Starting phenix.real_space_refine on Sat Aug 23 05:56:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k25_36828/08_2025/8k25_36828.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k25_36828/08_2025/8k25_36828.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k25_36828/08_2025/8k25_36828.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k25_36828/08_2025/8k25_36828.map" model { file = "/net/cci-nas-00/data/ceres_data/8k25_36828/08_2025/8k25_36828.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k25_36828/08_2025/8k25_36828.cif" } resolution = 3.4 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= 0.004 sd= 0.076 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 374 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 34 5.49 5 S 47 5.16 5 C 6226 2.51 5 N 1687 2.21 5 O 1967 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 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: 9961 Number of models: 1 Model: "" Number of chains: 8 Chain: "U" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 187 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 314 Unresolved non-hydrogen dihedrals: 202 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {' DC:plan': 1, ' DC:plan2': 1, ' DA:plan': 8, ' DA:plan2': 8, ' DT:plan': 4, ' DG:plan': 4, ' DG:plan2': 4} Unresolved non-hydrogen planarities: 194 Chain: "V" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 187 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Unresolved non-hydrogen bonds: 177 Unresolved non-hydrogen angles: 281 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {' DT:plan': 8, ' DC:plan': 4, ' DC:plan2': 4, ' DA:plan': 4, ' DA:plan2': 4, ' DG:plan': 1, ' DG:plan2': 1} Unresolved non-hydrogen planarities: 173 Chain: "A" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 614 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'TRANS': 79} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "a" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 594 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 79} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "D" Number of atoms: 2285 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 289, 2275 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 283} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'TRP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 18 Conformer: "B" Number of residues, atoms: 289, 2275 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 283} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'TRP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 18 bond proxies already assigned to first conformer: 2307 Chain: "d" Number of atoms: 1433 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 289, 1429 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 251} Link IDs: {'PTRANS': 5, 'TRANS': 283} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 930 Unresolved non-hydrogen angles: 1192 Unresolved non-hydrogen dihedrals: 787 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'GLN:plan1': 8, 'ARG:plan': 12, 'ASN:plan1': 18, 'TYR:plan': 14, 'HIS:plan': 9, 'GLU:plan': 15, 'ASP:plan': 16, 'PHE:plan': 13, 'TRP:plan': 4} Unresolved non-hydrogen planarities: 511 Conformer: "B" Number of residues, atoms: 289, 1429 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 251} Link IDs: {'PTRANS': 5, 'TRANS': 283} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 930 Unresolved non-hydrogen angles: 1192 Unresolved non-hydrogen dihedrals: 787 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'GLN:plan1': 8, 'ARG:plan': 12, 'ASN:plan1': 18, 'TYR:plan': 14, 'HIS:plan': 9, 'GLU:plan': 15, 'ASP:plan': 16, 'PHE:plan': 13, 'TRP:plan': 4} Unresolved non-hydrogen planarities: 511 bond proxies already assigned to first conformer: 1421 Chain: "E" Number of atoms: 2314 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 295, 2314 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 289} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "e" Number of atoms: 2347 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 295, 2339 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 289} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 295, 2339 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 289} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 2380 Time building chain proxies: 3.26, per 1000 atoms: 0.33 Number of scatterers: 9961 At special positions: 0 Unit cell: (89.1, 81.4, 151.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 47 16.00 P 34 15.00 O 1967 8.00 N 1687 7.00 C 6226 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 494.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2498 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 11 sheets defined 51.7% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 12 through 23 removed outlier: 3.507A pdb=" N LYS A 16 " --> pdb=" O PRO A 12 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 53 removed outlier: 3.745A pdb=" N GLY A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) Processing helix chain 'a' and resid 11 through 22 removed outlier: 3.725A pdb=" N LYS a 15 " --> pdb=" O GLN a 11 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS a 16 " --> pdb=" O PRO a 12 " (cutoff:3.500A) Processing helix chain 'a' and resid 38 through 51 Processing helix chain 'D' and resid 6 through 10 Processing helix chain 'D' and resid 57 through 65 Processing helix chain 'D' and resid 98 through 109 Processing helix chain 'D' and resid 110 through 123 Processing helix chain 'D' and resid 124 through 131 Processing helix chain 'D' and resid 144 through 159 removed outlier: 3.539A pdb=" N ALA D 159 " --> pdb=" O GLY D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 178 removed outlier: 3.615A pdb=" N THR D 171 " --> pdb=" O GLY D 167 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE D 172 " --> pdb=" O HIS D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 205 Processing helix chain 'D' and resid 205 through 221 removed outlier: 4.044A pdb=" N GLY D 211 " --> pdb=" O TYR D 207 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA D 219 " --> pdb=" O SER D 215 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU D 220 " --> pdb=" O SER D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 248 removed outlier: 4.705A pdb=" N ILE D 245 " --> pdb=" O ASP D 241 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE D 246 " --> pdb=" O VAL D 242 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR D 248 " --> pdb=" O ASP D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 262 removed outlier: 3.652A pdb=" N LEU D 254 " --> pdb=" O ILE D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 280 removed outlier: 3.526A pdb=" N PHE D 268 " --> pdb=" O SER D 264 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN D 279 " --> pdb=" O TYR D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 294 removed outlier: 3.755A pdb=" N ILE D 289 " --> pdb=" O LEU D 285 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG D 291 " --> pdb=" O ASN D 287 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU D 292 " --> pdb=" O ASN D 288 " (cutoff:3.500A) Processing helix chain 'd' and resid 6 through 10 removed outlier: 3.747A pdb=" N LYS d 10 " --> pdb=" O THR d 7 " (cutoff:3.500A) Processing helix chain 'd' and resid 58 through 67 Processing helix chain 'd' and resid 97 through 110 removed outlier: 3.533A