Starting phenix.real_space_refine on Tue Aug 26 07:22:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zyd_11557/08_2025/6zyd_11557_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zyd_11557/08_2025/6zyd_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_11557/08_2025/6zyd_11557.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zyd_11557/08_2025/6zyd_11557.map" model { file = "/net/cci-nas-00/data/ceres_data/6zyd_11557/08_2025/6zyd_11557_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zyd_11557/08_2025/6zyd_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-2.0-5787/lib/python3.9/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: 4.83, per 1000 atoms: 0.15 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: 1.85 Conformation dependent library (CDL) restraints added in 863.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.56 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: 5.73 Time building geometry restraints manager: 2.78 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: 0.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.140 Extract box with map and model: 0.290 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 24.170 Find NCS groups from input model: 0.230 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:6.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 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 aren 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 covalent geometry : bond 0.01651 (17206) covalent geometry : angle 1.19596 (23310) hydrogen bonds : bond 0.13074 ( 1196) hydrogen bonds : angle 7.26045 ( 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 : 0.561 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: 1.0016 time to fit residues: 241.3420 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 : 0.656 ------------------------------------------------------------------------------- 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: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 99 ASN E 272 GLN E 307 GLN E 329 GLN C 272 GLN C 307 GLN C 329 GLN A 272 GLN A 307 GLN A 329 GLN B 272 GLN B 307 GLN B 329 GLN D 272 GLN D 307 GLN D 329 GLN F 272 GLN F 307 GLN F 329 GLN G 99 ASN G 272 GLN G 307 GLN G 329 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.102947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.063899 restraints weight = 105380.140| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 2.50 r_work: 0.2750 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.5223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.049 0.265 17206 Z= 2.139 Angle : 1.924 12.858 23310 Z= 1.063 Chirality : 0.168 1.503 2772 Planarity : 0.012 0.092 2926 Dihedral : 21.623 176.740 2723 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 31.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 5.89 % Allowed : 16.46 % Favored : 77.64 % 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 aren not related in a simple way. whole: -4.40 (0.15), residues: 1778 helix: -2.48 (0.13), residues: 973 sheet: -2.40 (0.35), residues: 189 loop : -3.55 (0.17), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.003 ARG C 235 TYR 0.036 0.006 TYR B 291 PHE 0.028 0.005 PHE C 138 TRP 0.047 0.009 TRP A 302 HIS 0.008 0.003 HIS A 265 Details of bonding type rmsd covalent geometry : bond 0.04940 (17206) covalent geometry : angle 1.92384 (23310) hydrogen bonds : bond 0.09039 ( 1196) hydrogen bonds : angle 8.44414 ( 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 273 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 181 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 198 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.8768 (tt0) REVERT: E 256 GLU cc_start: 0.8927 (tt0) cc_final: 0.8615 (tm-30) REVERT: C 118 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7910 (tpp) REVERT: C 198 GLU cc_start: 0.9257 (tt0) cc_final: 0.8738 (tm-30) REVERT: C 232 MET cc_start: 0.9494 (ptt) cc_final: 0.9246 (ptm) REVERT: A 158 MET cc_start: 0.8856 (OUTLIER) cc_final: 0.8460 (mtm) REVERT: B 198 GLU cc_start: 0.9095 (pt0) cc_final: 0.8521 (pp20) REVERT: B 227 GLU cc_start: 0.9117 (tt0) cc_final: 0.8891 (tt0) REVERT: B 256 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8342 (tm-30) REVERT: D 198 GLU cc_start: 0.9070 (pt0) cc_final: 0.8563 (pp20) REVERT: D 232 MET cc_start: 0.9478 (ptt) cc_final: 0.9143 (ptt) REVERT: D 256 GLU cc_start: 0.8927 (tt0) cc_final: 0.8495 (tm-30) REVERT: F 118 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7802 (tpt) REVERT: G 256 GLU cc_start: 0.8929 (tt0) cc_final: 0.8539 (tm-30) outliers start: 92 outliers final: 54 residues processed: 251 average time/residue: 0.7738 time to fit residues: 225.6379 Evaluate side-chains 232 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 174 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 223 SER Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain F residue 195 THR Chi-restraints excluded: chain F residue 198 GLU Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 210 ASP Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 246 GLU Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain G residue 198 GLU Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 210 ASP Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 233 THR Chi-restraints excluded: chain G residue 313 ILE Chi-restraints excluded: chain G residue 314 ILE 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: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.098235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.061679 restraints weight = 109988.359| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 2.44 r_work: 0.2681 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2579 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.6294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.049 0.265 17206 Z= 2.136 Angle : 1.913 13.633 23310 Z= 1.056 Chirality : 0.170 1.515 2772 Planarity : 0.011 0.085 2926 Dihedral : 20.762 176.603 2723 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 33.