Starting phenix.real_space_refine on Fri Oct 30 01:08:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zyd_11557/10_2026/6zyd_11557_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zyd_11557/10_2026/6zyd_11557.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6zyd_11557/10_2026/6zyd_11557.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zyd_11557/10_2026/6zyd_11557.map" model { file = "/net/cci-nas-00/data/ceres_data/6zyd_11557/10_2026/6zyd_11557_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zyd_11557/10_2026/6zyd_11557_trim.cif" } resolution = 3.0 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= 0.010 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 P 7 5.49 5 S 70 5.16 5 C 10927 2.51 5 N 2849 2.21 5 O 3080 1.98 5 H 14490 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31423 Number of models: 1 Model: "" Number of chains: 14 Chain: "E" Number of atoms: 4438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 4438 Classifications: {'peptide': 323} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 7, 'TRANS': 315} Chain breaks: 1 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'UNK:plan-1': 67} Unresolved non-hydrogen planarities: 67 Chain: "C" Number of atoms: 4438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 4438 Classifications: {'peptide': 323} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 7, 'TRANS': 315} Chain breaks: 1 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'UNK:plan-1': 67} Unresolved non-hydrogen planarities: 67 Chain: "A" Number of atoms: 4438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 4438 Classifications: {'peptide': 323} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 7, 'TRANS': 315} Chain breaks: 1 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'UNK:plan-1': 67} Unresolved non-hydrogen planarities: 67 Chain: "B" Number of atoms: 4438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 4438 Classifications: {'peptide': 323} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 7, 'TRANS': 315} Chain breaks: 1 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'UNK:plan-1': 67} Unresolved non-hydrogen planarities: 67 Chain: "D" Number of atoms: 4438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 4438 Classifications: {'peptide': 323} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 7, 'TRANS': 315} Chain breaks: 1 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'UNK:plan-1': 67} Unresolved non-hydrogen planarities: 67 Chain: "F" Number of atoms: 4438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 4438 Classifications: {'peptide': 323} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 7, 'TRANS': 315} Chain breaks: 1 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'UNK:plan-1': 67} Unresolved non-hydrogen planarities: 67 Chain: "G" Number of atoms: 4438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 4438 Classifications: {'peptide': 323} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 7, 'TRANS': 315} Chain breaks: 1 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'UNK:plan-1': 67} Unresolved non-hydrogen planarities: 67 Chain: "E" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.29, per 1000 atoms: 0.17 Number of scatterers: 31423 At special positions: 0 Unit cell: (103.16, 104.223, 134.001, 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) S 70 16.00 P 7 15.00 O 3080 8.00 N 2849 7.00 C 10927 6.00 H 14490 1.00 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=0, symmetry=0 Time building additional restraints: 2.94 Conformation dependent library (CDL) restraints added in 767.6 milliseconds 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4270 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 15 sheets defined 78.2% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'E' and resid -66 through -47 removed outlier: 3.679A pdb=" N UNK E -55 " --> pdb=" O UNK E -59 " (cutoff:3.500A) Processing helix chain 'E' and resid -39 through -6 removed outlier: 4.854A pdb=" N UNK E -31 " --> pdb=" O UNK E -35 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N UNK E -30 " --> pdb=" O UNK E -34 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N UNK E -14 " --> pdb=" O UNK E -18 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N UNK E -13 " --> pdb=" O UNK E -17 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N UNK E -8 " --> pdb=" O UNK E -12 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 108 removed outlier: 3.850A pdb=" N THR E 91 " --> pdb=" O ALA E 87 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS E 108 " --> pdb=" O GLN E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 139 removed outlier: 3.638A pdb=" N VAL E 129 " --> pdb=" O THR E 125 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU E 130 " --> pdb=" O ILE E 126 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLU E 136 " --> pdb=" O LEU E 132 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N HIS E 137 " --> pdb=" O LEU E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 176 removed outlier: 5.322A pdb=" N ASP E 162 " --> pdb=" O MET E 158 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ILE E 163 " --> pdb=" O ALA E 159 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN E 166 " --> pdb=" O ASP E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 223 Processing helix chain 'E' and resid 229 through 232 Processing helix chain 'E' and resid 244 through 249 removed outlier: 3.567A pdb=" N ALA E 248 " --> pdb=" O TYR E 245 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ALA E 249 " --> pdb=" O GLU E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 263 Processing helix chain 'E' and resid 298 through 321 Processing helix chain 'C' and resid -65 through -47 removed outlier: 3.680A pdb=" N UNK C -55 " --> pdb=" O UNK C -59 " (cutoff:3.500A) Processing helix chain 'C' and resid -39 through -6 removed outlier: 4.853A pdb=" N UNK C -31 " --> pdb=" O UNK C -35 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N UNK C -30 " --> pdb=" O UNK C -34 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N UNK C -14 " --> pdb=" O UNK C -18 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N UNK C -13 " --> pdb=" O UNK C -17 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N UNK C -8 " --> pdb=" O UNK C -12 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 108 removed outlier: 3.850A pdb=" N THR C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS C 108 " --> pdb=" O GLN C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 139 removed outlier: 3.636A pdb=" N VAL C 129 " --> pdb=" O THR C 125 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU C 130 " --> pdb=" O ILE C 126 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N GLU C 136 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N HIS C 137 " --> pdb=" O LEU C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 176 removed outlier: 5.320A pdb=" N ASP C 162 " --> pdb=" O MET C 158 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ILE C 163 " --> pdb=" O ALA C 159 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN C 166 " --> pdb=" O ASP C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 223 Processing helix chain 'C' and resid 229 through 232 Processing helix chain 'C' and resid 244 through 249 removed outlier: 3.566A pdb=" N ALA C 248 " --> pdb=" O TYR C 245 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ALA C 249 " --> pdb=" O GLU C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 263 Processing helix chain 'C' and resid 298 through 321 Processing helix chain 'A' and resid -65 through -47 removed outlier: 3.680A pdb=" N UNK A -55 " --> pdb=" O UNK A -59 " (cutoff:3.500A) Processing helix chain 'A' and resid -39 through -6 removed outlier: 4.854A pdb=" N UNK A -31 " --> pdb=" O UNK A -35 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N UNK A -30 " --> pdb=" O UNK A -34 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N UNK A -14 " --> pdb=" O UNK A -18 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N UNK A -13 " --> pdb=" O UNK A -17 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N UNK A -8 " --> pdb=" O UNK A -12 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 108 removed outlier: 3.848A pdb=" N THR A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS A 108 " --> pdb=" O GLN A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 139 removed outlier: 3.637A pdb=" N VAL A 129 " --> pdb=" O THR A 125 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A 130 " --> pdb=" O ILE A 126 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N GLU A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N HIS A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 176 removed outlier: 5.321A pdb=" N ASP A 162 " --> pdb=" O MET A 158 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ILE A 163 " --> pdb=" O ALA A 159 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN A 166 " --> pdb=" O ASP A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 223 Processing helix chain 'A' and resid 229 through 232 Processing helix chain 'A' and resid 244 through 249 removed outlier: 3.567A pdb=" N ALA A 248 " --> pdb=" O TYR A 245 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ALA A 249 " --> pdb=" O GLU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 263 Processing helix chain 'A' and resid 298 through 321 Processing helix chain 'B' and resid -65 through -47 removed outlier: 3.680A pdb=" N UNK B -55 " --> pdb=" O UNK B -59 " (cutoff:3.500A) Processing helix chain 'B' and resid -39 through -6 removed outlier: 4.854A pdb=" N UNK B -31 " --> pdb=" O UNK B -35 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N UNK B -30 " --> pdb=" O UNK B -34 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N UNK B -14 " --> pdb=" O UNK B -18 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N UNK B -13 " --> pdb=" O UNK B -17 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N UNK B -8 " --> pdb=" O UNK B -12 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 108 removed outlier: 3.850A pdb=" N THR B 91 " --> pdb=" O ALA B 87 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS B 108 " --> pdb=" O GLN B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 139 removed outlier: 3.616A pdb=" N VAL B 129 " --> pdb=" O THR B 125 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU B 130 " --> pdb=" O ILE B 126 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLU B 136 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N HIS B 137 " --> pdb=" O LEU B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 176 removed outlier: 5.321A pdb=" N ASP B 162 " --> pdb=" O MET B 158 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ILE B 163 " --> pdb=" O ALA B 159 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN B 166 " --> pdb=" O ASP B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 223 Processing helix chain 'B' and resid 229 through 232 Processing helix chain 'B' and resid 244 through 249 removed outlier: 3.567A pdb=" N ALA B 248 " --> pdb=" O TYR B 245 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ALA B 249 " --> pdb=" O GLU B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 263 Processing helix chain 'B' and resid 298 through 321 Processing helix chain 'D' and resid -65 through -47 removed outlier: 3.679A pdb=" N UNK D -55 " --> pdb=" O UNK D -59 " (cutoff:3.500A) Processing helix chain 'D' and resid -39 through -6 removed outlier: 4.854A pdb=" N UNK D -31 " --> pdb=" O UNK D -35 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N UNK D -30 " --> pdb=" O UNK D -34 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N UNK D -14 " --> pdb=" O UNK D -18 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N UNK D -13 " --> pdb=" O UNK D -17 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N UNK D -8 " --> pdb=" O UNK D -12 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 108 removed outlier: 3.851A pdb=" N THR D 91 " --> pdb=" O ALA D 87 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS D 108 " --> pdb=" O GLN D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 139 removed outlier: 3.636A pdb=" N VAL D 129 " --> pdb=" O THR D 125 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU D 130 " --> pdb=" O ILE D 126 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLU D 136 " --> pdb=" O LEU D 132 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N HIS D 137 " --> pdb=" O LEU D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 176 removed outlier: 5.323A pdb=" N ASP D 162 " --> pdb=" O MET D 158 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ILE D 163 " --> pdb=" O ALA D 159 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN D 166 " --> pdb=" O ASP D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 223 Processing helix chain 'D' and resid 229 through 232 Processing helix chain 'D' and resid 244 through 249 removed outlier: 3.567A pdb=" N ALA D 248 " --> pdb=" O TYR D 245 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ALA D 249 " --> pdb=" O GLU D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 263 Processing helix chain 'D' and resid 298 through 321 Processing helix chain 'F' and resid -65 through -47 removed outlier: 3.680A pdb=" N UNK F -55 " --> pdb=" O UNK F -59 " (cutoff:3.500A) Processing helix chain 'F' and resid -39 through -6 removed outlier: 4.852A pdb=" N UNK F -31 " --> pdb=" O UNK F -35 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N UNK F -30 " --> pdb=" O UNK F -34 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N UNK F -14 " --> pdb=" O UNK F -18 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N UNK F -13 " --> pdb=" O UNK F -17 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N UNK F -8 " --> pdb=" O UNK F -12 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 108 removed outlier: 3.850A pdb=" N THR F 91 " --> pdb=" O ALA F 87 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS F 108 " --> pdb=" O GLN F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 139 removed outlier: 3.636A pdb=" N VAL F 129 " --> pdb=" O THR F 125 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU F 130 " --> pdb=" O ILE F 126 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLU F 136 " --> pdb=" O LEU F 132 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N HIS F 137 " --> pdb=" O LEU F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 176 removed outlier: 5.322A pdb=" N ASP F 162 " --> pdb=" O MET F 158 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ILE F 163 " --> pdb=" O ALA F 159 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN F 166 " --> pdb=" O ASP F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 219 through 223 Processing helix chain 'F' and resid 229 through 232 Processing helix chain 'F' and resid 244 through 249 removed outlier: 3.567A pdb=" N ALA F 248 " --> pdb=" O TYR F 245 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ALA F 249 " --> pdb=" O GLU F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 263 Processing helix chain 'F' and resid 298 through 321 Processing helix chain 'G' and resid -65 through -47 removed outlier: 3.680A pdb=" N UNK G -55 " --> pdb=" O UNK G -59 " (cutoff:3.500A) Processing helix chain 'G' and resid -39 through -6 removed outlier: 4.853A pdb=" N UNK G -31 " --> pdb=" O UNK G -35 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N UNK G -30 " --> pdb=" O UNK G -34 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N UNK G -14 " --> pdb=" O UNK G -18 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N UNK G -13 " --> pdb=" O UNK G -17 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N UNK G -8 " --> pdb=" O UNK G -12 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 108 