pdb=" N ASN d 103 " --> pdb=" O LYS d 99 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ASP d 110 " --> pdb=" O ARG d 106 " (cutoff:3.500A) Processing helix chain 'd' and resid 110 through 124 removed outlier: 3.508A pdb=" N SER d 116 " --> pdb=" O GLU d 112 " (cutoff:3.500A) Processing helix chain 'd' and resid 145 through 159 removed outlier: 4.093A pdb=" N GLN d 158 " --> pdb=" O LYS d 154 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA d 159 " --> pdb=" O GLY d 155 " (cutoff:3.500A) Processing helix chain 'd' and resid 167 through 184 removed outlier: 3.526A pdb=" N THR d 171 " --> pdb=" O GLY d 167 " (cutoff:3.500A) Processing helix chain 'd' and resid 205 through 210 Processing helix chain 'd' and resid 239 through 248 removed outlier: 4.431A pdb=" N ILE d 245 " --> pdb=" O ASP d 241 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE d 246 " --> pdb=" O VAL d 242 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR d 248 " --> pdb=" O ASP d 244 " (cutoff:3.500A) Processing helix chain 'd' and resid 251 through 261 Processing helix chain 'd' and resid 264 through 279 Processing helix chain 'd' and resid 280 through 294 removed outlier: 3.609A pdb=" N LYS d 290 " --> pdb=" O ILE d 286 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG d 291 " --> pdb=" O ASN d 287 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU d 292 " --> pdb=" O ASN d 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 67 Processing helix chain 'E' and resid 98 through 110 removed outlier: 4.149A pdb=" N GLN E 102 " --> pdb=" O THR E 98 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASP E 110 " --> pdb=" O ARG E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 132 Processing helix chain 'E' and resid 142 through 158 Processing helix chain 'E' and resid 161 through 184 Processing helix chain 'E' and resid 196 through 219 Processing helix chain 'E' and resid 236 through 247 removed outlier: 3.537A pdb=" N ASP E 244 " --> pdb=" O PHE E 240 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE E 245 " --> pdb=" O ASP E 241 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ILE E 246 " --> pdb=" O VAL E 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 262 Processing helix chain 'E' and resid 264 through 279 Processing helix chain 'E' and resid 280 through 295 removed outlier: 3.757A pdb=" N GLU E 295 " --> pdb=" O ARG E 291 " (cutoff:3.500A) Processing helix chain 'e' and resid 57 through 67 removed outlier: 4.143A pdb=" N ASN e 67 " --> pdb=" O MET e 63 " (cutoff:3.500A) Processing helix chain 'e' and resid 98 through 110 Processing helix chain 'e' and resid 110 through 132 Processing helix chain 'e' and resid 142 through 158 removed outlier: 3.606A pdb=" N SER e 146 " --> pdb=" O ASN e 142 " (cutoff:3.500A) Processing helix chain 'e' and resid 161 through 185 removed outlier: 3.505A pdb=" N LEU e 165 " --> pdb=" O SER e 161 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR e 184 " --> pdb=" O TYR e 180 " (cutoff:3.500A) Processing helix chain 'e' and resid 196 through 220 Processing helix chain 'e' and resid 236 through 248 removed outlier: 3.560A pdb=" N PHE e 240 " --> pdb=" O GLY e 236 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N ILE e 245 " --> pdb=" O ASP e 241 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ILE e 246 " --> pdb=" O VAL e 242 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR e 248 " --> pdb=" O ASP e 244 " (cutoff:3.500A) Processing helix chain 'e' and resid 250 through 262 Processing helix chain 'e' and resid 264 through 280 Processing helix chain 'e' and resid 281 through 295 Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 27 removed outlier: 3.533A pdb=" N GLU A 26 " --> pdb=" O GLU A 34 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 26 through 29 removed outlier: 5.981A pdb=" N THR a 32 " --> pdb=" O THR a 28 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 12 through 16 removed outlier: 7.761A pdb=" N ASN D 12 " --> pdb=" O VAL D 46 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE D 48 " --> pdb=" O ASN D 12 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N TYR D 14 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N LEU D 50 " --> pdb=" O TYR D 14 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU D 16 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N VAL D 46 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N PHE D 72 " --> pdb=" O VAL D 46 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE D 48 " --> pdb=" O PHE D 72 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'D' and resid 55 through 56 removed outlier: 3.780A pdb=" N ILE D 56 " --> pdb=" O ILE E 56 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE E 56 " --> pdb=" O ILE D 56 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 90 through 91 removed outlier: 3.804A pdb=" N ALA E 83 " --> pdb=" O TRP E 73 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ILE E 48 " --> pdb=" O PHE E 72 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N THR E 74 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N LEU E 50 " --> pdb=" O THR E 74 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N PHE E 47 " --> pdb=" O ASN E 12 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N TYR E 14 " --> pdb=" O PHE E 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'd' and resid 12 through 14 removed outlier: 8.086A pdb=" N ASN d 12 " --> pdb=" O PHE d 47 " (cutoff:3.500A) removed outlier: 9.479A pdb=" N GLY d 49 " --> pdb=" O ASN d 12 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N TYR d 14 " --> pdb=" O GLY d 49 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE d 72 " --> pdb=" O ILE d 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'd' and resid 21 through 24 Processing sheet with id=AA8, first strand: chain 'd' and resid 56 through 57 removed outlier: 3.764A pdb=" N ILE d 56 " --> pdb=" O ILE e 56 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE e 56 " --> pdb=" O ILE d 56 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'd' and resid 90 through 91 removed outlier: 3.694A pdb=" N ALA e 83 " --> pdb=" O TRP e 73 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ILE e 48 " --> pdb=" O PHE e 72 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N THR e 74 " --> pdb=" O ILE e 48 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N LEU e 50 " --> pdb=" O THR e 74 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N TYR e 14 " --> pdb=" O GLY e 49 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 19 through 23 Processing sheet with id=AB2, first strand: chain 'e' and resid 19 through 24 510 hydrogen bonds defined for protein. 