Starting phenix.real_space_refine on Thu Jul 2 20:21:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k25_36828/07_2026/8k25_36828.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k25_36828/07_2026/8k25_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_36828/07_2026/8k25_36828.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k25_36828/07_2026/8k25_36828.map" model { file = "/net/cci-nas-00/data/ceres_data/8k25_36828/07_2026/8k25_36828.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k25_36828/07_2026/8k25_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-dev-6108/lib/python3.11/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: 3.99, per 1000 atoms: 0.40 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: 0.89 Conformation dependent library (CDL) restraints added in 610.1 milliseconds 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: 1.11 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: 1.69 Time building geometry restraints manager: 1.17 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=" C3' DT U 6 " pdb=" O3' DT U 6 " ideal model delta sigma weight residual 1.435 1.484 -0.049 1.30e-02 5.92e+03 1.44e+01 bond pdb=" C3' DA U 9 " pdb=" C2' DA U 9 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.56e+00 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=" C3' DT V 12 " pdb=" C2' DT V 12 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.73e+00 ... (remaining 10151 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.35: 13557 3.35 - 6.69: 226 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: 1427 0.086 - 0.171: 194 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: 0.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.030 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5236 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 : 0.006 0.076 10156 Z= 0.294 Angle : 1.149 16.729 13841 Z= 0.616 Chirality : 0.057 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 are 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/Z covalent geometry : bond 0.00557 / 0.29 (10156) covalent geometry : angle 1.14894 / 0.62 (13841) hydrogen bonds : bond 0.15878 / 14.02 ( 510) hydrogen bonds : angle 7.59076 / 5.49 ( 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 : 0.375 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: 0.6551 (t80) cc_final: 0.5959 (t80) outliers start: 6 outliers final: 3 residues processed: 149 average time/residue: 0.0900 time to fit residues: 19.6913 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 : 0.272 ------------------------------------------------------------------------------- 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... ** A 61 ASN ** 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 = 0.5032 r_free = 0.5032 target = 0.218981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4738 r_free = 0.4738 target = 0.191260 restraints weight = 61932.209| |-----------------------------------------------------------------------------| r_work (start): 0.4741 rms_B_bonded: 10.70 r_work: 0.4287 rms_B_bonded: 10.47 restraints_weight: 2.0000 r_work: 0.4481 rms_B_bonded: 6.18 restraints_weight: 4.0000 r_work (final): 0.4481 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4494 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4494 r_free = 0.4494 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4494 r_free = 0.4494 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (6 function evaluations) r_final: 0.4494 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5762 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10156 Z= 0.121 Angle : 0.620 9.708 13841 Z= 0.327 Chirality : 0.041 0.156 1639 Planarity : 0.004 0.053 1712 Dihedral : 14.117 165.823 1773 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.01 % Favored : 93.91 % Rotamer: Outliers : 2.41 % Allowed : 27.70 % Favored : 69.89 % 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 are not related in a simple way. whole: -1.78 (0.22), residues: 1319 helix: -0.27 (0.19), residues: 692 sheet: -1.31 (0.70), residues: 66 loop : -2.33 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 144 TYR 0.033 0.001 TYR e 210 PHE 0.016 0.002 PHE D 152 TRP 0.029 0.002 TRP D 104 HIS 0.007 0.001 HIS D 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (10156) covalent geometry : angle 0.62007 / 0.33 (13841) hydrogen bonds : bond 0.03655 / 3.10 ( 510) hydrogen bonds : angle 4.97005 / 3.60 ( 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: 21 poor density : 148 time to evaluate : 0.226 Fit side-chains revert: symmetry clash REVERT: a 24 TYR cc_start: 0.6106 (m-80) cc_final: 0.5886 (m-80) REVERT: a 48 LYS cc_start: 0.7021 (ptpp) cc_final: 0.6683 (ptpp) REVERT: D 263 MET cc_start: 0.5535 (pmm) cc_final: 0.5226 (pmm) REVERT: e 13 MET cc_start: 0.5957 (tmm) cc_final: 0.5465 (tmm) REVERT: e 95 TYR cc_start: 0.3858 (OUTLIER) cc_final: 0.0289 (t80) REVERT: e 120 GLU cc_start: 0.7214 (tt0) cc_final: 0.6596 (tt0) REVERT: e 124 MET cc_start: 0.6785 (mmp) cc_final: 0.6483 (mmm) REVERT: e 256 PHE cc_start: 0.6930 (OUTLIER) cc_final: 0.6665 (t80) REVERT: e 257 HIS cc_start: 0.6667 (p-80) cc_final: 0.6309 (p-80) outliers start: 21 outliers final: 8 residues processed: 162 average time/residue: 0.0746 time to fit residues: 18.0587 Evaluate side-chains 142 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 132 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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 D residue 90 LEU Chi-restraints excluded: chain E residue 50 LEU 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: 0.8980 chunk 108 optimal weight: 7.9990 chunk 70 optimal weight: 0.9980 chunk 9 optimal weight: 8.9990 chunk 18 optimal weight: 0.0570 chunk 22 optimal weight: 0.0980 chunk 58 optimal weight: 0.0170 chunk 48 optimal weight: 9.9990 chunk 55 optimal weight: 9.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 ASN ** E 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 ASN ** 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 = 0.5042 r_free = 0.5042 target = 0.219709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4753 r_free = 0.4753 target = 0.192135 restraints weight = 59240.505| |-----------------------------------------------------------------------------| r_work (start): 0.4753 rms_B_bonded: 10.08 r_work (final): 0.4753 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4753 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4753 r_free = 0.4753 target_work(ls_wunit_k1) = 0.191 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4753 r_free = 0.4753 target_work(ls_wunit_k1) = 0.191 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.4753 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5310 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10156 Z= 0.107 Angle : 0.566 10.258 13841 Z= 0.297 Chirality : 0.041 0.214 1639 Planarity : 0.003 0.047 1712 Dihedral : 13.770 163.553 1767 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.09 % Favored : 93.84 % Rotamer: Outliers : 2.76 % Allowed : 27.36 % Favored : 69.89 % 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 are not related in a simple way. whole: -1.01 (0.23), residues: 1319 helix: 0.56 (0.20), residues: 688 sheet: -1.82 (0.62), residues: 80 loop : -2.11 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG e 291 TYR 0.040 0.001 TYR e 210 PHE 0.013 0.002 PHE D 152 TRP 0.027 0.002 TRP D 104 HIS 0.009 0.001 HIS D 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 (10156) covalent geometry : angle 0.56568 / 0.30 (13841) hydrogen bonds : bond 0.03114 / 2.61 ( 510) hydrogen bonds : angle 4.50037 / 3.22 ( 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 179 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 155 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: A 26 GLU cc_start: 0.7032 (pm20) cc_final: 0.6613 (pm20) REVERT: a 19 ARG cc_start: 0.7081 (OUTLIER) cc_final: 0.6734 (ptm160) REVERT: D 102 GLN cc_start: 0.6393 (mm110) cc_final: 0.6114 (mm110) REVERT: D 111 GLU cc_start: 0.5925 (mm-30) cc_final: 0.4296 (pt0) REVERT: E 124 MET cc_start: 0.7346 (ptp) cc_final: 0.7076 (ptp) REVERT: e 13 MET cc_start: 0.5570 (tmm) cc_final: 0.4419 (tmm) REVERT: e 95 TYR cc_start: 0.3752 (OUTLIER) cc_final: 0.0473 (t80) REVERT: e 120 GLU cc_start: 0.6257 (tt0) cc_final: 0.5812 (tt0) REVERT: e 256 PHE cc_start: 0.6395 (OUTLIER) cc_final: 0.6150 (t80) REVERT: e 257 HIS cc_start: 0.6539 (p-80) cc_final: 0.6167 (p-80) outliers start: 24 outliers final: 12 residues processed: 172 average time/residue: 0.0903 time to fit residues: 22.4553 Evaluate side-chains 150 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 0.424 ------------------------------------------------------------------------------- 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 19 ARG Chi-restraints excluded: chain a residue 56 VAL Chi-restraints excluded: chain a residue 76 SER Chi-restraints excluded: chain D residue 90 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 108 TRP Chi-restraints excluded: chain e residue 256 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 112 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 54 optimal weight: 10.0000 chunk 76 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 83 optimal weight: 0.0070 chunk 43 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.5202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 ASN ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 GLN ** E 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 HIS ** e 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4991 r_free = 0.4991 target = 0.214379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.185275 restraints weight = 53163.720| |-----------------------------------------------------------------------------| r_work (start): 0.4676 rms_B_bonded: 9.57 r_work: 0.4248 rms_B_bonded: 9.30 restraints_weight: 2.0000 r_work: 0.4425 rms_B_bonded: 5.69 restraints_weight: 4.0000 r_work (final): 0.4425 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4436 