removed outlier: 3.850A pdb=" N THR G 91 " --> pdb=" O ALA G 87 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS G 108 " --> pdb=" O GLN G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 139 removed outlier: 3.637A pdb=" N VAL G 129 " --> pdb=" O THR G 125 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU G 130 " --> pdb=" O ILE G 126 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLU G 136 " --> pdb=" O LEU G 132 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N HIS G 137 " --> pdb=" O LEU G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 176 removed outlier: 5.323A pdb=" N ASP G 162 " --> pdb=" O MET G 158 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ILE G 163 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN G 166 " --> pdb=" O ASP G 162 " (cutoff:3.500A) Processing helix chain 'G' and resid 219 through 223 Processing helix chain 'G' and resid 229 through 232 Processing helix chain 'G' and resid 244 through 249 removed outlier: 3.567A pdb=" N ALA G 248 " --> pdb=" O TYR G 245 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ALA G 249 " --> pdb=" O GLU G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 263 Processing helix chain 'G' and resid 298 through 321 Processing sheet with id=AA1, first strand: chain 'E' and resid 184 through 187 removed outlier: 6.482A pdb=" N SER E 187 " --> pdb=" O ILE E 192 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ILE E 192 " --> pdb=" O SER E 187 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LYS E 205 " --> pdb=" O ALA E 197 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N ILE E 199 " --> pdb=" O ILE E 203 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE E 203 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 226 through 227 removed outlier: 6.848A pdb=" N ILE D 203 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N ILE D 199 " --> pdb=" O ILE D 203 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LYS D 205 " --> pdb=" O ALA D 197 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ILE D 192 " --> pdb=" O SER D 187 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N SER D 187 " --> pdb=" O ILE D 192 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 235 through 243 removed outlier: 3.601A pdb=" N GLN E 280 " --> pdb=" O ASN E 287 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N MET E 289 " --> pdb=" O PHE E 278 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N PHE E 278 " --> pdb=" O MET E 289 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N TYR E 291 " --> pdb=" O VAL E 276 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N VAL E 276 " --> pdb=" O TYR E 291 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N PHE E 293 " --> pdb=" O LEU E 274 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N LEU E 274 " --> pdb=" O PHE E 293 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 328 through 331 removed outlier: 8.322A pdb=" N GLN D 329 " --> pdb=" O SER E 328 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N THR E 330 " --> pdb=" O GLN D 329 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N LEU D 331 " --> pdb=" O THR E 330 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N GLN G 329 " --> pdb=" O SER C 328 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N THR C 330 " --> pdb=" O GLN G 329 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N LEU G 331 " --> pdb=" O THR C 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 184 through 187 removed outlier: 6.480A pdb=" N SER C 187 " --> pdb=" O ILE C 192 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ILE C 192 " --> pdb=" O SER C 187 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LYS C 205 " --> pdb=" O ALA C 197 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ILE C 199 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE C 203 " --> pdb=" O ILE C 199 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 226 through 227 removed outlier: 6.850A pdb=" N ILE G 203 " --> pdb=" O ILE G 199 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ILE G 199 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LYS G 205 " --> pdb=" O ALA G 197 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ILE G 192 " --> pdb=" O SER G 187 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N SER G 187 " --> pdb=" O ILE G 192 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 235 through 243 removed outlier: 3.601A pdb=" N GLN C 280 " --> pdb=" O ASN C 287 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N MET C 289 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N PHE C 278 " --> pdb=" O MET C 289 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N TYR C 291 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N VAL C 276 " --> pdb=" O TYR C 291 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N PHE C 293 " --> pdb=" O LEU C 274 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N LEU C 274 " --> pdb=" O PHE C 293 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 184 through 187 removed outlier: 6.482A pdb=" N SER A 187 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ILE A 192 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LYS A 205 " --> pdb=" O ALA A 197 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ILE A 199 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE A 203 " --> pdb=" O ILE A 199 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 235 through 243 removed outlier: 3.602A pdb=" N GLN A 280 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N MET A 289 " --> pdb=" O PHE A 278 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N PHE A 278 " --> pdb=" O MET A 289 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N TYR A 291 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N VAL A 276 " --> pdb=" O TYR A 291 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N PHE A 293 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N LEU A 274 " --> pdb=" O PHE A 293 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 184 through 187 removed outlier: 6.481A pdb=" N SER B 187 " --> pdb=" O ILE B 192 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ILE B 192 " --> pdb=" O SER B 187 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LYS B 205 " --> pdb=" O ALA B 197 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N ILE B 199 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE B 203 " --> pdb=" O ILE B 199 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 235 through 243 removed outlier: 3.601A pdb=" N GLN B 280 " --> pdb=" O ASN B 287 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N MET B 289 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N PHE B 278 " --> pdb=" O MET B 289 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N TYR B 291 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N VAL B 276 " --> pdb=" O TYR B 291 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N PHE B 293 " --> pdb=" O LEU B 274 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N LEU B 274 " --> pdb=" O PHE B 293 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 235 through 243 removed outlier: 3.602A pdb=" N GLN D 280 " --> pdb=" O ASN D 287 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N MET D 289 " --> pdb=" O PHE D 278 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N PHE D 278 " --> pdb=" O MET D 289 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N TYR D 291 " --> pdb=" O VAL D 276 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N VAL D 276 " --> pdb=" O TYR D 291 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N PHE D 293 " --> pdb=" O LEU D 274 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N LEU D 274 " --> pdb=" O PHE D 293 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 184 through 187 removed outlier: 6.481A pdb=" N SER F 187 " --> pdb=" O ILE F 192 