1485 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: 1.13 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2701 1.34 - 1.46: 2299 1.46 - 1.58: 5012 1.58 - 1.70: 69 1.70 - 1.83: 75 Bond restraints: 10156 Sorted by residual: bond pdb=" C LEU e 252 " pdb=" N PRO e 253 " ideal model delta sigma weight residual 1.336 1.391 -0.055 1.20e-02 6.94e+03 2.13e+01 bond pdb=" CB ASN e 12 " pdb=" CG ASN e 12 " ideal model delta sigma weight residual 1.516 1.588 -0.072 2.50e-02 1.60e+03 8.20e+00 bond pdb=" CB LYS D 154 " pdb=" CG LYS D 154 " ideal model delta sigma weight residual 1.520 1.591 -0.071 3.00e-02 1.11e+03 5.58e+00 bond pdb=" CG LEU D 282 " pdb=" CD1 LEU D 282 " ideal model delta sigma weight residual 1.521 1.445 0.076 3.30e-02 9.18e+02 5.28e+00 bond pdb=" C GLN a 11 " pdb=" N PRO a 12 " ideal model delta sigma weight residual 1.334 1.387 -0.053 2.34e-02 1.83e+03 5.13e+00 ... (remaining 10151 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.35: 13558 3.35 - 6.69: 225 6.69 - 10.04: 41 10.04 - 13.38: 13 13.38 - 16.73: 4 Bond angle restraints: 13841 Sorted by residual: angle pdb=" CB LYS D 154 " pdb=" CG LYS D 154 " pdb=" CD LYS D 154 " ideal model delta sigma weight residual 111.30 126.80 -15.50 2.30e+00 1.89e-01 4.54e+01 angle pdb=" C LYS E 75 " pdb=" N GLY E 76 " pdb=" CA GLY E 76 " ideal model delta sigma weight residual 119.92 125.34 -5.42 9.60e-01 1.09e+00 3.19e+01 angle pdb=" CB MET E 61 " pdb=" CG MET E 61 " pdb=" SD MET E 61 " ideal model delta sigma weight residual 112.70 129.43 -16.73 3.00e+00 1.11e-01 3.11e+01 angle pdb=" CD1 LEU D 282 " pdb=" CG LEU D 282 " pdb=" CD2 LEU D 282 " ideal model delta sigma weight residual 110.80 98.56 12.24 2.20e+00 2.07e-01 3.09e+01 angle pdb=" C ASN E 279 " pdb=" N ASP E 280 " pdb=" CA ASP E 280 " ideal model delta sigma weight residual 122.82 129.85 -7.03 1.42e+00 4.96e-01 2.45e+01 ... (remaining 13836 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.06: 5847 34.06 - 68.12: 267 68.12 - 102.19: 14 102.19 - 136.25: 0 136.25 - 170.31: 1 Dihedral angle restraints: 6129 sinusoidal: 2250 harmonic: 3879 Sorted by residual: dihedral pdb=" CA LEU a 49 " pdb=" C LEU a 49 " pdb=" N ILE a 50 " pdb=" CA ILE a 50 " ideal model delta harmonic sigma weight residual 180.00 153.49 26.51 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA PHE a 8 " pdb=" C PHE a 8 " pdb=" N SER a 9 " pdb=" CA SER a 9 " ideal model delta harmonic sigma weight residual -180.00 -154.89 -25.11 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA ILE D 70 " pdb=" C ILE D 70 " pdb=" N VAL D 71 " pdb=" CA VAL D 71 " ideal model delta harmonic sigma weight residual 180.00 155.20 24.80 0 5.00e+00 4.00e-02 2.46e+01 ... (remaining 6126 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1442 0.086 - 0.171: 179 0.171 - 0.257: 17 0.257 - 0.342: 0 0.342 - 0.428: 1 Chirality restraints: 1639 Sorted by residual: chirality pdb=" CB VAL a 66 " pdb=" CA VAL a 66 " pdb=" CG1 VAL a 66 " pdb=" CG2 VAL a 66 " both_signs ideal model delta sigma weight residual False -2.63 -2.20 -0.43 2.00e-01 2.50e+01 4.58e+00 chirality pdb=" CB ILE a 70 " pdb=" CA ILE a 70 " pdb=" CG1 ILE a 70 " pdb=" CG2 ILE a 70 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CG LEU D 16 " pdb=" CB LEU D 16 " pdb=" CD1 LEU D 16 " pdb=" CD2 LEU D 16 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 1636 not shown) Planarity restraints: 1712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA E 213 " 0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C ALA E 213 " -0.060 2.00e-02 2.50e+03 pdb=" O ALA E 213 " 0.022 2.00e-02 2.50e+03 pdb=" N ARG E 214 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG E 96 " -0.055 5.00e-02 4.00e+02 8.31e-02 1.10e+01 pdb=" N PRO E 97 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO E 97 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO E 97 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN E 102 " -0.015 2.00e-02 2.50e+03 2.93e-02 8.61e+00 pdb=" C GLN E 102 " 0.051 2.00e-02 2.50e+03 pdb=" O GLN E 102 " -0.019 2.00e-02 2.50e+03 pdb=" N ASN E 103 " -0.017 2.00e-02 2.50e+03 ... (remaining 1709 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2476 2.80 - 3.32: 9237 3.32 - 3.85: 17505 3.85 - 4.37: 19174 4.37 - 4.90: 32408 Nonbonded interactions: 80800 Sorted by model distance: nonbonded pdb=" O ALA D 51 " pdb=" OG1 THR D 54 " model vdw 2.271 3.040 nonbonded pdb=" OG SER A 9 " pdb=" O GLY A 55 " model vdw 2.284 3.040 nonbonded pdb=" OG SER D 194 " pdb=" OD1 ASP D 196 " model vdw 2.291 3.040 nonbonded pdb=" O SER e 225 " pdb=" OG SER e 225 " model vdw 2.291 3.040 nonbonded pdb=" O ASP e 127 " pdb=" OG1 THR e 131 " model vdw 2.307 3.040 ... (remaining 80795 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 61 or (resid 62 through 64 and (nam \ e N or name CA or name C or name O or name CB )) or resid 65 through 76 or (resi \ d 77 through 78 and (name N or name CA or name C or name O or name CB )) or resi \ d 79 through 81)) selection = (chain 'a' and (resid 1 through 48 or (resid 49 and (name N or name CA or name C \ or name O or name CB )) or resid 50 through 81)) } ncs_group { reference = (chain 'D' and ((resid 1 through 25 and (name N or name CA or name C or name O o \ r name CB )) or resid 26 or (resid 27 through 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 or (resid 36 through 48 and (name N or nam \ e CA or name C or name O or name CB )) or resid 49 or (resid 50 through 52 and ( \ name N or name CA or name C or name O or name CB )) or resid 53 or (resid 54 thr \ ough 67 and (name N or name CA or name C or name O or name CB )) or resid 68 or \ (resid 69 through 105 and (name N or name CA or name C or name O or name CB )) o \ r (resid 107 through 136 and (name N or name CA or name C or name O or name CB ) \ ) or resid 137 or (resid 138 through 149 and (name N or name CA or name C or nam \ e O or name CB )) or (resid 151 through 154 and (name N or name CA or name C or \ name O or name CB )) or resid 155 or (resid 156 through 166 and (name N or name \ CA or name C or name O or name CB )) or resid 167 or (resid 168 through 169 and \ (name N or name CA or name C or name O or name CB )) or resid 170 or (resid 171 \ through 204 and (name N or name CA or name C or name O or name CB )) or resid 20 \ 5 or (resid 206 through 210 and (name N or name CA or name C or name O or name C \ B )) or resid 211 or (resid 212 through 220 and (name N or name CA or name C or \ name O or name CB )) or resid 221 or (resid 222 through 230 and (name N or name \ CA or name C or name O or name CB )) or resid 231 or (resid 232 through 235 and \ (name N or name CA or name C or name O or name CB )) or resid 236 through 237 or \ (resid 238 through 261 and (name N or name CA or name C or name O or name CB )) \ or resid 262 or (resid 263 through 286 and (name N or name CA or name C or name \ O or name CB )) or (resid 288 through 295 and (name N or name CA or name C or n \ ame O or name CB )))) selection = (chain 'E' and ((resid 1 through 25 and (name N or name CA or name C or name O o \ r name CB )) or resid 26 or (resid 27 through 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 or (resid 36 through 48 and (name N or nam \ e CA or name C or name O or name CB )) or resid 49 or (resid 50 through 52 and ( \ name N or name CA or name C or name O or name CB )) or resid 53 or (resid 54 thr \ ough 67 and (name N or name CA or name C or name O or name CB )) or resid 68 or \ (resid 69 through 75 and (name N or name CA or name C or name O or name CB )) or \ (resid 83 through 105 and (name N or name CA or name C or name O or name CB )) \ or (resid 107 through 136 and (name N or name CA or name C or name O or name CB \ )) or resid 137 or (resid 138 through 149 and (name N or name CA or name C or na \ me O or name CB )) or (resid 151 through 154 and (name N or name CA or name C or \ name O or name CB )) or resid 155 or (resid 156 through 166 and (name N or name \ CA or name C or name O or name CB )) or resid 167 or (resid 168 through 169 and \ (name N or name CA or name C or name O or name CB )) or resid 170 or (resid 171 \ through 204 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 