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 12.94 % Favored : 87.01 % Rotamer: Outliers : 13.65 % Allowed : 16.66 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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 aren not related in a simple way. whole: -4.91 (0.15), residues: 1778 helix: -3.00 (0.12), residues: 980 sheet: -2.71 (0.27), residues: 259 loop : -3.55 (0.19), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG B 231 TYR 0.033 0.006 TYR D 291 PHE 0.028 0.005 PHE B 221 TRP 0.044 0.008 TRP F 302 HIS 0.008 0.003 HIS F 320 Details of bonding type rmsd covalent geometry : bond 0.04941 (17206) covalent geometry : angle 1.91341 (23310) hydrogen bonds : bond 0.09106 ( 1196) hydrogen bonds : angle 8.77905 ( 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 381 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 213 poor density : 168 time to evaluate : 0.718 Fit side-chains revert: symmetry clash REVERT: E 148 PHE cc_start: 0.9097 (t80) cc_final: 0.8870 (t80) REVERT: E 274 LEU cc_start: 0.9510 (OUTLIER) cc_final: 0.9304 (tp) REVERT: C 111 ASP cc_start: 0.8505 (OUTLIER) cc_final: 0.8233 (t70) REVERT: C 118 MET cc_start: 0.8170 (tpt) cc_final: 0.7812 (tpp) REVERT: C 198 GLU cc_start: 0.9190 (tt0) cc_final: 0.8822 (tm-30) REVERT: A 158 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8608 (mtm) REVERT: A 198 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8652 (tt0) REVERT: A 274 LEU cc_start: 0.9545 (OUTLIER) cc_final: 0.9129 (tp) REVERT: B 158 MET cc_start: 0.9013 (OUTLIER) cc_final: 0.8762 (mtm) REVERT: B 198 GLU cc_start: 0.9153 (pt0) cc_final: 0.8649 (pp20) REVERT: B 199 ILE cc_start: 0.9699 (OUTLIER) cc_final: 0.9387 (mm) REVERT: B 227 GLU cc_start: 0.8861 (tt0) cc_final: 0.8643 (tt0) REVERT: B 256 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8527 (tm-30) REVERT: D 111 ASP cc_start: 0.8445 (OUTLIER) cc_final: 0.8234 (t0) REVERT: D 140 MET cc_start: 0.8059 (mmm) cc_final: 0.7737 (mpt) REVERT: D 198 GLU cc_start: 0.9050 (pt0) cc_final: 0.8616 (pp20) REVERT: D 256 GLU cc_start: 0.8904 (tt0) cc_final: 0.8583 (tm-30) REVERT: F 118 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.7838 (tpt) REVERT: F 199 ILE cc_start: 0.9685 (OUTLIER) cc_final: 0.9388 (mm) REVERT: F 232 MET cc_start: 0.9469 (ptt) cc_final: 0.9212 (ptm) REVERT: F 256 GLU cc_start: 0.9048 (OUTLIER) cc_final: 0.8635 (tp30) REVERT: F 274 LEU cc_start: 0.9518 (OUTLIER) cc_final: 0.9135 (tp) REVERT: G 111 ASP cc_start: 0.8453 (OUTLIER) cc_final: 0.8152 (t70) REVERT: G 256 GLU cc_start: 0.8969 (tt0) cc_final: 0.8681 (tm-30) outliers start: 213 outliers final: 109 residues processed: 342 average time/residue: 0.5684 time to fit residues: 238.5281 Evaluate side-chains 285 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 163 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 211 ASN Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 223 SER Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 319 SER Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain F residue 195 THR Chi-restraints excluded: chain F residue 198 GLU Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 210 ASP Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 292 CYS Chi-restraints excluded: chain F residue 294 THR Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 165 SER Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 210 ASP Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain G residue 319 SER 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: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.096976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.060423 restraints weight = 110565.610| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 2.49 r_work: 0.2681 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2578 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.6785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.049 0.263 17206 Z= 2.134 Angle : 1.888 12.495 23310 Z= 1.047 Chirality : 0.168 1.542 2772 Planarity : 0.012 0.091 2926 Dihedral : 20.770 173.774 2723 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 37.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.45 % Favored : 85.55 % Rotamer: Outliers : 13.84 % Allowed : 18.26 % Favored : 67.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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 aren not related in a simple way. whole: -5.33 (0.15), residues: 1778 helix: -3.22 (0.12), residues: 994 sheet: -3.11 (0.28), residues: 217 loop : -3.87 (0.20), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG D 231 TYR 0.032 0.006 TYR D 291 PHE 0.052 0.005 PHE B 101 TRP 0.042 0.008 TRP F 302 HIS 0.011 0.003 HIS F 320 Details of bonding type rmsd covalent geometry : bond 0.04933 (17206) covalent geometry : angle 1.88813 (23310) hydrogen bonds : bond 0.09207 ( 1196) hydrogen bonds : angle 8.96995 ( 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 371 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 216 poor density : 155 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 148 PHE cc_start: 0.9164 (t80) cc_final: 0.8903 (t80) REVERT: C 117 ILE cc_start: 0.7011 (OUTLIER) cc_final: 0.6794 (mt) REVERT: C 118 MET cc_start: 0.8172 (OUTLIER) cc_final: 0.7837 (tpp) REVERT: C 198 GLU cc_start: 0.9186 (tt0) cc_final: 0.8810 (tm-30) REVERT: C 199 ILE cc_start: 0.9762 (OUTLIER) cc_final: 0.9288 (mm) REVERT: C 256 GLU cc_start: 0.8868 (mm-30) cc_final: 0.8339 (tm-30) REVERT: A 158 MET cc_start: 0.8938 (OUTLIER) cc_final: 0.8629 (mtm) REVERT: A 198 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8657 (tt0) REVERT: A 214 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8909 (tp) REVERT: B 158 MET cc_start: 0.9010 (OUTLIER) cc_final: 0.8654 (mtm) REVERT: B 198 GLU cc_start: 0.9121 (pt0) cc_final: 0.8655 (pp20) REVERT: