Starting phenix.real_space_refine on Mon Sep 14 21:08:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6et5_3951/09_2026/6et5_3951.cif Found real_map, /net/cci-nas-00/data/ceres_data/6et5_3951/09_2026/6et5_3951.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6et5_3951/09_2026/6et5_3951.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6et5_3951/09_2026/6et5_3951.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6et5_3951/09_2026/6et5_3951.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6et5_3951/09_2026/6et5_3951.map" model { file = "/net/cci-nas-00/data/ceres_data/6et5_3951/09_2026/6et5_3951.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6et5_3951/09_2026/6et5_3951.cif" } resolution = 2.87 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= 0.001 sd= 0.004 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: 6 Type Number sf(0) Gaussians Fe 5 7.16 5 Mg 38 5.21 5 S 45 5.16 5 C 22073 2.51 5 N 4821 2.21 5 O 5012 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 100 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31994 Number of models: 1 Model: "" Number of chains: 92 Chain: "C" Number of atoms: 2603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2603 Classifications: {'peptide': 333} Link IDs: {'PCIS': 3, 'PTRANS': 24, 'TRANS': 305} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 2171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2171 Classifications: {'peptide': 273} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 257} Chain: "M" Number of atoms: 2555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2555 Classifications: {'peptide': 323} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 303} Chain: "H" Number of atoms: 2018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2018 Classifications: {'peptide': 258} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 239} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "z" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 487 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "1" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 436 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "2" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 199 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 2, 'TRANS': 21} Chain: "F" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 487 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "K" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 487 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "P" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 487 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "S" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 487 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "V" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 487 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "Y" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 487 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "b" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 487 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "e" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 487 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "h" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 487 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "k" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 487 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "n" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 487 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "q" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 487 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "t" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 487 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "w" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 487 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "3" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 487 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "6" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 487 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 436 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "N" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 436 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "Q" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 436 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "T" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 436 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "W" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 436 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "Z" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 436 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "c" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 436 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "f" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 436 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "i" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 436 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "l" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 436 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "o" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 436 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "r" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 436 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "u" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 436 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "x" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 436 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "4" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 436 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "7" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 436 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "I" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 199 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 2, 'TRANS': 21} Chain: "O" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 199 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 2, 'TRANS': 21} Chain: "R" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 199 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 2, 'TRANS': 21} Chain: "U" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 199 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 2, 'TRANS': 21} Chain: "X" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 199 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 2, 'TRANS': 21} Chain: "a" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 199 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 2, 'TRANS': 21} Chain: "d" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 199 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 2, 'TRANS': 21} Chain: "g" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 199 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 2, 'TRANS': 21} Chain: "j" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 199 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 2, 'TRANS': 21} Chain: "m" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 199 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 2, 'TRANS': 21} Chain: "p" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 199 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 2, 'TRANS': 21} Chain: "s" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 199 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 2, 'TRANS': 21} Chain: "v" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 199 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 2, 'TRANS': 21} Chain: "y" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 199 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 2, 'TRANS': 21} Chain: "5" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 199 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 2, 'TRANS': 21} Chain: "C" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 172 Unusual residues: {'HEM': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "L" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 256 Unusual residues: {' FE': 1, 'BCB': 2, 'BPB': 1, 'UQ9': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "M" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 331 Unusual residues: {'BCB': 2, 'BPB': 1, 'LDA': 1, 'MQ9': 1, 'NS5': 1, 'SO4': 4} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 31 Unusual residues: {'LDA': 1, 'SO4': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "z" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCB': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCB': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCB': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCB': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCB': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCB': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCB': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCB': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCB': 1} Classifications: {'undetermined': 1} Chain: "h" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCB': 1} Classifications: {'undetermined': 1} Chain: "k" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCB': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCB': 1} Classifications: {'undetermined': 1} Chain: "q" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCB': 1} Classifications: {'undetermined': 1} Chain: "t" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCB': 1} Classifications: {'undetermined': 1} Chain: "w" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCB': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCB': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 124 Unusual residues: {'BCB': 1, 'UQ9': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "c" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "f" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "i" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "l" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "o" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "r" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "u" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "x" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "7" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'BCB': 1, 'NS0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.58, per 1000 atoms: 0.21 Number of scatterers: 31994 At special positions: 0 Unit cell: (145.22, 145.22, 147.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 5 26.01 S 45 16.00 Mg 38 11.99 O 5012 8.00 N 4821 7.00 C 22073 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=60, symmetry=0 Number of additional bonds: simple=60, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.27 Conformation dependent library (CDL) restraints added in 1.3 seconds 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6526 Finding SS restraints... Secondary structure from input PDB file: 146 helices and 9 sheets defined 59.0% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'C' and resid 24 through 35 Processing helix chain 'C' and resid 51 through 56 removed outlier: 3.572A pdb=" N VAL C 55 " --> pdb=" O PRO C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 82 Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'C' and resid 101 through 121 removed outlier: 4.216A pdb=" N VAL C 105 " --> pdb=" O LYS C 101 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG C 109 " --> pdb=" O VAL C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 126 Processing helix chain 'C' and resid 131 through 137 removed outlier: 4.060A pdb=" N CYS C 135 " --> pdb=" O THR C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 170 No H-bonds generated for 'chain 'C' and resid 168 through 170' Processing helix chain 'C' and resid 171 through 178 Processing helix chain 'C' and resid 179 through 181 No H-bonds generated for 'chain 'C' and resid 179 through 181' Processing helix chain 'C' and resid 188 through 194 Processing helix chain 'C' and resid 216 through 220 Processing helix chain 'C' and resid 223 through 241 Processing helix chain 'C' and resid 243 through 247 Processing helix chain 'C' and resid 249 through 253 removed outlier: 3.643A pdb=" N PHE C 253 " --> pdb=" O ALA C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 260 Processing helix chain 'C' and resid 261 through 281 removed outlier: 3.864A pdb=" N ALA C 265 " --> pdb=" O THR C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 removed outlier: 3.630A pdb=" N ASN C 286 " --> pdb=" O ALA C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 310 removed outlier: 4.161A pdb=" N CYS C 308 " --> pdb=" O ASP C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 319 Processing helix chain 'L' and resid 6 through 10 Processing helix chain 'L' and resid 18 through 23 removed outlier: 4.421A pdb=" N PHE L 22 " --> pdb=" O GLY L 18 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP L 23 " --> pdb=" O GLY L 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 18 through 23' Processing helix chain 'L' and resid 31 through 55 Processing helix chain 'L' and resid 70 through 74 Processing helix chain 'L' and resid 83 through 112 Processing helix chain 'L' and resid 115 through 133 removed outlier: 3.691A pdb=" N VAL L 123 " --> pdb=" O LEU L 119 " (cutoff:3.500A) Proline residue: L 124 - end of helix Processing helix chain 'L' and resid 133 through 140 Processing helix chain 'L' and resid 141 through 145 removed outlier: 3.847A pdb=" N HIS L 144 " --> pdb=" O SER L 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 149 through 164 removed outlier: 4.034A pdb=" N LEU L 154 " --> pdb=" O ILE L 150 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N TYR L 164 " --> pdb=" O PHE L 160 " (cutoff:3.500A) Processing helix chain 'L' and resid 166 through 169 Processing helix chain 'L' and resid 170 through 199 Processing helix chain 'L' and resid 208 through 220 removed outlier: 3.507A pdb=" N GLU L 212 " --> pdb=" O THR L 208 " (cutoff:3.500A) Processing helix chain 'L' and resid 225 through 251 removed outlier: 4.012A pdb=" N HIS L 230 " --> pdb=" O ALA L 226 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N PHE L 241 " --> pdb=" O ALA L 237 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N PHE L 246 " --> pdb=" O LEU L 242 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY L 247 " --> pdb=" O THR L 243 " (cutoff:3.500A) Processing helix chain 'L' and resid 258 through 263 removed outlier: 3.820A pdb=" N TRP L 262 " --> pdb=" O GLY L 258 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N TRP L 263 " --> pdb=" O TRP L 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 258 through 263' Processing helix chain 'L' and resid 263 through 268 Processing helix chain 'M' and resid 2 through 6 removed outlier: 4.103A