05 or (resid 206 through 210 and (name N or name CA or name C or name O or name \ CB )) or resid 211 or (resid 212 through 220 and (name N or name CA or name C or \ name O or name CB )) or resid 221 or (resid 222 through 230 and (name N or name \ CA or name C or name O or name CB )) or resid 231 or (resid 232 through 235 and \ (name N or name CA or name C or name O or name CB )) or resid 236 through 237 o \ r (resid 238 through 261 and (name N or name CA or name C or name O or name CB ) \ ) or resid 262 or (resid 263 through 286 and (name N or name CA or name C or nam \ e O or name CB )) or (resid 288 through 295 and (name N or name CA or name C or \ name O or name CB )))) selection = (chain 'd' and (resid 1 through 105 or resid 107 through 149 or resid 151 throug \ h 286 or resid 288 through 295)) selection = (chain 'e' and ((resid 1 through 25 and (name N or name CA or name C or name O o \ r name CB )) or resid 26 or (resid 27 through 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 or (resid 36 through 48 and (name N or nam \ e CA or name C or name O or name CB )) or resid 49 or (resid 50 through 52 and ( \ name N or name CA or name C or name O or name CB )) or resid 53 or (resid 54 thr \ ough 67 and (name N or name CA or name C or name O or name CB )) or resid 68 or \ (resid 69 through 75 and (name N or name CA or name C or name O or name CB )) or \ (resid 83 through 105 and (name N or name CA or name C or name O or name CB )) \ or (resid 107 through 136 and (name N or name CA or name C or name O or name CB \ )) or resid 137 or (resid 138 through 149 and (name N or name CA or name C or na \ me O or name CB )) or (resid 151 through 154 and (name N or name CA or name C or \ name O or name CB )) or resid 155 or (resid 156 through 166 and (name N or name \ CA or name C or name O or name CB )) or resid 167 or (resid 168 through 169 and \ (name N or name CA or name C or name O or name CB )) or resid 170 or (resid 171 \ through 204 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 05 or (resid 206 through 210 and (name N or name CA or name C or name O or name \ CB )) or resid 211 or (resid 212 through 220 and (name N or name CA or name C or \ name O or name CB )) or resid 221 or (resid 222 through 230 and (name N or name \ CA or name C or name O or name CB )) or resid 231 or (resid 232 through 235 and \ (name N or name CA or name C or name O or name CB )) or resid 236 through 237 o \ r (resid 238 through 261 and (name N or name CA or name C or name O or name CB ) \ ) or resid 262 or (resid 263 through 286 and (name N or name CA or name C or nam \ e O or name CB )) or (resid 288 through 295 and (name N or name CA or name C or \ name O or name CB )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.05 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: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.160 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5207 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 : 0.005 0.076 10156 Z= 0.255 Angle : 1.139 16.729 13841 Z= 0.602 Chirality : 0.056 0.428 1639 Planarity : 0.006 0.083 1712 Dihedral : 18.395 170.311 3631 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.15 % Favored : 92.77 % Rotamer: Outliers : 0.69 % Allowed : 30.00 % Favored : 69.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -3.18 (0.20), residues: 1319 helix: -1.79 (0.16), residues: 678 sheet: -2.00 (0.63), residues: 70 loop : -2.42 (0.24), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 125 TYR 0.046 0.003 TYR e 210 PHE 0.029 0.003 PHE A 8 TRP 0.045 0.004 TRP D 104 HIS 0.015 0.002 HIS e 30 Details of bonding type rmsd covalent geometry : bond 0.00543 (10156) covalent geometry : angle 1.13914 (13841) hydrogen bonds : bond 0.15878 ( 510) hydrogen bonds : angle 7.59076 ( 1485) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 148 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 111 GLU cc_start: 0.6158 (mm-30) cc_final: 0.3807 (pm20) REVERT: e 86 ILE cc_start: 0.7395 (mp) cc_final: 0.7135 (mt) REVERT: e 284 TYR cc_start: 0.6550 (t80) cc_final: 0.5959 (t80) outliers start: 6 outliers final: 3 residues processed: 149 average time/residue: 0.0807 time to fit residues: 17.5176 Evaluate side-chains 143 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 140 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 132 HIS Chi-restraints excluded: chain e residue 108 TRP Chi-restraints excluded: chain e residue 281 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 0.0170 chunk 122 optimal weight: 0.1980 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 9.9990 overall best weight: 0.5820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 58 ASN e 279 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5031 r_free = 0.5031 target = 0.218907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4739 r_free = 0.4739 target = 0.191248 restraints weight = 61552.928| |-----------------------------------------------------------------------------| r_work (start): 0.4741 rms_B_bonded: 10.57 r_work: 0.4283 rms_B_bonded: 10.51 restraints_weight: 2.0000 r_work: 0.4472 rms_B_bonded: 6.33 restraints_weight: 4.0000 r_work (final): 0.4472 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4488 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4488 r_free = 0.4488 target_work(ls_wunit_k1) = 0.170 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4488 r_free = 0.4488 target_work(ls_wunit_k1) = 0.170 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4488 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5733 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10156 Z= 0.124 Angle : 0.620 9.690 13841 Z= 0.326 Chirality : 0.041 0.151 1639 Planarity : 0.004 0.052 1712 Dihedral : 13.919 169.119 1773 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.24 % Favored : 93.68 % Rotamer: Outliers : 2.53 % Allowed : 27.82 % Favored : 69.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.81 (0.22), residues: 1319 helix: -0.31 (0.19), residues: 693 sheet: -1.37 (0.69), residues: 66 loop : -2.33 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 144 TYR 0.037 0.001 TYR e 210 PHE 0.016 0.002 PHE D 152 TRP 0.028 0.002 TRP D 104 HIS 0.007 0.001 HIS D 30 Details of bonding type rmsd covalent geometry : bond 0.00263 (10156) covalent geometry : angle 0.62039 (13841) hydrogen bonds : bond 0.03704 ( 510) hydrogen bonds : angle 4.98580 ( 1485) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: a 24 TYR cc_start: 0.6020 (m-80) cc_final: 0.5762 (m-80) REVERT: a 31 ASN cc_start: 0.7718 (OUTLIER) cc_final: 0.7314 (t0) REVERT: a 48 LYS cc_start: 0.7007 (ptpp) cc_final: 0.6632 (ptpp) REVERT: D 263 MET cc_start: 0.5407 (pmm) cc_final: 0.5095 (pmm) REVERT: e 13 MET cc_start: 0.5986 (tmm) cc_final: 0.5537 (tmm) REVERT: e 95 TYR cc_start: 0.3906 (OUTLIER) cc_final: 0.0294 (t80) REVERT: e 120 GLU cc_start: 0.7179 (tt0) cc_final: 0.6564 (tt0) REVERT: e 124 MET cc_start: 0.6679 (mmp) cc_final: 0.6432 (mmm) REVERT: e 256 PHE cc_start: 0.6965 (OUTLIER) cc_final: 0.6687 (t80) REVERT: e 257 HIS cc_start: 0.6658 (p-80) cc_final: 0.6282 (p-80) outliers start: 22 outliers final: 10 residues processed: 163 average time/residue: 0.0800 time to fit residues: 19.4436 Evaluate side-chains 147 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain a residue 31 ASN Chi-restraints excluded: chain a residue 56 