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ILE F 192 " --> pdb=" O SER F 187 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LYS F 205 " --> pdb=" O ALA F 197 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N ILE F 199 " --> pdb=" O ILE F 203 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE F 203 " --> pdb=" O ILE F 199 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 235 through 243 removed outlier: 3.602A pdb=" N GLN F 280 " --> pdb=" O ASN F 287 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N MET F 289 " --> pdb=" O PHE F 278 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N PHE F 278 " --> pdb=" O MET F 289 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N TYR F 291 " --> pdb=" O VAL F 276 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N VAL F 276 " --> pdb=" O TYR F 291 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N PHE F 293 " --> pdb=" O LEU F 274 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N LEU F 274 " --> pdb=" O PHE F 293 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 235 through 243 removed outlier: 3.603A pdb=" N GLN G 280 " --> pdb=" O ASN G 287 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N MET G 289 " --> pdb=" O PHE G 278 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N PHE G 278 " --> pdb=" O MET G 289 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N TYR G 291 " --> pdb=" O VAL G 276 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N VAL G 276 " --> pdb=" O TYR G 291 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N PHE G 293 " --> pdb=" O LEU G 274 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N LEU G 274 " --> pdb=" O PHE G 293 " (cutoff:3.500A) 1196 hydrogen bonds defined for protein. 3441 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: 7.33 Time building geometry restraints manager: 3.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 14476 1.02 - 1.21: 21 1.21 - 1.41: 6972 1.41 - 1.61: 10087 1.61 - 1.81: 140 Bond restraints: 31696 Sorted by residual: bond pdb=" SG CYS C 292 " pdb=" HG CYS C 292 " ideal model delta sigma weight residual 1.200 1.340 -0.140 2.00e-02 2.50e+03 4.92e+01 bond pdb=" SG CYS A 292 " pdb=" HG CYS A 292 " ideal model delta sigma weight residual 1.200 1.340 -0.140 2.00e-02 2.50e+03 4.91e+01 bond pdb=" SG CYS E 292 " pdb=" HG CYS E 292 " ideal model delta sigma weight residual 1.200 1.340 -0.140 2.00e-02 2.50e+03 4.90e+01 bond pdb=" SG CYS G 292 " pdb=" HG CYS G 292 " ideal model delta sigma weight residual 1.200 1.340 -0.140 2.00e-02 2.50e+03 4.89e+01 bond pdb=" SG CYS B 292 " pdb=" HG CYS B 292 " ideal model delta sigma weight residual 1.200 1.339 -0.139 2.00e-02 2.50e+03 4.85e+01 ... (remaining 31691 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.86: 55924 5.86 - 11.71: 76 11.71 - 17.57: 14 17.57 - 23.43: 7 23.43 - 29.29: 35 Bond angle restraints: 56056 Sorted by residual: angle pdb=" CG2 THR A 113 " pdb=" CB THR A 113 " pdb=" HB THR A 113 " ideal model delta sigma weight residual 108.00 78.71 29.29 3.00e+00 1.11e-01 9.53e+01 angle pdb=" CG2 THR D 113 " pdb=" CB THR D 113 " pdb=" HB THR D 113 " ideal model delta sigma weight residual 108.00 78.72 29.28 3.00e+00 1.11e-01 9.53e+01 angle pdb=" CG2 THR E 113 " pdb=" CB THR E 113 " pdb=" HB THR E 113 " ideal model delta sigma weight residual 108.00 78.75 29.25 3.00e+00 1.11e-01 9.51e+01 angle pdb=" CG2 THR C 113 " pdb=" CB THR C 113 " pdb=" HB THR C 113 " ideal model delta sigma weight residual 108.00 78.76 29.24 3.00e+00 1.11e-01 9.50e+01 angle pdb=" CG2 THR B 113 " pdb=" CB THR B 113 " pdb=" HB THR B 113 " ideal model delta sigma weight residual 108.00 78.77 29.23 3.00e+00 1.11e-01 9.50e+01 ... (remaining 56051 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.28: 14735 35.28 - 70.56: 469 70.56 - 105.84: 28 105.84 - 141.12: 21 141.12 - 176.40: 21 Dihedral angle restraints: 15274 sinusoidal: 7686 harmonic: 7588 Sorted by residual: dihedral pdb=" CA ILE G 192 " pdb=" C ILE G 192 " pdb=" N GLU G 193 " pdb=" CA GLU G 193 " ideal model delta harmonic sigma weight residual 180.00 -154.09 -25.91 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA ILE C 192 " pdb=" C ILE C 192 " pdb=" N GLU C 193 " pdb=" CA GLU C 193 " ideal model delta harmonic sigma weight residual -180.00 -154.09 -25.91 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA ILE A 192 " pdb=" C ILE A 192 " pdb=" N GLU A 193 " pdb=" CA GLU A 193 " ideal model delta harmonic sigma weight residual -180.00 -154.11 -25.89 0 5.00e+00 4.00e-02 2.68e+01 ... (remaining 15271 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.293: 2758 0.293 - 0.585: 0 0.585 - 0.878: 0 0.878 - 1.170: 0 1.170 - 1.463: 14 Chirality restraints: 2772 Sorted by residual: chirality pdb=" CB THR G 113 " pdb=" CA THR G 113 " pdb=" OG1 THR G 113 " pdb=" CG2 THR G 113 " both_signs ideal model delta sigma weight residual False 2.55 1.09 1.46 2.00e-01 2.50e+01 5.35e+01 chirality pdb=" CB THR C 113 " pdb=" CA THR C 113 " pdb=" OG1 THR C 113 " pdb=" CG2 THR C 113 " both_signs ideal model delta sigma weight residual False 2.55 1.09 1.46 2.00e-01 2.50e+01 5.32e+01 chirality pdb=" CB THR F 113 " pdb=" CA THR F 113 " pdb=" OG1 THR F 113 " pdb=" CG2 THR F 113 " both_signs ideal model delta sigma weight residual False 2.55 1.09 1.46 2.00e-01 2.50e+01 5.31e+01 ... (remaining 2769 not shown) Planarity restraints: 4662 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 282 " -0.014 2.00e-02 2.50e+03 2.75e-02 7.58e+00 pdb=" N ASP B 283 " 0.047 2.00e-02 2.50e+03 pdb=" CA ASP B 283 " -0.012 2.00e-02 2.50e+03 pdb=" H ASP B 283 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA F 282 " 0.014 2.00e-02 2.50e+03 2.75e-02 7.56e+00 pdb=" N ASP F 283 " -0.047 2.00e-02 2.50e+03 pdb=" CA ASP F 283 " 0.012 2.00e-02 2.50e+03 pdb=" H ASP F 283 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU F 133 " 0.014 2.00e-02 2.50e+03 2.74e-02 7.49e+00 pdb=" N TYR F 134 " -0.047 2.00e-02 2.50e+03 pdb=" CA TYR F 134 " 0.012 2.00e-02 2.50e+03 pdb=" H TYR F 134 " 0.021 2.00e-02 2.50e+03 ... (remaining 4659 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.12: 836 2.12 - 2.74: 55292 2.74 - 3.36: 82860 3.36 - 3.98: 108368 3.98 - 4.60: 172239 Nonbonded interactions: 419595 Sorted by model distance: nonbonded pdb="HD12 ILE E 268 " pdb=" HG CYS E 292 " model vdw 1.506 2.440 nonbonded pdb="HD12 ILE F 268 " pdb=" HG CYS F 292 " model vdw 1.528 2.440 nonbonded pdb=" HA3 GLY E 144 " pdb="HD23 LEU F 133 " model vdw 1.672 2.440 nonbonded pdb="HD23 LEU C 133 " pdb=" HA3 GLY G 144 " model vdw 1.678 2.440 nonbonded pdb="HD23 LEU E 133 " pdb=" HA3 GLY D 144 " model vdw 1.692 2.440 ... (remaining 419590 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: 0.07 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'C' selection = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'G' } 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: 0.