pdb=" N THR M 5 " --> pdb=" O ASP M 2 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 41 Processing helix chain 'M' and resid 51 through 77 removed outlier: 4.097A pdb=" N GLY M 55 " --> pdb=" O LEU M 51 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL M 77 " --> pdb=" O MET M 73 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 88 Processing helix chain 'M' and resid 89 through 91 No H-bonds generated for 'chain 'M' and resid 89 through 91' Processing helix chain 'M' and resid 110 through 138 Processing helix chain 'M' and resid 142 through 160 removed outlier: 3.504A pdb=" N ALA M 151 " --> pdb=" O ASN M 147 " (cutoff:3.500A) Processing helix chain 'M' and resid 160 through 167 Processing helix chain 'M' and resid 168 through 172 removed outlier: 3.559A pdb=" N GLU M 171 " --> pdb=" O SER M 168 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 191 removed outlier: 3.643A pdb=" N ILE M 181 " --> pdb=" O ILE M 177 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU M 184 " --> pdb=" O HIS M 180 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR M 185 " --> pdb=" O ILE M 181 " (cutoff:3.500A) Processing helix chain 'M' and resid 193 through 196 Processing helix chain 'M' and resid 197 through 224 Processing helix chain 'M' and resid 225 through 228 Processing helix chain 'M' and resid 231 through 238 Processing helix chain 'M' and resid 240 through 255 Processing helix chain 'M' and resid 259 through 285 removed outlier: 4.313A pdb=" N HIS M 264 " --> pdb=" O ILE M 260 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG M 265 " --> pdb=" O GLU M 261 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N MET M 275 " --> pdb=" O SER M 271 " (cutoff:3.500A) Processing helix chain 'M' and resid 291 through 299 Processing helix chain 'M' and resid 314 through 318 Processing helix chain 'H' and resid 12 through 31 removed outlier: 3.715A pdb=" N TYR H 18 " --> pdb=" O GLN H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 36 Processing helix chain 'H' and resid 37 through 39 No H-bonds generated for 'chain 'H' and resid 37 through 39' Processing helix chain 'H' and resid 106 through 111 Processing helix chain 'H' and resid 112 through 116 Processing helix chain 'H' and resid 199 through 201 No H-bonds generated for 'chain 'H' and resid 199 through 201' Processing helix chain 'H' and resid 214 through 221 removed outlier: 3.624A pdb=" N ALA H 219 " --> pdb=" O GLU H 216 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL H 221 " --> pdb=" O PHE H 218 " (cutoff:3.500A) Processing helix chain 'H' and resid 231 through 249 removed outlier: 3.742A pdb=" N TYR H 242 " --> pdb=" O VAL H 238 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LEU H 247 " --> pdb=" O ALA H 243 " (cutoff:3.500A) Processing helix chain 'H' and resid 250 through 254 Processing helix chain 'z' and resid 7 through 9 No H-bonds generated for 'chain 'z' and resid 7 through 9' Processing helix chain 'z' and resid 10 through 16 removed outlier: 4.040A pdb=" N ASP z 16 " --> pdb=" O TRP z 12 " (cutoff:3.500A) Processing helix chain 'z' and resid 16 through 40 Processing helix chain '1' and resid 16 through 42 removed outlier: 3.552A pdb=" N THR 1 42 " --> pdb=" O TYR 1 38 " (cutoff:3.500A) Processing helix chain '2' and resid 18 through 35 Proline residue: 2 27 - end of helix removed outlier: 3.941A pdb=" N TYR 2 35 " --> pdb=" O ILE 2 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 9 No H-bonds generated for 'chain 'F' and resid 7 through 9' Processing helix chain 'F' and resid 10 through 16 removed outlier: 3.697A pdb=" N ILE F 14 " --> pdb=" O LYS F 10 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP F 16 " --> pdb=" O TRP F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 40 Processing helix chain 'K' and resid 7 through 9 No H-bonds generated for 'chain 'K' and resid 7 through 9' Processing helix chain 'K' and resid 10 through 16 removed outlier: 3.810A pdb=" N ASP K 16 " --> pdb=" O TRP K 12 " (cutoff:3.500A) Processing helix chain 'K' and resid 16 through 41 Processing helix chain 'P' and resid 7 through 9 No H-bonds generated for 'chain 'P' and resid 7 through 9' Processing helix chain 'P' and resid 10 through 16 removed outlier: 3.832A pdb=" N ASP P 16 " --> pdb=" O TRP P 12 " (cutoff:3.500A) Processing helix chain 'P' and resid 16 through 41 Processing helix chain 'S' and resid 7 through 9 No H-bonds generated for 'chain 'S' and resid 7 through 9' Processing helix chain 'S' and resid 10 through 15 Processing helix chain 'S' and resid 16 through 40 Processing helix chain 'V' and resid 7 through 9 No H-bonds generated for 'chain 'V' and resid 7 through 9' Processing helix chain 'V' and resid 10 through 16 removed outlier: 3.715A pdb=" N ASP V 16 " --> pdb=" O TRP V 12 " (cutoff:3.500A) Processing helix chain 'V' and resid 16 through 40 Processing helix chain 'Y' and resid 7 through 9 No H-bonds generated for 'chain 'Y' and resid 7 through 9' Processing helix chain 'Y' and resid 10 through 16 removed outlier: 3.880A pdb=" N ASP Y 16 " --> pdb=" O TRP Y 12 " (cutoff:3.500A) Processing helix chain 'Y' and resid 16 through 40 Processing helix chain 'b' and resid 7 through 9 No H-bonds generated for 'chain 'b' and resid 7 through 9' Processing helix chain 'b' and resid 10 through 16 removed outlier: 3.817A pdb=" N ASP b 16 " --> pdb=" O TRP b 12 " (cutoff:3.500A) Processing helix chain 'b' and resid 16 through 40 Processing helix chain 'e' and resid 7 through 9 No H-bonds generated for 'chain 'e' and resid 7 through 9' Processing helix chain 'e' and resid 10 through 16 removed outlier: 3.935A pdb=" N ASP e 16 " --> pdb=" O TRP e 12 " (cutoff:3.500A) Processing helix chain 'e' and resid 16 through 40 Processing helix chain 'h' and resid 7 through 9 No H-bonds generated for 'chain 'h' and resid 7 through 9' Processing helix chain 'h' and resid 10 through 16 removed outlier: 3.791A pdb=" N ASP h 16 " --> pdb=" O TRP h 12 " (cutoff:3.500A) Processing helix chain 'h' and resid 16 through 41 Processing helix chain 'k' and resid 7 through 9 No H-bonds generated for 'chain 'k' and resid 7 through 9' Processing helix chain 'k' and resid 10 through 16 removed outlier: 3.550A pdb=" N ASP k 16 " --> pdb=" O TRP k 12 " (cutoff:3.500A) Processing helix chain 'k' and resid 16 through 41 Processing helix chain 'n' and resid 7 through 9 No H-bonds generated for 'chain 'n' and resid 7 through 9' Processing helix chain 'n' and resid 10 through 16 removed outlier: 3.523A pdb=" N ASP n 16 " --> pdb=" O TRP n 12 " (cutoff:3.500A) Processing helix chain 'n' and resid 16 through 41 Processing helix chain 'q' and resid 7 through 9 No H-bonds generated for 'chain 'q' and resid 7 through 9' Processing helix chain 'q' and resid 10 through 16 removed outlier: 3.751A pdb=" N ASP q 16 " --> pdb=" O TRP q 12 " (cutoff:3.500A) Processing helix chain 'q' and resid 16 through 40 Processing helix chain 't' and resid 7 through 10 Processing helix chain 't' and resid 11 through 16 removed outlier: 3.600A pdb=" N ASP t 16 " --> pdb=" O TRP t 12 " (cutoff:3.500A) Processing helix chain 't' and resid 16 through 40 Processing helix chain 'w' and resid 7 through 9 No H-bonds generated for 'chain 'w' and resid 7 through 9' Processing helix chain 'w' and resid 10 through 16 removed outlier: 3.825A pdb=" N ASP w 16 " --> pdb=" O TRP w 12 " (cutoff:3.500A) Processing helix chain 'w' and resid 16 through 41 Processing helix chain '3' and resid 7 through 9 No H-bonds generated for 'chain '3' and resid 7 through 9' Processing helix chain '3' and resid 10 through 16 removed outlier: 3.502A pdb=" N ILE 3 14 " --> pdb=" O LYS 3 10 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASP 3 16 " --> pdb=" O TRP 3 12 " (cutoff:3.500A) Processing helix chain '3' and resid 16 through 41 Processing helix chain '6' and resid 7 through 9 No H-bonds generated for 'chain '6' and resid 7 through 9' Processing helix chain '6' and resid 10 through 16 removed outlier: 3.599A pdb=" N ILE 6 14 " --> pdb=" O LYS 6 10 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP 6 16 " --> pdb=" O TRP 6 12 " (cutoff:3.500A) Processing helix chain '6' and resid 16 through 40 removed outlier: 3.846A pdb=" N ALA 6 23 " --> pdb=" O ARG 6 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 44 Processing helix chain 'N' and resid 16 through 44 Processing helix chain 'Q' and resid 16 through 44 Processing helix chain 'T' and resid 16 through 44 removed outlier: 3.540A pdb=" N ALA T 43 " --> pdb=" O LEU T 39 " (cutoff:3.500A) Processing helix chain 'W' and resid 16 through 44 removed outlier: 3.572A pdb=" N LEU W 30 " --> pdb=" O THR W 26 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 44 Processing helix chain 'c' and resid 16 through 44 Processing helix chain 'f' and resid 16 through 44 Processing helix chain 'i' and resid 16 through 44 Processing helix chain 'l' and resid 16 through 44 Processing helix chain 'o' and resid 16 through 44 Processing helix chain 'r' and resid 16 through 42 Processing helix chain 'u' and resid 16 through 44 Processing helix chain 'x' and resid 16 through 44 removed outlier: 3.602A pdb=" N THR x 42 " --> pdb=" O TYR x 38 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA x 43 " --> pdb=" O LEU x 39 " (cutoff:3.500A) Processing helix chain '4' and resid 16 through 44 removed outlier: 3.546A pdb=" N ALA 4 43 " --> pdb=" O LEU 4 39 " (cutoff:3.500A) Processing helix chain '7' and resid 16 through 44 removed outlier: 3.647A pdb=" N ALA 7 43 " --> pdb=" O LEU 7 39 " (cutoff:3.500A) Processing helix chain 'I' and resid 18 through 35 Proline residue: I 27 - end of helix removed outlier: 3.960A pdb=" N TYR I 35 " --> pdb=" O ILE I 31 " (cutoff:3.500A) Processing helix chain 'O' and resid 18 through 35 Proline residue: O 27 - end of helix removed outlier: 3.856A pdb=" N TYR O 35 " --> pdb=" O ILE O 31 " (cutoff:3.500A) Processing helix chain 'R' and resid 18 through 35 Proline residue: R 27 - end of helix removed outlier: 3.849A pdb=" N TYR R 35 " --> pdb=" O ILE R 31 " (cutoff:3.500A) Processing helix chain 'U' and resid 18 through 35 Proline residue: U 27 - end of helix removed outlier: 4.110A pdb=" N TYR U 35 " --> pdb=" O ILE U 31 " (cutoff:3.500A) Processing helix chain 'X' and resid 18 through 35 Proline residue: X 27 - end of helix removed outlier: 4.004A pdb=" N TYR X 35 " --> pdb=" O ILE X 31 " (cutoff:3.500A) Processing helix chain 'a' and resid 18 through 35 Proline residue: a 27 - end of helix removed outlier: 4.044A pdb=" N TYR a 35 " --> pdb=" O ILE a 31 " (cutoff:3.500A) Processing helix chain 'd' and resid 18 through 35 Proline residue: d 27 - end of helix removed outlier: 3.921A pdb=" N TYR d 35 " --> pdb=" O ILE d 31 " (cutoff:3.500A) Processing helix chain 'g' and resid 18 through 35 Proline residue: g 27 - end of helix removed outlier: 4.023A pdb=" N TYR g 35 " --> pdb=" O ILE g 31 " (cutoff:3.500A) Processing helix chain 'j' and resid 18 through 35 Proline residue: j 27 - end of helix removed outlier: 3.852A pdb=" N TYR j 35 " --> pdb=" O ILE j 31 " (cutoff:3.500A) Processing helix chain 'm' and resid 18 through 35 Proline residue: m 27 - end of helix removed outlier: 3.830A pdb=" N TYR m 35 " --> pdb=" O ILE m 31 " (cutoff:3.500A) Processing helix chain 'p' and resid 18 through 35 Proline residue: p 27 - end of helix removed outlier: 3.853A pdb=" N TYR p 35 " --> pdb=" O ILE p 31 " (cutoff:3.500A) Processing helix chain 's' and resid 18 through 35 Proline residue: s 27 - end of helix removed outlier: 3.983A pdb=" N TYR s 35 " --> pdb=" O ILE s 31 " (cutoff:3.500A) Processing helix chain 'v' and resid 18 through 35 Proline residue: v 27 - end of helix removed outlier: 4.043A pdb=" N TYR v 35 " --> pdb=" O ILE v 31 " (cutoff:3.500A) Processing helix chain 'y' and resid 18 through 35 Proline residue: y 27 - end of helix removed outlier: 3.978A pdb=" N TYR y 35 " --> pdb=" O ILE y 31 " (cutoff:3.500A) Processing helix chain '5' and resid 18 through 35 Proline residue: 5 27 - end of helix removed outlier: 3.777A pdb=" N TYR 5 35 " --> pdb=" O ILE 5 31 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 8 through 9 Processing sheet with id=AA2, first strand: chain 'L' and resid 25 through 26 Processing sheet with id=AA3, first strand: chain 'M' and resid 12 through 13 Processing sheet with id=AA4, first strand: chain 'M' and resid 28 through 29 Processing sheet with id=AA5, first strand: chain 'H' and resid 5 through 7 removed outlier: 6.122A pdb=" N LEU H 10 " --> pdb=" O LEU H 6 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 66 through 69 Processing sheet with id=AA7, first strand: chain 'H' and resid 90 through 92 Processing sheet with id=AA8, first strand: chain 'H' and resid 134 through 136 removed outlier: 6.679A pdb=" N GLU H 184 " --> pdb=" O THR H 169 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU H 171 " --> pdb=" O TYR H 182 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N TYR H 182 " --> pdb=" O LEU H 171 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL H 173 " --> pdb=" O PHE H 180 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N PHE H 180 " --> pdb=" O VAL H 173 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ARG H 192 " --> pdb=" O VAL H 187 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 134 through 136 removed outlier: 3.641A pdb=" N GLY H 166 " --> pdb=" O VAL H 157 " (cutoff:3.500A) 1418 hydrogen bonds defined for protein. 4125 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: 5.92 Time building geometry restraints manager: 4.