VAL Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain e residue 95 TYR Chi-restraints excluded: chain e residue 140 VAL Chi-restraints excluded: chain e residue 256 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 86 optimal weight: 2.9990 chunk 121 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 18 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 58 optimal weight: 0.5980 chunk 48 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 ASN E 89 HIS ** e 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5020 r_free = 0.5020 target = 0.217281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.183910 restraints weight = 58984.067| |-----------------------------------------------------------------------------| r_work (start): 0.4650 rms_B_bonded: 8.74 r_work: 0.4317 rms_B_bonded: 8.72 restraints_weight: 2.0000 r_work: 0.4496 rms_B_bonded: 5.16 restraints_weight: 4.0000 r_work (final): 0.4496 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4516 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4516 r_free = 0.4516 target_work(ls_wunit_k1) = 0.172 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4516 r_free = 0.4516 target_work(ls_wunit_k1) = 0.172 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4516 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5739 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10156 Z= 0.120 Angle : 0.575 10.937 13841 Z= 0.302 Chirality : 0.041 0.203 1639 Planarity : 0.003 0.048 1712 Dihedral : 13.643 169.544 1767 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.00 % Favored : 92.92 % Rotamer: Outliers : 3.45 % Allowed : 26.78 % Favored : 69.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.13 (0.23), residues: 1319 helix: 0.48 (0.20), residues: 693 sheet: -2.09 (0.53), residues: 98 loop : -2.15 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG e 291 TYR 0.019 0.001 TYR E 198 PHE 0.015 0.002 PHE D 152 TRP 0.028 0.002 TRP D 104 HIS 0.009 0.001 HIS D 30 Details of bonding type rmsd covalent geometry : bond 0.00261 (10156) covalent geometry : angle 0.57471 (13841) hydrogen bonds : bond 0.03159 ( 510) hydrogen bonds : angle 4.52777 ( 1485) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 151 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: A 26 GLU cc_start: 0.7537 (pm20) cc_final: 0.7235 (pm20) REVERT: A 70 ILE cc_start: 0.6525 (OUTLIER) cc_final: 0.6246 (pt) REVERT: a 31 ASN cc_start: 0.7697 (OUTLIER) cc_final: 0.7470 (t0) REVERT: a 48 LYS cc_start: 0.7167 (ptpp) cc_final: 0.6939 (ptpp) REVERT: D 16 LEU cc_start: 0.5490 (OUTLIER) cc_final: 0.5262 (mt) REVERT: D 102 GLN cc_start: 0.6952 (mm110) cc_final: 0.6319 (mm110) REVERT: D 111 GLU cc_start: 0.5996 (mm-30) cc_final: 0.4345 (pt0) REVERT: E 124 MET cc_start: 0.7958 (ptp) cc_final: 0.7703 (ptp) REVERT: E 187 GLU cc_start: 0.6557 (tp30) cc_final: 0.6351 (tp30) REVERT: e 95 TYR cc_start: 0.3908 (OUTLIER) cc_final: 0.0037 (t80) REVERT: e 251 ILE cc_start: 0.7192 (mm) cc_final: 0.6983 (mm) REVERT: e 256 PHE cc_start: 0.7242 (OUTLIER) cc_final: 0.6945 (t80) REVERT: e 257 HIS cc_start: 0.6776 (p-80) cc_final: 0.6353 (p-80) outliers start: 30 outliers final: 13 residues processed: 174 average time/residue: 0.1001 time to fit residues: 24.9433 Evaluate side-chains 155 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain a residue 31 ASN Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain e residue 95 TYR Chi-restraints excluded: chain e residue 108 TRP Chi-restraints excluded: chain e residue 210 TYR Chi-restraints excluded: chain e residue 256 PHE Chi-restraints excluded: chain e residue 263 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 112 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 42 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 54 optimal weight: 0.3980 chunk 76 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 GLN ** E 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 168 HIS ** e 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4990 r_free = 0.4990 target = 0.214503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.185708 restraints weight = 53279.006| |-----------------------------------------------------------------------------| r_work (start): 0.4677 rms_B_bonded: 9.48 r_work: 0.4252 rms_B_bonded: 9.36 restraints_weight: 2.0000 r_work: 0.4431 rms_B_bonded: 5.68 restraints_weight: 4.0000 r_work (final): 0.4431 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4445 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4445 r_free = 0.4445 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4445 r_free = 0.4445 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4445 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5852 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10156 Z= 0.141 Angle : 0.616 15.556 13841 Z= 0.318 Chirality : 0.042 0.169 1639 Planarity : 0.003 0.038 1712 Dihedral : 13.669 169.628 1767 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.70 % Favored : 93.23 % Rotamer: Outliers : 3.56 % Allowed : 27.70 % Favored : 68.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.97 (0.24), residues: 1319 helix: 0.66 (0.20), residues: 698 sheet: -2.12 (0.54), residues: 96 loop : -2.18 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 214 TYR 0.014 0.001 TYR D 14 PHE 0.021 0.002 PHE e 152 TRP 0.023 0.002 TRP D 104 HIS 0.009 0.001 HIS D 30 Details of bonding type rmsd covalent geometry : bond 0.00312 (10156) covalent geometry : angle 0.61554 (13841) hydrogen bonds : bond 0.03320 ( 510) hydrogen bonds : angle 4.52435 ( 1485) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: A 26 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7344 (pm20) REVERT: A 40 GLN cc_start: 0.6896 (pt0) cc_final: 0.6512 (pt0) REVERT: a 31 ASN cc_start: 0.7692 (OUTLIER) cc_final: 0.7248 (t0) REVERT: D 16 LEU cc_start: 0.5888 (OUTLIER) cc_final: 0.5654 (mt) REVERT: D 111 GLU cc_start: 0.5686 (mm-30) cc_final: 0.4311 (pt0) REVERT: E 287 ASN cc_start: 0.8520 (t0) cc_final: 0.8272 (t0) REVERT: E 288 ASN cc_start: 0.7197 (m-40) cc_final: 0.6688 (m-40) REVERT: e 13 MET cc_start: 0.6225 (tmm) cc_final: 0.5662 (tmm) REVERT: e 95 TYR cc_start: 0.4131 (OUTLIER) cc_final: 0.0102 (t80) REVERT: e 251 ILE cc_start: 0.7160 (mm) cc_final: 0.6959 (mm) REVERT: e 256 PHE cc_start: 0.7306 (OUTLIER) cc_final: 0.7003 (t80) outliers start: 31 outliers final: 21 residues processed: 168 average time/residue: 0.0840 time to fit residues: 20.4009 Evaluate side-chains 158 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain a residue 31 ASN Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain a residue 81 VAL Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 44 ASN Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain e residue 95 TYR Chi-restraints excluded: chain e residue 108 TRP Chi-restraints excluded: chain e residue 256 PHE Chi-restraints excluded: chain e residue 263 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 43 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 126 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 92 optimal weight: 7.9990 chunk 20 optimal weight: 0.4980 chunk 60 optimal weight: 7.9990 chunk 33 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 overall best weight: 1.