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4436 r_free = 0.4436 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4436 r_free = 0.4436 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.4436 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5916 moved from start: 0.2337 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= 0.155 Angle : 0.627 12.953 13841 Z= 0.328 Chirality : 0.043 0.173 1639 Planarity : 0.003 0.037 1712 Dihedral : 13.825 165.183 1767 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.00 % Favored : 92.92 % Rotamer: Outliers : 3.68 % Allowed : 27.47 % Favored : 68.85 % 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 are not related in a simple way. whole: -1.04 (0.24), residues: 1319 helix: 0.58 (0.20), residues: 700 sheet: -1.97 (0.57), residues: 91 loop : -2.23 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 270 TYR 0.016 0.002 TYR e 210 PHE 0.019 0.002 PHE e 152 TRP 0.030 0.002 TRP D 104 HIS 0.007 0.001 HIS D 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (10156) covalent geometry : angle 0.62676 / 0.33 (13841) hydrogen bonds : bond 0.03469 / 2.88 ( 510) hydrogen bonds : angle 4.59585 / 3.30 ( 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 173 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 141 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: A 26 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7373 (pm20) REVERT: A 40 GLN cc_start: 0.6908 (pt0) cc_final: 0.6556 (pt0) REVERT: D 102 GLN cc_start: 0.7025 (mm110) cc_final: 0.6567 (mm110) REVERT: D 111 GLU cc_start: 0.5803 (mm-30) cc_final: 0.4280 (pt0) REVERT: E 106 ARG cc_start: 0.5678 (OUTLIER) cc_final: 0.5260 (mtt-85) REVERT: E 124 MET cc_start: 0.8003 (ptp) cc_final: 0.7757 (ptp) REVERT: e 13 MET cc_start: 0.6282 (tmm) cc_final: 0.5708 (tmm) REVERT: e 95 TYR cc_start: 0.4138 (OUTLIER) cc_final: 0.0075 (t80) REVERT: e 256 PHE cc_start: 0.7187 (OUTLIER) cc_final: 0.6936 (t80) outliers start: 32 outliers final: 17 residues processed: 166 average time/residue: 0.0873 time to fit residues: 20.7938 Evaluate side-chains 156 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 1 MET 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 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 98 THR Chi-restraints excluded: chain E residue 106 ARG 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: 6.9990 chunk 10 optimal weight: 2.9990 chunk 126 optimal weight: 9.9990 chunk 30 optimal weight: 7.9990 chunk 92 optimal weight: 0.0670 chunk 20 optimal weight: 0.0470 chunk 60 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 106 optimal weight: 9.9990 overall best weight: 2.0222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN ** e 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 168 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4952 r_free = 0.4952 target = 0.210774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.181965 restraints weight = 53856.267| |-----------------------------------------------------------------------------| r_work (start): 0.4638 rms_B_bonded: 10.07 r_work: 0.4196 rms_B_bonded: 9.64 restraints_weight: 2.0000 r_work: 0.4377 rms_B_bonded: 5.80 restraints_weight: 4.0000 r_work (final): 0.4377 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4389 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4389 r_free = 0.4389 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4389 r_free = 0.4389 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.4389 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6012 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 10156 Z= 0.182 Angle : 0.651 11.158 13841 Z= 0.344 Chirality : 0.043 0.163 1639 Planarity : 0.003 0.030 1712 Dihedral : 13.999 166.867 1767 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.61 % Favored : 92.31 % Rotamer: Outliers : 5.17 % Allowed : 25.86 % Favored : 68.97 % 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 are not related in a simple way. whole: -1.12 (0.24), residues: 1319 helix: 0.58 (0.20), residues: 696 sheet: -1.57 (0.55), residues: 99 loop : -2.44 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 125 TYR 0.016 0.002 TYR e 284 PHE 0.016 0.002 PHE D 152 TRP 0.025 0.003 TRP E 104 HIS 0.006 0.001 HIS D 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 (10156) covalent geometry : angle 0.65071 / 0.34 (13841) hydrogen bonds : bond 0.03618 / 3.01 ( 510) hydrogen bonds : angle 4.76866 / 3.43 ( 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 183 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 138 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7382 (pm20) REVERT: D 3 LYS cc_start: 0.5554 (pttm) cc_final: 0.4647 (mtmm) REVERT: D 102 GLN cc_start: 0.7201 (mm110) cc_final: 0.6717 (mm110) REVERT: D 111 GLU cc_start: 0.5993 (mm-30) cc_final: 0.4749 (pt0) REVERT: D 223 ASP cc_start: 0.2369 (OUTLIER) cc_final: 0.2121 (t0) REVERT: E 106 ARG cc_start: 0.6048 (OUTLIER) cc_final: 0.5580 (mtt-85) REVERT: e 95 TYR cc_start: 