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.37: 9597 1.37 - 1.55: 22726 1.55 - 1.73: 703 1.73 - 1.90: 62 1.90 - 2.08: 164 Bond restraints: 33252 Sorted by residual: bond pdb=" CAB BCB q 101 " pdb=" CBB BCB q 101 " ideal model delta sigma weight residual 1.510 1.209 0.301 2.30e-02 1.89e+03 1.71e+02 bond pdb=" C2 UQ9 L 304 " pdb=" O2 UQ9 L 304 " ideal model delta sigma weight residual 1.213 1.426 -0.213 2.00e-02 2.50e+03 1.14e+02 bond pdb=" C2 UQ9 6 101 " pdb=" O2 UQ9 6 101 " ideal model delta sigma weight residual 1.213 1.423 -0.210 2.00e-02 2.50e+03 1.10e+02 bond pdb=" C28 UQ9 L 304 " pdb=" C29 UQ9 L 304 " ideal model delta sigma weight residual 1.335 1.534 -0.199 2.00e-02 2.50e+03 9.90e+01 bond pdb=" C48 UQ9 L 304 " pdb=" C49 UQ9 L 304 " ideal model delta sigma weight residual 1.336 1.534 -0.198 2.00e-02 2.50e+03 9.79e+01 ... (remaining 33247 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.31: 43171 5.31 - 10.63: 2287 10.63 - 15.94: 427 15.94 - 21.26: 126 21.26 - 26.57: 6 Bond angle restraints: 46017 Sorted by residual: angle pdb=" C TRP P 48 " pdb=" CA TRP P 48 " pdb=" CB TRP P 48 " ideal model delta sigma weight residual 111.82 97.11 14.71 1.28e+00 6.10e-01 1.32e+02 angle pdb=" C TRP e 48 " pdb=" CA TRP e 48 " pdb=" CB TRP e 48 " ideal model delta sigma weight residual 111.82 97.36 14.46 1.28e+00 6.10e-01 1.28e+02 angle pdb=" C TRP b 48 " pdb=" CA TRP b 48 " pdb=" CB TRP b 48 " ideal model delta sigma weight residual 111.73 96.55 15.18 1.42e+00 4.96e-01 1.14e+02 angle pdb=" N TYR L 164 " pdb=" CA TYR L 164 " pdb=" C TYR L 164 " ideal model delta sigma weight residual 110.17 93.58 16.59 1.61e+00 3.86e-01 1.06e+02 angle pdb=" N ILE G 47 " pdb=" CA ILE G 47 " pdb=" C ILE G 47 " ideal model delta sigma weight residual 110.42 119.83 -9.41 9.60e-01 1.09e+00 9.60e+01 ... (remaining 46012 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.58: 16751 35.58 - 71.15: 949 71.15 - 106.73: 120 106.73 - 142.31: 16 142.31 - 177.88: 9 Dihedral angle restraints: 17845 sinusoidal: 7747 harmonic: 10098 Sorted by residual: dihedral pdb=" CBD BCB 6 102 " pdb=" CGD BCB 6 102 " pdb=" O2D BCB 6 102 " pdb=" CED BCB 6 102 " ideal model delta sinusoidal sigma weight residual -180.00 -59.22 -120.78 1 5.00e+00 4.00e-02 5.81e+02 dihedral pdb=" C1 BCB u 101 " pdb=" CGA BCB u 101 " pdb=" O2A BCB u 101 " pdb=" CBA BCB u 101 " ideal model delta sinusoidal sigma weight residual -180.00 -2.12 -177.88 1 6.00e+00 2.78e-02 5.33e+02 dihedral pdb=" C1 BCB i 101 " pdb=" CGA BCB i 101 " pdb=" O2A BCB i 101 " pdb=" CBA BCB i 101 " ideal model delta sinusoidal sigma weight residual 180.00 2.81 177.19 1 6.00e+00 2.78e-02 5.33e+02 ... (remaining 17842 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.045: 4798 1.045 - 2.089: 13 2.089 - 3.134: 0 3.134 - 4.178: 0 4.178 - 5.223: 2 Chirality restraints: 4813 Sorted by residual: chirality pdb=" C13 BPB M 407 " pdb=" C12 BPB M 407 " pdb=" C14 BPB M 407 " pdb=" C15 BPB M 407 " both_signs ideal model delta sigma weight residual False 2.60 -2.63 5.22 2.00e-01 2.50e+01 6.82e+02 chirality pdb=" C13 BPB L 303 " pdb=" C12 BPB L 303 " pdb=" C14 BPB L 303 " pdb=" C15 BPB L 303 " both_signs ideal model delta sigma weight residual False 2.60 -2.54 5.13 2.00e-01 2.50e+01 6.59e+02 chirality pdb=" CA LEU P 40 " pdb=" N LEU P 40 " pdb=" C LEU P 40 " pdb=" CB LEU P 40 " both_signs ideal model delta sigma weight residual False 2.51 1.19 1.32 2.00e-01 2.50e+01 4.34e+01 ... (remaining 4810 not shown) Planarity restraints: 5558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 UQ9 6 101 " 0.144 2.00e-02 2.50e+03 2.58e-01 1.99e+03 pdb=" C1M UQ9 6 101 " 0.227 2.00e-02 2.50e+03 pdb=" C2 UQ9 6 101 " 0.254 2.00e-02 2.50e+03 pdb=" C3 UQ9 6 101 " 0.153 2.00e-02 2.50e+03 pdb=" C4 UQ9 6 101 " 0.043 2.00e-02 2.50e+03 pdb=" C5 UQ9 6 101 " -0.051 2.00e-02 2.50e+03 pdb=" C6 UQ9 6 101 " 0.004 2.00e-02 2.50e+03 pdb=" C7 UQ9 6 101 " -0.040 2.00e-02 2.50e+03 pdb=" O2 UQ9 6 101 " -0.738 2.00e-02 2.50e+03 pdb=" O3 UQ9 6 101 " 0.230 2.00e-02 2.50e+03 pdb=" O4 UQ9 6 101 " -0.053 2.00e-02 2.50e+03 pdb=" O5 UQ9 6 101 " -0.173 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 UQ9 L 304 " 0.152 2.00e-02 2.50e+03 2.56e-01 1.97e+03 pdb=" C1M UQ9 L 304 " 0.224 2.00e-02 2.50e+03 pdb=" C2 UQ9 L 304 " 0.253 2.00e-02 2.50e+03 pdb=" C3 UQ9 L 304 " 0.144 2.00e-02 2.50e+03 pdb=" C4 UQ9 L 304 " 0.020 2.00e-02 2.50e+03 pdb=" C5 UQ9 L 304 " -0.051 2.00e-02 2.50e+03 pdb=" C6 UQ9 L 304 " 0.035 2.00e-02 2.50e+03 pdb=" C7 UQ9 L 304 " -0.059 2.00e-02 2.50e+03 pdb=" O2 UQ9 L 304 " -0.733 2.00e-02 2.50e+03 pdb=" O3 UQ9 L 304 " 0.229 2.00e-02 2.50e+03 pdb=" O4 UQ9 L 304 " -0.044 2.00e-02 2.50e+03 pdb=" O5 UQ9 L 304 " -0.173 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA NS0 i 102 " 0.295 2.00e-02 2.50e+03 3.23e-01 1.30e+03 pdb=" CB NS0 i 102 " -0.589 2.00e-02 2.50e+03 pdb=" CG NS0 i 102 " 0.293 2.00e-02 2.50e+03 pdb=" CD1 NS0 i 102 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 NS0 i 102 " -0.006 2.00e-02 2.50e+03 ... (remaining 5555 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.25: 32 2.25 - 2.92: 13033 2.92 - 3.58: 46804 3.58 - 4.24: 80731 4.24 - 4.90: 130118 Nonbonded interactions: 270718 Sorted by model distance: nonbonded pdb=" CD1 ILE f 47 " pdb=" CD1 LEU d 17 " model vdw 1.592 3.880 nonbonded pdb=" CD1 ILE N 47 " pdb=" CD1 LEU I 17 " model vdw 1.701 3.880 nonbonded pdb=" O TRP L 25 " pdb=" NH2 ARG 3 19 " model vdw 1.791 3.120 nonbonded pdb=" CG1 ILE 1 21 " pdb=" C8 NS0 1 102 " model vdw 1.856 3.088 nonbonded pdb=" O ALA 6 23 " pdb=" CD2 TYR 6 27 " model vdw 1.863 3.340 ... (remaining 270713 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 '1' selection = chain '4' selection = chain '7' selection = chain 'G' selection = chain 'N' selection = chain 'Q' selection = chain 'T' selection = chain 'W' selection = chain 'Z' selection = chain 'c' selection = chain 'f' selection = chain 'i' selection = chain 'l' selection = chain 'o' selection = chain 'r' selection = chain 'u' selection = chain 'x' } ncs_group { reference = chain '2' selection = chain '5' selection = chain 'I' selection = chain 'O' selection = chain 'R' selection = chain 'U' selection = chain 'X' selection = chain 'a' selection = chain 'd' selection = chain 'g' selection = chain 'j' selection = chain 'm' selection = chain 'p' selection = chain 's' selection = chain 'v' selection = chain 'y' } ncs_group { reference = (chain '3' and resid 1 through 58) selection = (chain '6' and resid 1 through 58) selection = (chain 'F' and resid 1 through 58) selection = (chain 'K' and resid 1 through 58) selection = (chain 'P' and resid 1 through 58) selection = (chain 'S' and resid 1 through 58) selection = (chain 'V' and resid 1 through 58) selection = (chain 'Y' and resid 1 through 58) selection = (chain 'b' and resid 1 through 58) selection = (chain 'e' and resid 1 through 58) selection = (chain 'h' and resid 1 through 58) selection = (chain 'k' and resid 1 through 58) selection = (chain 'n' and resid 1 through 58) selection = (chain 'q' and resid 1 through 58) selection = (chain 't' and resid 1 through 58) selection = (chain 'w' and resid 1 through 58) selection = (chain 'z' and resid 1 through 58) } 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: 0.790 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: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 28.750 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.110 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:9.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 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 0.767 33312 Z= 1.737 Angle : 2.859 26.570 46017 Z= 1.477 Chirality : 0.206 5.223 4813 Planarity : 0.029 0.350 5558 Dihedral : 21.558 177.884 11319 Min Nonbonded Distance : 1.592 Molprobity Statistics. All-atom Clashscore : 33.23 Ramachandran Plot: Outliers : 4.08 % Allowed : 12.22 % Favored : 83.70 % Rotamer: Outliers : 8.13 % Allowed : 12.88 % Favored : 79.00 % Cbeta Deviations : 6.19 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 1.42 % Twisted General : 1.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.05 (0.11), residues: 3380 helix: -2.60 (0.09), residues: 1693 sheet: -2.28 (0.87), residues: 26 loop : -4.33 (0.12), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 146 TYR 0.056 0.005 TYR C 227 PHE 0.045 0.005 PHE L 62 TRP 0.056 0.007 TRP L 86 HIS 0.019 0.004 HIS L 230 Details of bonding type rmsd/Z covalent geometry : bond 0.02514 / 1.30 (33252) covalent geometry : angle 2.85920 / 1.48 (46017) hydrogen bonds : bond 0.21483 / 14.47 ( 1416) hydrogen bonds : angle 8.44019 / 5.98 ( 4125) Misc. bond : bond 0.27642 / 18.41 ( 60) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 951 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 238 poor density : 713 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 74 MET cc_start: 0.9558 (mmp) cc_final: 0.9288 (mmt) REVERT: C 110 MET cc_start: 0.9562 (mmt) cc_final: 0.9159 (mmt) REVERT: C 113 MET cc_start: 0.9602 (ttp) cc_final: 0.9345 (ttp) REVERT: C 123 GLN cc_start: 0.9482 (OUTLIER) cc_final: 0.9254 (pm20) REVERT: C 233 MET cc_start: 0.9340 (mmp) cc_final: 0.8443 (mmt) REVERT: C 252 THR cc_start: 0.9671 (OUTLIER) cc_final: 0.9464 (p) REVERT: C 273 MET cc_start: 0.9485 (ttp) cc_final: 0.9284 (ttt) REVERT: L 23 ASP cc_start: 0.9598 (t0) cc_final: 0.9271 (t0) REVERT: L 106 GLU cc_start: 0.9754 (mt-10) cc_final: 0.9545 (mm-30) REVERT: L 204 ASP cc_start: 0.9350 (m-30) cc_final: 0.9107 (m-30) REVERT: L 228 SER cc_start: 0.9564 (OUTLIER) cc_final: 0.9272 (p) REVERT: M 244 GLU cc_start: 0.9367 (mt-10) cc_final: 0.9020 (mm-30) REVERT: H 133 LYS cc_start: 0.9616 (OUTLIER) cc_final: 0.9324 (ttmp) REVERT: H 161 ASP cc_start: 0.9380 (OUTLIER) cc_final: 0.8716 (p0) REVERT: H 217 GLN cc_start: 0.8968 (OUTLIER) cc_final: 0.8564 (pm20) REVERT: H 237 LYS cc_start: 0.9674 (OUTLIER) cc_final: 0.9384 (mmtp) REVERT: H 239 SER cc_start: 0.9859 (m) cc_final: 0.9623 (p) REVERT: 2 34 THR cc_start: 0.9477 (m) cc_final: 0.9249 (p) REVERT: F 31 ILE cc_start: 0.9722 (OUTLIER) cc_final: 0.9424 (pp) REVERT: F 44 ARG cc_start: 0.9439 (OUTLIER) cc_final: 0.8727 (ttt-90) REVERT: K 18 ARG cc_start: 0.9333 (mtm110) cc_final: 0.8777 (tmt170) REVERT: b 44 ARG cc_start: 0.9500 (OUTLIER) cc_final: 0.8943 (mtm180) REVERT: h 43 ASP cc_start: 0.9780 (m-30) cc_final: 0.9482 (m-30) REVERT: h 51 GLN cc_start: 0.9537 (tp40) cc_final: 0.9330 (mm-40) REVERT: k 56 LYS cc_start: 0.9319 (tmtp) cc_final: 0.9008 (mppt) REVERT: w 52 ARG cc_start: 0.9348 (mtm-85) cc_final: 0.9078 (ppt170) REVERT: 3 16 ASP cc_start: 0.9333 (t0) cc_final: 0.8688 (t0) REVERT: 3 27 TYR cc_start: 0.9342 (t80) cc_final: 0.9118 (t80) REVERT: 3 44 ARG cc_start: 0.9473 (OUTLIER) cc_final: 0.9243 (mtp-110) REVERT: 6 4 TYR cc_start: 0.8997 (OUTLIER) cc_final: 0.7339 (m-10) REVERT: c 44 ARG cc_start: 0.9497 (OUTLIER) cc_final: 0.9264 (mmp80) REVERT: l 29 TYR cc_start: 0.9512 (t80) cc_final: 0.9279 (t80) REVERT: o 16 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8802 (ptpt) REVERT: r 16 LYS cc_start: 0.9253 (OUTLIER) cc_final: 0.8930 (mttp) REVERT: d 16 ASN cc_start: 0.6804 (OUTLIER) cc_final: 0.6364 (t0) REVERT: s 35 TYR cc_start: 0.9453 (m-80) cc_final: 0.8938 (m-10) outliers start: 238 outliers final: 56 residues processed: 873 average time/residue: 0.5194 time to fit residues: 558.8287 Evaluate side-chains 536 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 464 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 132 CYS Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain L residue 228 SER Chi-restraints excluded: chain M residue 126 SER Chi-restraints excluded: chain M residue 194 PHE Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 133 LYS Chi-restraints excluded: chain H residue 161 ASP Chi-restraints excluded: chain H residue 209 VAL Chi-restraints excluded: chain H residue 217 GLN Chi-restraints excluded: chain H residue 237 LYS Chi-restraints excluded: chain H residue 238 VAL Chi-restraints excluded: chain 1 residue 6 SER Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 44 ARG Chi-restraints excluded: chain b residue 44 ARG Chi-restraints excluded: chain w residue 19 ARG Chi-restraints excluded: chain w residue 21 LEU Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain 3 residue 44 ARG Chi-restraints excluded: chain 6 residue 4 TYR Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain Q residue 14 GLU Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain W residue 27 VAL Chi-restraints excluded: chain Z residue 14 GLU Chi-restraints excluded: chain Z residue 55 VAL Chi-restraints excluded: chain c residue 14 GLU Chi-restraints excluded: chain c residue 23 VAL Chi-restraints excluded: chain c residue 44 ARG Chi-restraints excluded: chain f residue 13 GLU Chi-restraints excluded: chain f residue 16 LYS Chi-restraints excluded: chain f residue 27 VAL Chi-restraints excluded: chain i residue 14 GLU Chi-restraints excluded: chain i residue 23 VAL Chi-restraints excluded: chain i residue 27 VAL Chi-restraints excluded: chain l residue 14 GLU Chi-restraints excluded: chain l residue 36 VAL Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain o residue 16 LYS Chi-restraints excluded: chain o residue 25 SER Chi-restraints excluded: chain o residue 34 VAL Chi-restraints excluded: chain r residue 14 GLU Chi-restraints excluded: chain r residue 16 LYS Chi-restraints excluded: chain r residue 23 VAL Chi-restraints excluded: chain r residue 36 VAL Chi-restraints excluded: chain r residue 55 VAL Chi-restraints excluded: chain u residue 14 GLU Chi-restraints excluded: chain u residue 23 VAL Chi-restraints excluded: chain x residue 14 GLU Chi-restraints excluded: chain x residue 16 LYS Chi-restraints excluded: chain 4 residue 34 VAL Chi-restraints excluded: chain 4 residue 55 VAL Chi-restraints excluded: chain 7 residue 14 GLU Chi-restraints excluded: chain 7 residue 34 VAL Chi-restraints excluded: chain 7 residue 55 VAL Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain d residue 16 ASN Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain s residue 17 LEU Chi-restraints excluded: chain s residue 26 ILE Chi-restraints excluded: chain y residue 14 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.0970 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.0010 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 3.9990 overall best weight: 3.2190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 54 GLN L 55 GLN L 144 HIS L 211 HIS L 239 ASN H 58 GLN H 106 ASN ** q 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 46 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.062710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.044196 restraints weight = 113242.950| |-----------------------------------------------------------------------------| r_work (start): 0.2684 rms_B_bonded: 4.26 r_work: 0.2519 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.681 33312 Z= 0.233 Angle : 1.143 17.360 46017 Z= 0.508 Chirality : 0.055 0.971 4813 Planarity : 0.006 0.076 5558 Dihedral : 20.077 179.446 5268 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.50 % Allowed : 9.14 % Favored : 90.36 % Rotamer: Outliers : 5.53 % Allowed : 22.98 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % 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: -2.18 (0.14), residues: 3380 helix: 0.28 (0.11), residues: 1792 sheet: 0.06 (1.08), residues: 22 loop : -3.77 (0.14), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG b 52 TYR 0.017 0.002 TYR 6 27 PHE 0.027 0.002 PHE 7 18 TRP 0.041 0.003 TRP O 15 HIS 0.011 0.001 HIS M 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.23 (33252) covalent geometry : angle 1.14326 / 0.51 (46017) hydrogen bonds : bond 0.06989 / 4.70 ( 1416) hydrogen bonds : angle 5.33520 / 3.74 ( 4125) Misc. bond : bond 0.10757 / 4.80 ( 60) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 753 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 591 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 37 GLN cc_start: 0.9168 (OUTLIER) cc_final: 0.8674 (mp10) REVERT: C 110 MET cc_start: 0.9724 (mmt) cc_final: 0.8840 (mmt) REVERT: C 113 MET cc_start: 0.9761 (ttp) cc_final: 0.9212 (ttp) REVERT: C 146 ARG cc_start: 0.9174 (OUTLIER) cc_final: 0.8744 (mmm-85) REVERT: C 149 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8431 (pm20) REVERT: C 238 ASP cc_start: 0.9642 (t0) cc_final: 0.9325 (t0) REVERT: C 252 THR cc_start: 0.9431 (OUTLIER) cc_final: 0.9018 (p) REVERT: C 312 VAL cc_start: 0.9334 (OUTLIER) cc_final: 0.9088 (m) REVERT: L 23 ASP cc_start: 0.9001 (t0) cc_final: 0.8498 (t0) REVERT: L 29 TYR cc_start: 0.9441 (m-80) cc_final: 0.9049 (m-80) REVERT: L 60 ASP cc_start: 0.8541 (t0) cc_final: 0.8144 (t0) REVERT: L 148 TYR cc_start: 0.9365 (m-80) cc_final: 0.9132 (m-10) REVERT: L 204 ASP cc_start: 0.8774 (m-30) cc_final: 0.8390 (m-30) REVERT: L 210 GLU cc_start: 0.8862 (mp0) cc_final: 0.8643 (mp0) REVERT: M 22 GLU cc_start: 0.9121 (tm-30) cc_final: 0.8514 (tm-30) REVERT: M 26 ASN cc_start: 0.9622 (m-40) cc_final: 0.9150 (p0) REVERT: M 171 GLU cc_start: 0.9505 (OUTLIER) cc_final: 0.9066 (mp0) REVERT: M 193 ASN cc_start: 0.9379 (t0) cc_final: 0.8822 (t0) REVERT: H 66 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8233 (mtpt) REVERT: H 92 GLN cc_start: 0.8933 (pm20) cc_final: 0.8275 (pm20) REVERT: H 102 GLN cc_start: 0.8911 (mt0) cc_final: 0.8493 (pm20) REVERT: H 131 LYS cc_start: 0.9154 (mtpt) cc_final: 0.8888 (mtpp) REVERT: H 133 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8732 (tppp) REVERT: H 204 LYS cc_start: 0.7972 (mmmm) cc_final: 0.7756 (mmmm) REVERT: H 217 GLN cc_start: 0.9068 (OUTLIER) cc_final: 0.8603 (pm20) REVERT: H 239 SER cc_start: 0.9729 (m) cc_final: 0.9414 (p) REVERT: z 56 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8318 (tptp) REVERT: 2 34 THR cc_start: 0.9347 (m) cc_final: 0.8990 (p) REVERT: F 43 ASP cc_start: 0.9130 (m-30) cc_final: 0.8920 (m-30) REVERT: F 52 ARG cc_start: 0.8750 (mtm-85) cc_final: 0.8361 (mtm-85) REVERT: K 10 LYS cc_start: 0.9739 (OUTLIER) cc_final: 0.9403 (mmmm) REVERT: K 18 ARG cc_start: 0.9106 (mtm110) cc_final: 0.8673 (tmt170) REVERT: P 43 ASP cc_start: 0.9035 (m-30) cc_final: 0.8617 (t0) REVERT: S 10 LYS cc_start: 0.9672 (OUTLIER) cc_final: 0.9267 (mmmm) REVERT: Y 16 ASP cc_start: 0.8917 (t0) cc_final: 0.8440 (t0) REVERT: e 51 GLN cc_start: 0.9143 (mm-40) cc_final: 0.8516 (mm-40) REVERT: e 56 LYS cc_start: 0.8973 (tmmt) cc_final: 0.8732 (tptp) REVERT: k 20 VAL cc_start: 0.9678 (t) cc_final: 0.9464 (p) REVERT: n 11 LEU cc_start: 0.9769 (tp) cc_final: 0.9358 (pt) REVERT: q 10 LYS cc_start: 0.9593 (OUTLIER) cc_final: 0.9348 (mmmm) REVERT: q 25 PHE cc_start: 0.9080 (t80) cc_final: 0.8784 (t80) REVERT: w 51 GLN cc_start: 0.9048 (mm-40) cc_final: 0.8832 (mm-40) REVERT: 3 16 ASP cc_start: 0.8315 (t0) cc_final: 0.7831 (t0) REVERT: 3 44 ARG cc_start: 0.9060 (OUTLIER) cc_final: 0.8848 (mtm180) REVERT: 3 49 GLU cc_start: 0.8975 (mm-30) cc_final: 0.8610 (tp30) REVERT: 6 18 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.8526 (mpt90) REVERT: 6 51 GLN cc_start: 0.8762 (mm-40) cc_final: 0.8488 (tp-100) REVERT: 6 56 LYS cc_start: 0.8226 (tmmm) cc_final: 0.7838 (tptp) REVERT: G 36 VAL cc_start: 0.9686 (t) cc_final: 0.9330 (p) REVERT: Q 16 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8174 (ptpt) REVERT: W 16 LYS cc_start: 0.9127 (OUTLIER) cc_final: 0.8766 (ptpp) REVERT: Z 16 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8756 (pmtt) REVERT: o 36 VAL cc_start: 0.9798 (t) cc_final: 0.9558 (p) REVERT: r 16 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8608 (mttp) REVERT: r 50 ILE cc_start: 0.9615 (pp) cc_final: 0.9234 (mp) REVERT: O 24 LEU cc_start: 0.9668 (mm) cc_final: 0.9126 (mm) REVERT: d 24 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.8998 (mm) REVERT: g 24 LEU cc_start: 0.9439 (mt) cc_final: 0.8941 (mt) outliers start: 162 outliers final: 38 residues processed: 694 average time/residue: 0.4391 time to fit residues: 386.9663 Evaluate side-chains 540 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 482 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain M residue 41 ILE Chi-restraints excluded: chain M residue 126 SER Chi-restraints excluded: chain M residue 171 GLU Chi-restraints excluded: chain M residue 194 PHE Chi-restraints excluded: chain H residue 24 ILE Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 66 LYS Chi-restraints excluded: chain H residue 133 LYS Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 205 LYS Chi-restraints excluded: chain H residue 217 GLN Chi-restraints excluded: chain H residue 236 ASP Chi-restraints excluded: chain z residue 56 LYS Chi-restraints excluded: chain 1 residue 6 SER Chi-restraints excluded: chain 1 residue 39 LEU Chi-restraints excluded: chain K residue 10 LYS Chi-restraints excluded: chain S residue 10 LYS Chi-restraints excluded: chain Y residue 4 TYR Chi-restraints excluded: chain h residue 14 ILE Chi-restraints excluded: chain q residue 10 LYS Chi-restraints excluded: chain q residue 47 TRP Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain w residue 21 LEU Chi-restraints excluded: chain 3 residue 44 ARG Chi-restraints excluded: chain 3 residue 47 TRP Chi-restraints excluded: chain 6 residue 18 ARG Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain Q residue 16 LYS Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain W residue 16 LYS Chi-restraints excluded: chain Z residue 16 LYS Chi-restraints excluded: chain Z residue 55 VAL Chi-restraints excluded: chain c residue 23 VAL Chi-restraints excluded: chain f residue 25 SER Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain o residue 55 VAL Chi-restraints excluded: chain r residue 16 LYS Chi-restraints excluded: chain r residue 27 VAL Chi-restraints excluded: chain r residue 55 VAL Chi-restraints excluded: chain u residue 23 VAL Chi-restraints excluded: chain 4 residue 47 ILE Chi-restraints excluded: chain 4 residue 55 VAL Chi-restraints excluded: chain 7 residue 55 VAL Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain a residue 24 LEU Chi-restraints excluded: chain d residue 24 LEU Chi-restraints excluded: chain g residue 29 ILE Chi-restraints excluded: chain j residue 29 ILE Chi-restraints excluded: chain m residue 13 SER Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain s residue 31 ILE Chi-restraints excluded: chain v residue 21 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 164 optimal weight: 10.0000 chunk 272 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 161 optimal weight: 10.0000 chunk 68 optimal weight: 0.9980 chunk 19 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 226 optimal weight: 4.9990 chunk 304 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 28 optimal weight: 8.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 4 GLN S 46 ASN q 46 ASN 3 46 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.063472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.045062 restraints weight = 112664.496| |-----------------------------------------------------------------------------| r_work (start): 0.2713 rms_B_bonded: 4.23 r_work: 0.2551 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.681 33312 Z= 0.192 Angle : 1.007 15.802 46017 Z= 0.437 Chirality : 0.048 0.697 4813 Planarity : 0.005 0.069 5558 Dihedral : 18.260 179.663 5164 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.41 % Allowed : 8.67 % Favored : 90.92 % Rotamer: Outliers : 4.51 % Allowed : 25.27 % Favored : 70.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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: -1.22 (0.15), residues: 3380 helix: 1.18 (0.12), residues: 1787 sheet: 0.86 (1.10), residues: 22 loop : -3.46 (0.15), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG e 52 TYR 0.019 0.001 TYR V 27 PHE 0.022 0.001 PHE 7 18 TRP 0.029 0.002 TRP m 30 HIS 0.010 0.001 HIS o 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.19 (33252) covalent geometry : angle 1.00692 / 0.44 (46017) hydrogen bonds : bond 0.05967 / 4.03 ( 1416) hydrogen bonds : angle 5.07382 / 3.54 ( 4125) Misc. bond : bond 0.10348 / 4.37 ( 60) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 567 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 37 GLN cc_start: 0.9226 (OUTLIER) cc_final: 0.8779 (mp10) REVERT: C 110 MET cc_start: 0.9702 (mmt) cc_final: 0.8654 (mmt) REVERT: C 113 MET cc_start: 0.9772 (ttp) cc_final: 0.9311 (ttp) REVERT: C 146 ARG cc_start: 0.9176 (OUTLIER) cc_final: 0.8834 (mmm-85) REVERT: C 149 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8265 (pm20) REVERT: C 238 ASP cc_start: 0.9600 (t0) cc_final: 0.9285 (t0) REVERT: C 252 THR cc_start: 0.9309 (OUTLIER) cc_final: 0.8819 (p) REVERT: L 23 ASP cc_start: 0.8934 (t0) cc_final: 0.8513 (t0) REVERT: L 29 TYR cc_start: 0.9430 (m-80) cc_final: 0.9167 (m-80) REVERT: L 60 ASP cc_start: 0.8653 (t0) cc_final: 0.8221 (t0) REVERT: L 148 TYR cc_start: 0.9340 (m-80) cc_final: 0.9096 (m-10) REVERT: L 204 ASP cc_start: 0.8887 (m-30) cc_final: 0.8493 (m-30) REVERT: L 210 GLU cc_start: 0.9034 (mp0) cc_final: 0.8768 (mp0) REVERT: L 212 GLU cc_start: 0.9455 (OUTLIER) cc_final: 0.8901 (pm20) REVERT: M 9 GLN cc_start: 0.8986 (mt0) cc_final: 0.8583 (mt0) REVERT: M 22 GLU cc_start: 0.9126 (tm-30) cc_final: 0.8605 (tm-30) REVERT: M 26 ASN cc_start: 0.9655 (m-40) cc_final: 0.9236 (p0) REVERT: M 97 LYS cc_start: 0.9525 (mttt) cc_final: 0.9270 (mmmm) REVERT: M 171 GLU cc_start: 0.9453 (OUTLIER) cc_final: 0.9160 (mp0) REVERT: M 193 ASN cc_start: 0.9427 (t0) cc_final: 0.8920 (t0) REVERT: M 194 PHE cc_start: 0.9719 (OUTLIER) cc_final: 0.9500 (t80) REVERT: H 66 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8247 (mtpt) REVERT: H 92 GLN cc_start: 0.9024 (pm20) cc_final: 0.8390 (pm20) REVERT: H 102 GLN cc_start: 0.8892 (mt0) cc_final: 0.8522 (pm20) REVERT: H 131 LYS cc_start: 0.9185 (mtpt) cc_final: 0.8976 (mtpp) REVERT: H 239 SER cc_start: 0.9726 (m) cc_final: 0.9414 (p) REVERT: z 16 ASP cc_start: 0.9070 (t0) cc_final: 0.8846 (t0) REVERT: 2 34 THR cc_start: 0.9430 (m) cc_final: 0.9215 (p) REVERT: F 35 ILE cc_start: 0.9704 (OUTLIER) cc_final: 0.9467 (mp) REVERT: F 43 ASP cc_start: 0.9177 (m-30) cc_final: 0.8940 (m-30) REVERT: F 52 ARG cc_start: 0.8775 (mtm-85) cc_final: 0.8535 (mtm-85) REVERT: K 10 LYS cc_start: 0.9698 (OUTLIER) cc_final: 0.9372 (mmmm) REVERT: K 18 ARG cc_start: 0.9118 (mtm110) cc_final: 0.8673 (tmt170) REVERT: P 16 ASP cc_start: 0.9058 (t0) cc_final: 0.8425 (t0) REVERT: P 19 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7947 (tpp-160) REVERT: P 43 ASP cc_start: 0.9094 (m-30) cc_final: 0.8396 (t0) REVERT: P 52 ARG cc_start: 0.8754 (mtm180) cc_final: 0.8296 (mtm-85) REVERT: S 10 LYS cc_start: 0.9678 (OUTLIER) cc_final: 0.9273 (mmmm) REVERT: S 16 ASP cc_start: 0.8766 (t0) cc_final: 0.8372 (t0) REVERT: S 19 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7713 (tpp-160) REVERT: V 52 ARG cc_start: 0.9324 (ttp80) cc_final: 0.9121 (ttp-110) REVERT: Y 16 ASP cc_start: 0.8774 (t0) cc_final: 0.8244 (t0) REVERT: e 10 LYS cc_start: 0.9503 (OUTLIER) cc_final: 0.9020 (mmtp) REVERT: e 16 ASP cc_start: 0.8635 (t0) cc_final: 0.7946 (t0) REVERT: e 51 GLN cc_start: 0.9142 (mm-40) cc_final: 0.8781 (mm-40) REVERT: e 56 LYS cc_start: 0.9046 (tmmt) cc_final: 0.8811 (tptp) REVERT: h 16 ASP cc_start: 0.8542 (t0) cc_final: 0.7990 (t0) REVERT: h 27 TYR cc_start: 0.9412 (t80) cc_final: 0.9211 (t80) REVERT: h 52 ARG cc_start: 0.9084 (mtp-110) cc_final: 0.8833 (mtp-110) REVERT: k 20 VAL cc_start: 0.9641 (t) cc_final: 0.9426 (p) REVERT: k 56 LYS cc_start: 0.8758 (tppt) cc_final: 0.8179 (mppt) REVERT: n 11 LEU cc_start: 0.9752 (tp) cc_final: 0.9353 (pt) REVERT: n 16 ASP cc_start: 0.8543 (t0) cc_final: 0.8071 (t0) REVERT: q 10 LYS cc_start: 0.9539 (OUTLIER) cc_final: 0.9263 (mmmm) REVERT: q 14 ILE cc_start: 0.8777 (tp) cc_final: 0.7837 (tp) REVERT: q 25 PHE cc_start: 0.9053 (t80) cc_final: 0.8781 (t80) REVERT: t 16 ASP cc_start: 0.8774 (t0) cc_final: 0.8306 (t0) REVERT: 3 16 ASP cc_start: 0.8402 (t0) cc_final: 0.7983 (t0) REVERT: 3 43 ASP cc_start: 0.9485 (m-30) cc_final: 0.8971 (m-30) REVERT: 3 44 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.8093 (mtp85) REVERT: 3 49 GLU cc_start: 0.8960 (mm-30) cc_final: 0.8712 (tp30) REVERT: 6 56 LYS cc_start: 0.8457 (tmmm) cc_final: 0.8060 (tptp) REVERT: G 36 VAL cc_start: 0.9665 (t) cc_final: 0.9336 (p) REVERT: T 36 VAL cc_start: 0.9639 (t) cc_final: 0.9264 (p) REVERT: W 16 LYS cc_start: 0.9168 (OUTLIER) cc_final: 0.8863 (ptpp) REVERT: o 36 VAL cc_start: 0.9744 (t) cc_final: 0.9497 (p) REVERT: 7 54 TRP cc_start: 0.9347 (OUTLIER) cc_final: 0.7519 (t60) REVERT: O 24 LEU cc_start: 0.9528 (OUTLIER) cc_final: 0.9235 (mm) REVERT: d 24 LEU cc_start: 0.9327 (mm) cc_final: 0.8971 (mm) REVERT: g 24 LEU cc_start: 0.9226 (mt) cc_final: 0.8988 (mt) REVERT: p 28 THR cc_start: 0.9362 (m) cc_final: 0.9135 (p) outliers start: 132 outliers final: 40 residues processed: 651 average time/residue: 0.4214 time to fit residues: 354.2948 Evaluate side-chains 559 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 500 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain L residue 212 GLU Chi-restraints excluded: chain M residue 41 ILE Chi-restraints excluded: chain M residue 171 GLU Chi-restraints excluded: chain M residue 194 PHE Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 66 LYS Chi-restraints excluded: chain H residue 205 LYS Chi-restraints excluded: chain H residue 236 ASP Chi-restraints excluded: chain z residue 35 ILE Chi-restraints excluded: chain 1 residue 39 LEU Chi-restraints excluded: chain 2 residue 21 LEU Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain K residue 10 LYS Chi-restraints excluded: chain P residue 19 ARG Chi-restraints excluded: chain S residue 10 LYS Chi-restraints excluded: chain S residue 19 ARG Chi-restraints excluded: chain Y residue 4 TYR Chi-restraints excluded: chain e residue 10 LYS Chi-restraints excluded: chain e residue 47 TRP Chi-restraints excluded: chain h residue 35 ILE Chi-restraints excluded: chain k residue 14 ILE Chi-restraints excluded: chain q residue 2 THR Chi-restraints excluded: chain q residue 10 LYS Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain t residue 43 ASP Chi-restraints excluded: chain 3 residue 19 ARG Chi-restraints excluded: chain 3 residue 44 ARG Chi-restraints excluded: chain 3 residue 51 GLN Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain Q residue 3 LEU Chi-restraints excluded: chain W residue 16 LYS Chi-restraints excluded: chain Z residue 55 VAL Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain f residue 25 SER Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain o residue 55 VAL Chi-restraints excluded: chain r residue 16 LYS Chi-restraints excluded: chain u residue 55 VAL Chi-restraints excluded: chain x residue 16 LYS Chi-restraints excluded: chain x residue 55 VAL Chi-restraints excluded: chain 4 residue 13 GLU Chi-restraints excluded: chain 4 residue 55 VAL Chi-restraints excluded: chain 7 residue 47 ILE Chi-restraints excluded: chain 7 residue 54 TRP Chi-restraints excluded: chain 7 residue 55 VAL Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain R residue 29 ILE Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain a residue 24 LEU Chi-restraints excluded: chain g residue 31 ILE Chi-restraints excluded: chain m residue 13 SER Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain s residue 31 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 244 optimal weight: 0.5980 chunk 39 optimal weight: 0.0770 chunk 307 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 105 optimal weight: 4.9990 chunk 212 optimal weight: 10.0000 chunk 4 optimal weight: 30.0000 chunk 23 optimal weight: 0.0060 chunk 292 optimal weight: 7.9990 chunk 159 optimal weight: 6.9990 chunk 275 optimal weight: 0.9980 overall best weight: 0.9356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 214 GLN M 4 GLN S 46 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.065214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.047022 restraints weight = 111792.223| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 4.27 r_work: 0.2627 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.4262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.517 33312 Z= 0.155 Angle : 0.917 15.438 46017 Z= 0.391 Chirality : 0.045 0.286 4813 Planarity : 0.005 0.072 5558 Dihedral : 17.234 179.237 5149 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.49 % Favored : 91.12 % Rotamer: Outliers : 4.54 % Allowed : 25.38 % Favored : 70.