B 199 ILE cc_start: 0.9714 (OUTLIER) cc_final: 0.9409 (mm) REVERT: B 256 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8580 (tm-30) REVERT: D 198 GLU cc_start: 0.9040 (pt0) cc_final: 0.8668 (pp20) REVERT: D 256 GLU cc_start: 0.8914 (tt0) cc_final: 0.8589 (tm-30) REVERT: F 117 ILE cc_start: 0.7141 (OUTLIER) cc_final: 0.6878 (mt) REVERT: F 118 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.7879 (tpt) REVERT: F 140 MET cc_start: 0.7114 (OUTLIER) cc_final: 0.6649 (mpt) REVERT: F 199 ILE cc_start: 0.9706 (OUTLIER) cc_final: 0.9400 (mm) REVERT: F 274 LEU cc_start: 0.9533 (OUTLIER) cc_final: 0.9120 (tp) REVERT: G 111 ASP cc_start: 0.8523 (OUTLIER) cc_final: 0.8314 (t70) REVERT: G 198 GLU cc_start: 0.9195 (pt0) cc_final: 0.8618 (pp20) REVERT: G 199 ILE cc_start: 0.9720 (OUTLIER) cc_final: 0.9416 (mm) REVERT: G 232 MET cc_start: 0.9431 (ptt) cc_final: 0.9121 (ptt) REVERT: G 256 GLU cc_start: 0.8982 (tt0) cc_final: 0.8676 (tm-30) outliers start: 216 outliers final: 126 residues processed: 337 average time/residue: 0.5514 time to fit residues: 228.4572 Evaluate side-chains 288 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 147 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 137 HIS Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 223 SER Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 319 SER Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 138 PHE Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 117 ILE Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 138 PHE Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 195 THR Chi-restraints excluded: chain F residue 198 GLU Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 210 ASP Chi-restraints excluded: chain F residue 211 ASN Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 92 ILE Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 165 SER Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 210 ASP Chi-restraints excluded: chain G residue 211 ASN Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 246 GLU Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 313 ILE Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain G residue 319 SER Chi-restraints excluded: chain G residue 330 THR 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: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.096880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.060255 restraints weight = 110969.474| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 2.50 r_work: 0.2667 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2563 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.7001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.049 0.262 17206 Z= 2.132 Angle : 1.874 13.350 23310 Z= 1.038 Chirality : 0.169 1.553 2772 Planarity : 0.012 0.096 2926 Dihedral : 20.815 176.966 2723 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 38.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.13 % Favored : 84.87 % Rotamer: Outliers : 15.70 % Allowed : 17.81 % Favored : 66.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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 aren not related in a simple way. whole: -5.46 (0.14), residues: 1778 helix: -3.28 (0.12), residues: 987 sheet: -3.05 (0.29), residues: 217 loop : -4.09 (0.18), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG D 231 TYR 0.032 0.006 TYR D 291 PHE 0.046 0.005 PHE A 101 TRP 0.042 0.008 TRP F 302 HIS 0.014 0.004 HIS A 137 Details of bonding type rmsd covalent geometry : bond 0.04930 (17206) covalent geometry : angle 1.87446 (23310) hydrogen bonds : bond 0.09142 ( 1196) hydrogen bonds : angle 9.00711 ( 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 389 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 245 poor density : 144 time to evaluate : 0.725 Fit side-chains REVERT: E 148 PHE cc_start: 0.9155 (t80) cc_final: 0.8903 (t80) REVERT: C 117 ILE cc_start: 0.7002 (OUTLIER) cc_final: 0.6786 (mt) REVERT: C 118 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7831 (tpp) REVERT: C 198 GLU cc_start: 0.9190 (tt0) cc_final: 0.8785 (tm-30) REVERT: C 256 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8440 (tm-30) REVERT: A 158 MET cc_start: 0.8946 (OUTLIER) cc_final: 0.8636 (mtm) REVERT: A 198 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8636 (tt0) REVERT: A 214 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8893 (tp) REVERT: B 158 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.8752 (mtm) REVERT: B 198 GLU cc_start: 0.9129 (pt0) cc_final: 0.8636 (pp20) REVERT: B 199 ILE cc_start: 0.9740 (OUTLIER) cc_final: 0.9418 (mm) REVERT: B 214 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.8645 (tp) REVERT: B 256 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8586 (tm-30) REVERT: D 198 GLU cc_start: 0.9068 (pt0) cc_final: 0.8705 (pp20) REVERT: D 256 GLU cc_start: 0.8915 (tt0) cc_final: 0.8561 (tm-30) REVERT: F 117 ILE cc_start: 0.7093 (OUTLIER) cc_final: 0.6846 (mt) REVERT: F 118 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.7852 (tpt) REVERT: F 199 ILE cc_start: 0.9707 (OUTLIER) cc_final: 0.9383 (mm) REVERT: F 256 GLU cc_start: 0.9074 (OUTLIER) cc_final: 0.8711 (tp30) REVERT: F 274 LEU cc_start: 0.9534 (OUTLIER) cc_final: 0.9152 (tp) REVERT: G 111 ASP cc_start: 0.8495 (OUTLIER) cc_final: 0.8231 (t70) REVERT: G 198 GLU cc_start: 0.9046 (pt0) cc_final: 0.8516 (pp20) REVERT: G 199 ILE cc_start: 0.9717 (OUTLIER) cc_final: 0.9407 (mm) REVERT: G 256 GLU cc_start: 0.8999 (tt0) cc_final: 0.8678 (tm-30) outliers start: 245 outliers final: 144 residues processed: 357 average time/residue: 0.5346 time to fit residues: 235.6068 Evaluate side-chains 300 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 141 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 223 SER Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 319 SER Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 138 PHE Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 