0.4350 (OUTLIER) cc_final: 0.0050 (t80) REVERT: e 256 PHE cc_start: 0.7225 (OUTLIER) cc_final: 0.6915 (t80) outliers start: 45 outliers final: 27 residues processed: 174 average time/residue: 0.0845 time to fit residues: 21.2390 Evaluate side-chains 166 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 0.366 ------------------------------------------------------------------------------- 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 70 ILE Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain a residue 37 ILE 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 44 ASN Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain D residue 223 ASP Chi-restraints excluded: chain D residue 226 PHE 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 106 ARG Chi-restraints excluded: chain E residue 158 GLN Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 202 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 63 optimal weight: 30.0000 chunk 59 optimal weight: 30.0000 chunk 110 optimal weight: 0.2980 chunk 66 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 70 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 98 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 27 GLN ** 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** ** e 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 168 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4960 r_free = 0.4960 target = 0.211759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4679 r_free = 0.4679 target = 0.183953 restraints weight = 60927.070| |-----------------------------------------------------------------------------| r_work (start): 0.4665 rms_B_bonded: 9.75 r_work (final): 0.4665 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4665 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4665 r_free = 0.4665 target_work(ls_wunit_k1) = 0.183 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4665 r_free = 0.4665 target_work(ls_wunit_k1) = 0.183 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.4665 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5559 moved from start: 0.3042 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= 0.153 Angle : 0.631 11.947 13841 Z= 0.328 Chirality : 0.042 0.158 1639 Planarity : 0.003 0.033 1712 Dihedral : 13.936 165.224 1767 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.53 % Favored : 92.39 % Rotamer: Outliers : 4.94 % Allowed : 26.44 % Favored : 68.62 % 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 are not related in a simple way. whole: -1.10 (0.24), residues: 1319 helix: 0.62 (0.20), residues: 702 sheet: -1.66 (0.54), residues: 103 loop : -2.48 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 125 TYR 0.023 0.002 TYR E 284 PHE 0.016 0.002 PHE e 152 TRP 0.022 0.002 TRP D 104 HIS 0.007 0.001 HIS D 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (10156) covalent geometry : angle 0.63081 / 0.33 (13841) hydrogen bonds : bond 0.03375 / 2.77 ( 510) hydrogen bonds : angle 4.66054 / 3.38 ( 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 184 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 141 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6879 (pm20) REVERT: D 3 LYS cc_start: 0.5376 (pttm) cc_final: 0.4571 (mtmm) REVERT: D 102 GLN cc_start: 0.6693 (mm110) cc_final: 0.6306 (mm110) REVERT: D 111 GLU cc_start: 0.5634 (mm-30) cc_final: 0.4602 (pt0) REVERT: e 13 MET cc_start: 0.6240 (tmm) cc_final: 0.5767 (tmm) REVERT: e 18 ARG cc_start: 0.3204 (OUTLIER) cc_final: 0.1255 (mmt180) REVERT: e 95 TYR cc_start: 0.3978 (OUTLIER) cc_final: 0.0470 (t80) outliers start: 43 outliers final: 27 residues processed: 175 average time/residue: 0.0920 time to fit residues: 23.0077 Evaluate side-chains 167 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 137 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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 78 THR Chi-restraints excluded: chain a residue 58 VAL 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 138 VAL Chi-restraints excluded: chain D residue 215 SER 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 98 THR Chi-restraints excluded: chain E residue 158 GLN Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 202 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 25 optimal weight: 0.6980 chunk 37 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 123 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 70 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 93 optimal weight: 20.0000 chunk 119 optimal weight: 20.0000 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 27 GLN ** 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** ** e 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 279 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4948 r_free = 0.4948 target = 0.210612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.181969 restraints weight = 51560.092| |-----------------------------------------------------------------------------| r_work (start): 