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 279 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 = 0.4959 r_free = 0.4959 target = 0.211586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.182493 restraints weight = 53728.176| |-----------------------------------------------------------------------------| r_work (start): 0.4643 rms_B_bonded: 9.15 r_work: 0.4237 rms_B_bonded: 9.14 restraints_weight: 2.0000 r_work: 0.4418 rms_B_bonded: 5.41 restraints_weight: 4.0000 r_work (final): 0.4418 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4429 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4429 r_free = 0.4429 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4429 r_free = 0.4429 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4429 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5913 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 10156 Z= 0.163 Angle : 0.632 11.981 13841 Z= 0.330 Chirality : 0.042 0.175 1639 Planarity : 0.003 0.033 1712 Dihedral : 13.751 170.212 1767 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.46 % Favored : 92.47 % Rotamer: Outliers : 4.60 % Allowed : 26.90 % Favored : 68.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.01 (0.24), residues: 1319 helix: 0.67 (0.20), residues: 698 sheet: -1.64 (0.52), residues: 104 loop : -2.38 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 291 TYR 0.020 0.002 TYR E 284 PHE 0.017 0.002 PHE e 152 TRP 0.028 0.002 TRP D 104 HIS 0.007 0.001 HIS D 30 Details of bonding type rmsd covalent geometry : bond 0.00368 (10156) covalent geometry : angle 0.63224 (13841) hydrogen bonds : bond 0.03396 ( 510) hydrogen bonds : angle 4.63782 ( 1485) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 130 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7386 (pm20) REVERT: a 31 ASN cc_start: 0.7571 (OUTLIER) cc_final: 0.7225 (t0) REVERT: D 16 LEU cc_start: 0.5818 (OUTLIER) cc_final: 0.5607 (mt) REVERT: D 111 GLU cc_start: 0.5653 (mm-30) cc_final: 0.4508 (pt0) REVERT: e 95 TYR cc_start: 0.4323 (OUTLIER) cc_final: -0.0022 (t80) REVERT: e 245 ILE cc_start: 0.7143 (OUTLIER) cc_final: 0.6936 (mm) REVERT: e 256 PHE cc_start: 0.7288 (OUTLIER) cc_final: 0.6990 (t80) outliers start: 40 outliers final: 26 residues processed: 161 average time/residue: 0.0940 time to fit residues: 22.2619 Evaluate side-chains 158 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain a residue 31 ASN Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain a residue 81 VAL Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 44 ASN Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain e residue 32 HIS Chi-restraints excluded: chain e residue 95 TYR Chi-restraints excluded: chain e residue 108 TRP Chi-restraints excluded: chain e residue 140 VAL Chi-restraints excluded: chain e residue 210 TYR Chi-restraints excluded: chain e residue 245 ILE Chi-restraints excluded: chain e residue 256 PHE Chi-restraints excluded: chain e residue 263 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 63 optimal weight: 30.0000 chunk 59 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 chunk 70 optimal weight: 7.9990 chunk 69 optimal weight: 0.2980 chunk 19 optimal weight: 0.6980 chunk 98 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN D 36 ASN ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 132 HIS e 279 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4992 r_free = 0.4992 target = 0.214855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.186440 restraints weight = 60882.587| |-----------------------------------------------------------------------------| r_work (start): 0.4694 rms_B_bonded: 9.56 r_work: 0.4281 rms_B_bonded: 9.33 restraints_weight: 2.0000 r_work: 0.4461 rms_B_bonded: 5.58 restraints_weight: 4.0000 r_work (final): 0.4461 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4475 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4475 r_free = 0.4475 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4475 r_free = 0.4475 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4475 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5801 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10156 Z= 0.118 Angle : 0.594 12.105 13841 Z= 0.305 Chirality : 0.041 0.154 1639 Planarity : 0.003 0.033 1712 Dihedral : 13.560 169.060 1767 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.32 % Favored : 93.61 % Rotamer: Outliers : 4.48 % Allowed : 26.21 % Favored : 69.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.86 (0.24), residues: 1319 helix: 0.85 (0.21), residues: 697 sheet: -2.34 (0.52), residues: 99 loop : -2.21 (0.27), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 125 TYR 0.021 0.001 TYR e 284 PHE 0.016 0.002 PHE e 152 TRP 0.025 0.002 TRP D 104 HIS 0.008 0.001 HIS D 30 Details of bonding type rmsd covalent geometry : bond 0.00264 (10156) covalent geometry : angle 0.59390 (13841) hydrogen bonds : bond 0.03063 ( 510) hydrogen bonds : angle 4.43069 ( 1485) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 149 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: A 26 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7429 (pm20) REVERT: a 31 ASN cc_start: 0.7612 (OUTLIER) cc_final: 0.7010 (t0) REVERT: D 3 LYS cc_start: 0.5292 (pttm) cc_final: 0.4247 (mtmm) REVERT: D 27 GLN cc_start: 0.6282 (OUTLIER) cc_final: 0.5749 (mt0) REVERT: D 111 GLU cc_start: 0.5488 (mm-30) cc_final: 0.4516 (pm20) REVERT: E 95 TYR cc_start: 0.5059 (OUTLIER) cc_final: 0.3635 (t80) REVERT: E 124 MET cc_start: 0.7719 (ptp) cc_final: 0.7513 (ptp) REVERT: e 13 MET cc_start: 0.6246 (tmm) cc_final: 0.5672 (tmm) REVERT: e 18 ARG cc_start: 0.2550 (OUTLIER) cc_final: 0.1037 (mmt180) REVERT: e 95 TYR cc_start: 0.4113 (OUTLIER) cc_final: -0.0186 (t80) REVERT: e 256 PHE cc_start: 0.7242 (OUTLIER) cc_final: 0.6976 (t80) outliers start: 39 outliers final: 23 residues processed: 176 average time/residue: 0.0946 time to fit residues: 24.3792 Evaluate side-chains 165 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 135 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain a residue 31 ASN Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain D residue 27 GLN Chi-restraints excluded: chain D residue 44 ASN Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 230 HIS Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain e residue 18 ARG Chi-restraints excluded: chain e residue 95 TYR Chi-restraints excluded: chain e residue 108 TRP Chi-restraints excluded: chain e residue 140 VAL Chi-restraints excluded: chain e residue 210 TYR Chi-restraints excluded: chain e residue 256 PHE Chi-restraints excluded: chain e residue 263 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 25 optimal weight: 0.5980 chunk 37 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 123 optimal weight: 0.9980 chunk 42 optimal weight: 0.0470 chunk 70 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 54 optimal weight: 0.0060 chunk 73 optimal weight: 3.9990 chunk 93 optimal weight: 0.0050 chunk 119 optimal weight: 7.9990 overall best weight: 0.3308 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN D 12 ASN ** D 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5016 r_free = 0.5016 target = 0.217288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4739 r_free = 0.4739 target = 0.190080 restraints weight = 51681.794| |-----------------------------------------------------------------------------| r_work (start): 0.4732 rms_B_bonded: 8.15 r_work (final): 0.4732 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4730 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4730 r_free = 0.4730 target_work(ls_wunit_k1) = 0.189 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4730 r_free = 0.4730 target_work(ls_wunit_k1) = 0.189 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4730 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5370 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10156 Z= 0.113 Angle : 0.597 11.724 13841 Z= 0.308 Chirality : 0.042 0.243 1639 Planarity : 0.003 0.030 1712 Dihedral : 13.473 169.083 1767 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.39 % Favored : 93.53 % Rotamer: Outliers : 3.22 % Allowed : 28.51 % Favored : 68.