138 PHE Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain F residue 117 ILE Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain F residue 195 THR Chi-restraints excluded: chain F residue 198 GLU Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 210 ASP Chi-restraints excluded: chain F residue 211 ASN Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 292 CYS Chi-restraints excluded: chain F residue 294 THR Chi-restraints excluded: chain F residue 316 ILE Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 165 SER Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 210 ASP Chi-restraints excluded: chain G residue 211 ASN Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 246 GLU Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 254 ILE Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 313 ILE Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain G residue 319 SER Chi-restraints excluded: chain G residue 330 THR 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: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.096883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.059775 restraints weight = 111264.193| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 2.52 r_work: 0.2665 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2562 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.7185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.049 0.257 17206 Z= 2.132 Angle : 1.874 13.960 23310 Z= 1.039 Chirality : 0.169 1.639 2772 Planarity : 0.012 0.098 2926 Dihedral : 20.807 176.808 2723 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 40.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.19 % Favored : 84.81 % Rotamer: Outliers : 14.86 % Allowed : 19.09 % Favored : 66.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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 aren not related in a simple way. whole: -5.55 (0.14), residues: 1778 helix: -3.29 (0.12), residues: 987 sheet: -3.10 (0.29), residues: 217 loop : -4.25 (0.17), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 231 TYR 0.031 0.006 TYR D 291 PHE 0.039 0.005 PHE F 101 TRP 0.042 0.008 TRP F 302 HIS 0.012 0.005 HIS F 320 Details of bonding type rmsd covalent geometry : bond 0.04933 (17206) covalent geometry : angle 1.87449 (23310) hydrogen bonds : bond 0.09211 ( 1196) hydrogen bonds : angle 9.06971 ( 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 378 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 232 poor density : 146 time to evaluate : 0.744 Fit side-chains revert: symmetry clash REVERT: E 148 PHE cc_start: 0.9169 (t80) cc_final: 0.8924 (t80) REVERT: E 256 GLU cc_start: 0.8871 (tm-30) cc_final: 0.8564 (tm-30) REVERT: C 117 ILE cc_start: 0.7018 (OUTLIER) cc_final: 0.6804 (mt) REVERT: C 118 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7840 (tpp) REVERT: C 198 GLU cc_start: 0.9208 (tt0) cc_final: 0.8762 (tm-30) REVERT: C 199 ILE cc_start: 0.9772 (OUTLIER) cc_final: 0.9327 (mm) REVERT: C 256 GLU cc_start: 0.8968 (mm-30) cc_final: 0.8445 (tm-30) REVERT: A 158 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8623 (mtm) REVERT: A 214 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8875 (tp) REVERT: A 256 GLU cc_start: 0.8868 (tm-30) cc_final: 0.8492 (tm-30) REVERT: B 93 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7619 (mmpt) REVERT: B 158 MET cc_start: 0.9008 (OUTLIER) cc_final: 0.8705 (mtm) REVERT: B 198 GLU cc_start: 0.9095 (pt0) cc_final: 0.8696 (pp20) REVERT: B 199 ILE cc_start: 0.9727 (OUTLIER) cc_final: 0.9417 (mm) REVERT: B 214 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.8643 (tp) REVERT: B 256 GLU cc_start: 0.8865 (mt-10) cc_final: 0.8579 (tm-30) REVERT: D 198 GLU cc_start: 0.9024 (pt0) cc_final: 0.8710 (pp20) REVERT: D 256 GLU cc_start: 0.8908 (tt0) cc_final: 0.8519 (tm-30) REVERT: F 93 LYS cc_start: 0.7719 (OUTLIER) cc_final: 0.7517 (mmpt) REVERT: F 117 ILE cc_start: 0.7093 (OUTLIER) cc_final: 0.6852 (mt) REVERT: F 118 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.7863 (tpt) REVERT: F 140 MET cc_start: 0.7536 (OUTLIER) cc_final: 0.6972 (mpt) REVERT: F 199 ILE cc_start: 0.9696 (OUTLIER) cc_final: 0.9368 (mm) REVERT: F 256 GLU cc_start: 0.9104 (OUTLIER) cc_final: 0.8709 (tp30) REVERT: F 274 LEU cc_start: 0.9529 (OUTLIER) cc_final: 0.9137 (tp) REVERT: G 198 GLU cc_start: 0.9068 (pt0) cc_final: 0.8683 (pp20) REVERT: G 199 ILE cc_start: 0.9711 (OUTLIER) cc_final: 0.9384 (mm) REVERT: G 256 GLU cc_start: 0.8997 (tt0) cc_final: 0.8643 (tm-30) outliers start: 232 outliers final: 157 residues processed: 346 average time/residue: 0.5660 time to fit residues: 241.5684 Evaluate side-chains 317 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 143 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 211 ASN Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 223 SER Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 319 SER Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 138 PHE Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 138 PHE Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 138 PHE Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 176 ASP Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 93 LYS Chi-restraints excluded: chain F residue 117 ILE Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 138 PHE Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 195 THR Chi-restraints excluded: chain F residue 198 GLU Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 210 ASP Chi-restraints excluded: chain F residue 211 ASN Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 292 CYS Chi-restraints excluded: chain F residue 294 THR Chi-restraints excluded: chain F residue 316 ILE Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 92 ILE Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 165 SER Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain G residue 176 