0.4640 rms_B_bonded: 8.92 r_work: 0.4229 rms_B_bonded: 8.89 restraints_weight: 2.0000 r_work: 0.4405 rms_B_bonded: 5.32 restraints_weight: 4.0000 r_work (final): 0.4405 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4416 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4416 r_free = 0.4416 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4416 r_free = 0.4416 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.4416 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5979 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 10156 Z= 0.167 Angle : 0.641 11.772 13841 Z= 0.336 Chirality : 0.043 0.157 1639 Planarity : 0.003 0.035 1712 Dihedral : 13.987 166.190 1767 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.14 % Favored : 91.78 % Rotamer: Outliers : 4.37 % Allowed : 27.01 % Favored : 68.62 % 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 are not related in a simple way. whole: -1.13 (0.24), residues: 1319 helix: 0.58 (0.20), residues: 704 sheet: -1.80 (0.52), residues: 101 loop : -2.46 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 125 TYR 0.020 0.002 TYR e 284 PHE 0.015 0.002 PHE a 68 TRP 0.021 0.002 TRP D 104 HIS 0.007 0.001 HIS D 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.17 (10156) covalent geometry : angle 0.64055 / 0.34 (13841) hydrogen bonds : bond 0.03506 / 2.87 ( 510) hydrogen bonds : angle 4.71939 / 3.42 ( 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 183 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 145 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7421 (pm20) REVERT: D 3 LYS cc_start: 0.5370 (pttm) cc_final: 0.4553 (mtmm) REVERT: D 102 GLN cc_start: 0.7049 (mm110) cc_final: 0.6657 (mm110) REVERT: D 111 GLU cc_start: 0.5741 (mm-30) cc_final: 0.4875 (pm20) REVERT: D 263 MET cc_start: 0.5709 (pmm) cc_final: 0.5097 (pmm) REVERT: E 30 HIS cc_start: 0.4714 (OUTLIER) cc_final: 0.4473 (p-80) REVERT: e 13 MET cc_start: 0.6389 (tmm) cc_final: 0.5802 (tmm) REVERT: e 18 ARG cc_start: 0.3083 (OUTLIER) cc_final: 0.1293 (mmt180) REVERT: e 95 TYR cc_start: 0.4398 (OUTLIER) cc_final: 0.0020 (t80) outliers start: 38 outliers final: 29 residues processed: 174 average time/residue: 0.0922 time to fit residues: 22.7659 Evaluate side-chains 176 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 143 time to evaluate : 0.373 ------------------------------------------------------------------------------- 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 59 VAL Chi-restraints excluded: chain a residue 13 ILE 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 23 VAL Chi-restraints excluded: chain D residue 44 ASN Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 188 PHE Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain E residue 30 HIS Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 56 ILE 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 158 GLN Chi-restraints excluded: chain E residue 162 PHE Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 202 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 115 optimal weight: 0.6980 chunk 33 optimal weight: 7.9990 chunk 37 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 114 optimal weight: 0.3980 chunk 3 optimal weight: 0.0060 chunk 44 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 overall best weight: 0.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 27 GLN ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4978 r_free = 0.4978 target = 0.213434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.186191 restraints weight = 58028.198| |-----------------------------------------------------------------------------| r_work (start): 0.4694 rms_B_bonded: 9.09 r_work (final): 0.4694 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4693 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4693 r_free = 0.4693 target_work(ls_wunit_k1) = 0.185 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4693 r_free = 0.4693 target_work(ls_wunit_k1) = 0.185 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.4693 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5492 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10156 Z= 0.126 Angle : 0.610 12.456 13841 Z= 0.316 Chirality : 0.042 0.177 1639 Planarity : 0.003 0.031 1712 Dihedral : 13.856 164.297 1767 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.08 % Favored : 92.85 % Rotamer: Outliers : 4.02 % Allowed : 27.24 % 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 are not related in a simple way. whole: -0.76 (0.24), residues: 1319 helix: 0.84 (0.20), residues: 695 sheet: -1.30 (0.58), residues: 89 loop : -2.24 (0.27), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 125 TYR 0.024 0.002 TYR e 284 PHE 0.018 0.002 PHE e 152 TRP 0.022 0.002 TRP D 104 HIS 0.008 0.001 HIS D 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (10156) covalent geometry : angle 0.61029 / 0.32 (13841) hydrogen bonds : bond 0.03159 / 2.57 ( 510) hydrogen bonds : angle 4.52436 / 3.28 ( 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 