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.59 (0.24), residues: 1319 helix: 1.02 (0.21), residues: 687 sheet: -1.47 (0.52), residues: 110 loop : -2.12 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 291 TYR 0.024 0.002 TYR E 284 PHE 0.023 0.002 PHE E 226 TRP 0.024 0.002 TRP D 104 HIS 0.011 0.001 HIS D 30 Details of bonding type rmsd covalent geometry : bond 0.00246 (10156) covalent geometry : angle 0.59665 (13841) hydrogen bonds : bond 0.03013 ( 510) hydrogen bonds : angle 4.37838 ( 1485) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 145 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.7130 (pm20) cc_final: 0.6846 (pm20) REVERT: a 31 ASN cc_start: 0.7137 (OUTLIER) cc_final: 0.6563 (t0) REVERT: D 102 GLN cc_start: 0.6295 (mm110) cc_final: 0.5896 (mm110) REVERT: D 111 GLU cc_start: 0.5311 (mm-30) cc_final: 0.4712 (pt0) REVERT: E 95 TYR cc_start: 0.4782 (OUTLIER) cc_final: 0.3793 (t80) REVERT: e 18 ARG cc_start: 0.2520 (OUTLIER) cc_final: 0.0916 (mmt180) REVERT: e 95 TYR cc_start: 0.3897 (OUTLIER) cc_final: 0.0135 (t80) outliers start: 28 outliers final: 19 residues processed: 164 average time/residue: 0.0992 time to fit residues: 23.3509 Evaluate side-chains 160 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain a residue 31 ASN Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain D residue 230 HIS Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 106 ARG Chi-restraints excluded: chain E residue 158 GLN Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain e residue 18 ARG Chi-restraints excluded: chain e residue 95 TYR Chi-restraints excluded: chain e residue 108 TRP Chi-restraints excluded: chain e residue 140 VAL Chi-restraints excluded: chain e residue 210 TYR Chi-restraints excluded: chain e residue 263 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 115 optimal weight: 0.9980 chunk 33 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 9 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 chunk 114 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 127 optimal weight: 0.8980 chunk 50 optimal weight: 6.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 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 = 0.4986 r_free = 0.4986 target = 0.214087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.186124 restraints weight = 58295.391| |-----------------------------------------------------------------------------| r_work (start): 0.4691 rms_B_bonded: 9.47 r_work: 0.4267 rms_B_bonded: 9.35 restraints_weight: 2.0000 r_work: 0.4445 rms_B_bonded: 5.60 restraints_weight: 4.0000 r_work (final): 0.4445 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4453 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4453 r_free = 0.4453 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4453 r_free = 0.4453 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4453 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5846 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10156 Z= 0.140 Angle : 0.618 12.054 13841 Z= 0.321 Chirality : 0.043 0.234 1639 Planarity : 0.003 0.037 1712 Dihedral : 13.510 169.936 1767 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.85 % Favored : 93.07 % Rotamer: Outliers : 3.91 % Allowed : 28.16 % Favored : 67.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.69 (0.24), residues: 1319 helix: 0.90 (0.21), residues: 703 sheet: -1.51 (0.51), residues: 109 loop : -2.20 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 291 TYR 0.049 0.002 TYR e 284 PHE 0.013 0.002 PHE D 152 TRP 0.022 0.002 TRP D 104 HIS 0.006 0.001 HIS D 30 Details of bonding type rmsd covalent geometry : bond 0.00318 (10156) covalent geometry : angle 0.61776 (13841) hydrogen bonds : bond 0.03180 ( 510) hydrogen bonds : angle 4.48735 ( 1485) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 135 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7523 (pm20) REVERT: a 31 ASN cc_start: 0.7716 (OUTLIER) cc_final: 0.7385 (t0) REVERT: D 3 LYS cc_start: 0.5212 (pttm) cc_final: 0.3998 (mtpp) REVERT: D 102 GLN cc_start: 0.7053 (mm110) cc_final: 0.6580 (mm110) REVERT: D 111 GLU cc_start: 0.5303 (mm-30) cc_final: 0.4528 (pt0) REVERT: D 261 GLN cc_start: 0.7278 (OUTLIER) cc_final: 0.6222 (mp10) REVERT: E 95 TYR cc_start: 0.5350 (OUTLIER) cc_final: 0.4344 (t80) REVERT: E 101 MET cc_start: 0.3703 (mmm) cc_final: 0.3475 (mmm) REVERT: e 13 MET cc_start: 0.6318 (tmm) cc_final: 0.5419 (ttm) REVERT: e 18 ARG cc_start: 0.2463 (OUTLIER) cc_final: 0.1000 (mmt180) REVERT: e 95 TYR cc_start: 0.4267 (OUTLIER) cc_final: -0.0139 (t80) outliers start: 34 outliers final: 24 residues processed: 159 average time/residue: 0.0949 time to fit residues: 22.0246 Evaluate side-chains 159 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 129 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain a residue 31 ASN Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 44 ASN Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 261 GLN Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 158 GLN Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain e residue 18 ARG Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 32 HIS Chi-restraints excluded: chain e residue 95 TYR Chi-restraints excluded: chain e residue 108 TRP Chi-restraints excluded: chain e residue 140 VAL Chi-restraints excluded: chain e residue 210 TYR Chi-restraints excluded: chain e residue 263 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 57 optimal weight: 5.9990 chunk 114 optimal weight: 0.8980 chunk 91 optimal weight: 20.0000 chunk 6 optimal weight: 0.8980 chunk 90 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 56 optimal weight: 20.0000 chunk 49 optimal weight: 9.9990 chunk 103 optimal weight: 9.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 HIS ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 257 HIS ** 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 = 0.4900 r_free = 0.4900 target = 0.205829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.170752 restraints weight = 57828.164| |-----------------------------------------------------------------------------| r_work (start): 0.4494 rms_B_bonded: 7.66 r_work: 0.4217 rms_B_bonded: 7.23 restraints_weight: 2.0000 r_work (final): 0.4217 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4232 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4232 r_free = 0.4232 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4232 r_free = 0.4232 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4232 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6157 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 10156 Z= 0.255 Angle : 0.759 12.467 13841 Z= 0.399 Chirality : 0.047 0.253 1639 Planarity : 0.004 0.043 1712 Dihedral : 14.050 170.562 1767 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 19.