ASP Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 210 ASP Chi-restraints excluded: chain G residue 211 ASN Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 246 GLU Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 268 ILE Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 313 ILE Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain G residue 319 SER Chi-restraints excluded: chain G residue 330 THR 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: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.096003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.059587 restraints weight = 113638.439| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 2.43 r_work: 0.2701 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2605 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.7273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.049 0.257 17206 Z= 2.131 Angle : 1.873 13.211 23310 Z= 1.038 Chirality : 0.168 1.526 2772 Planarity : 0.012 0.100 2926 Dihedral : 20.544 179.452 2723 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 40.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.42 % Favored : 83.58 % Rotamer: Outliers : 14.41 % Allowed : 20.44 % Favored : 65.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 aren not related in a simple way. whole: -5.57 (0.14), residues: 1778 helix: -3.26 (0.12), residues: 987 sheet: -3.12 (0.29), residues: 217 loop : -4.34 (0.16), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 231 TYR 0.033 0.006 TYR G 134 PHE 0.042 0.005 PHE A 101 TRP 0.041 0.008 TRP F 302 HIS 0.019 0.005 HIS C 137 Details of bonding type rmsd covalent geometry : bond 0.04930 (17206) covalent geometry : angle 1.87324 (23310) hydrogen bonds : bond 0.09134 ( 1196) hydrogen bonds : angle 9.06835 ( 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 370 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 225 poor density : 145 time to evaluate : 0.852 Fit side-chains revert: symmetry clash REVERT: E 93 LYS cc_start: 0.7725 (OUTLIER) cc_final: 0.7436 (mmpt) REVERT: E 148 PHE cc_start: 0.9132 (t80) cc_final: 0.8869 (t80) REVERT: E 198 GLU cc_start: 0.8988 (OUTLIER) cc_final: 0.8779 (tt0) REVERT: E 256 GLU cc_start: 0.9064 (tm-30) cc_final: 0.8705 (tm-30) REVERT: C 117 ILE cc_start: 0.7277 (OUTLIER) cc_final: 0.7038 (mt) REVERT: C 118 MET cc_start: 0.8170 (OUTLIER) cc_final: 0.7948 (tpp) REVERT: C 198 GLU cc_start: 0.9104 (tt0) cc_final: 0.8761 (tm-30) REVERT: A 158 MET cc_start: 0.9020 (OUTLIER) cc_final: 0.8723 (mtm) REVERT: A 214 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.8977 (tp) REVERT: B 158 MET cc_start: 0.9036 (OUTLIER) cc_final: 0.8773 (mtm) REVERT: B 198 GLU cc_start: 0.9062 (pt0) cc_final: 0.8718 (pp20) REVERT: B 199 ILE cc_start: 0.9745 (OUTLIER) cc_final: 0.9452 (mm) REVERT: B 214 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.8717 (tp) REVERT: D 198 GLU cc_start: 0.9030 (pt0) cc_final: 0.8727 (pp20) REVERT: D 246 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8457 (mp0) REVERT: D 256 GLU cc_start: 0.8953 (tt0) cc_final: 0.8617 (tm-30) REVERT: F 117 ILE cc_start: 0.7217 (OUTLIER) cc_final: 0.6958 (mt) REVERT: F 118 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.7916 (tpt) REVERT: F 140 MET cc_start: 0.7664 (OUTLIER) cc_final: 0.7056 (mpt) REVERT: F 199 ILE cc_start: 0.9716 (OUTLIER) cc_final: 0.9387 (mm) REVERT: F 256 GLU cc_start: 0.9086 (OUTLIER) cc_final: 0.8697 (tp30) REVERT: F 274 LEU cc_start: 0.9548 (OUTLIER) cc_final: 0.9127 (tp) REVERT: G 101 PHE cc_start: 0.4879 (OUTLIER) cc_final: 0.4216 (t80) REVERT: G 198 GLU cc_start: 0.8983 (pt0) cc_final: 0.8662 (pp20) REVERT: G 256 GLU cc_start: 0.9078 (tt0) cc_final: 0.8738 (tm-30) outliers start: 225 outliers final: 168 residues processed: 340 average time/residue: 0.6836 time to fit residues: 284.7984 Evaluate side-chains 328 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 143 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 93 LYS Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 211 ASN Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 223 SER Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 319 SER Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 138 PHE Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 138 PHE Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 148 PHE Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 112 ILE Chi-restraints excluded: chain F residue 117 ILE Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 138 PHE Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 195 THR Chi-restraints excluded: chain F residue 198 GLU Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 210 ASP Chi-restraints excluded: chain F residue 211 ASN Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 225 SER Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 292 CYS Chi-restraints excluded: chain F residue 294 THR Chi-restraints excluded: chain F residue 316 ILE Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 101 PHE Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 165 SER Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain G residue 176 ASP Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 210 ASP Chi-restraints excluded: chain G residue 211 ASN Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 246 GLU Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 254 ILE Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 268 ILE Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 313 ILE Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain G residue 319 SER Chi-restraints excluded: chain G residue 330 THR 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: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.096801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.059748 restraints weight = 112474.257| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 2.53 r_work: 0.2668 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2564 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.7374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.049 0.254 17206 Z= 2.131 Angle : 1.876 13.167 23310 Z= 1.039 Chirality : 0.168 1.530 2772 Planarity : 0.012 0.101 2926 Dihedral : 20.470 179.570 2723 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 41.