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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: 3380 helix: 1.35 (0.12), residues: 1801 sheet: 0.23 (0.99), residues: 32 loop : -3.23 (0.15), residues: 1547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG S 52 TYR 0.024 0.001 TYR V 27 PHE 0.025 0.001 PHE 7 22 TRP 0.028 0.002 TRP m 30 HIS 0.006 0.001 HIS M 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.15 (33252) covalent geometry : angle 0.91712 / 0.39 (46017) hydrogen bonds : bond 0.05051 / 3.41 ( 1416) hydrogen bonds : angle 4.85184 / 3.37 ( 4125) Misc. bond : bond 0.07600 / 3.01 ( 60) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 726 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 593 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 37 GLN cc_start: 0.9215 (OUTLIER) cc_final: 0.8731 (mp10) REVERT: C 110 MET cc_start: 0.9667 (mmt) cc_final: 0.8747 (mmt) REVERT: C 113 MET cc_start: 0.9759 (ttp) cc_final: 0.9279 (ttp) REVERT: C 146 ARG cc_start: 0.9113 (OUTLIER) cc_final: 0.8811 (mmm-85) REVERT: C 149 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8173 (pm20) REVERT: C 238 ASP cc_start: 0.9531 (t0) cc_final: 0.9217 (t0) REVERT: C 252 THR cc_start: 0.9123 (OUTLIER) cc_final: 0.8724 (t) REVERT: L 23 ASP cc_start: 0.8838 (t0) cc_final: 0.8609 (t0) REVERT: L 60 ASP cc_start: 0.8691 (t0) cc_final: 0.8297 (t0) REVERT: L 106 GLU cc_start: 0.9332 (OUTLIER) cc_final: 0.9110 (tp30) REVERT: L 204 ASP cc_start: 0.8936 (m-30) cc_final: 0.8558 (m-30) REVERT: L 210 GLU cc_start: 0.9046 (mp0) cc_final: 0.8769 (mp0) REVERT: L 212 GLU cc_start: 0.9422 (OUTLIER) cc_final: 0.8929 (pm20) REVERT: L 214 GLN cc_start: 0.9297 (OUTLIER) cc_final: 0.8888 (tp40) REVERT: M 9 GLN cc_start: 0.9000 (mt0) cc_final: 0.8540 (mt0) REVERT: M 22 GLU cc_start: 0.9128 (tm-30) cc_final: 0.8595 (tm-30) REVERT: M 26 ASN cc_start: 0.9650 (m-40) cc_final: 0.9313 (p0) REVERT: M 171 GLU cc_start: 0.9402 (mm-30) cc_final: 0.9161 (mp0) REVERT: M 193 ASN cc_start: 0.9391 (t0) cc_final: 0.8926 (t0) REVERT: H 66 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8295 (mtpt) REVERT: H 92 GLN cc_start: 0.9192 (pm20) cc_final: 0.8611 (pm20) REVERT: H 102 GLN cc_start: 0.8859 (mt0) cc_final: 0.8619 (pm20) REVERT: H 217 GLN cc_start: 0.9468 (mt0) cc_final: 0.8962 (mp10) REVERT: H 239 SER cc_start: 0.9715 (m) cc_final: 0.9392 (p) REVERT: F 52 ARG cc_start: 0.8741 (mtm-85) cc_final: 0.8474 (mtm-85) REVERT: F 54 LEU cc_start: 0.9024 (mp) cc_final: 0.8765 (pp) REVERT: K 10 LYS cc_start: 0.9686 (OUTLIER) cc_final: 0.9440 (mmmm) REVERT: K 16 ASP cc_start: 0.8312 (t0) cc_final: 0.7368 (t0) REVERT: K 18 ARG cc_start: 0.9105 (mtm110) cc_final: 0.8699 (tmt170) REVERT: K 43 ASP cc_start: 0.9241 (m-30) cc_final: 0.9022 (m-30) REVERT: P 16 ASP cc_start: 0.8782 (t0) cc_final: 0.8050 (t0) REVERT: P 19 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7768 (tpp-160) REVERT: P 52 ARG cc_start: 0.8670 (mtm180) cc_final: 0.8290 (mtm-85) REVERT: S 10 LYS cc_start: 0.9623 (OUTLIER) cc_final: 0.9269 (mmmm) REVERT: S 16 ASP cc_start: 0.8719 (t0) cc_final: 0.8047 (t0) REVERT: V 52 ARG cc_start: 0.9280 (ttp80) cc_final: 0.9047 (ttp80) REVERT: Y 15 LEU cc_start: 0.9418 (tp) cc_final: 0.9008 (tm) REVERT: Y 51 GLN cc_start: 0.8908 (mm-40) cc_final: 0.8605 (tp-100) REVERT: e 10 LYS cc_start: 0.9500 (OUTLIER) cc_final: 0.9018 (mmtp) REVERT: h 15 LEU cc_start: 0.9161 (tp) cc_final: 0.8958 (tp) REVERT: h 16 ASP cc_start: 0.8296 (t0) cc_final: 0.7677 (OUTLIER) REVERT: h 52 ARG cc_start: 0.9106 (mtp-110) cc_final: 0.8810 (mtm-85) REVERT: k 42 THR cc_start: 0.9712 (p) cc_final: 0.9505 (t) REVERT: k 56 LYS cc_start: 0.8846 (tppt) cc_final: 0.8159 (mppt) REVERT: n 3 GLU cc_start: 0.7353 (pp20) cc_final: 0.7088 (pm20) REVERT: n 11 LEU cc_start: 0.9747 (tp) cc_final: 0.9351 (pt) REVERT: n 16 ASP cc_start: 0.8394 (t0) cc_final: 0.7931 (t0) REVERT: n 56 LYS cc_start: 0.8929 (tppt) cc_final: 0.8698 (tppt) REVERT: q 10 LYS cc_start: 0.9570 (OUTLIER) cc_final: 0.9087 (mmtp) REVERT: q 16 ASP cc_start: 0.8155 (t0) cc_final: 0.7532 (t0) REVERT: q 25 PHE cc_start: 0.9043 (t80) cc_final: 0.8767 (t80) REVERT: q 43 ASP cc_start: 0.9064 (m-30) cc_final: 0.8838 (m-30) REVERT: t 16 ASP cc_start: 0.8517 (t0) cc_final: 0.7993 (t0) REVERT: t 54 LEU cc_start: 0.9003 (mm) cc_final: 0.8749 (mt) REVERT: 3 16 ASP cc_start: 0.8202 (t0) cc_final: 0.7707 (t0) REVERT: 3 43 ASP cc_start: 0.9399 (m-30) cc_final: 0.9035 (m-30) REVERT: 3 49 GLU cc_start: 0.8898 (mm-30) cc_final: 0.8552 (tp30) REVERT: 6 16 ASP cc_start: 0.8026 (t0) cc_final: 0.7140 (t0) REVERT: 6 27 TYR cc_start: 0.9155 (m-10) cc_final: 0.8847 (m-10) REVERT: G 36 VAL cc_start: 0.9635 (t) cc_final: 0.9308 (p) REVERT: Z 17 GLU cc_start: 0.9000 (OUTLIER) cc_final: 0.8792 (pm20) REVERT: o 36 VAL cc_start: 0.9679 (t) cc_final: 0.9394 (p) REVERT: O 24 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9232 (mm) REVERT: s 34 THR cc_start: 0.9560 (OUTLIER) cc_final: 0.9278 (p) REVERT: 5 31 ILE cc_start: 0.9200 (OUTLIER) cc_final: 0.8972 (mt) outliers start: 133 outliers final: 34 residues processed: 675 average time/residue: 0.4306 time to fit residues: 373.2964 Evaluate side-chains 563 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 513 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 212 GLU Chi-restraints excluded: chain L residue 214 GLN Chi-restraints excluded: chain M residue 210 CYS Chi-restraints excluded: chain M residue 282 ILE Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 66 LYS Chi-restraints excluded: chain z residue 35 ILE Chi-restraints excluded: chain 1 residue 35 ILE Chi-restraints excluded: chain 1 residue 39 LEU Chi-restraints excluded: chain K residue 10 LYS Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain P residue 19 ARG Chi-restraints excluded: chain S residue 10 LYS Chi-restraints excluded: chain Y residue 4 TYR Chi-restraints excluded: chain e residue 10 LYS Chi-restraints excluded: chain e residue 47 TRP Chi-restraints excluded: chain h residue 43 ASP Chi-restraints excluded: chain k residue 14 ILE Chi-restraints excluded: chain n residue 20 VAL Chi-restraints excluded: chain q residue 2 THR Chi-restraints excluded: chain q residue 10 LYS Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain 3 residue 19 ARG Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain Q residue 3 LEU Chi-restraints excluded: chain Z residue 17 GLU Chi-restraints excluded: chain Z residue 55 VAL Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain f residue 25 SER Chi-restraints excluded: chain i residue 55 VAL Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain o residue 55 VAL Chi-restraints excluded: chain u residue 55 VAL Chi-restraints excluded: chain x residue 16 LYS Chi-restraints excluded: chain x residue 55 VAL Chi-restraints excluded: chain 4 residue 30 LEU Chi-restraints excluded: chain 4 residue 47 ILE Chi-restraints excluded: chain 4 residue 55 VAL Chi-restraints excluded: chain 7 residue 55 VAL Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain m residue 13 SER Chi-restraints excluded: chain s residue 34 THR Chi-restraints excluded: chain 5 residue 31 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 225 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 202 optimal weight: 9.9990 chunk 244 optimal weight: 20.0000 chunk 59 optimal weight: 7.9990 chunk 308 optimal weight: 0.9990 chunk 99 optimal weight: 8.9990 chunk 36 optimal weight: 9.9990 chunk 82 optimal weight: 0.9990 chunk 173 optimal weight: 10.0000 chunk 204 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 257 ASN q 46 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.064201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.046199 restraints weight = 113412.023| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 4.35 r_work: 0.2588 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.4417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.653 33312 Z= 0.183 Angle : 0.932 18.139 46017 Z= 0.395 Chirality : 0.045 0.358 4813 Planarity : 0.005 0.069 5558 Dihedral : 16.880 179.901 5137 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.44 % Allowed : 8.79 % Favored : 90.77 % Rotamer: Outliers : 3.86 % Allowed : 26.81 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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: -0.65 (0.15), residues: 3380 helix: 1.59 (0.12), residues: 1776 sheet: 0.29 (1.01), residues: 32 loop : -3.07 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG q 52 TYR 0.026 0.001 TYR V 27 PHE 0.024 0.001 PHE H 96 TRP 0.035 0.002 TRP m 30 HIS 0.005 0.001 HIS L 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.18 (33252) covalent geometry : angle 0.93240 / 0.39 (46017) hydrogen bonds : bond 0.05072 / 3.43 ( 1416) hydrogen bonds : angle 4.88175 / 3.40 ( 4125) Misc. bond : bond 0.09486 / 3.83 ( 60) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 536 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 37 GLN cc_start: 0.9290 (OUTLIER) cc_final: 0.8799 (mp10) REVERT: C 110 MET cc_start: 0.9696 (mmt) cc_final: 0.8695 (mmt) REVERT: C 113 MET cc_start: 0.9776 (ttp) cc_final: 0.9402 (ttp) REVERT: C 146 ARG cc_start: 0.9086 (OUTLIER) cc_final: 0.8662 (mmm-85) REVERT: C 149 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8206 (pm20) REVERT: C 238 ASP cc_start: 0.9535 (t0) cc_final: 0.9205 (t0) REVERT: C 252 THR cc_start: 0.9226 (OUTLIER) cc_final: 0.8740 (p) REVERT: L 23 ASP cc_start: 0.8886 (t0) cc_final: 0.8659 (t0) REVERT: L 60 ASP cc_start: 0.8794 (t0) cc_final: 0.8472 (t0) REVERT: L 106 GLU cc_start: 0.9373 (OUTLIER) cc_final: 0.8914 (mm-30) REVERT: L 148 TYR cc_start: 0.9267 (m-10) cc_final: 0.9005 (m-80) REVERT: L 204 ASP cc_start: 0.8953 (m-30) cc_final: 0.8554 (m-30) REVERT: L 210 GLU cc_start: 0.9091 (mp0) cc_final: 0.8814 (mp0) REVERT: M 9 GLN cc_start: 0.9039 (mt0) cc_final: 0.8578 (mt0) REVERT: M 22 GLU cc_start: 0.9118 (tm-30) cc_final: 0.8591 (tm-30) REVERT: M 26 ASN cc_start: 0.9643 (m-40) cc_final: 0.9325 (p0) REVERT: M 171 GLU cc_start: 0.9421 (mm-30) cc_final: 0.9160 (mp0) REVERT: M 193 ASN cc_start: 0.9442 (t0) cc_final: 0.8982 (t0) REVERT: H 36 ASP cc_start: 0.8993 (OUTLIER) cc_final: 0.8640 (t0) REVERT: H 66 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8288 (mtpt) REVERT: H 92 GLN cc_start: 0.9217 (pm20) cc_final: 0.8580 (pm20) REVERT: H 102 GLN cc_start: 0.8817 (mt0) cc_final: 0.8593 (pm20) REVERT: H 134 ILE cc_start: 0.9565 (mt) cc_final: 0.9258 (mm) REVERT: H 239 SER cc_start: 0.9712 (m) cc_final: 0.9376 (p) REVERT: z 49 GLU cc_start: 0.9162 (OUTLIER) cc_final: 0.8934 (tp30) REVERT: 2 34 THR cc_start: 0.9727 (OUTLIER) cc_final: 0.9347 (p) REVERT: F 54 LEU cc_start: 0.8981 (mp) cc_final: 0.8745 (pp) REVERT: K 10 LYS cc_start: 0.9699 (OUTLIER) cc_final: 0.9465 (mmmm) REVERT: K 16 ASP cc_start: 0.8438 (t0) cc_final: 0.7467 (t0) REVERT: K 18 ARG cc_start: 0.9200 (mtm110) cc_final: 0.8722 (tmt170) REVERT: K 43 ASP cc_start: 0.9260 (m-30) cc_final: 0.9040 (m-30) REVERT: P 16 ASP cc_start: 0.8769 (t0) cc_final: 0.7985 (t0) REVERT: P 52 ARG cc_start: 0.8727 (mtm180) cc_final: 0.8328 (mtm-85) REVERT: S 10 LYS cc_start: 0.9649 (OUTLIER) cc_final: 0.9320 (mmtp) REVERT: S 16 ASP cc_start: 0.8709 (t0) cc_final: 0.8192 (t0) REVERT: S 19 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7577 (tpp-160) REVERT: S 43 ASP cc_start: 0.9254 (m-30) cc_final: 0.9051 (m-30) REVERT: V 52 ARG cc_start: 0.9322 (ttp80) cc_final: 0.8772 (ttp80) REVERT: Y 14 ILE cc_start: 0.9412 (mp) cc_final: 0.9116 (tp) REVERT: Y 51 GLN cc_start: 0.9073 (mm-40) cc_final: 0.8837 (tp-100) REVERT: e 10 LYS cc_start: 0.9525 (OUTLIER) cc_final: 0.9027 (mmtp) REVERT: h 16 ASP cc_start: 0.8369 (t0) cc_final: 0.7760 (OUTLIER) REVERT: h 52 ARG cc_start: 0.9196 (mtp-110) cc_final: 0.8920 (mtm-85) REVERT: n 11 LEU cc_start: 0.9774 (tp) cc_final: 0.9372 (pt) REVERT: n 16 ASP cc_start: 0.8476 (t0) cc_final: 0.7972 (t0) REVERT: n 56 LYS cc_start: 0.8945 (tppt) cc_final: 0.8720 (tppt) REVERT: q 10 LYS cc_start: 0.9583 (OUTLIER) cc_final: 0.9139 (mmtp) REVERT: q 16 ASP cc_start: 0.8316 (t0) cc_final: 0.7714 (t0) REVERT: q 25 PHE cc_start: 0.9081 (t80) cc_final: 0.8802 (t80) REVERT: t 16 ASP cc_start: 0.8558 (t0) cc_final: 0.7996 (t0) REVERT: t 52 ARG cc_start: 0.9180 (mtp-110) cc_final: 0.8894 (mtp-110) REVERT: 3 16 ASP cc_start: 0.8325 (t0) cc_final: 0.7916 (t0) REVERT: 3 43 ASP cc_start: 0.9467 (m-30) cc_final: 0.9027 (m-30) REVERT: 6 16 ASP cc_start: 0.7984 (t0) cc_final: 0.7251 (t0) REVERT: G 36 VAL cc_start: 0.9603 (t) cc_final: 0.9310 (p) REVERT: Z 13 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7692 (tm-30) REVERT: Z 17 GLU cc_start: 0.9029 (OUTLIER) cc_final: 0.8812 (pm20) REVERT: o 36 VAL cc_start: 0.9719 (t) cc_final: 0.9446 (p) REVERT: r 16 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8722 (mttp) REVERT: I 31 ILE cc_start: 0.9582 (OUTLIER) cc_final: 0.9366 (mt) REVERT: O 24 LEU cc_start: 0.9506 (OUTLIER) cc_final: 0.9264 (mm) REVERT: s 34 THR cc_start: 0.9598 (t) cc_final: 0.9386 (p) outliers start: 113 outliers final: 42 residues processed: 605 average time/residue: 0.4254 time to fit residues: 332.1560 Evaluate side-chains 550 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 490 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain M residue 282 ILE Chi-restraints excluded: chain H residue 36 ASP Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 66 LYS Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 236 ASP Chi-restraints excluded: chain z residue 35 ILE