0.8363 (OUTLIER) cc_final: 0.8117 (m-30) outliers start: 53 outliers final: 28 residues processed: 302 average time/residue: 0.7203 time to fit residues: 251.0391 Evaluate side-chains 320 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 280 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain 6 residue 14 GLU Chi-restraints excluded: chain 6 residue 25 SER Chi-restraints excluded: chain w residue 10 ILE Chi-restraints excluded: chain x residue 25 SER Chi-restraints excluded: chain x residue 43 ILE Chi-restraints excluded: chain v residue 43 ILE Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain q residue 30 MET Chi-restraints excluded: chain q residue 37 SER Chi-restraints excluded: chain q residue 39 GLU Chi-restraints excluded: chain o residue 35 LEU Chi-restraints excluded: chain p residue 7 SER Chi-restraints excluded: chain m residue 2 SER Chi-restraints excluded: chain k residue 46 LEU Chi-restraints excluded: chain l residue 17 GLN Chi-restraints excluded: chain f residue 39 LEU Chi-restraints excluded: chain b residue 18 GLU Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain 7 residue 2 SER Chi-restraints excluded: chain 7 residue 46 LEU Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain H residue 77 GLU Chi-restraints excluded: chain H residue 128 HIS Chi-restraints excluded: chain H residue 146 THR Chi-restraints excluded: chain H residue 234 ASP Chi-restraints excluded: chain L residue 203 LYS Chi-restraints excluded: chain L residue 211 ASP Chi-restraints excluded: chain L residue 217 PHE Chi-restraints excluded: chain M residue 6 ASN Chi-restraints excluded: chain M residue 29 GLU Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 217 PHE Chi-restraints excluded: chain M residue 307 ASP Chi-restraints excluded: chain 0 residue 13 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 227 optimal weight: 0.8980 chunk 244 optimal weight: 1.9990 chunk 174 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 158 optimal weight: 4.9990 chunk 66 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 278 optimal weight: 9.9990 chunk 68 optimal weight: 7.9990 chunk 57 optimal weight: 20.0000 chunk 21 optimal weight: 9.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 40 HIS g 50 ASN c 50 ASN L 167 HIS 9 50 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.122489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.090965 restraints weight = 32744.401| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 1.27 r_work: 0.2920 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 29582 Z= 0.175 Angle : 0.803 17.878 40558 Z= 0.314 Chirality : 0.041 0.223 3979 Planarity : 0.004 0.059 4873 Dihedral : 22.403 179.901 5668 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.95 % Allowed : 13.46 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.15), residues: 2823 helix: 2.68 (0.12), residues: 1615 sheet: -0.63 (0.80), residues: 27 loop : -1.04 (0.16), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG e 15 TYR 0.021 0.002 TYR L 165 PHE 0.022 0.002 PHE o 23 TRP 0.032 0.002 TRP p 47 HIS 0.012 0.001 HIS M 183 Details of bonding type rmsd covalent geometry : bond 0.00416 (29540) covalent geometry : angle 0.80316 (40556) SS BOND : bond 0.00091 ( 1) SS BOND : angle 0.38611 ( 2) hydrogen bonds : bond 0.08130 ( 1449) hydrogen bonds : angle 3.46498 ( 4032) Misc. bond : bond 0.01667 ( 41) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 283 time to evaluate : 1.002 Fit side-chains revert: symmetry clash REVERT: A 9 THR cc_start: 0.5679 (OUTLIER) cc_final: 0.5387 (m) REVERT: A 24 MET cc_start: 0.8155 (ttt) cc_final: 0.7831 (ttt) REVERT: 6 14 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7502 (mt-10) REVERT: w 45 GLU cc_start: 0.7416 (mm-30) cc_final: 0.7062 (mm-30) REVERT: q 20 GLN cc_start: 0.7852 (tt0) cc_final: 0.7541 (tt0) REVERT: q 30 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.7576 (tmm) REVERT: q 39 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6949 (tt0) REVERT: q 50 ASN cc_start: 0.6654 (t0) cc_final: 0.6412 (m-40) REVERT: o 3 LYS cc_start: 0.8613 (mttt) cc_final: 0.7700 (mtpt) REVERT: o 15 ARG cc_start: 0.7012 (mtp85) cc_final: 0.6634 (mtp-110) REVERT: o 35 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7433 (mp) REVERT: m 1 MET cc_start: 0.6348 (ptm) cc_final: 0.6020 (ptp) REVERT: k 46 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7711 (mp) REVERT: j 18 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7366 (mm-30) REVERT: 7 46 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7830 (tp) REVERT: L 211 ASP cc_start: 0.8371 (OUTLIER) cc_final: 0.7893 (m-30) REVERT: L 217 PHE cc_start: 0.8818 (OUTLIER) cc_final: 0.8344 (t80) REVERT: M 215 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8378 (tp) REVERT: M 217 PHE cc_start: 0.8928 (OUTLIER) cc_final: 0.6493 (t80) REVERT: M 219 MET cc_start: 0.8842 (mtp) cc_final: 0.8403 (mtp) REVERT: M 307 ASP cc_start: 0.8361 (OUTLIER) cc_final: 0.8114 (m-30) outliers start: 47 outliers final: 30 residues processed: 301 average time/residue: 0.7166 time to fit residues: 249.5171 Evaluate side-chains 324 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 281 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain 6 residue 14 GLU Chi-restraints excluded: chain 6 residue 25 SER Chi-restraints excluded: chain w residue 10 ILE Chi-restraints excluded: chain x residue 25 SER Chi-restraints excluded: chain x residue 43 ILE Chi-restraints excluded: chain v residue 43 ILE Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain q residue 30 MET Chi-restraints excluded: chain q residue 37 SER Chi-restraints excluded: chain q residue 39 GLU Chi-restraints excluded: chain r residue 43 ILE Chi-restraints excluded: chain o residue 35 LEU Chi-restraints excluded: chain p residue 7 SER Chi-restraints excluded: chain m residue 2 SER Chi-restraints excluded: chain k residue 46 LEU Chi-restraints excluded: chain l residue 17 GLN Chi-restraints excluded: chain f residue 39 LEU Chi-restraints excluded: chain b residue 18 GLU Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain j residue 18 GLU Chi-restraints excluded: chain 7 residue 2 SER Chi-restraints excluded: chain 7 residue 46 LEU Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain H residue 77 GLU Chi-restraints excluded: chain H residue 128 HIS Chi-restraints excluded: chain H residue 146 THR Chi-restraints excluded: chain H residue 234 ASP Chi-restraints excluded: chain L residue 203 LYS Chi-restraints excluded: chain L residue 211 ASP Chi-restraints excluded: chain L residue 217 PHE Chi-restraints excluded: chain M residue 6 ASN Chi-restraints excluded: chain M residue 29 GLU Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 217 PHE Chi-restraints excluded: chain M residue 275 VAL Chi-restraints excluded: chain M residue 307 ASP Chi-restraints excluded: chain 0 residue 13 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 101 optimal weight: 7.9990 chunk 187 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 257 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 138 optimal weight: 9.9990 chunk 201 optimal weight: 8.9990 chunk 236 optimal weight: 2.9990 chunk 212 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: q 20 GLN g 50 ASN c 50 ASN 9 50 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.122198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.090767 restraints weight = 32554.655| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.27 r_work: 0.2917 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 29582 Z= 0.177 Angle : 0.810 18.582 40558 Z= 0.318 Chirality : 0.041 0.236 3979 Planarity : 0.004 0.060 4873 Dihedral : 22.382 179.927 5668 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.86 % Allowed : 13.62 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.15), residues: 2823 helix: 2.66 (0.12), residues: 1615 sheet: -0.66 (1.01), residues: 17 loop : -1.07 (0.16), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 1 14 TYR 0.020 0.002 TYR L 165 PHE 0.021 0.002 PHE 5 25 TRP 0.035 0.002 TRP p 47 HIS 0.012 0.001 HIS M 183 Details of bonding type rmsd covalent geometry : bond 0.00420 (29540) covalent geometry : angle 0.81035 (40556) SS BOND : bond 0.00054 ( 1) SS BOND : angle 0.33890 ( 2) hydrogen bonds : bond 0.08257 ( 1449) hydrogen bonds : angle 3.48846 ( 4032) Misc. bond : bond 0.01528 ( 41) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5646 Ramachandran restraints generated. 