184 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 149 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.6935 (pm20) REVERT: D 3 LYS cc_start: 0.5230 (pttm) cc_final: 0.4362 (mtmm) REVERT: D 102 GLN cc_start: 0.6567 (mm110) cc_final: 0.6247 (mm110) REVERT: D 111 GLU cc_start: 0.5338 (mm-30) cc_final: 0.4582 (pm20) REVERT: e 13 MET cc_start: 0.6070 (tmm) cc_final: 0.5581 (tmm) REVERT: e 18 ARG cc_start: 0.3420 (OUTLIER) cc_final: 0.1343 (mmt180) REVERT: e 95 TYR cc_start: 0.3722 (OUTLIER) cc_final: 0.0146 (t80) outliers start: 35 outliers final: 26 residues processed: 171 average time/residue: 0.0945 time to fit residues: 22.8964 Evaluate side-chains 172 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 143 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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 59 VAL Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain a residue 81 VAL Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 40 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 E residue 42 TYR 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 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 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: 8.9990 chunk 114 optimal weight: 1.9990 chunk 91 optimal weight: 20.0000 chunk 6 optimal weight: 0.8980 chunk 90 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 42 optimal weight: 0.0570 chunk 56 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 overall best weight: 2.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 230 HIS ** 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 = 0.4934 r_free = 0.4934 target = 0.209245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.181900 restraints weight = 57894.626| |-----------------------------------------------------------------------------| r_work (start): 0.4644 rms_B_bonded: 9.97 r_work (final): 0.4644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4644 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4644 r_free = 0.4644 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4644 r_free = 0.4644 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (6 function evaluations) r_final: 0.4644 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5629 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 10156 Z= 0.195 Angle : 0.693 12.155 13841 Z= 0.362 Chirality : 0.044 0.195 1639 Planarity : 0.004 0.036 1712 Dihedral : 14.007 166.662 1767 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.90 % Favored : 91.02 % Rotamer: Outliers : 3.68 % Allowed : 27.93 % Favored : 68.39 % 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 are not related in a simple way. whole: -1.08 (0.24), residues: 1319 helix: 0.59 (0.20), residues: 706 sheet: -1.70 (0.56), residues: 88 loop : -2.42 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 AARG E 106 TYR 0.031 0.002 TYR D 177 PHE 0.018 0.002 PHE e 152 TRP 0.023 0.003 TRP E 104 HIS 0.007 0.001 HIS E 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.20 (10156) covalent geometry : angle 0.69330 / 0.36 (13841) hydrogen bonds : bond 0.03680 / 3.04 ( 510) hydrogen bonds : angle 4.84935 / 3.53 ( 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 176 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 144 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6784 (pm20) REVERT: D 3 LYS cc_start: 0.5494 (pttm) cc_final: 0.4728 (mtmm) REVERT: D 102 GLN cc_start: 0.6707 (mm110) cc_final: 0.6385 (mm110) REVERT: D 111 GLU cc_start: 0.5617 (mm-30) cc_final: 0.4722 (pm20) REVERT: D 226 PHE cc_start: 0.7900 (OUTLIER) cc_final: 0.7594 (m-80) REVERT: D 263 MET cc_start: 0.5501 (pmm) cc_final: 0.5066 (pmm) REVERT: e 13 MET cc_start: 0.6178 (tmm) cc_final: 0.5615 (tmm) REVERT: e 18 ARG cc_start: 0.3373 (OUTLIER) cc_final: 0.1619 (mmt180) REVERT: e 95 TYR cc_start: 0.4456 (OUTLIER) cc_final: 0.0781 (t80) outliers start: 32 outliers final: 27 residues processed: 166 average time/residue: 0.0968 time to fit residues: 22.7307 Evaluate side-chains 172 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 141 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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 59 VAL 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 188 PHE Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain D residue 226 PHE 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 158 GLN Chi-restraints excluded: chain E residue 162 PHE Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 202 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 67 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 58 optimal weight: 0.5980 chunk 131 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 23 optimal weight: 0.0070 overall best weight: 1.7202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 230 HIS ** 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 = 0.4942 r_free = 0.4942 target = 0.209577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.175897 restraints weight = 