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.37 % Favored : 83.63 % Rotamer: Outliers : 14.93 % Allowed : 20.76 % Favored : 64.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 aren not related in a simple way. whole: -5.60 (0.14), residues: 1778 helix: -3.27 (0.12), residues: 980 sheet: -3.15 (0.29), residues: 217 loop : -4.41 (0.16), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 231 TYR 0.034 0.006 TYR G 134 PHE 0.043 0.005 PHE C 101 TRP 0.041 0.008 TRP F 302 HIS 0.026 0.006 HIS A 137 Details of bonding type rmsd covalent geometry : bond 0.04930 (17206) covalent geometry : angle 1.87622 (23310) hydrogen bonds : bond 0.09188 ( 1196) hydrogen bonds : angle 9.11549 ( 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 369 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 233 poor density : 136 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 148 PHE cc_start: 0.9150 (t80) cc_final: 0.8909 (t80) REVERT: E 198 GLU cc_start: 0.8991 (OUTLIER) cc_final: 0.8774 (tt0) REVERT: E 256 GLU cc_start: 0.9014 (OUTLIER) cc_final: 0.8647 (tm-30) REVERT: C 117 ILE cc_start: 0.7082 (OUTLIER) cc_final: 0.6863 (mt) REVERT: C 118 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7848 (tpp) REVERT: C 198 GLU cc_start: 0.9229 (OUTLIER) cc_final: 0.8760 (tm-30) REVERT: A 118 MET cc_start: 0.8160 (tpt) cc_final: 0.7860 (tpp) REVERT: A 158 MET cc_start: 0.8989 (OUTLIER) cc_final: 0.8661 (mtm) REVERT: A 214 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8882 (tp) REVERT: A 256 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8554 (tm-30) REVERT: B 158 MET cc_start: 0.9030 (OUTLIER) cc_final: 0.8699 (mtm) REVERT: B 198 GLU cc_start: 0.9110 (pt0) cc_final: 0.8680 (pp20) REVERT: B 199 ILE cc_start: 0.9708 (OUTLIER) cc_final: 0.9399 (mm) REVERT: B 214 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.8651 (tp) REVERT: B 256 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8588 (tm-30) REVERT: D 198 GLU cc_start: 0.9059 (pt0) cc_final: 0.8731 (pp20) REVERT: D 246 GLU cc_start: 0.8979 (OUTLIER) cc_final: 0.8402 (mp0) REVERT: D 256 GLU cc_start: 0.8922 (tt0) cc_final: 0.8530 (tm-30) REVERT: F 117 ILE cc_start: 0.7082 (OUTLIER) cc_final: 0.6839 (mt) REVERT: F 118 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.7854 (tpt) REVERT: F 140 MET cc_start: 0.7494 (OUTLIER) cc_final: 0.6948 (mpt) REVERT: F 199 ILE cc_start: 0.9714 (OUTLIER) cc_final: 0.9366 (mm) REVERT: F 256 GLU cc_start: 0.9087 (OUTLIER) cc_final: 0.8698 (tp30) REVERT: F 274 LEU cc_start: 0.9532 (OUTLIER) cc_final: 0.9127 (tp) REVERT: G 101 PHE cc_start: 0.4680 (OUTLIER) cc_final: 0.4072 (t80) REVERT: G 111 ASP cc_start: 0.8311 (OUTLIER) cc_final: 0.8095 (t0) REVERT: G 198 GLU cc_start: 0.9049 (pt0) cc_final: 0.8657 (pp20) REVERT: G 256 GLU cc_start: 0.9006 (tt0) cc_final: 0.8622 (tm-30) outliers start: 233 outliers final: 172 residues processed: 341 average time/residue: 0.6271 time to fit residues: 264.9719 Evaluate side-chains 327 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 135 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 211 ASN Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 223 SER Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 225 SER Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 319 SER Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 138 PHE Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 138 PHE Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 148 PHE Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 112 ILE Chi-restraints excluded: chain F residue 117 ILE Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 138 PHE Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 148 PHE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 195 THR Chi-restraints excluded: chain F residue 198 GLU Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 210 ASP Chi-restraints excluded: chain F residue 211 ASN Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 225 SER Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 292 CYS Chi-restraints excluded: chain F residue 294 THR Chi-restraints excluded: chain F residue 316 ILE Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 101 PHE Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 165 SER Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain G residue 176 ASP Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 210 ASP Chi-restraints excluded: chain G residue 211 ASN Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 246 GLU Chi-restraints excluded: chain G residue 254 ILE Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 268 ILE Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 313 ILE Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain G residue 319 SER Chi-restraints excluded: chain G residue 330 THR 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: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.096785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.059743 restraints weight = 112444.626| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 2.52 r_work: 0.2665 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2559 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.7427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.049 0.255 17206 Z= 2.131 Angle : 1.879 12.808 23310 Z= 1.041 Chirality : 0.168 1.526 2772 Planarity : 0.012 0.102 2926 Dihedral : 20.405 177.993 2723 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 42.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.99 % Favored : 83.01 % Rotamer: Outliers : 13.84 % Allowed : 22.17 % Favored : 64.