2823 Oldfield, 0 Emsley, 2823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 277 time to evaluate : 1.138 Fit side-chains revert: symmetry clash REVERT: A 9 THR cc_start: 0.5708 (OUTLIER) cc_final: 0.5426 (m) REVERT: A 24 MET cc_start: 0.8157 (ttt) cc_final: 0.7855 (ttt) REVERT: 6 14 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7506 (mt-10) REVERT: w 45 GLU cc_start: 0.7409 (mm-30) cc_final: 0.7089 (mm-30) REVERT: q 20 GLN cc_start: 0.7822 (tt0) cc_final: 0.7570 (tt0) REVERT: q 30 MET cc_start: 0.7829 (OUTLIER) cc_final: 0.7579 (tmm) REVERT: q 39 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.6953 (tt0) REVERT: o 3 LYS cc_start: 0.8612 (mttt) cc_final: 0.7636 (mtpt) REVERT: o 15 ARG cc_start: 0.7011 (mtp85) cc_final: 0.6683 (mtp-110) REVERT: o 35 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7398 (mp) REVERT: m 1 MET cc_start: 0.6488 (ptm) cc_final: 0.6174 (ptp) REVERT: k 46 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7731 (mp) REVERT: j 18 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7380 (mm-30) REVERT: 7 46 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7792 (tp) REVERT: L 211 ASP cc_start: 0.8379 (OUTLIER) cc_final: 0.7902 (m-30) REVERT: L 217 PHE cc_start: 0.8824 (OUTLIER) cc_final: 0.8388 (t80) REVERT: M 140 MET cc_start: 0.8464 (mtp) cc_final: 0.8222 (mtm) REVERT: M 215 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8384 (tp) REVERT: M 217 PHE cc_start: 0.8936 (OUTLIER) cc_final: 0.6503 (t80) REVERT: M 219 MET cc_start: 0.8844 (mtp) cc_final: 0.8490 (mtp) REVERT: M 307 ASP cc_start: 0.8363 (OUTLIER) cc_final: 0.8117 (m-30) outliers start: 45 outliers final: 30 residues processed: 294 average time/residue: 0.7270 time to fit residues: 246.8942 Evaluate side-chains 320 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 277 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain 6 residue 14 GLU Chi-restraints excluded: chain 6 residue 25 SER Chi-restraints excluded: chain w residue 10 ILE Chi-restraints excluded: chain x residue 25 SER Chi-restraints excluded: chain x residue 43 ILE Chi-restraints excluded: chain v residue 43 ILE Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain q residue 30 MET Chi-restraints excluded: chain q residue 37 SER Chi-restraints excluded: chain q residue 39 GLU Chi-restraints excluded: chain r residue 43 ILE Chi-restraints excluded: chain o residue 35 LEU Chi-restraints excluded: chain m residue 2 SER Chi-restraints excluded: chain k residue 46 LEU Chi-restraints excluded: chain l residue 17 GLN Chi-restraints excluded: chain f residue 39 LEU Chi-restraints excluded: chain b residue 18 GLU Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain j residue 18 GLU Chi-restraints excluded: chain 7 residue 2 SER Chi-restraints excluded: chain 7 residue 46 LEU Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain H residue 77 GLU Chi-restraints excluded: chain H residue 128 HIS Chi-restraints excluded: chain H residue 146 THR Chi-restraints excluded: chain H residue 234 ASP Chi-restraints excluded: chain L residue 114 MET Chi-restraints excluded: chain L residue 203 LYS Chi-restraints excluded: chain L residue 211 ASP Chi-restraints excluded: chain L residue 217 PHE Chi-restraints excluded: chain M residue 6 ASN Chi-restraints excluded: chain M residue 29 GLU Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 217 PHE Chi-restraints excluded: chain M residue 275 VAL Chi-restraints excluded: chain M residue 307 ASP Chi-restraints excluded: chain 0 residue 13 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 162 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 276 optimal weight: 0.7980 chunk 203 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 219 optimal weight: 7.9990 chunk 132 optimal weight: 9.9990 chunk 133 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 262 optimal weight: 4.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 50 ASN c 50 ASN 9 50 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.123259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.091797 restraints weight = 32655.712| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.27 r_work: 0.2933 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 29582 Z= 0.160 Angle : 0.769 19.092 40558 Z= 0.300 Chirality : 0.040 0.200 3979 Planarity : 0.004 0.059 4873 Dihedral : 22.002 179.978 5668 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.90 % Allowed : 13.62 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.15), residues: 2823 helix: 2.77 (0.12), residues: 1616 sheet: -0.62 (0.79), residues: 27 loop : -1.01 (0.16), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 82 TYR 0.017 0.002 TYR L 165 PHE 0.020 0.002 PHE o 23 TRP 0.036 0.002 TRP p 47 HIS 0.011 0.001 HIS M 183 Details of bonding type rmsd covalent geometry : bond 0.00372 (29540) covalent geometry : angle 0.76926 (40556) SS BOND : bond 0.00059 ( 1) SS BOND : angle 0.35977 ( 2) hydrogen bonds : bond 0.07639 ( 1449) hydrogen bonds : angle 3.41292 ( 4032) Misc. bond : bond 0.01578 ( 41) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11948.12 seconds wall clock time: 203 minutes 17.66 seconds (12197.66 seconds total)