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.60 % Favored : 91.32 % Rotamer: Outliers : 4.14 % Allowed : 27.82 % Favored : 68.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.34 (0.24), residues: 1319 helix: 0.43 (0.20), residues: 698 sheet: -2.31 (0.47), residues: 115 loop : -2.44 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 214 TYR 0.046 0.003 TYR e 284 PHE 0.017 0.002 PHE D 152 TRP 0.045 0.003 TRP E 104 HIS 0.007 0.002 HIS E 30 Details of bonding type rmsd covalent geometry : bond 0.00573 (10156) covalent geometry : angle 0.75859 (13841) hydrogen bonds : bond 0.04098 ( 510) hydrogen bonds : angle 5.16991 ( 1485) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 141 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7586 (pm20) REVERT: a 31 ASN cc_start: 0.7919 (OUTLIER) cc_final: 0.7397 (t0) REVERT: D 111 GLU cc_start: 0.5895 (mm-30) cc_final: 0.4952 (pm20) REVERT: E 95 TYR cc_start: 0.6015 (OUTLIER) cc_final: 0.5680 (t80) REVERT: e 18 ARG cc_start: 0.3055 (OUTLIER) cc_final: 0.1392 (mmt180) REVERT: e 95 TYR cc_start: 0.5114 (OUTLIER) cc_final: 0.0735 (t80) outliers start: 36 outliers final: 27 residues processed: 167 average time/residue: 0.0907 time to fit residues: 21.9593 Evaluate side-chains 167 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain a residue 3 ILE Chi-restraints excluded: chain a residue 31 ASN Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain a residue 81 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 44 ASN Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 158 GLN Chi-restraints excluded: chain E residue 162 PHE Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain e residue 18 ARG Chi-restraints excluded: chain e residue 32 HIS Chi-restraints excluded: chain e residue 95 TYR Chi-restraints excluded: chain e residue 108 TRP Chi-restraints excluded: chain e residue 210 TYR Chi-restraints excluded: chain e residue 263 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 58 optimal weight: 0.0040 chunk 131 optimal weight: 2.9990 chunk 105 optimal weight: 0.0970 chunk 2 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 chunk 23 optimal weight: 0.9980 overall best weight: 1.0194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 ASN ** D 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 92 GLN ** 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 = 0.4945 r_free = 0.4945 target = 0.210155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.176981 restraints weight = 54056.014| |-----------------------------------------------------------------------------| r_work (start): 0.4568 rms_B_bonded: 7.98 r_work: 0.4272 rms_B_bonded: 7.50 restraints_weight: 2.0000 r_work (final): 0.4272 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4287 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4287 r_free = 0.4287 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4286 r_free = 0.4286 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4286 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6008 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10156 Z= 0.149 Angle : 0.673 12.858 13841 Z= 0.348 Chirality : 0.044 0.221 1639 Planarity : 0.003 0.038 1712 Dihedral : 13.795 168.862 1767 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.00 % Favored : 92.92 % Rotamer: Outliers : 3.45 % Allowed : 28.85 % Favored : 67.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.12 (0.24), residues: 1319 helix: 0.53 (0.20), residues: 704 sheet: -2.19 (0.48), residues: 112 loop : -2.24 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG a 19 TYR 0.052 0.002 TYR e 284 PHE 0.022 0.002 PHE e 152 TRP 0.023 0.003 TRP E 108 HIS 0.006 0.001 HIS D 30 Details of bonding type rmsd covalent geometry : bond 0.00336 (10156) covalent geometry : angle 0.67312 (13841) hydrogen bonds : bond 0.03429 ( 510) hydrogen bonds : angle 4.78502 ( 1485) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 148 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7560 (pm20) REVERT: A 40 GLN cc_start: 0.7237 (pm20) cc_final: 0.6985 (pm20) REVERT: a 31 ASN cc_start: 0.7932 (OUTLIER) cc_final: 0.7187 (t0) REVERT: D 3 LYS cc_start: 0.5565 (pttm) cc_final: 0.4666 (mtmm) REVERT: D 102 GLN cc_start: 0.7073 (mm110) cc_final: 0.6778 (mm110) REVERT: D 111 GLU cc_start: 0.5645 (mm-30) cc_final: 0.4425 (pm20) REVERT: e 18 ARG cc_start: 0.2755 (OUTLIER) cc_final: 0.1097 (mmt180) REVERT: e 95 TYR cc_start: 0.5093 (OUTLIER) cc_final: 0.0845 (t80) REVERT: e 101 MET cc_start: 0.5410 (mmt) cc_final: 0.4695 (mmp) outliers start: 30 outliers final: 23 residues processed: 167 average time/residue: 0.0999 time to fit residues: 23.9549 Evaluate side-chains 165 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 138 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain a residue 31 ASN Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain a residue 81 VAL Chi-restraints excluded: chain D residue 44 ASN Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 158 GLN Chi-restraints excluded: chain E residue 162 PHE Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain e residue 18 ARG Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 32 HIS Chi-restraints excluded: chain e residue 67 ASN Chi-restraints excluded: chain e residue 95 TYR Chi-restraints excluded: chain e residue 108 TRP Chi-restraints excluded: chain e residue 210 TYR Chi-restraints excluded: chain e residue 263 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 86 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 114 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 34 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 ASN ** D 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 ASN ** e 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4950 r_free = 0.4950 target = 0.210631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.182933 restraints weight = 43525.698| |-----------------------------------------------------------------------------| r_work (start): 0.4649 rms_B_bonded: 7.70 r_work (final): 0.4649 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4649 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4649 r_free = 0.4649 target_work(ls_wunit_k1) = 0.182 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4649 r_free = 0.4649 target_work(ls_wunit_k1) = 0.182 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4649 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5568 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10156 Z= 0.147 Angle : 0.666 12.576 13841 Z= 0.346 Chirality : 0.044 0.213 1639 Planarity : 0.003 0.040 1712 Dihedral : 13.681 169.533 1767 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.53 % Favored : 92.39 % Rotamer: Outliers : 2.99 % Allowed : 29.89 % Favored : 67.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.03 (0.24), residues: 1319 helix: 0.64 (0.20), residues: 704 sheet: -2.20 (0.46), residues: 117 loop : -2.23 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG a 19 TYR 0.052 0.002 TYR e 284 PHE 0.020 0.002 PHE e 152 TRP 0.023 0.002 TRP E 104 HIS 0.007 0.001 HIS D 30 Details of bonding type rmsd covalent geometry : bond 0.00333 (10156) covalent geometry : angle 0.66557 (13841) hydrogen bonds : bond 0.03353 ( 510) hydrogen bonds : angle 4.72476 ( 1485) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3139.88 seconds wall clock time: 54 minutes 38.95 seconds (3278.95 seconds total)