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 aren not related in a simple way. whole: -5.63 (0.14), residues: 1778 helix: -3.28 (0.12), residues: 980 sheet: -3.15 (0.29), residues: 217 loop : -4.43 (0.16), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 231 TYR 0.036 0.006 TYR E 134 PHE 0.039 0.005 PHE A 101 TRP 0.041 0.008 TRP F 302 HIS 0.023 0.006 HIS E 137 Details of bonding type rmsd covalent geometry : bond 0.04930 (17206) covalent geometry : angle 1.87875 (23310) hydrogen bonds : bond 0.09186 ( 1196) hydrogen bonds : angle 9.13275 ( 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 350 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 216 poor density : 134 time to evaluate : 0.634 Fit side-chains REVERT: E 148 PHE cc_start: 0.9161 (t80) cc_final: 0.8927 (t80) REVERT: E 198 GLU cc_start: 0.9015 (OUTLIER) cc_final: 0.8809 (tt0) REVERT: E 256 GLU cc_start: 0.9050 (OUTLIER) cc_final: 0.8665 (tm-30) REVERT: C 117 ILE cc_start: 0.7109 (OUTLIER) cc_final: 0.6884 (mt) REVERT: C 118 MET cc_start: 0.8078 (OUTLIER) cc_final: 0.7790 (tpp) REVERT: C 198 GLU cc_start: 0.9218 (OUTLIER) cc_final: 0.8745 (tm-30) REVERT: C 256 GLU cc_start: 0.9006 (mm-30) cc_final: 0.8441 (tm-30) REVERT: A 118 MET cc_start: 0.8187 (tpt) cc_final: 0.7895 (tpp) REVERT: A 158 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8648 (mtm) REVERT: A 198 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.8619 (tt0) REVERT: A 214 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8876 (tp) REVERT: A 256 GLU cc_start: 0.8973 (OUTLIER) cc_final: 0.8595 (tm-30) REVERT: B 158 MET cc_start: 0.9037 (mmm) cc_final: 0.8722 (mtm) REVERT: B 198 GLU cc_start: 0.9104 (pt0) cc_final: 0.8672 (pp20) REVERT: B 199 ILE cc_start: 0.9709 (OUTLIER) cc_final: 0.9399 (mm) REVERT: B 214 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.8648 (tp) REVERT: D 198 GLU cc_start: 0.9060 (pt0) cc_final: 0.8709 (pp20) REVERT: D 246 GLU cc_start: 0.8995 (OUTLIER) cc_final: 0.8421 (mp0) REVERT: D 256 GLU cc_start: 0.8926 (tt0) cc_final: 0.8528 (tm-30) REVERT: F 117 ILE cc_start: 0.7076 (OUTLIER) cc_final: 0.6825 (mt) REVERT: F 118 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.7852 (tpt) REVERT: F 140 MET cc_start: 0.7521 (OUTLIER) cc_final: 0.6968 (mpt) REVERT: F 199 ILE cc_start: 0.9709 (OUTLIER) cc_final: 0.9362 (mm) REVERT: F 256 GLU cc_start: 0.9089 (OUTLIER) cc_final: 0.8703 (tp30) REVERT: F 274 LEU cc_start: 0.9527 (OUTLIER) cc_final: 0.9153 (tp) REVERT: G 101 PHE cc_start: 0.4685 (OUTLIER) cc_final: 0.4072 (t80) REVERT: G 111 ASP cc_start: 0.8280 (OUTLIER) cc_final: 0.8071 (t0) REVERT: G 198 GLU cc_start: 0.9045 (pt0) cc_final: 0.8541 (pp20) REVERT: G 256 GLU cc_start: 0.9008 (tt0) cc_final: 0.8625 (tm-30) outliers start: 216 outliers final: 167 residues processed: 326 average time/residue: 0.5948 time to fit residues: 238.4466 Evaluate side-chains 321 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 134 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 93 LYS Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 138 PHE Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 211 ASN Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 223 SER Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 225 SER Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 319 SER Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 148 PHE Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 112 ILE Chi-restraints excluded: chain F residue 117 ILE Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 138 PHE Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 148 PHE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 195 THR Chi-restraints excluded: chain F residue 198 GLU Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 210 ASP Chi-restraints excluded: chain F residue 211 ASN Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 225 SER Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 292 CYS Chi-restraints excluded: chain F residue 294 THR Chi-restraints excluded: chain F residue 316 ILE Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 101 PHE Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 165 SER Chi-restraints excluded: chain G residue 176 ASP Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 210 ASP Chi-restraints excluded: chain G residue 211 ASN Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 246 GLU Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 254 ILE Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 268 ILE Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 313 ILE Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain G residue 319 SER Chi-restraints excluded: chain G residue 330 THR 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: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 270 GLN ** G 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.096802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.059739 restraints weight = 112541.371| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 2.54 r_work: 0.2669 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2565 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.7451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.049 0.254 17206 Z= 2.131 Angle : 1.884 12.573 23310 Z= 1.041 Chirality : 0.168 1.521 2772 Planarity : 0.012 0.102 2926 Dihedral : 20.394 176.649 2723 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 42.