Chi-restraints excluded: chain z residue 49 GLU Chi-restraints excluded: chain 1 residue 39 LEU Chi-restraints excluded: chain 2 residue 34 THR Chi-restraints excluded: chain K residue 10 LYS Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain P residue 31 ILE Chi-restraints excluded: chain S residue 10 LYS Chi-restraints excluded: chain S residue 19 ARG Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain Y residue 4 TYR Chi-restraints excluded: chain e residue 10 LYS Chi-restraints excluded: chain h residue 43 ASP Chi-restraints excluded: chain n residue 20 VAL Chi-restraints excluded: chain n residue 35 ILE Chi-restraints excluded: chain q residue 2 THR Chi-restraints excluded: chain q residue 10 LYS Chi-restraints excluded: chain q residue 56 LYS Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain 3 residue 19 ARG Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain Q residue 3 LEU Chi-restraints excluded: chain Q residue 47 ILE Chi-restraints excluded: chain Z residue 13 GLU Chi-restraints excluded: chain Z residue 17 GLU Chi-restraints excluded: chain Z residue 55 VAL Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain f residue 25 SER Chi-restraints excluded: chain i residue 55 VAL Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain o residue 55 VAL Chi-restraints excluded: chain r residue 16 LYS Chi-restraints excluded: chain u residue 55 VAL Chi-restraints excluded: chain x residue 16 LYS Chi-restraints excluded: chain x residue 55 VAL Chi-restraints excluded: chain 4 residue 47 ILE Chi-restraints excluded: chain 4 residue 55 VAL Chi-restraints excluded: chain 7 residue 47 ILE Chi-restraints excluded: chain 7 residue 55 VAL Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain R residue 29 ILE Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain j residue 21 LEU Chi-restraints excluded: chain j residue 33 LEU Chi-restraints excluded: chain p residue 29 ILE Chi-restraints excluded: chain v residue 21 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 219 optimal weight: 30.0000 chunk 134 optimal weight: 5.9990 chunk 133 optimal weight: 9.9990 chunk 19 optimal weight: 0.1980 chunk 265 optimal weight: 7.9990 chunk 105 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 162 optimal weight: 8.9990 chunk 289 optimal weight: 9.9990 chunk 59 optimal weight: 3.9990 chunk 313 optimal weight: 10.0000 overall best weight: 4.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.062752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.044925 restraints weight = 114197.148| |-----------------------------------------------------------------------------| r_work (start): 0.2718 rms_B_bonded: 4.05 r_work: 0.2552 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.789 33312 Z= 0.226 Angle : 0.950 16.166 46017 Z= 0.403 Chirality : 0.047 0.327 4813 Planarity : 0.005 0.057 5558 Dihedral : 16.637 179.719 5137 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.47 % Favored : 90.09 % Rotamer: Outliers : 4.34 % Allowed : 26.84 % Favored : 68.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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: -0.58 (0.15), residues: 3380 helix: 1.65 (0.12), residues: 1777 sheet: -0.39 (0.96), residues: 36 loop : -3.03 (0.16), residues: 1567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG q 52 TYR 0.031 0.001 TYR s 35 PHE 0.032 0.001 PHE 7 22 TRP 0.026 0.002 TRP m 30 HIS 0.007 0.001 HIS L 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.23 (33252) covalent geometry : angle 0.94950 / 0.40 (46017) hydrogen bonds : bond 0.05287 / 3.57 ( 1416) hydrogen bonds : angle 4.91965 / 3.44 ( 4125) Misc. bond : bond 0.11787 / 5.00 ( 60) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 515 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 37 GLN cc_start: 0.9305 (OUTLIER) cc_final: 0.8753 (mp10) REVERT: C 110 MET cc_start: 0.9712 (mmt) cc_final: 0.8856 (mmt) REVERT: C 146 ARG cc_start: 0.9129 (OUTLIER) cc_final: 0.8887 (mmm-85) REVERT: C 149 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8193 (pm20) REVERT: C 238 ASP cc_start: 0.9546 (t0) cc_final: 0.9211 (t0) REVERT: C 252 THR cc_start: 0.9255 (OUTLIER) cc_final: 0.8804 (p) REVERT: L 23 ASP cc_start: 0.8979 (t0) cc_final: 0.8651 (t0) REVERT: L 29 TYR cc_start: 0.9514 (m-80) cc_final: 0.9054 (m-80) REVERT: L 60 ASP cc_start: 0.8922 (t0) cc_final: 0.8496 (t0) REVERT: L 148 TYR cc_start: 0.9296 (m-10) cc_final: 0.9018 (m-80) REVERT: L 204 ASP cc_start: 0.9020 (m-30) cc_final: 0.8644 (m-30) REVERT: L 210 GLU cc_start: 0.9207 (mp0) cc_final: 0.9003 (mp0) REVERT: L 212 GLU cc_start: 0.9425 (pt0) cc_final: 0.8976 (pm20) REVERT: M 9 GLN cc_start: 0.9083 (mt0) cc_final: 0.8628 (mt0) REVERT: M 22 GLU cc_start: 0.9130 (tm-30) cc_final: 0.8599 (tm-30) REVERT: M 26 ASN cc_start: 0.9649 (m-40) cc_final: 0.9324 (p0) REVERT: M 171 GLU cc_start: 0.9434 (OUTLIER) cc_final: 0.9044 (mp0) REVERT: M 193 ASN cc_start: 0.9476 (t0) cc_final: 0.9019 (t0) REVERT: H 66 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8274 (mtpt) REVERT: H 92 GLN cc_start: 0.9240 (pm20) cc_final: 0.8762 (pm20) REVERT: H 102 GLN cc_start: 0.8799 (mt0) cc_final: 0.8573 (pm20) REVERT: H 134 ILE cc_start: 0.9584 (mt) cc_final: 0.9286 (mm) REVERT: F 54 LEU cc_start: 0.8923 (mp) cc_final: 0.8700 (pp) REVERT: K 10 LYS cc_start: 0.9690 (OUTLIER) cc_final: 0.9442 (mmmm) REVERT: K 16 ASP cc_start: 0.8507 (t0) cc_final: 0.7352 (t0) REVERT: K 18 ARG cc_start: 0.9200 (mtm110) cc_final: 0.8694 (tmt170) REVERT: K 43 ASP cc_start: 0.9299 (m-30) cc_final: 0.9091 (m-30) REVERT: P 16 ASP cc_start: 0.8741 (t0) cc_final: 0.7828 (t0) REVERT: P 19 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7453 (tpp-160) REVERT: P 52 ARG cc_start: 0.8778 (mtm180) cc_final: 0.8396 (mtm-85) REVERT: S 10 LYS cc_start: 0.9653 (OUTLIER) cc_final: 0.9308 (mmtp) REVERT: S 16 ASP cc_start: 0.8795 (t0) cc_final: 0.8286 (t0) REVERT: S 19 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7542 (tpp-160) REVERT: V 43 ASP cc_start: 0.9235 (m-30) cc_final: 0.8556 (m-30) REVERT: V 52 ARG cc_start: 0.9320 (ttp80) cc_final: 0.8743 (ttp80) REVERT: e 10 LYS cc_start: 0.9515 (OUTLIER) cc_final: 0.9048 (mmtp) REVERT: h 16 ASP cc_start: 0.8423 (t0) cc_final: 0.7850 (t0) REVERT: h 52 ARG cc_start: 0.9252 (mtp-110) cc_final: 0.9002 (mtm-85) REVERT: n 3 GLU cc_start: 0.7404 (pp20) cc_final: 0.7010 (pm20) REVERT: n 11 LEU cc_start: 0.9778 (tp) cc_final: 0.9489 (tm) REVERT: n 16 ASP cc_start: 0.8546 (t0) cc_final: 0.8001 (t0) REVERT: n 56 LYS cc_start: 0.8944 (tppt) cc_final: 0.8685 (tppt) REVERT: q 10 LYS cc_start: 0.9562 (OUTLIER) cc_final: 0.9154 (mmtp) REVERT: q 16 ASP cc_start: 0.8401 (t0) cc_final: 0.7814 (t0) REVERT: t 16 ASP cc_start: 0.8560 (t0) cc_final: 0.7992 (t0) REVERT: 3 16 ASP cc_start: 0.8396 (t0) cc_final: 0.7879 (t0) REVERT: 3 43 ASP cc_start: 0.9422 (m-30) cc_final: 0.9059 (m-30) REVERT: 6 16 ASP cc_start: 0.8094 (t0) cc_final: 0.7249 (t0) REVERT: G 36 VAL cc_start: 0.9656 (t) cc_final: 0.9374 (p) REVERT: o 36 VAL cc_start: 0.9761 (t) cc_final: 0.9510 (p) REVERT: x 16 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8456 (pmmt) REVERT: O 24 LEU cc_start: 0.9560 (OUTLIER) cc_final: 0.9312 (mm) REVERT: d 21 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.9239 (tm) REVERT: d 34 THR cc_start: 0.9599 (OUTLIER) cc_final: 0.9259 (p) REVERT: j 21 LEU cc_start: 0.9494 (mp) cc_final: 0.9266 (mm) REVERT: p 34 THR cc_start: 0.9640 (t) cc_final: 0.9363 (p) outliers start: 127 outliers final: 52 residues processed: 595 average time/residue: 0.4185 time to fit residues: 319.3804 Evaluate side-chains 547 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 479 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain L residue 242 LEU Chi-restraints excluded: chain M residue 171 GLU Chi-restraints excluded: chain M residue 194 PHE Chi-restraints excluded: chain M residue 282 ILE Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 66 LYS Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 205 LYS Chi-restraints excluded: chain H residue 236 ASP Chi-restraints excluded: chain 1 residue 39 LEU Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain K residue 10 LYS Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain P residue 19 ARG Chi-restraints excluded: chain P residue 31 ILE Chi-restraints excluded: chain S residue 10 LYS Chi-restraints excluded: chain S residue 19 ARG Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain Y residue 4 TYR Chi-restraints excluded: chain e residue 10 LYS Chi-restraints excluded: chain h residue 41 SER Chi-restraints excluded: chain h residue 43 ASP Chi-restraints excluded: chain n residue 20 VAL Chi-restraints excluded: chain n residue 35 ILE Chi-restraints excluded: chain q residue 2 THR Chi-restraints excluded: chain q residue 10 LYS Chi-restraints excluded: chain q residue 56 LYS Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain 3 residue 15 LEU Chi-restraints excluded: chain 3 residue 19 ARG Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain Q residue 3 LEU Chi-restraints excluded: chain Q residue 47 ILE Chi-restraints excluded: chain T residue 13 GLU Chi-restraints excluded: chain Z residue 13 GLU Chi-restraints excluded: chain Z residue 55 VAL Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain f residue 2 ASP Chi-restraints excluded: chain f residue 25 SER Chi-restraints excluded: chain i residue 13 GLU Chi-restraints excluded: chain i residue 55 VAL Chi-restraints excluded: chain l residue 21 ILE Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain o residue 55 VAL Chi-restraints excluded: chain u residue 13 GLU Chi-restraints excluded: chain u residue 55 VAL Chi-restraints excluded: chain x residue 16 LYS Chi-restraints excluded: chain x residue 21 ILE Chi-restraints excluded: chain x residue 55 VAL Chi-restraints excluded: chain 4 residue 30 LEU Chi-restraints excluded: chain 4 residue 47 ILE Chi-restraints excluded: chain 4 residue 55 VAL Chi-restraints excluded: chain 7 residue 47 ILE Chi-restraints excluded: chain 7 residue 55 VAL Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain d residue 21 LEU Chi-restraints excluded: chain d residue 34 THR Chi-restraints excluded: chain j residue 33 LEU Chi-restraints excluded: chain v residue 21 LEU Chi-restraints excluded: chain y residue 34 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 107 optimal weight: 20.0000 chunk 67 optimal weight: 9.9990 chunk 272 optimal weight: 1.9990 chunk 195 optimal weight: 10.0000 chunk 153 optimal weight: 0.9980 chunk 162 optimal weight: 7.9990 chunk 171 optimal weight: 8.9990 chunk 176 optimal weight: 0.9990 chunk 123 optimal weight: 0.9980 chunk 41 optimal weight: 6.9990 chunk 248 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.064649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.046626 restraints weight = 112604.039| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 4.25 r_work: 0.2627 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.4875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.598 33312 Z= 0.150 Angle : 0.919 16.014 46017 Z= 0.389 Chirality : 0.045 0.263 4813 Planarity : 0.005 0.088 5558 Dihedral : 16.319 179.692 5137 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.14 % Favored : 91.48 % Rotamer: Outliers : 2.90 % Allowed : 28.62 % Favored : 68.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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: -0.57 (0.15), residues: 3380 helix: 1.58 (0.12), residues: 1780 sheet: 0.28 (1.00), residues: 32 loop : -2.94 (0.16), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG S 52 TYR 0.028 0.001 TYR V 27 PHE 0.019 0.001 PHE L 235 TRP 0.037 0.002 TRP m 30 HIS 0.004 0.001 HIS M 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 (33252) covalent geometry : angle 0.91926 / 0.39 (46017) hydrogen bonds : bond 0.04737 / 3.20 ( 1416) hydrogen bonds : angle 4.79485 / 3.35 ( 4125) Misc. bond : bond 0.08491 / 3.56 ( 60) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 569 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 37 GLN cc_start: 0.9272 (OUTLIER) cc_final: 0.8781 (mp10) REVERT: C 110 MET cc_start: 0.9788 (mmt) cc_final: 0.8670 (mmt) REVERT: C 146 ARG cc_start: 0.9032 (OUTLIER) cc_final: 0.8677 (mmm-85) REVERT: C 149 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8064 (pm20) REVERT: C 188 ASP cc_start: 0.9243 (t0) cc_final: 0.8807 (t0) REVERT: C 233 MET cc_start: 0.9602 (mmp) cc_final: 0.8816 (mmt) REVERT: C 238 ASP cc_start: 0.9504 (t0) cc_final: 0.9154 (t0) REVERT: C 252 THR cc_start: 0.9164 (OUTLIER) cc_final: 0.8673 (p) REVERT: L 23 ASP cc_start: 0.8866 (t0) cc_final: 0.8595 (t0) REVERT: L 29 TYR cc_start: 0.9457 (m-80) cc_final: 0.9084 (m-80) REVERT: L 60 ASP cc_start: 0.8833 (t0) cc_final: 0.8356 (t0) REVERT: L 106 GLU cc_start: 0.9345 (tt0) cc_final: 0.9102 (mm-30) REVERT: L 127 MET cc_start: 0.9586 (tpp) cc_final: 0.9275 (tpp) REVERT: L 148 TYR cc_start: 0.9267 (m-10) cc_final: 0.9013 (m-80) REVERT: L 204 ASP cc_start: 0.8971 (m-30) cc_final: 0.8573 (m-30) REVERT: L 212 GLU cc_start: 0.9409 (pt0) cc_final: 0.9030 (pm20) REVERT: M 9 GLN cc_start: 0.9085 (mt0) cc_final: 0.8629 (mt0) REVERT: M 22 GLU cc_start: 0.9080 (tm-30) cc_final: 0.8527 (tm-30) REVERT: M 26 ASN cc_start: 0.9644 (m-40) cc_final: 0.9353 (p0) REVERT: M 171 GLU cc_start: 0.9414 (mm-30) cc_final: 0.9128 (mp0) REVERT: M 193 ASN cc_start: 0.9437 (t0) cc_final: 0.9016 (t0) REVERT: H 36 ASP cc_start: 0.8969 (OUTLIER) cc_final: 0.8674 (t0) REVERT: H 66 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8300 (mtpp) REVERT: H 92 GLN cc_start: 0.9277 (pm20) cc_final: 0.8774 (pm20) REVERT: H 101 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8863 (mm) REVERT: H 102 GLN cc_start: 0.8823 (mt0) cc_final: 0.8596 (pm20) REVERT: H 217 GLN cc_start: 0.9532 (mt0) cc_final: 0.9006 (mp10) REVERT: H 220 ASN cc_start: 0.9527 (m110) cc_final: 0.9148 (m-40) REVERT: H 236 ASP cc_start: 0.9193 (OUTLIER) cc_final: 0.8781 (t70) REVERT: F 54 LEU cc_start: 0.8942 (mp) cc_final: 0.8717 (pp) REVERT: K 10 LYS cc_start: 0.9678 (OUTLIER) cc_final: 0.9474 (mmmm) REVERT: K 16 ASP cc_start: 0.8415 (t0) cc_final: 0.7267 (t0) REVERT: K 18 ARG cc_start: 0.9194 (mtm110) cc_final: 0.8695 (tmt170) REVERT: K 29 THR cc_start: 0.9632 (m) cc_final: 0.9424 (m) REVERT: K 43 ASP cc_start: 0.9210 (m-30) cc_final: 0.8615 (t0) REVERT: P 16 ASP cc_start: 0.8610 (t0) cc_final: 0.7825 (t0) REVERT: P 52 ARG cc_start: 0.8696 (mtm180) cc_final: 0.8279 (mtm-85) REVERT: S 10 LYS cc_start: 0.9631 (OUTLIER) cc_final: 0.9389 (mmtp) REVERT: S 16 ASP cc_start: 0.8619 (t0) cc_final: 0.8105 (t0) REVERT: S 19 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7552 (tpp-160) REVERT: S 49 GLU cc_start: 0.8991 (tm-30) cc_final: 0.8674 (tp30) REVERT: S 52 ARG cc_start: 0.8929 (mtm110) cc_final: 0.8578 (mtm-85) REVERT: V 43 ASP cc_start: 0.9196 (m-30) cc_final: 0.8500 (m-30) REVERT: V 52 ARG cc_start: 