54312.494| |-----------------------------------------------------------------------------| r_work (start): 0.4561 rms_B_bonded: 7.54 r_work (final): 0.4561 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4561 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4561 r_free = 0.4561 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4561 r_free = 0.4561 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (5 function evaluations) r_final: 0.4561 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5814 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10156 Z= 0.168 Angle : 0.672 12.099 13841 Z= 0.349 Chirality : 0.044 0.173 1639 Planarity : 0.003 0.039 1712 Dihedral : 13.953 165.504 1767 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.14 % Favored : 91.78 % Rotamer: Outliers : 3.91 % Allowed : 27.82 % 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 are not related in a simple way. whole: -1.09 (0.24), residues: 1319 helix: 0.62 (0.20), residues: 705 sheet: -2.25 (0.50), residues: 103 loop : -2.32 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 AARG E 106 TYR 0.025 0.002 TYR e 284 PHE 0.019 0.002 PHE e 152 TRP 0.023 0.003 TRP E 104 HIS 0.006 0.001 HIS E 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (10156) covalent geometry : angle 0.67203 / 0.35 (13841) hydrogen bonds : bond 0.03494 / 2.88 ( 510) hydrogen bonds : angle 4.77221 / 3.48 ( 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 170 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 136 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.7156 (pm20) REVERT: D 3 LYS cc_start: 0.5380 (pttm) cc_final: 0.4602 (mtmm) REVERT: D 102 GLN cc_start: 0.6831 (mm110) cc_final: 0.6503 (mm110) REVERT: D 111 GLU cc_start: 0.5492 (mm-30) cc_final: 0.4617 (pm20) REVERT: D 226 PHE cc_start: 0.8353 (OUTLIER) cc_final: 0.8102 (m-80) REVERT: D 263 MET cc_start: 0.5592 (pmm) cc_final: 0.5088 (pmm) REVERT: E 124 MET cc_start: 0.7355 (ptp) cc_final: 0.6948 (ptp) REVERT: e 13 MET cc_start: 0.6376 (tmm) cc_final: 0.5831 (tmm) REVERT: e 18 ARG cc_start: 0.2988 (OUTLIER) cc_final: 0.1233 (mmt180) REVERT: e 95 TYR cc_start: 0.4795 (OUTLIER) cc_final: 0.1218 (t80) outliers start: 34 outliers final: 27 residues processed: 160 average time/residue: 0.0929 time to fit residues: 21.2876 Evaluate side-chains 167 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 0.388 ------------------------------------------------------------------------------- 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 59 VAL Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain a residue 81 VAL Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 44 ASN Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 188 PHE Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain D residue 226 PHE 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 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 67 ASN Chi-restraints excluded: chain e residue 95 TYR Chi-restraints excluded: chain e residue 101 MET 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: 0.9990 chunk 53 optimal weight: 20.0000 chunk 114 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 126 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 92 GLN ** 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 = 0.4965 r_free = 0.4965 target = 0.211938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.183731 restraints weight = 43489.768| |-----------------------------------------------------------------------------| r_work (start): 0.4661 rms_B_bonded: 7.69 r_work (final): 0.4661 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4662 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4662 r_free = 0.4662 target_work(ls_wunit_k1) = 0.183 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4662 r_free = 0.4662 target_work(ls_wunit_k1) = 0.183 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (6 function evaluations) r_final: 0.4662 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5596 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10156 Z= 0.132 Angle : 0.646 12.232 13841 Z= 0.330 Chirality : 0.042 0.166 1639 Planarity : 0.003 0.036 1712 Dihedral : 13.838 164.494 1767 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.22 % Favored : 91.70 % Rotamer: Outliers : 3.45 % Allowed : 28.05 % 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 are not related in a simple way. whole: -0.84 (0.24), residues: 1319 helix: 0.78 (0.20), residues: 707 sheet: -2.04 (0.51), residues: 103 loop : -2.18 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 AARG E 106 TYR 0.026 0.002 TYR e 284 PHE 0.019 0.002 PHE e 152 TRP 0.026 0.002 TRP E 73 HIS 0.006 0.001 HIS E 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (10156) covalent geometry : angle 0.64611 / 0.33 (13841) hydrogen bonds : bond 0.03220 / 2.66 ( 510) hydrogen bonds : angle 4.58353 / 3.35 ( 1485) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2324.37 seconds wall clock time: 40 minutes 44.91 seconds (2444.91 seconds total)