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 0.530 Check model and map are aligned: 0.050 Set scattering table: 0.090 Process input model: 28.270 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 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 : 0.017 0.107 17206 Z= 0.674 Angle : 1.196 16.094 23310 Z= 0.630 Chirality : 0.120 1.463 2772 Planarity : 0.007 0.067 2926 Dihedral : 19.712 176.400 6055 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.12 (0.17), residues: 1778 helix: -1.47 (0.13), residues: 938 sheet: -2.68 (0.28), residues: 259 loop : -2.47 (0.24), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 235 TYR 0.015 0.002 TYR D 291 PHE 0.013 0.002 PHE E 148 TRP 0.013 0.003 TRP E 201 HIS 0.004 0.002 HIS B 265 Details of bonding type rmsd/Z covalent geometry : bond 0.01651 / 0.67 (17206) covalent geometry : angle 1.19596 / 0.63 (23310) hydrogen bonds : bond 0.13074 / 8.33 ( 1196) hydrogen bonds : angle 7.26045 / 4.79 ( 3441) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Evaluate side-chains 214 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.899 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 130 LEU cc_start: 0.8585 (mt) cc_final: 0.8195 (pp) REVERT: E 256 GLU cc_start: 0.7625 (tt0) cc_final: 0.7385 (mt-10) REVERT: C 130 LEU cc_start: 0.8507 (mt) cc_final: 0.8084 (pp) REVERT: C 198 GLU cc_start: 0.8406 (tt0) cc_final: 0.8168 (tt0) REVERT: C 232 MET cc_start: 0.8051 (ptt) cc_final: 0.7837 (ptt) REVERT: A 130 LEU cc_start: 0.8544 (mt) cc_final: 0.8125 (pp) REVERT: B 130 LEU cc_start: 0.8504 (mt) cc_final: 0.8111 (pp) REVERT: B 227 GLU cc_start: 0.8173 (tt0) cc_final: 0.7911 (tt0) REVERT: D 130 LEU cc_start: 0.8501 (mt) cc_final: 0.8146 (pp) REVERT: D 227 GLU cc_start: 0.8138 (tt0) cc_final: 0.7925 (tt0) REVERT: D 256 GLU cc_start: 0.7716 (tt0) cc_final: 0.7436 (mt-10) REVERT: F 130 LEU cc_start: 0.8604 (mt) cc_final: 0.8163 (pp) REVERT: G 130 LEU cc_start: 0.8558 (mt) cc_final: 0.8094 (pp) REVERT: G 256 GLU cc_start: 0.7730 (tt0) cc_final: 0.7486 (mt-10) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.9839 time to fit residues: 240.2632 Evaluate side-chains 128 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: [] chunk None optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 99 ASN E 329 GLN C 99 ASN C 329 GLN A 99 ASN A 329 GLN B 99 ASN B 329 GLN D 99 ASN D 329 GLN F 99 ASN F 329 GLN G 99 ASN G 329 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.117442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.076890 restraints weight = 94290.839| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.58 r_work: 0.3054 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 17206 Z= 0.241 Angle : 0.703 11.428 23310 Z= 0.377 Chirality : 0.107 1.436 2772 Planarity : 0.004 0.044 2926 Dihedral : 19.206 160.680 2723 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.90 % Allowed : 7.62 % Favored : 91.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.80 (0.19), residues: 1778 helix: 0.74 (0.15), residues: 931 sheet: -1.51 (0.31), residues: 238 loop : -2.07 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 116 TYR 0.013 0.001 TYR B 291 PHE 0.007 0.001 PHE C 324 TRP 0.006 0.001 TRP B 201 HIS 0.003 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.24 (17206) covalent geometry : angle 0.70308 / 0.38 (23310) hydrogen bonds : bond 0.04136 / 2.71 ( 1196) hydrogen bonds : angle 5.13878 / 3.40 ( 3441) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Evaluate side-chains 172 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 158 time to evaluate : 0.798 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: symmetry clash revert: symmetry clash REVERT: E 130 LEU cc_start: 0.8615 (mt) cc_final: 0.8270 (pp) REVERT: E 198 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8293 (tt0) REVERT: E 256 GLU cc_start: 0.8641 (tt0) cc_final: 0.8177 (tm-30) REVERT: C 118 MET cc_start: 0.7596 (tpt) cc_final: 0.7186 (tmm) REVERT: C 130 LEU cc_start: 0.8508 (mt) cc_final: 0.8148 (pp) REVERT: C 198 GLU cc_start: 0.9068 (tt0) cc_final: 0.8865 (pt0) REVERT: A 130 LEU cc_start: 0.8612 (mt) cc_final: 0.8233 (pp) REVERT: B 118 MET cc_start: 0.7742 (tpt) cc_final: 0.7540 (tpp) REVERT: B 130 LEU cc_start: 0.8541 (mt) cc_final: 0.8224 (pp) REVERT: B 227 GLU cc_start: 0.8851 (tt0) cc_final: 0.8613 (tt0) REVERT: B 256 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8331 (tm-30) REVERT: D 118 MET cc_start: 0.7468 (tpp) cc_final: 0.7119 (tmm) REVERT: D 130 LEU cc_start: 0.8616 (mt) cc_final: 0.8309 (pp) REVERT: D 256 GLU cc_start: 0.8733 (tt0) cc_final: 0.8252 (tm-30) REVERT: D 261 MET cc_start: 0.9217 (tmm) cc_final: 0.8993 (tmm) REVERT: F 118 MET cc_start: 0.7749 (tpt) cc_final: 0.7208 (tmm) REVERT: F 130 LEU cc_start: 0.8614 (mt) cc_final: 0.8275 (pp) REVERT: F 261 MET cc_start: 0.9354 (tmm) cc_final: 0.8995 (tmm) REVERT: G 118 MET cc_start: 0.7437 (tpp) cc_final: 0.7110 (tmm) REVERT: G 130 LEU cc_start: 0.8563 (mt) cc_final: 0.8229 (pp) REVERT: G 198 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8266 (tt0) REVERT: G 256 GLU cc_start: 0.8722 (tt0) cc_final: 0.8201 (tm-30) outliers start: 14 outliers final: 1 residues processed: 167 average time/residue: 1.0489 time to fit residues: 198.4448 Evaluate side-chains 142 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 139 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 198 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: [] chunk None optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 307 GLN C 307 GLN A 307 GLN B 307 GLN D 307 GLN F 307 GLN G 307 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.111924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.073234 restraints weight = 96894.731| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.39 r_work: 0.2963 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 17206 Z= 0.227 Angle : 0.674 11.768 23310 Z= 0.360 Chirality : 0.108 1.463 2772 Planarity : 0.004 0.051 2926 Dihedral : 16.665 149.492 2723 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.41 % Allowed : 9.42 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.28 (0.20), residues: 1778 helix: 1.73 (0.16), residues: 938 sheet: -1.47 (0.32), residues: 273 loop : -1.58 (0.24), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 116 TYR 0.011 0.001 TYR B 291 PHE 0.007 0.001 PHE C 324 TRP 0.006 0.001 TRP B 201 HIS 0.003 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.23 (17206) covalent geometry : angle 0.67420 / 0.36 (23310) hydrogen bonds : bond 0.03725 / 2.45 ( 1196) hydrogen bonds : angle 4.53570 / 3.01 ( 3441) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Evaluate side-chains 199 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 177 time to evaluate : 0.823 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: symmetry clash revert: symmetry clash REVERT: E 118 MET cc_start: 0.7788 (tpp) cc_final: 0.7186 (tmm) REVERT: E 130 LEU cc_start: 0.8717 (mt) cc_final: 0.8373 (pp) REVERT: C 118 MET cc_start: 0.7899 (tpt) cc_final: 0.7251 (tmm) REVERT: C 130 LEU cc_start: 0.8658 (mt) cc_final: 0.8370 (pp) REVERT: C 261 MET cc_start: 0.9240 (tmm) cc_final: 0.9032 (tmm) REVERT: A 130 LEU cc_start: 0.8653 (mt) cc_final: 0.8385 (pp) REVERT: A 261 MET cc_start: 0.9335 (tmm) cc_final: 0.9049 (tmm) REVERT: B 118 MET cc_start: 0.7925 (tpt) cc_final: 0.7699 (tpp) REVERT: B 130 LEU cc_start: 0.8622 (mt) cc_final: 0.8380 (pp) REVERT: B 227 GLU cc_start: 0.8654 (tt0) cc_final: 0.8434 (tt0) REVERT: B 256 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8522 (tm-30) REVERT: D 118 MET cc_start: 0.7723 (tpp) cc_final: 0.7272 (tmm) REVERT: D 130 LEU cc_start: 0.8685 (mt) cc_final: 0.8436 (pp) REVERT: D 198 GLU cc_start: 0.8618 (pt0) cc_final: 0.8293 (pp20) REVERT: D 261 MET cc_start: 0.9333 (tmm) cc_final: 0.9065 (tmm) REVERT: F 118 MET cc_start: 0.7893 (tpt) cc_final: 0.7484 (tpp) REVERT: F 130 LEU cc_start: 0.8728 (mt) cc_final: 0.8443 (pp) REVERT: G 130 LEU cc_start: 0.8676 (mt) cc_final: 0.8427 (pp) REVERT: G 256 GLU cc_start: 0.8738 (tt0) cc_final: 0.8431 (tm-30) outliers start: 22 outliers final: 2 residues processed: 192 average time/residue: 1.0146 time to fit residues: 221.5279 Evaluate side-chains 147 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 145 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain G residue 131 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: [] chunk None optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.3893 r_free = 0.3893 target = 0.112008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.072048 restraints weight = 98484.977| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.42 r_work: 0.2941 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17206 Z= 0.216 Angle : 0.652 11.786 23310 Z= 0.349 Chirality : 0.108 1.467 2772 Planarity : 0.003 0.037 2926 Dihedral : 15.738 156.410 2723 