0.9288 (ttp80) cc_final: 0.8721 (ttp80) REVERT: e 3 GLU cc_start: 0.7117 (OUTLIER) cc_final: 0.6367 (pp20) REVERT: e 10 LYS cc_start: 0.9488 (OUTLIER) cc_final: 0.9088 (mmtp) REVERT: h 16 ASP cc_start: 0.8262 (t0) cc_final: 0.7711 (t0) REVERT: h 52 ARG cc_start: 0.9194 (mtp-110) cc_final: 0.8701 (mtm-85) REVERT: n 3 GLU cc_start: 0.7384 (pp20) cc_final: 0.7095 (pm20) REVERT: n 11 LEU cc_start: 0.9756 (tp) cc_final: 0.9447 (tm) REVERT: n 16 ASP cc_start: 0.8451 (t0) cc_final: 0.7893 (t0) REVERT: n 56 LYS cc_start: 0.9018 (tppt) cc_final: 0.8746 (tppt) REVERT: q 10 LYS cc_start: 0.9578 (OUTLIER) cc_final: 0.9164 (mmtp) REVERT: q 16 ASP cc_start: 0.8344 (t0) cc_final: 0.7799 (t0) REVERT: t 16 ASP cc_start: 0.8400 (t0) cc_final: 0.7824 (t0) REVERT: w 30 VAL cc_start: 0.9682 (t) cc_final: 0.9467 (p) REVERT: 3 16 ASP cc_start: 0.8333 (t0) cc_final: 0.7911 (t0) REVERT: 3 43 ASP cc_start: 0.9298 (m-30) cc_final: 0.8955 (m-30) REVERT: 6 16 ASP cc_start: 0.7861 (t0) cc_final: 0.7090 (t0) REVERT: 6 52 ARG cc_start: 0.8672 (ptp-110) cc_final: 0.8295 (ptt180) REVERT: 6 54 LEU cc_start: 0.8928 (mm) cc_final: 0.8683 (mm) REVERT: G 36 VAL cc_start: 0.9611 (t) cc_final: 0.9323 (p) REVERT: o 36 VAL cc_start: 0.9706 (t) cc_final: 0.9443 (p) REVERT: r 16 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8736 (mttp) REVERT: u 36 VAL cc_start: 0.9538 (t) cc_final: 0.9141 (p) REVERT: x 16 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8679 (ptpt) REVERT: d 21 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9208 (tm) REVERT: d 34 THR cc_start: 0.9433 (t) cc_final: 0.9109 (p) REVERT: j 21 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9278 (mm) outliers start: 85 outliers final: 37 residues processed: 624 average time/residue: 0.4013 time to fit residues: 324.7551 Evaluate side-chains 559 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 504 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 305 CYS Chi-restraints excluded: chain M residue 210 CYS Chi-restraints excluded: chain M residue 282 ILE Chi-restraints excluded: chain H residue 36 ASP Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 66 LYS Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 236 ASP Chi-restraints excluded: chain 1 residue 39 LEU Chi-restraints excluded: chain 1 residue 47 ILE Chi-restraints excluded: chain K residue 10 LYS Chi-restraints excluded: chain S residue 10 LYS Chi-restraints excluded: chain S residue 19 ARG Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain Y residue 15 LEU Chi-restraints excluded: chain e residue 3 GLU Chi-restraints excluded: chain e residue 10 LYS Chi-restraints excluded: chain h residue 31 ILE Chi-restraints excluded: chain h residue 43 ASP Chi-restraints excluded: chain n residue 20 VAL Chi-restraints excluded: chain n residue 35 ILE Chi-restraints excluded: chain q residue 2 THR Chi-restraints excluded: chain q residue 10 LYS Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain 3 residue 15 LEU Chi-restraints excluded: chain 3 residue 19 ARG Chi-restraints excluded: chain 3 residue 42 THR Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain Q residue 3 LEU Chi-restraints excluded: chain Q residue 47 ILE Chi-restraints excluded: chain Z residue 13 GLU Chi-restraints excluded: chain Z residue 55 VAL Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain f residue 2 ASP Chi-restraints excluded: chain f residue 25 SER Chi-restraints excluded: chain i residue 55 VAL Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain o residue 55 VAL Chi-restraints excluded: chain r residue 16 LYS Chi-restraints excluded: chain u residue 55 VAL Chi-restraints excluded: chain x residue 16 LYS Chi-restraints excluded: chain x residue 55 VAL Chi-restraints excluded: chain 4 residue 47 ILE Chi-restraints excluded: chain 4 residue 55 VAL Chi-restraints excluded: chain 7 residue 47 ILE Chi-restraints excluded: chain 7 residue 55 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain d residue 21 LEU Chi-restraints excluded: chain j residue 21 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 186 optimal weight: 7.9990 chunk 220 optimal weight: 8.9990 chunk 79 optimal weight: 5.9990 chunk 265 optimal weight: 7.9990 chunk 123 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 267 optimal weight: 20.0000 chunk 206 optimal weight: 10.0000 chunk 75 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.061492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.043362 restraints weight = 116090.898| |-----------------------------------------------------------------------------| r_work (start): 0.2697 rms_B_bonded: 4.24 r_work: 0.2537 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.4747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.862 33312 Z= 0.304 Angle : 1.012 17.762 46017 Z= 0.434 Chirality : 0.049 0.316 4813 Planarity : 0.005 0.064 5558 Dihedral : 16.266 179.821 5136 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.41 % Allowed : 9.82 % Favored : 89.76 % Rotamer: Outliers : 3.35 % Allowed : 28.83 % Favored : 67.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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: -0.57 (0.15), residues: 3380 helix: 1.61 (0.12), residues: 1790 sheet: 0.09 (0.99), residues: 32 loop : -3.00 (0.16), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG S 52 TYR 0.032 0.001 TYR V 27 PHE 0.035 0.002 PHE H 96 TRP 0.030 0.002 TRP d 30 HIS 0.009 0.001 HIS L 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00741 / 0.30 (33252) covalent geometry : angle 1.01185 / 0.43 (46017) hydrogen bonds : bond 0.05379 / 3.64 ( 1416) hydrogen bonds : angle 5.01522 / 3.52 ( 4125) Misc. bond : bond 0.13393 / 6.10 ( 60) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 464 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 37 GLN cc_start: 0.9330 (OUTLIER) cc_final: 0.8770 (mp10) REVERT: C 146 ARG cc_start: 0.9186 (OUTLIER) cc_final: 0.8895 (mmm-85) REVERT: C 149 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8147 (pm20) REVERT: C 238 ASP cc_start: 0.9572 (t0) cc_final: 0.9223 (t0) REVERT: C 252 THR cc_start: 0.9202 (OUTLIER) cc_final: 0.9001 (t) REVERT: L 23 ASP cc_start: 0.9047 (t0) cc_final: 0.8649 (t0) REVERT: L 60 ASP cc_start: 0.8946 (t0) cc_final: 0.8508 (t0) REVERT: L 106 GLU cc_start: 0.9436 (tt0) cc_final: 0.9141 (tp30) REVERT: L 127 MET cc_start: 0.9657 (tpp) cc_final: 0.9333 (tpp) REVERT: L 204 ASP cc_start: 0.9015 (m-30) cc_final: 0.8643 (m-30) REVERT: L 212 GLU cc_start: 0.9435 (pt0) cc_final: 0.9045 (pm20) REVERT: M 9 GLN cc_start: 0.9139 (mt0) cc_final: 0.8693 (mt0) REVERT: M 22 GLU cc_start: 0.9144 (tm-30) cc_final: 0.8575 (tm-30) REVERT: M 26 ASN cc_start: 0.9645 (m-40) cc_final: 0.9354 (p0) REVERT: M 171 GLU cc_start: 0.9457 (OUTLIER) cc_final: 0.9020 (mp0) REVERT: M 193 ASN cc_start: 0.9518 (t0) cc_final: 0.9049 (t0) REVERT: H 36 ASP cc_start: 0.8926 (OUTLIER) cc_final: 0.8607 (t0) REVERT: H 66 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8242 (mtpp) REVERT: H 92 GLN cc_start: 0.9235 (pm20) cc_final: 0.8708 (pm20) REVERT: H 101 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8835 (mm) REVERT: H 102 GLN cc_start: 0.8794 (mt0) cc_final: 0.8568 (pm20) REVERT: H 220 ASN cc_start: 0.9552 (m110) cc_final: 0.9178 (m-40) REVERT: F 54 LEU cc_start: 0.8974 (mp) cc_final: 0.8708 (pp) REVERT: K 10 LYS cc_start: 0.9707 (OUTLIER) cc_final: 0.9458 (mmmm) REVERT: K 16 ASP cc_start: 0.8550 (t0) cc_final: 0.7387 (t0) REVERT: K 18 ARG cc_start: 0.9138 (mtm110) cc_final: 0.8681 (tmt170) REVERT: K 43 ASP cc_start: 0.9316 (m-30) cc_final: 0.8690 (t0) REVERT: P 16 ASP cc_start: 0.8719 (t0) cc_final: 0.7938 (t0) REVERT: P 52 ARG cc_start: 0.8697 (mtm180) cc_final: 0.8332 (mtm-85) REVERT: S 10 LYS cc_start: 0.9661 (OUTLIER) cc_final: 0.9360 (mmtp) REVERT: S 16 ASP cc_start: 0.8785 (t0) cc_final: 0.8271 (t0) REVERT: S 19 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7569 (tpp-160) REVERT: V 43 ASP cc_start: 0.9323 (m-30) cc_final: 0.8689 (m-30) REVERT: V 52 ARG cc_start: 0.9317 (ttp80) cc_final: 0.8793 (ttp80) REVERT: Y 14 ILE cc_start: 0.9482 (mp) cc_final: 0.9259 (tp) REVERT: e 10 LYS cc_start: 0.9517 (OUTLIER) cc_final: 0.9046 (mmtp) REVERT: h 16 ASP cc_start: 0.8452 (t0) cc_final: 0.7823 (t0) REVERT: h 43 ASP cc_start: 0.9180 (OUTLIER) cc_final: 0.8514 (t0) REVERT: h 52 ARG cc_start: 0.9058 (mtp-110) cc_final: 0.8770 (mtp-110) REVERT: n 11 LEU cc_start: 0.9779 (tp) cc_final: 0.9477 (tm) REVERT: n 16 ASP cc_start: 0.8570 (t0) cc_final: 0.8004 (t0) REVERT: n 56 LYS cc_start: 0.9048 (tppt) cc_final: 0.8765 (tppt) REVERT: q 10 LYS cc_start: 0.9584 (OUTLIER) cc_final: 0.9178 (mmtp) REVERT: q 16 ASP cc_start: 0.8456 (t0) cc_final: 0.7896 (t0) REVERT: t 16 ASP cc_start: 0.8512 (t0) cc_final: 0.7912 (t0) REVERT: 3 16 ASP cc_start: 0.8434 (t0) cc_final: 0.7924 (t0) REVERT: 3 43 ASP cc_start: 0.9407 (m-30) cc_final: 0.9082 (m-30) REVERT: 6 16 ASP cc_start: 0.7997 (t0) cc_final: 0.7192 (t0) REVERT: 6 54 LEU cc_start: 0.9005 (mm) cc_final: 0.8792 (mm) REVERT: G 36 VAL cc_start: 0.9657 (t) cc_final: 0.9396 (p) REVERT: o 36 VAL cc_start: 0.9779 (t) cc_final: 0.9535 (p) REVERT: u 36 VAL cc_start: 0.9627 (t) cc_final: 0.9288 (p) REVERT: x 16 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8430 (ptmt) REVERT: d 21 LEU cc_start: 0.9506 (OUTLIER) cc_final: 0.9279 (tm) REVERT: d 34 THR cc_start: 0.9431 (t) cc_final: 0.9123 (p) REVERT: j 21 LEU cc_start: 0.9521 (OUTLIER) cc_final: 0.9300 (mm) outliers start: 98 outliers final: 51 residues processed: 532 average time/residue: 0.4341 time to fit residues: 296.3609 Evaluate side-chains 519 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 451 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain L residue 205 LYS Chi-restraints excluded: chain M residue 156 LEU Chi-restraints excluded: chain M residue 171 GLU Chi-restraints excluded: chain M residue 282 ILE Chi-restraints excluded: chain H residue 36 ASP Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 66 LYS Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 205 LYS Chi-restraints excluded: chain H residue 236 ASP Chi-restraints excluded: chain z residue 35 ILE Chi-restraints excluded: chain 1 residue 39 LEU Chi-restraints excluded: chain 1 residue 47 ILE Chi-restraints excluded: chain K residue 10 LYS Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain P residue 31 ILE Chi-restraints excluded: chain S residue 10 LYS Chi-restraints excluded: chain S residue 19 ARG Chi-restraints excluded: chain Y residue 15 LEU Chi-restraints excluded: chain e residue 10 LYS Chi-restraints excluded: chain h residue 43 ASP Chi-restraints excluded: chain n residue 20 VAL Chi-restraints excluded: chain n residue 35 ILE Chi-restraints excluded: chain q residue 2 THR Chi-restraints excluded: chain q residue 10 LYS Chi-restraints excluded: chain t residue 15 LEU Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain 3 residue 15 LEU Chi-restraints excluded: chain 3 residue 19 ARG Chi-restraints excluded: chain 3 residue 21 LEU Chi-restraints excluded: chain 3 residue 42 THR Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain Q residue 3 LEU Chi-restraints excluded: chain Q residue 47 ILE Chi-restraints excluded: chain T residue 13 GLU Chi-restraints excluded: chain Z residue 13 GLU Chi-restraints excluded: chain Z residue 55 VAL Chi-restraints excluded: chain c residue 55 VAL Chi-restraints excluded: chain f residue 2 ASP Chi-restraints excluded: chain f residue 25 SER Chi-restraints excluded: chain i residue 13 GLU Chi-restraints excluded: chain i residue 55 VAL Chi-restraints excluded: chain l residue 21 ILE Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain o residue 55 VAL Chi-restraints excluded: chain u residue 13 GLU Chi-restraints excluded: chain u residue 55 VAL Chi-restraints excluded: chain x residue 16 LYS Chi-restraints excluded: chain x residue 21 ILE Chi-restraints excluded: chain x residue 55 VAL Chi-restraints excluded: chain 4 residue 47 ILE Chi-restraints excluded: chain 4 residue 55 VAL Chi-restraints excluded: chain 7 residue 47 ILE Chi-restraints excluded: chain 7 residue 55 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain d residue 21 LEU Chi-restraints excluded: chain d residue 23 ILE Chi-restraints excluded: chain j residue 21 LEU Chi-restraints excluded: chain m residue 21 LEU Chi-restraints excluded: chain s residue 24 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 21 optimal weight: 0.5980 chunk 219 optimal weight: 10.0000 chunk 58 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 223 optimal weight: 0.1980 chunk 64 optimal weight: 4.9990 chunk 314 optimal weight: 4.9990 chunk 272 optimal weight: 5.9990 chunk 113 optimal weight: 8.9990 chunk 133 optimal weight: 10.0000 chunk 80 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.064906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.046600 restraints weight = 111774.744| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 4.31 r_work: 0.2607 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.5039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.667 33312 Z= 0.160 Angle : 0.952 16.267 46017 Z= 0.407 Chirality : 0.046 0.257 4813 Planarity : 0.005 0.053 5558 Dihedral : 16.079 179.207 5136 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.20 % Favored : 91.45 % Rotamer: Outliers : 2.29 % Allowed : 29.99 % Favored : 67.