Starting phenix.real_space_refine on Wed Aug 5 13:53:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k25_36828/08_2026/8k25_36828.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k25_36828/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8k25_36828/08_2026/8k25_36828.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k25_36828/08_2026/8k25_36828.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k25_36828/08_2026/8k25_36828.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k25_36828/08_2026/8k25_36828.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.076 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 374 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 34 5.49 5 S 47 5.16 5 C 6226 2.51 5 N 1687 2.21 5 O 1967 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/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: 2.81, per 1000 atoms: 0.28 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: 0.66 Conformation dependent library (CDL) restraints added in 585.8 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: 0.84 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: 1.07 Time building geometry restraints manager: 0.92 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: 0.600 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.070 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.950 ------------------------------------------------------------------------------- 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= 0.295 Angle : 1.149 16.729 13841 Z= 0.617 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 1.14942 / 0.62 (13841) hydrogen bonds : bond 0.15878 / 14.07 ( 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 : 0.382 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: 0.0806 time to fit residues: 18.0207 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 : 0.355 ------------------------------------------------------------------------------- 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 = 0.5030 r_free = 0.5030 target = 0.218909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4740 r_free = 0.4740 target = 0.191264 restraints weight = 61988.933| |-----------------------------------------------------------------------------| r_work (start): 0.4742 rms_B_bonded: 10.64 r_work: 0.4283 rms_B_bonded: 10.54 restraints_weight: 2.0000 r_work: 0.4471 rms_B_bonded: 6.35 restraints_weight: 4.0000 r_work (final): 0.4471 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4482 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4482 r_free = 0.4482 target_work(ls_wunit_k1) = 0.170 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4482 r_free = 0.4482 target_work(ls_wunit_k1) = 0.170 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (6 function evaluations) r_final: 0.4482 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5772 moved from start: 0.1418 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= 0.124 Angle : 0.617 9.568 13841 Z= 0.325 Chirality : 0.041 0.161 1639 Planarity : 0.003 0.054 1712 Dihedral : 14.119 166.488 1773 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.94 % Favored : 93.99 % Rotamer: Outliers : 2.41 % Allowed : 27.59 % Favored : 70.00 % 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: -1.77 (0.22), residues: 1319 helix: -0.26 (0.19), residues: 692 sheet: -1.33 (0.69), residues: 66 loop : -2.32 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 144 TYR 0.036 0.001 TYR e 210 PHE 0.017 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 0.00255 / 0.12 (10156) covalent geometry : angle 0.61657 / 0.32 (13841) hydrogen bonds : bond 0.03625 / 3.10 ( 510) hydrogen bonds : angle 4.94137 / 3.58 ( 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 : 0.260 Fit side-chains revert: symmetry clash REVERT: a 24 TYR cc_start: 0.6136 (m-80) cc_final: 0.5925 (m-80) REVERT: a 48 LYS cc_start: 0.7016 (ptpp) cc_final: 0.6671 (ptpp) REVERT: D 263 MET cc_start: 0.5533 (pmm) cc_final: 0.5212 (pmm) REVERT: e 13 MET cc_start: 0.5994 (tmm) cc_final: 0.5502 (tmm) REVERT: e 95 TYR cc_start: 0.3856 (OUTLIER) cc_final: 0.0305 (t80) REVERT: e 120 GLU cc_start: 0.7238 (tt0) cc_final: 0.6610 (tt0) REVERT: e 124 MET cc_start: 0.6776 (mmp) cc_final: 0.6551 (mmm) REVERT: e 256 PHE cc_start: 0.6948 (OUTLIER) cc_final: 0.6679 (t80) REVERT: e 257 HIS cc_start: 0.6655 (p-80) cc_final: 0.6283 (p-80) outliers start: 21 outliers final: 9 residues processed: 162 average time/residue: 0.0722 time to fit residues: 17.5106 Evaluate side-chains 143 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 0.266 ------------------------------------------------------------------------------- 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 86 ILE Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain e residue 95 TYR Chi-restraints excluded: chain e residue 140 VAL Chi-restraints excluded: chain e residue 256 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 86 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 18 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 chunk 80 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 ASN E 89 HIS ** E 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.5014 