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.28 % Allowed : 11.40 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.79 (0.20), residues: 1778 helix: 2.13 (0.16), residues: 938 sheet: -0.51 (0.35), residues: 238 loop : -1.69 (0.22), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 235 TYR 0.011 0.001 TYR B 291 PHE 0.008 0.001 PHE D 168 TRP 0.005 0.001 TRP A 184 HIS 0.003 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.22 (17206) covalent geometry : angle 0.65161 / 0.35 (23310) hydrogen bonds : bond 0.03503 / 2.31 ( 1196) hydrogen bonds : angle 4.30303 / 2.86 ( 3441) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Evaluate side-chains 183 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 163 time to evaluate : 0.874 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: symmetry clash revert: symmetry clash REVERT: E 130 LEU cc_start: 0.8713 (mt) cc_final: 0.8353 (pp) REVERT: E 136 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7310 (pm20) REVERT: C 116 ARG cc_start: 0.8114 (ttt90) cc_final: 0.7876 (ttt90) REVERT: C 130 LEU cc_start: 0.8681 (mt) cc_final: 0.8432 (pp) REVERT: C 224 ILE cc_start: 0.8639 (OUTLIER) cc_final: 0.8310 (pt) REVERT: C 232 MET cc_start: 0.9061 (ptt) cc_final: 0.8752 (ptm) REVERT: C 333 MET cc_start: 0.8870 (mmm) cc_final: 0.8662 (mmm) REVERT: A 130 LEU cc_start: 0.8611 (mt) cc_final: 0.8334 (pp) REVERT: A 224 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8316 (pt) REVERT: A 261 MET cc_start: 0.9331 (tmm) cc_final: 0.9000 (tmm) REVERT: B 118 MET cc_start: 0.8038 (tpt) cc_final: 0.7806 (tpp) REVERT: B 130 LEU cc_start: 0.8568 (mt) cc_final: 0.8331 (pp) REVERT: B 224 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8342 (pt) REVERT: B 227 GLU cc_start: 0.8695 (tt0) cc_final: 0.8481 (tt0) REVERT: B 256 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8557 (tm-30) REVERT: D 198 GLU cc_start: 0.8738 (pt0) cc_final: 0.8393 (pp20) REVERT: F 118 MET cc_start: 0.7829 (tpt) cc_final: 0.7197 (tmm) REVERT: F 130 LEU cc_start: 0.8710 (mt) cc_final: 0.8402 (pp) REVERT: F 224 ILE cc_start: 0.8610 (OUTLIER) cc_final: 0.8282 (pt) REVERT: G 118 MET cc_start: 0.7924 (tpp) cc_final: 0.7415 (tmm) REVERT: G 130 LEU cc_start: 0.8643 (mt) cc_final: 0.8352 (pp) REVERT: G 224 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8365 (pt) REVERT: G 256 GLU cc_start: 0.8791 (tt0) cc_final: 0.8497 (tm-30) outliers start: 20 outliers final: 1 residues processed: 177 average time/residue: 0.9209 time to fit residues: 188.0673 Evaluate side-chains 157 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 150 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain G residue 224 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: [] chunk None optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.3902 r_free = 0.3902 target = 0.111977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.072216 restraints weight = 101239.198| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.35 r_work: 0.2977 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 17206 Z= 0.214 Angle : 0.651 11.770 23310 Z= 0.347 Chirality : 0.108 1.457 2772 Planarity : 0.003 0.031 2926 Dihedral : 15.153 157.075 2723 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.09 % Allowed : 12.36 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.97 (0.20), residues: 1778 helix: 2.28 (0.16), residues: 931 sheet: -1.08 (0.33), residues: 273 loop : -1.25 (0.23), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 235 TYR 0.011 0.001 TYR B 291 PHE 0.025 0.001 PHE F 138 TRP 0.004 0.001 TRP G 201 HIS 0.003 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.21 (17206) covalent geometry : angle 0.65070 / 0.35 (23310) hydrogen bonds : bond 0.03418 / 2.25 ( 1196) hydrogen bonds : angle 4.18064 / 2.78 ( 3441) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Evaluate side-chains 179 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 162 time to evaluate : 0.996 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 118 MET cc_start: 0.7955 (tpt) cc_final: 0.7109 (tmm) REVERT: E 130 LEU cc_start: 0.8756 (mt) cc_final: 0.8428 (pp) REVERT: E 145 LEU cc_start: 0.7385 (OUTLIER) cc_final: 0.7118 (mp) REVERT: E 148 PHE cc_start: 0.8838 (t80) cc_final: 0.8529 (t80) REVERT: C 116 ARG cc_start: 0.8143 (ttt90) cc_final: 0.7913 (ttt90) REVERT: C 118 MET cc_start: 0.8130 (tpt) cc_final: 0.7304 (tmm) REVERT: C 130 LEU cc_start: 0.8692 (mt) cc_final: 0.8444 (pp) REVERT: C 142 LEU cc_start: 0.7891 (tt) cc_final: 0.7650 (tm) REVERT: C 198 GLU cc_start: 0.8845 (pt0) cc_final: 0.8512 (pp20) REVERT: C 224 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8406 (pt) REVERT: C 232 MET cc_start: 0.9080 (ptt) cc_final: 0.8822 (ptm) REVERT: A 130 LEU cc_start: 0.8656 (mt) cc_final: 0.8390 (pp) REVERT: A 148 PHE cc_start: 0.9030 (t80) cc_final: 0.8673 (t80) REVERT: A 261 MET cc_start: 0.9292 (tmm) cc_final: 0.8993 (tmm) REVERT: B 116 ARG cc_start: 0.8288 (mtp-110) cc_final: 0.7406 (ttt90) REVERT: B 118 MET cc_start: 0.8107 (tpt) cc_final: 0.7868 (tpp) REVERT: B 130 LEU cc_start: 0.8634 (mt) cc_final: 0.8411 (pp) REVERT: B 198 GLU cc_start: 0.8768 (pt0) cc_final: 0.8197 (pp20) REVERT: D 118 MET cc_start: 0.7896 (tpp) cc_final: 0.7317 (tmm) REVERT: D 198 GLU cc_start: 0.8841 (pt0) cc_final: 0.8494 (pp20) REVERT: D 261 MET cc_start: 0.9305 (tmm) cc_final: 0.9065 (tmm) REVERT: F 118 MET cc_start: 0.7918 (tpt) cc_final: 0.7603 (tpp) REVERT: F 130 LEU cc_start: 0.8739 (mt) cc_final: 0.8532 (pp) REVERT: G 130 LEU cc_start: 0.8720 (mt) cc_final: 0.8456 (pp) REVERT: G 224 ILE cc_start: 0.8775 (OUTLIER) cc_final: 0.8409 (pt) REVERT: G 256 GLU cc_start: 0.8861 (tt0) cc_final: 0.8625 (tm-30) REVERT: G 261 MET cc_start: 0.9221 (tmm) cc_final: 0.8901 (tmm) outliers start: 17 outliers final: 4 residues processed: 176 average time/residue: 0.9332 time to fit residues: 189.1529 Evaluate side-chains 157 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 150 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 224 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: [] chunk None optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.3895 r_free = 0.3895 target = 0.111659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.072079 restraints weight = 100893.995| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.36 r_work: 0.2972 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 17206 Z= 0.211 Angle : 0.649 11.807 23310 Z= 0.346 Chirality : 0.108 1.468 2772 Planarity : 0.003 0.024 2926 Dihedral : 14.862 159.281 2723 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.96 % Allowed : 13.26 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.95 (0.20), residues: 1778 helix: 2.41 (0.16), residues: 931 sheet: -1.67 (0.29), residues: 357 loop : -1.01 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 235 TYR 0.010 0.001 TYR B 291 PHE 0.006 0.001 PHE F 209 TRP 0.007 0.001 TRP F 184 HIS 0.003 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.21 (17206) covalent geometry : angle 0.64863 / 0.35 (23310) hydrogen bonds : bond 0.03343 / 2.21 ( 1196) hydrogen bonds : angle 4.12608 / 2.75 ( 3441) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Evaluate side-chains 186 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 171 time to evaluate : 0.765 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: E 130 LEU cc_start: 0.8710 (mt) cc_final: 0.8434 (pp) REVERT: E 140 MET cc_start: 0.7515 (mmm) cc_final: 0.7294 (mmt) REVERT: E 145 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.7117 (mp) REVERT: E 148 PHE cc_start: 0.8867 (t80) cc_final: 0.8555 (t80) REVERT: C 116 ARG cc_start: 0.8166 (ttt90) cc_final: 0.7869 (ttt90) REVERT: C 130 LEU cc_start: 0.8699 (mt) cc_final: 0.8447 (pp) REVERT: C 142 LEU cc_start: 0.7889 (tt) cc_final: 0.7645 (tm) REVERT: C 148 PHE cc_start: 0.8849 (t80) cc_final: 0.8610 (t80) REVERT: C 198 GLU cc_start: 0.8864 (pt0) cc_final: 0.8512 (pp20) REVERT: C 232 MET cc_start: 0.9118 (ptt) cc_final: 0.8895 (ptm) REVERT: C 261 MET cc_start: 0.9256 (tmm) cc_final: 0.8995 (tmm) REVERT: A 130 LEU cc_start: 0.8590 (mt) cc_final: 0.8320 (pp) REVERT: A 148 PHE cc_start: 0.9037 (t80) cc_final: 0.8752 (t80) REVERT: B 116 ARG cc_start: 0.8276 (mtp-110) cc_final: 0.7423 (ttt90) REVERT: B 118 MET cc_start: 0.8124 (tpt) cc_final: 0.7848 (tpp) REVERT: B 130 LEU cc_start: 0.8650 (mt) cc_final: 0.8425 (pp) REVERT: B 148 PHE cc_start: 0.9038 (t80) cc_final: 0.8730 (t80) REVERT: B 198 GLU cc_start: 0.8784 (pt0) cc_final: 0.8241 (pp20) REVERT: D 198 GLU cc_start: 0.8862 (pt0) cc_final: 0.8500 (pp20) REVERT: F 118 MET cc_start: 0.7875 (tpt) cc_final: 0.7455 (tpp) REVERT: F 130 LEU cc_start: 0.8737 (mt) cc_final: 0.8533 (pp) REVERT: F 148 PHE cc_start: 0.8972 (t80) cc_final: 0.8650 (t80) REVERT: G 118 MET cc_start: 0.7994 (tpp) cc_final: 0.7408 (tmm) REVERT: G 130 LEU cc_start: 0.8694 (mt) cc_final: 0.8386 (pp) REVERT: G 224 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8391 (pt) REVERT: G 256 GLU cc_start: 0.8857 (tt0) cc_final: 0.8614 (tm-30) outliers start: 15 outliers final: 7 residues processed: 182 average time/residue: 0.8971 time to fit residues: 189.4391 Evaluate side-chains 157 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 148 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain G residue 224 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: [] chunk None optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.3893 r_free = 0.3893 target = 0.111555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.072060 restraints weight = 101821.744| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.38 r_work: 0.2966 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.4762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 17206 Z= 0.209 Angle : 0.655 11.792 23310 Z= 0.348 Chirality : 0.108 1.470 2772 Planarity : 0.003 0.025 2926 Dihedral : 14.612 159.002 2723 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.09 % Allowed : 14.16 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.07 (0.20), residues: 1778 helix: 2.54 (0.16), residues: 924 sheet: -1.66 (0.29), residues: 357 loop : -0.93 (0.25), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 202 TYR 0.011 0.001 TYR B 291 PHE 0.029 0.001 PHE G 138 TRP 0.008 0.001 TRP D 184 HIS 0.003 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.21 (17206) covalent geometry : angle 0.65548 / 0.35 (23310) hydrogen bonds : bond 0.03308 / 2.18 ( 1196) hydrogen bonds : angle 4.09783 / 2.72 ( 3441) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Evaluate side-chains 180 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 163 time to evaluate : 0.839 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: symmetry clash REVERT: E 130 LEU cc_start: 0.8698 (mt) cc_final: 0.8434 (pp) REVERT: E 145 LEU cc_start: 0.7393 (OUTLIER) cc_final: 0.7127 (mp) REVERT: E 148 PHE cc_start: 0.8885 (t80) cc_final: 0.8658 (t80) REVERT: C 116 ARG cc_start: 0.8187 (ttt90) cc_final: 0.7911 (ttt90) REVERT: C 130 LEU cc_start: 0.8706 (mt) cc_final: 0.8450 (pp) REVERT: C 142 LEU cc_start: 0.7761 (tt) cc_final: 0.7536 (tm) REVERT: C 148 PHE cc_start: 0.8873 (t80) cc_final: 0.8665 (t80) REVERT: C 198 GLU cc_start: 0.8858 (pt0) cc_final: 0.8505 (pp20) REVERT: C 261 MET cc_start: 0.9259 (tmm) cc_final: 0.8997 (tmm) REVERT: A 130 LEU cc_start: 0.8575 (mt) cc_final: 0.8340 (pp) REVERT: A 148 PHE cc_start: 0.9048 (t80) cc_final: 0.8777 (t80) REVERT: B 116 ARG cc_start: 0.8268 (mtp-110) cc_final: 0.7403 (ttt90) REVERT: B 118 MET cc_start: 0.8078 (tpt) cc_final: 0.7839 (tpp) REVERT: B 142 LEU cc_start: 0.7749 (tt) cc_final: 0.7529 (tm) REVERT: B 148 PHE cc_start: 0.9058 (t80) cc_final: 0.8778 (t80) REVERT: B 198 GLU cc_start: 0.8790 (pt0) cc_final: 0.8241 (pp20) REVERT: B 224 ILE cc_start: 0.8793 (OUTLIER) cc_final: 0.8383 (pt) REVERT: D 118 MET cc_start: 0.7912 (tpp) cc_final: 0.7321 (tmm) REVERT: D 148 PHE cc_start: 0.9054 (t80) cc_final: 0.8787 (t80) REVERT: D 198 GLU cc_start: 0.8868 (pt0) cc_final: 0.8500 (pp20) REVERT: F 118 MET cc_start: 0.7888 (tpt) cc_final: 0.7529 (tpp) REVERT: F 142 LEU cc_start: 0.7786 (tt) cc_final: 0.7576 (tm) REVERT: F 148 PHE cc_start: 0.8996 (t80) cc_final: 0.8710 (t80) REVERT: F 224 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8332 (pt) REVERT: G 118 MET cc_start: 0.8039 (tpp) cc_final: 0.7428 (tmm) REVERT: G 130 LEU cc_start: 0.8773 (mt) cc_final: 0.8536 (pp) REVERT: G 148 PHE cc_start: 0.8901 (t80) cc_final: 0.8701 (t80) REVERT: G 224 ILE cc_start: 0.8769 (OUTLIER) cc_final: 0.8395 (pt) REVERT: G 256 GLU cc_start: 0.8855 (tt0) cc_final: 0.8623 (tm-30) outliers start: 17 outliers final: 6 residues processed: 179 average time/residue: 0.8947 time to fit residues: 186.0934 Evaluate side-chains 157 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 147 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain G residue 224 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: [] chunk None optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.3870 r_free = 0.3870 target = 0.111416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.071986 restraints weight = 99562.178| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.46 r_work: 0.2949 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.4960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 17206 Z= 0.209 Angle : 0.657 11.801 23310 Z= 0.348 Chirality : 0.108 1.468 2772 Planarity : 0.002 0.020 2926 Dihedral : 14.486 160.738 2723 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.83 % Allowed : 15.37 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.17 (0.20), residues: 1778 helix: 2.56 (0.16), residues: 924 sheet: -1.17 (0.30), residues: 322 loop : -1.18 (0.24), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 235 TYR 0.010 0.001 TYR B 291 PHE 0.019 0.001 PHE B 138 TRP 0.006 0.001 TRP E 184 HIS 0.003 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.21 (17206) covalent geometry : angle 0.65656 / 0.35 (23310) hydrogen bonds : bond 0.03286 / 2.17 ( 1196) hydrogen bonds : angle 4.08320 / 2.72 ( 3441) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Evaluate side-chains 165 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 152 time to evaluate : 0.885 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: symmetry clash REVERT: E 130 LEU cc_start: 0.8653 (mt) cc_final: 0.8379 (pp) REVERT: E 138 PHE cc_start: 0.7508 (m-80) cc_final: 0.7274 (m-80) REVERT: E 301 GLU cc_start: 0.9051 (OUTLIER) cc_final: 0.8795 (mt-10) REVERT: C 116 ARG cc_start: 0.8192 (ttt90) cc_final: 0.7896 (ttt90) REVERT: C 118 MET cc_start: 0.8032 (tpt) cc_final: 0.7825 (tpt) REVERT: C 130 LEU cc_start: 0.8687 (mt) cc_final: 0.8434 (pp) REVERT: C 142 LEU cc_start: 0.7768 (tt) cc_final: 0.7541 (tm) REVERT: C 198 GLU cc_start: 0.8836 (pt0) cc_final: 0.8439 (pp20) REVERT: C 261 MET cc_start: 0.9280 (tmm) cc_final: 0.8969 (tmm) REVERT: A 130 LEU cc_start: 0.8570 (mt) cc_final: 0.8330 (pp) REVERT: A 148 PHE cc_start: 0.9048 (t80) cc_final: 0.8814 (t80) REVERT: B 116 ARG cc_start: 0.8263 (mtp-110) cc_final: 0.7420 (ttt90) REVERT: B 118 MET cc_start: 0.8059 (tpt) cc_final: 0.7823 (tpp) REVERT: B 148 PHE cc_start: 0.9068 (t80) cc_final: 0.8817 (t80) REVERT: B 198 GLU cc_start: 0.8786 (pt0) cc_final: 0.8160 (pp20) REVERT: B 224 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8297 (pt) REVERT: D 148 PHE cc_start: 0.9041 (t80) cc_final: 0.8806 (t80) REVERT: D 198 GLU cc_start: 0.8887 (pt0) cc_final: 0.8474 (pp20) REVERT: F 118 MET cc_start: 0.7832 (tpt) cc_final: 0.7477 (tpp) REVERT: F 148 PHE cc_start: 0.9001 (t80) cc_final: 0.8733 (t80) REVERT: G 130 LEU cc_start: 0.8676 (mt) cc_final: 0.8455 (pp) REVERT: G 224 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8299 (pt) REVERT: G 256 GLU cc_start: 0.8769 (tt0) cc_final: 0.8492 (tm-30) outliers start: 