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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: -0.61 (0.15), residues: 3380 helix: 1.51 (0.12), residues: 1784 sheet: 0.19 (0.99), residues: 32 loop : -2.93 (0.16), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG 6 52 TYR 0.031 0.001 TYR V 27 PHE 0.031 0.001 PHE H 96 TRP 0.028 0.002 TRP d 30 HIS 0.004 0.001 HIS M 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.16 (33252) covalent geometry : angle 0.95219 / 0.41 (46017) hydrogen bonds : bond 0.04870 / 3.28 ( 1416) hydrogen bonds : angle 4.88618 / 3.42 ( 4125) Misc. bond : bond 0.09638 / 4.16 ( 60) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 518 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 37 GLN cc_start: 0.9278 (OUTLIER) cc_final: 0.8743 (mp10) REVERT: C 146 ARG cc_start: 0.9037 (OUTLIER) cc_final: 0.8656 (mmm-85) REVERT: C 149 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8040 (pm20) REVERT: C 188 ASP cc_start: 0.9221 (t0) cc_final: 0.8764 (t0) REVERT: C 233 MET cc_start: 0.9584 (mmp) cc_final: 0.8884 (mmt) REVERT: C 238 ASP cc_start: 0.9507 (t0) cc_final: 0.9156 (t0) REVERT: C 252 THR cc_start: 0.9190 (OUTLIER) cc_final: 0.8828 (p) REVERT: L 23 ASP cc_start: 0.8860 (t0) cc_final: 0.8552 (t0) REVERT: L 60 ASP cc_start: 0.8939 (t0) cc_final: 0.8494 (t0) REVERT: L 106 GLU cc_start: 0.9414 (tt0) cc_final: 0.9159 (tp30) REVERT: L 148 TYR cc_start: 0.9281 (m-10) cc_final: 0.9073 (m-80) REVERT: L 204 ASP cc_start: 0.9027 (m-30) cc_final: 0.8652 (m-30) REVERT: L 212 GLU cc_start: 0.9387 (pt0) cc_final: 0.9040 (pm20) REVERT: M 9 GLN cc_start: 0.9130 (mt0) cc_final: 0.8686 (mt0) REVERT: M 22 GLU cc_start: 0.9091 (tm-30) cc_final: 0.8524 (tm-30) REVERT: M 26 ASN cc_start: 0.9620 (m-40) cc_final: 0.9419 (OUTLIER) REVERT: M 171 GLU cc_start: 0.9394 (OUTLIER) cc_final: 0.9025 (mp0) REVERT: M 193 ASN cc_start: 0.9457 (t0) cc_final: 0.9052 (t0) REVERT: H 36 ASP cc_start: 0.8974 (OUTLIER) cc_final: 0.8693 (t0) REVERT: H 66 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8327 (mtpp) REVERT: H 92 GLN cc_start: 0.9265 (pm20) cc_final: 0.8796 (pm20) REVERT: H 101 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8851 (mm) REVERT: H 102 GLN cc_start: 0.8822 (mt0) cc_final: 0.8595 (pm20) REVERT: H 217 GLN cc_start: 0.9568 (mt0) cc_final: 0.9111 (mp10) REVERT: H 220 ASN cc_start: 0.9529 (m110) cc_final: 0.9166 (m-40) REVERT: F 54 LEU cc_start: 0.8978 (mp) cc_final: 0.8746 (pp) REVERT: K 16 ASP cc_start: 0.8440 (t0) cc_final: 0.7315 (t0) REVERT: K 18 ARG cc_start: 0.9119 (mtm110) cc_final: 0.8666 (tmt170) REVERT: K 29 THR cc_start: 0.9653 (m) cc_final: 0.9237 (p) REVERT: K 43 ASP cc_start: 0.9237 (m-30) cc_final: 0.8665 (t0) REVERT: P 16 ASP cc_start: 0.8580 (t0) cc_final: 0.7809 (t0) REVERT: P 52 ARG cc_start: 0.8638 (mtm180) cc_final: 0.8290 (mtm-85) REVERT: S 10 LYS cc_start: 0.9633 (OUTLIER) cc_final: 0.9395 (mmtp) REVERT: S 16 ASP cc_start: 0.8738 (t0) cc_final: 0.8182 (t0) REVERT: S 19 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7592 (tpp-160) REVERT: V 43 ASP cc_start: 0.9208 (m-30) cc_final: 0.8561 (m-30) REVERT: V 52 ARG cc_start: 0.9264 (ttp80) cc_final: 0.8724 (ttp80) REVERT: Y 14 ILE cc_start: 0.9428 (mp) cc_final: 0.9223 (tp) REVERT: b 56 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8680 (tptp) REVERT: e 10 LYS cc_start: 0.9484 (OUTLIER) cc_final: 0.9063 (mmtp) REVERT: h 16 ASP cc_start: 0.8423 (t0) cc_final: 0.7756 (t0) REVERT: h 43 ASP cc_start: 0.8911 (m-30) cc_final: 0.8634 (OUTLIER) REVERT: n 3 GLU cc_start: 0.7290 (pp20) cc_final: 0.6912 (pm20) REVERT: n 11 LEU cc_start: 0.9743 (tp) cc_final: 0.9540 (tm) REVERT: n 16 ASP cc_start: 0.8386 (t0) cc_final: 0.7808 (t0) REVERT: q 10 LYS cc_start: 0.9566 (OUTLIER) cc_final: 0.9174 (mmtp) REVERT: q 16 ASP cc_start: 0.8354 (t0) cc_final: 0.7776 (t0) REVERT: t 16 ASP cc_start: 0.8369 (t0) cc_final: 0.7715 (t0) REVERT: w 30 VAL cc_start: 0.9719 (t) cc_final: 0.9489 (p) REVERT: 3 16 ASP cc_start: 0.8304 (t0) cc_final: 0.7857 (t0) REVERT: 3 43 ASP cc_start: 0.9302 (m-30) cc_final: 0.8977 (m-30) REVERT: 6 16 ASP cc_start: 0.7855 (t0) cc_final: 0.7028 (t0) REVERT: 6 52 ARG cc_start: 0.8625 (ptp-110) cc_final: 0.8320 (ptt180) REVERT: 6 54 LEU cc_start: 0.8898 (mm) cc_final: 0.8681 (mm) REVERT: G 36 VAL cc_start: 0.9619 (t) cc_final: 0.9344 (p) REVERT: o 36 VAL cc_start: 0.9752 (t) cc_final: 0.9494 (p) REVERT: o 55 VAL cc_start: 0.9140 (OUTLIER) cc_final: 0.8900 (p) REVERT: u 36 VAL cc_start: 0.9565 (t) cc_final: 0.9155 (p) REVERT: x 16 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8524 (ptpt) REVERT: 4 36 VAL cc_start: 0.9613 (t) cc_final: 0.9315 (p) REVERT: d 21 LEU cc_start: 0.9454 (OUTLIER) cc_final: 0.9245 (tm) REVERT: d 34 THR cc_start: 0.9444 (t) cc_final: 0.9145 (p) REVERT: j 21 LEU cc_start: 0.9503 (OUTLIER) cc_final: 0.9287 (mm) outliers start: 67 outliers final: 36 residues processed: 563 average time/residue: 0.4081 time to fit residues: 298.7161 Evaluate side-chains 546 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 495 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain M residue 171 GLU Chi-restraints excluded: chain M residue 282 ILE Chi-restraints excluded: chain H residue 36 ASP Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 66 LYS Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain 1 residue 39 LEU Chi-restraints excluded: chain 1 residue 47 ILE Chi-restraints excluded: chain S residue 10 LYS Chi-restraints excluded: chain S residue 19 ARG Chi-restraints excluded: chain Y residue 15 LEU Chi-restraints excluded: chain b residue 56 LYS Chi-restraints excluded: chain e residue 10 LYS Chi-restraints excluded: chain n residue 20 VAL Chi-restraints excluded: chain n residue 35 ILE Chi-restraints excluded: chain q residue 2 THR Chi-restraints excluded: chain q residue 10 LYS Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain 3 residue 19 ARG Chi-restraints excluded: chain 3 residue 42 THR Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain Q residue 3 LEU Chi-restraints excluded: chain Q residue 47 ILE Chi-restraints excluded: chain W residue 16 LYS Chi-restraints excluded: chain Z residue 13 GLU Chi-restraints excluded: chain Z residue 55 VAL Chi-restraints excluded: chain f residue 2 ASP Chi-restraints excluded: chain i residue 13 GLU Chi-restraints excluded: chain i residue 30 LEU Chi-restraints excluded: chain i residue 55 VAL Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain o residue 55 VAL Chi-restraints excluded: chain u residue 55 VAL Chi-restraints excluded: chain x residue 16 LYS Chi-restraints excluded: chain x residue 55 VAL Chi-restraints excluded: chain 4 residue 47 ILE Chi-restraints excluded: chain 4 residue 55 VAL Chi-restraints excluded: chain 7 residue 47 ILE Chi-restraints excluded: chain 7 residue 55 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain d residue 21 LEU Chi-restraints excluded: chain j residue 21 LEU Chi-restraints excluded: chain m residue 21 LEU Chi-restraints excluded: chain p residue 24 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 128 optimal weight: 0.8980 chunk 275 optimal weight: 1.9990 chunk 219 optimal weight: 4.9990 chunk 138 optimal weight: 0.0980 chunk 60 optimal weight: 10.0000 chunk 262 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 178 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.064805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.047038 restraints weight = 111766.674| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 4.20 r_work: 0.2623 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.5154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.686 33312 Z= 0.166 Angle : 0.943 17.337 46017 Z= 0.407 Chirality : 0.046 0.317 4813 Planarity : 0.005 0.064 5558 Dihedral : 15.903 179.597 5136 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.08 % Favored : 90.53 % Rotamer: Outliers : 1.71 % Allowed : 30.77 % Favored : 67.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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: -0.59 (0.15), residues: 3380 helix: 1.52 (0.12), residues: 1784 sheet: 0.14 (0.97), residues: 32 loop : -2.89 (0.16), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG Y 52 TYR 0.032 0.001 TYR V 27 PHE 0.034 0.001 PHE 7 22 TRP 0.048 0.002 TRP j 30 HIS 0.004 0.001 HIS L 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.17 (33252) covalent geometry : angle 0.94265 / 0.41 (46017) hydrogen bonds : bond 0.04784 / 3.22 ( 1416) hydrogen bonds : angle 4.85461 / 3.40 ( 4125) Misc. bond : bond 0.09564 / 3.70 ( 60) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6760 Ramachandran restraints generated. 3380 Oldfield, 0 Emsley, 3380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 517 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 37 GLN cc_start: 0.9233 (OUTLIER) cc_final: 0.8658 (mp10) REVERT: C 110 MET cc_start: 0.9636 (mmt) cc_final: 0.8872 (mmt) REVERT: C 146 ARG cc_start: 0.9011 (OUTLIER) cc_final: 0.8670 (mmm-85) REVERT: C 149 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8054 (pm20) REVERT: C 188 ASP cc_start: 0.9217 (t0) cc_final: 0.8764 (t0) REVERT: C 233 MET cc_start: 0.9590 (mmp) cc_final: 0.8900 (mmt) REVERT: C 238 ASP cc_start: 0.9486 (t0) cc_final: 0.9150 (t0) REVERT: C 252 THR cc_start: 0.9070 (OUTLIER) cc_final: 0.8720 (p) REVERT: L 23 ASP cc_start: 0.8878 (t0) cc_final: 0.8572 (t0) REVERT: L 60 ASP cc_start: 0.8962 (t0) cc_final: 0.8503 (t0) REVERT: L 106 GLU cc_start: 0.9420 (tt0) cc_final: 0.9120 (tp30) REVERT: L 127 MET cc_start: 0.9475 (tpp) cc_final: 0.9275 (tpp) REVERT: L 204 ASP cc_start: 0.9025 (m-30) cc_final: 0.8666 (m-30) REVERT: L 212 GLU cc_start: 0.9385 (pt0) cc_final: 0.9097 (pm20) REVERT: M 9 GLN cc_start: 0.9126 (mt0) cc_final: 0.8681 (mt0) REVERT: M 22 GLU cc_start: 0.9103 (tm-30) cc_final: 0.8546 (tm-30) REVERT: M 171 GLU cc_start: 0.9399 (OUTLIER) cc_final: 0.9122 (mp0) REVERT: M 193 ASN cc_start: 0.9461 (t0) cc_final: 0.9061 (t0) REVERT: H 36 ASP cc_start: 0.8971 (OUTLIER) cc_final: 0.8726 (t0) REVERT: H 66 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8378 (mtpp) REVERT: H 92 GLN cc_start: 0.9272 (pm20) cc_final: 0.8774 (pm20) REVERT: H 101 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8867 (mm) REVERT: H 102 GLN cc_start: 0.8830 (mt0) cc_final: 0.8613 (pm20) REVERT: H 217 GLN cc_start: 0.9586 (mt0) cc_final: 0.9102 (mp10) REVERT: H 220 ASN cc_start: 0.9528 (m110) cc_final: 0.9162 (m-40) REVERT: F 54 LEU cc_start: 0.8965 (mp) cc_final: 0.8679 (pp) REVERT: K 16 ASP cc_start: 0.8477 (t0) cc_final: 0.7379 (t0) REVERT: K 18 ARG cc_start: 0.9110 (mtm110) cc_final: 0.8720 (tmt170) REVERT: K 29 THR cc_start: 0.9651 (m) cc_final: 0.9241 (p) REVERT: K 43 ASP cc_start: 0.9220 (m-30) cc_final: 0.8660 (t0) REVERT: P 16 ASP cc_start: 0.8542 (t0) cc_final: 0.7797 (t0) REVERT: P 52 ARG cc_start: 0.8631 (mtm180) cc_final: 0.8281 (mtm-85) REVERT: S 10 LYS cc_start: 0.9653 (OUTLIER) cc_final: 0.9383 (mmtp) REVERT: S 16 ASP cc_start: 0.8692 (t0) cc_final: 0.8160 (t0) REVERT: S 19 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7643 (tpp-160) REVERT: V 43 ASP cc_start: 0.9186 (m-30) cc_final: 0.8527 (m-30) REVERT: V 52 ARG cc_start: 0.9266 (ttp80) cc_final: 0.8734 (ttp80) REVERT: Y 14 ILE cc_start: 0.9466 (mp) cc_final: 0.9249 (tp) REVERT: e 10 LYS cc_start: 0.9486 (OUTLIER) cc_final: 0.9088 (mmtp) REVERT: h 16 ASP cc_start: 0.8383 (t0) cc_final: 0.7721 (t0) REVERT: h 43 ASP cc_start: 0.8820 (m-30) cc_final: 0.8581 (m-30) REVERT: h 52 ARG cc_start: 0.9012 (mtp-110) cc_final: 0.8625 (mtm-85) REVERT: n 3 GLU cc_start: 0.7225 (pp20) cc_final: 0.6768 (pm20) REVERT: n 16 ASP cc_start: 0.8334 (t0) cc_final: 0.7764 (t0) REVERT: q 10 LYS cc_start: 0.9568 (OUTLIER) cc_final: 0.9173 (mmtp) REVERT: q 16 ASP cc_start: 0.8343 (t0) cc_final: 0.7767 (t0) REVERT: t 16 ASP cc_start: 0.8311 (t0) cc_final: 0.7670 (t0) REVERT: w 16 ASP cc_start: 0.8216 (t0) cc_final: 0.7646 (t0) REVERT: 3 16 ASP cc_start: 0.8237 (t0) cc_final: 0.7736 (t0) REVERT: 3 43 ASP cc_start: 0.9279 (m-30) cc_final: 0.8954 (m-30) REVERT: 6 16 ASP cc_start: 0.7801 (t0) cc_final: 0.7048 (t0) REVERT: 6 52 ARG cc_start: 0.8607 (ptp-110) cc_final: 0.8332 (ptt180) REVERT: o 36 VAL cc_start: 0.9754 (t) cc_final: 0.9497 (p) REVERT: o 55 VAL cc_start: 0.9151 (OUTLIER) cc_final: 0.8912 (p) REVERT: u 36 VAL cc_start: 0.9591 (t) cc_final: 0.9240 (p) REVERT: 4 36 VAL cc_start: 0.9628 (t) cc_final: 0.9331 (p) REVERT: d 21 LEU cc_start: 0.9505 (OUTLIER) cc_final: 0.9289 (tm) REVERT: d 34 THR cc_start: 0.9424 (t) cc_final: 0.9165 (p) REVERT: j 21 LEU cc_start: 0.9504 (OUTLIER) cc_final: 0.9295 (mm) REVERT: s 17 LEU cc_start: 0.7390 (mt) cc_final: 0.6996 (mt) outliers start: 50 outliers final: 31 residues processed: 548 average time/residue: 0.3884 time to fit residues: 278.8975 Evaluate side-chains 539 residues out of total 2928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 493 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 146 ARG Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain M residue 26 ASN Chi-restraints excluded: chain M residue 171 GLU Chi-restraints excluded: chain M residue 282 ILE Chi-restraints excluded: chain H residue 36 ASP Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 66 LYS Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain 1 residue 39 LEU Chi-restraints excluded: chain 1 residue 47 ILE Chi-restraints excluded: chain S residue 10 LYS Chi-restraints excluded: chain S residue 19 ARG Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain e residue 10 LYS Chi-restraints excluded: chain n residue 20 VAL Chi-restraints excluded: chain n residue 35 ILE Chi-restraints excluded: chain q residue 2 THR Chi-restraints excluded: chain q residue 10 LYS Chi-restraints excluded: chain t residue 31 ILE Chi-restraints excluded: chain 3 residue 19 ARG Chi-restraints excluded: chain 3 residue 42 THR Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain Q residue 3 LEU Chi-restraints excluded: chain Q residue 47 ILE Chi-restraints excluded: chain Z residue 55 VAL Chi-restraints excluded: chain i residue 30 LEU Chi-restraints excluded: chain i residue 55 VAL Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain o residue 55 VAL Chi-restraints excluded: chain u residue 55 VAL Chi-restraints excluded: chain x residue 55 VAL Chi-restraints excluded: chain 4 residue 47 ILE Chi-restraints excluded: chain 4 residue 55 VAL Chi-restraints excluded: chain 7 residue 47 ILE Chi-restraints excluded: chain 7 residue 55 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain d residue 21 LEU Chi-restraints excluded: chain j residue 21 LEU Chi-restraints excluded: chain v residue 29 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 98 optimal weight: 5.9990 chunk 53 optimal weight: 0.5980 chunk 163 optimal weight: 0.7980 chunk 174 optimal weight: 0.2980 chunk 122 optimal weight: 30.0000 chunk 4 optimal weight: 20.0000 chunk 193 optimal weight: 9.9990 chunk 219 optimal weight: 7.9990 chunk 203 optimal weight: 10.0000 chunk 225 optimal weight: 0.9990 chunk 177 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.066058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.048185 restraints weight = 111123.485| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 4.30 r_work: 0.2660 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.5333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.613 33312 Z= 0.154 Angle : 0.948 19.743 46017 Z= 0.408 Chirality : 0.046 0.272 4813 Planarity : 0.005 0.056 5558 Dihedral : 15.784 179.696 5136 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.43 % Favored : 91.18 % Rotamer: Outliers : 1.57 % Allowed : 31.22 % Favored : 67.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % 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: -0.63 (0.15), residues: 3380 helix: 1.51 (0.12), residues: 1767 sheet: 0.22 (0.94), residues: 32 loop : -2.90 (0.16), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG Y 52 TYR 0.034 0.001 TYR V 27 PHE 0.030 0.001 PHE H 96 TRP 0.036 0.002 TRP j 30 HIS 0.003 0.001 HIS M 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.15 (33252) covalent geometry : angle 0.94780 / 0.41 (46017) hydrogen bonds : bond 0.04605 / 3.11 ( 1416) hydrogen bonds : angle 4.84580 / 3.39 ( 4125) Misc. bond : bond 0.08473 / 3.37 ( 60) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9428.68 seconds wall clock time: 161 minutes 39.38 seconds (9699.38 seconds total)