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.59 % Favored : 83.41 % Rotamer: Outliers : 12.94 % Allowed : 23.06 % Favored : 64.00 % 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 aren not related in a simple way. whole: -5.65 (0.14), residues: 1778 helix: -3.29 (0.12), residues: 980 sheet: -3.17 (0.29), residues: 217 loop : -4.45 (0.16), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 231 TYR 0.038 0.006 TYR E 134 PHE 0.037 0.005 PHE A 101 TRP 0.041 0.008 TRP F 302 HIS 0.021 0.006 HIS E 137 Details of bonding type rmsd covalent geometry : bond 0.04933 (17206) covalent geometry : angle 1.88366 (23310) hydrogen bonds : bond 0.09212 ( 1196) hydrogen bonds : angle 9.16427 ( 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 334 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 132 time to evaluate : 0.823 Fit side-chains revert: symmetry clash REVERT: E 148 PHE cc_start: 0.9149 (t80) cc_final: 0.8917 (t80) REVERT: E 198 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8778 (tt0) REVERT: E 256 GLU cc_start: 0.9046 (OUTLIER) cc_final: 0.8657 (tm-30) REVERT: C 117 ILE cc_start: 0.7106 (OUTLIER) cc_final: 0.6880 (mt) REVERT: C 118 MET cc_start: 0.8073 (OUTLIER) cc_final: 0.7842 (tpp) REVERT: C 198 GLU cc_start: 0.9230 (OUTLIER) cc_final: 0.8757 (tm-30) REVERT: A 118 MET cc_start: 0.8202 (tpt) cc_final: 0.7905 (tpp) REVERT: A 158 MET cc_start: 0.8967 (OUTLIER) cc_final: 0.8640 (mtm) REVERT: A 198 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8592 (tt0) REVERT: A 214 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8885 (tp) REVERT: A 256 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.8597 (tm-30) REVERT: B 158 MET cc_start: 0.9038 (mmm) cc_final: 0.8697 (mtm) REVERT: B 198 GLU cc_start: 0.9107 (pt0) cc_final: 0.8679 (pp20) REVERT: B 199 ILE cc_start: 0.9707 (OUTLIER) cc_final: 0.9398 (mm) REVERT: B 214 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.8657 (tp) REVERT: D 198 GLU cc_start: 0.9046 (pt0) cc_final: 0.8725 (pp20) REVERT: D 246 GLU cc_start: 0.8986 (OUTLIER) cc_final: 0.8427 (mp0) REVERT: D 256 GLU cc_start: 0.8920 (tt0) cc_final: 0.8530 (tm-30) REVERT: F 117 ILE cc_start: 0.7074 (OUTLIER) cc_final: 0.6823 (mt) REVERT: F 118 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.7847 (tpt) REVERT: F 140 MET cc_start: 0.7510 (OUTLIER) cc_final: 0.6960 (mpt) REVERT: F 199 ILE cc_start: 0.9709 (OUTLIER) cc_final: 0.9359 (mm) REVERT: F 256 GLU cc_start: 0.9091 (OUTLIER) cc_final: 0.8704 (tp30) REVERT: F 274 LEU cc_start: 0.9537 (OUTLIER) cc_final: 0.9149 (tp) REVERT: G 101 PHE cc_start: 0.4681 (OUTLIER) cc_final: 0.4070 (t80) REVERT: G 198 GLU cc_start: 0.9103 (pt0) cc_final: 0.8673 (pp20) REVERT: G 256 GLU cc_start: 0.9010 (tt0) cc_final: 0.8631 (tm-30) outliers start: 202 outliers final: 170 residues processed: 316 average time/residue: 0.5726 time to fit residues: 223.4218 Evaluate side-chains 319 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 130 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 93 LYS Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 211 ASN Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 223 SER Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 225 SER Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 319 SER Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 101 PHE Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 148 PHE Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 148 PHE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 101 PHE Chi-restraints excluded: chain F residue 112 ILE Chi-restraints excluded: chain F residue 117 ILE Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 138 PHE Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 148 PHE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 195 THR Chi-restraints excluded: chain F residue 198 GLU Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 210 ASP Chi-restraints excluded: chain F residue 211 ASN Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 225 SER Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 292 CYS Chi-restraints excluded: chain F residue 294 THR Chi-restraints excluded: chain F residue 316 ILE Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 101 PHE Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 165 SER Chi-restraints excluded: chain G residue 176 ASP Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain G residue 204 THR Chi-restraints excluded: chain G residue 210 ASP Chi-restraints excluded: chain G residue 211 ASN Chi-restraints excluded: chain G residue 223 SER Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 246 GLU Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 254 ILE Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 268 ILE Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 313 ILE Chi-restraints excluded: chain G residue 314 ILE Chi-restraints excluded: chain G residue 319 SER Chi-restraints excluded: chain G residue 330 THR 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: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.096856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.059715 restraints weight = 112914.602| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 2.53 r_work: 0.2662 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2558 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.7471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.049 0.254 17206 Z= 2.132 Angle : 1.885 12.893 23310 Z= 1.042 Chirality : 0.168 1.522 2772 Planarity : 0.012 0.103 2926 Dihedral : 20.357 176.110 2723 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 42.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.70 % Favored : 83.30 % Rotamer: Outliers : 13.13 % Allowed : 22.87 % Favored : 64.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 aren not related in a simple way. whole: -5.67 (0.14), residues: 1778 helix: -3.31 (0.12), residues: 980 sheet: -3.16 (0.29), residues: 217 loop : -4.47 (0.16), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 231 TYR 0.039 0.006 TYR E 134 PHE 0.038 0.005 PHE A 101 TRP 0.041 0.008 TRP F 302 HIS 0.019 0.006 HIS A 137 Details of bonding type rmsd covalent geometry : bond 0.04934 (17206) covalent geometry : angle 1.88493 (23310) hydrogen bonds : bond 0.09221 ( 1196) hydrogen bonds : angle 9.19322 ( 3441) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12318.71 seconds wall clock time: 208 minutes 33.20 seconds (12513.20 seconds total)