13 outliers final: 7 residues processed: 163 average time/residue: 0.9419 time to fit residues: 176.4181 Evaluate side-chains 156 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 146 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 301 GLU Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain G residue 224 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: [] chunk None optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.3867 r_free = 0.3867 target = 0.111311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.071952 restraints weight = 99559.183| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.43 r_work: 0.2940 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.5119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 17206 Z= 0.208 Angle : 0.665 11.794 23310 Z= 0.351 Chirality : 0.108 1.466 2772 Planarity : 0.002 0.021 2926 Dihedral : 14.363 162.846 2723 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.96 % Allowed : 16.02 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.20 (0.20), residues: 1778 helix: 2.59 (0.16), residues: 924 sheet: -1.28 (0.30), residues: 329 loop : -1.09 (0.24), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 116 TYR 0.010 0.001 TYR B 291 PHE 0.021 0.001 PHE E 148 TRP 0.005 0.001 TRP G 299 HIS 0.003 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.21 (17206) covalent geometry : angle 0.66493 / 0.35 (23310) hydrogen bonds : bond 0.03260 / 2.15 ( 1196) hydrogen bonds : angle 4.05765 / 2.70 ( 3441) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Evaluate side-chains 167 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 152 time to evaluate : 0.800 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: E 130 LEU cc_start: 0.8673 (mt) cc_final: 0.8415 (pp) REVERT: E 138 PHE cc_start: 0.7424 (m-80) cc_final: 0.7187 (m-80) REVERT: E 301 GLU cc_start: 0.9073 (OUTLIER) cc_final: 0.8817 (mt-10) REVERT: C 116 ARG cc_start: 0.8218 (ttt90) cc_final: 0.7938 (ttt90) REVERT: C 130 LEU cc_start: 0.8683 (mt) cc_final: 0.8413 (pp) REVERT: C 198 GLU cc_start: 0.8828 (pt0) cc_final: 0.8420 (pp20) REVERT: C 261 MET cc_start: 0.9288 (tmm) cc_final: 0.8954 (tmm) REVERT: A 130 LEU cc_start: 0.8589 (mt) cc_final: 0.8363 (pp) REVERT: A 148 PHE cc_start: 0.9016 (t80) cc_final: 0.8774 (t80) REVERT: B 116 ARG cc_start: 0.8268 (mtp-110) cc_final: 0.7423 (ttt90) REVERT: B 118 MET cc_start: 0.8084 (tpt) cc_final: 0.7856 (tpp) REVERT: B 142 LEU cc_start: 0.7730 (tt) cc_final: 0.7526 (tm) REVERT: B 148 PHE cc_start: 0.9078 (t80) cc_final: 0.8809 (t80) REVERT: B 198 GLU cc_start: 0.8795 (pt0) cc_final: 0.8164 (pp20) REVERT: B 224 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8307 (pt) REVERT: D 148 PHE cc_start: 0.9043 (t80) cc_final: 0.8826 (t80) REVERT: D 198 GLU cc_start: 0.8882 (pt0) cc_final: 0.8470 (pp20) REVERT: F 118 MET cc_start: 0.7839 (tpt) cc_final: 0.7500 (tpp) REVERT: F 148 PHE cc_start: 0.9028 (t80) cc_final: 0.8803 (t80) REVERT: G 118 MET cc_start: 0.7947 (tpp) cc_final: 0.7414 (tmt) REVERT: G 130 LEU cc_start: 0.8687 (mt) cc_final: 0.8430 (pp) REVERT: G 224 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8232 (pt) REVERT: G 256 GLU cc_start: 0.8769 (tt0) cc_final: 0.8494 (tm-30) outliers start: 15 outliers final: 6 residues processed: 164 average time/residue: 0.9329 time to fit residues: 176.5637 Evaluate side-chains 154 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 145 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 301 GLU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain G residue 224 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: [] chunk None optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.3865 r_free = 0.3865 target = 0.111220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.071883 restraints weight = 99578.711| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.42 r_work: 0.2937 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.5250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 17206 Z= 0.208 Angle : 0.668 11.832 23310 Z= 0.352 Chirality : 0.109 1.475 2772 Planarity : 0.002 0.021 2926 Dihedral : 14.284 162.107 2723 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.77 % Allowed : 16.66 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.17 (0.20), residues: 1778 helix: 2.55 (0.16), residues: 924 sheet: -1.28 (0.30), residues: 329 loop : -1.07 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 116 TYR 0.011 0.001 TYR B 291 PHE 0.023 0.001 PHE C 138 TRP 0.005 0.001 TRP G 299 HIS 0.004 0.001 HIS C 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.21 (17206) covalent geometry : angle 0.66770 / 0.35 (23310) hydrogen bonds : bond 0.03250 / 2.14 ( 1196) hydrogen bonds : angle 4.05247 / 2.69 ( 3441) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Residue LYS 205 is missing expected H atoms. Skipping. Evaluate side-chains 161 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 149 time to evaluate : 0.901 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: symmetry clash revert: symmetry clash REVERT: E 118 MET cc_start: 0.8035 (tpt) cc_final: 0.7652 (tpp) REVERT: E 130 LEU cc_start: 0.8649 (mt) cc_final: 0.8442 (pp) REVERT: C 116 ARG cc_start: 0.8260 (ttt90) cc_final: 0.7987 (ttt90) REVERT: C 198 GLU cc_start: 0.8835 (pt0) cc_final: 0.8424 (pp20) REVERT: C 261 MET cc_start: 0.9289 (tmm) cc_final: 0.8946 (tmm) REVERT: A 130 LEU cc_start: 0.8573 (mt) cc_final: 0.8329 (pp) REVERT: B 116 ARG cc_start: 0.8267 (mtp-110) cc_final: 0.7422 (ttt90) REVERT: B 118 MET cc_start: 0.8066 (tpt) cc_final: 0.7857 (tpp) REVERT: B 142 LEU cc_start: 0.7737 (tt) cc_final: 0.7534 (tm) REVERT: B 148 PHE cc_start: 0.9065 (t80) cc_final: 0.8814 (t80) REVERT: B 198 GLU cc_start: 0.8803 (pt0) cc_final: 0.8171 (pp20) REVERT: B 224 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8301 (pt) REVERT: D 148 PHE cc_start: 0.9037 (t80) cc_final: 0.8830 (t80) REVERT: D 198 GLU cc_start: 0.8883 (pt0) cc_final: 0.8467 (pp20) REVERT: F 118 MET cc_start: 0.7838 (tpt) cc_final: 0.7504 (tpp) REVERT: G 118 MET cc_start: 0.7931 (tpp) cc_final: 0.7368 (tmm) REVERT: G 130 LEU cc_start: 0.8679 (mt) cc_final: 0.8433 (pp) REVERT: G 224 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8248 (pt) REVERT: G 256 GLU cc_start: 0.8769 (tt0) cc_final: 0.8492 (tm-30) outliers start: 12 outliers final: 6 residues processed: 159 average time/residue: 0.9564 time to fit residues: 175.2659 Evaluate side-chains 151 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 143 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain G residue 224 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: [] chunk None optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.3866 r_free = 0.3866 target = 0.111303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.072025 restraints weight = 99769.788| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.43 r_work: 0.2945 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.5362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 17206 Z= 0.208 Angle : 0.669 11.812 23310 Z= 0.352 Chirality : 0.109 1.471 2772 Planarity : 0.002 0.021 2926 Dihedral : 14.102 158.993 2723 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.90 % Allowed : 16.85 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.16 (0.20), residues: 1778 helix: 2.53 (0.16), residues: 924 sheet: -1.27 (0.30), residues: 329 loop : -1.07 (0.24), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 116 TYR 0.011 0.001 TYR B 291 PHE 0.024 0.001 PHE C 138 TRP 0.004 0.001 TRP G 299 HIS 0.003 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.21 (17206) covalent geometry : angle 0.66880 / 0.35 (23310) hydrogen bonds : bond 0.03241 / 2.13 ( 1196) hydrogen bonds : angle 4.05710 / 2.69 ( 3441) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11405.74 seconds wall clock time: 193 minutes 5.91 seconds (11585.91 seconds total)