r_free = 0.5014 target = 0.216806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4709 r_free = 0.4709 target = 0.187928 restraints weight = 58972.327| |-----------------------------------------------------------------------------| r_work (start): 0.4704 rms_B_bonded: 10.59 r_work: 0.4247 rms_B_bonded: 10.35 restraints_weight: 2.0000 r_work: 0.4435 rms_B_bonded: 6.27 restraints_weight: 4.0000 r_work (final): 0.4435 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4451 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4451 r_free = 0.4451 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4451 r_free = 0.4451 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.4451 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5853 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10156 Z= 0.124 Angle : 0.582 10.609 13841 Z= 0.307 Chirality : 0.041 0.203 1639 Planarity : 0.003 0.048 1712 Dihedral : 13.869 164.770 1767 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.77 % Favored : 93.15 % Rotamer: Outliers : 2.99 % Allowed : 27.59 % Favored : 69.43 % 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: -1.15 (0.23), residues: 1319 helix: 0.46 (0.20), residues: 691 sheet: -2.16 (0.53), residues: 100 loop : -2.14 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG e 291 TYR 0.017 0.001 TYR E 198 PHE 0.015 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 0.00266 / 0.12 (10156) covalent geometry : angle 0.58250 / 0.31 (13841) hydrogen bonds : bond 0.03267 / 2.75 ( 510) hydrogen bonds : angle 4.59643 / 3.29 ( 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 177 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 26 GLU cc_start: 0.7584 (pm20) cc_final: 0.7270 (pm20) REVERT: a 48 LYS cc_start: 0.7048 (ptpp) cc_final: 0.6782 (ptpp) REVERT: D 16 LEU cc_start: 0.5637 (OUTLIER) cc_final: 0.5426 (mt) REVERT: D 102 GLN cc_start: 0.6878 (mm110) cc_final: 0.6419 (mm110) REVERT: D 111 GLU cc_start: 0.6038 (mm-30) cc_final: 0.4217 (pt0) REVERT: E 124 MET cc_start: 0.7978 (ptp) cc_final: 0.7704 (ptp) REVERT: E 287 ASN cc_start: 0.8556 (t0) cc_final: 0.8256 (t0) REVERT: e 95 TYR cc_start: 0.3969 (OUTLIER) cc_final: 0.0070 (t80) REVERT: e 120 GLU cc_start: 0.7274 (tt0) cc_final: 0.6620 (tt0) REVERT: e 256 PHE cc_start: 0.7208 (OUTLIER) cc_final: 0.6921 (t80) REVERT: e 257 HIS cc_start: 0.6760 (p-80) cc_final: 0.6352 (p-80) outliers start: 26 outliers final: 12 residues processed: 171 average time/residue: 0.0811 time to fit residues: 19.9361 Evaluate side-chains 152 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 0.315 ------------------------------------------------------------------------------- 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 58 VAL Chi-restraints excluded: chain D residue 16 LEU 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 210 TYR 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: 7.9990 chunk 3 optimal weight: 0.0050 chunk 27 optimal weight: 0.8980 chunk 42 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 54 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 83 optimal weight: 0.0970 chunk 43 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 overall best weight: 0.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 GLN ** E 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5006 r_free = 0.5006 target = 0.216188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.187265 restraints weight = 53361.879| |-----------------------------------------------------------------------------| r_work (start): 0.4690 rms_B_bonded: 9.90 r_work: 0.4260 rms_B_bonded: 9.67 restraints_weight: 2.0000 r_work: 0.4444 rms_B_bonded: 5.83 restraints_weight: 4.0000 r_work (final): 0.4444 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4457 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4457 r_free = 0.4457 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4457 r_free = 0.4457 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.4457 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5855 moved from start: 0.2193 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= 0.126 Angle : 0.597 12.281 13841 Z= 0.309 Chirality : 0.042 0.177 1639 Planarity : 0.003 0.039 1712 Dihedral : 13.868 165.484 1767 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.39 % Favored : 93.53 % Rotamer: Outliers : 3.91 % Allowed : 27.47 % 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: -0.90 (0.24), residues: 1319 helix: 0.71 (0.20), residues: 691 sheet: -1.92 (0.57), residues: 91 loop : -2.13 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG a 19 TYR 0.011 0.001 TYR e 210 PHE 0.017 0.002 PHE e 152 TRP 0.029 0.002 TRP D 104 HIS 0.008 0.001 HIS D 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (10156) covalent geometry : angle 0.59699 / 0.31 (13841) hydrogen bonds : bond 0.03204 / 2.66 ( 510) hydrogen bonds : angle 4.51030 / 3.25 ( 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: 34 poor density : 139 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7327 (pm20) REVERT: A 70 ILE cc_start: 0.6571 (OUTLIER) cc_final: 0.6283 (pt) REVERT: D 16 LEU cc_start: 0.5762 (OUTLIER) cc_final: 0.5541 (mt) REVERT: D 102 GLN cc_start: 0.6989 (mm110) cc_final: 0.6513 (mm110) REVERT: D 111 GLU cc_start: 0.5821 (mm-30) cc_final: 0.4310 (pt0) REVERT: E 106 ARG cc_start: 0.5708 (OUTLIER) cc_final: 0.5275 (mtt-85) REVERT: E 124 MET cc_start: 0.7992 (ptp) cc_final: 0.7742 (ptp) REVERT: e 13 MET cc_start: 0.5992 (tmm) cc_final: 0.5328 (tmm) REVERT: e 95 TYR cc_start: 0.4062 (OUTLIER) cc_final: 0.0016 (t80) REVERT: e 256 PHE cc_start: 0.7194 (OUTLIER) cc_final: 0.6883 (t80) outliers start: 34 outliers final: 22 residues processed: 163 average time/residue: 0.0715 time to fit residues: 17.0899 Evaluate side-chains 160 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain a residue 81 VAL Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 44 ASN Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 106 ARG Chi-restraints excluded: chain E residue 158 GLN Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain e residue 95 TYR Chi-restraints excluded: chain e residue 108 TRP Chi-restraints excluded: chain e residue 256 PHE Chi-restraints excluded: chain e residue 263 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 43 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 126 optimal weight: 9.9990 chunk 30 optimal weight: 7.9990 chunk 92 optimal weight: 6.9990 chunk 20 optimal weight: 0.0170 chunk 60 optimal weight: 5.9990 chunk 33 optimal weight: 20.0000 chunk 21 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 overall best weight: 2.3422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 134 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4944 r_free = 0.4944 target = 0.210144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.181249 restraints weight = 53824.643| |-----------------------------------------------------------------------------| r_work (start): 0.4627 rms_B_bonded: 9.29 r_work: 0.4222 rms_B_bonded: 8.73 restraints_weight: 2.0000 r_work: 0.4397 rms_B_bonded: 5.22 restraints_weight: 4.0000 r_work (final): 0.4397 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4410 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4410 r_free = 0.4410 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4410 r_free = 0.4410 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.4410 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6006 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 10156 Z= 0.200 Angle : 0.669 11.710 13841 Z= 0.354 Chirality : 0.044 0.175 1639 Planarity : 0.003 0.039 1712 Dihedral : 14.112 168.148 1767 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.84 % Favored : 92.09 % Rotamer: Outliers : 5.17 % Allowed : 26.09 % 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: -1.24 (0.24), residues: 1319 helix: 0.48 (0.20), residues: 702 sheet: -1.79 (0.52), residues: 104 loop : -2.50 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 125 TYR 0.016 0.002 TYR D 14 PHE 0.017 0.002 PHE e 152 TRP 0.027 0.003 TRP D 104 HIS 0.005 0.001 HIS D 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.20 (10156) covalent geometry : angle 0.66909 / 0.35 (13841) hydrogen bonds : bond 0.03796 / 3.17 ( 510) hydrogen bonds : angle 4.84823 / 3.50 ( 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 178 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 133 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: A 26 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7442 (pm20) REVERT: D 102 GLN cc_start: 0.7203 (mm110) cc_final: 0.6738 (mm110) REVERT: D 111 GLU cc_start: 0.6013 (mm-30) cc_final: 0.4622 (pt0) REVERT: E 106 ARG cc_start: 0.6025 (OUTLIER) cc_final: 0.5581 (mtt-85) REVERT: E 287 ASN cc_start: 0.8316 (t0) cc_final: 0.8076 (t0) REVERT: E 288 ASN cc_start: 0.7102 (m-40) cc_final: 0.6710 (m-40) REVERT: e 95 TYR cc_start: 0.4304 (OUTLIER) cc_final: 0.0031 (t80) REVERT: e 256 PHE cc_start: 0.7169 (OUTLIER) cc_final: 0.6935 (t80) outliers start: 45 outliers final: 28 residues processed: 168 average time/residue: 0.0687 time to fit residues: 16.8461 Evaluate side-chains 157 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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 61 ASN Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain a residue 13 ILE Chi-restraints excluded: chain a residue 19 ARG 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 129 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 226 PHE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 106 ARG Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain e residue 32 HIS 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: 40.0000 chunk 59 optimal weight: 30.0000 chunk 110 optimal weight: 0.4980 chunk 66 optimal weight: 0.2980 chunk 41 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 chunk 69 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 ASN ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 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 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 168 HIS ** e 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 279 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4956 r_free = 0.4956 target = 0.211278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.182621 restraints weight = 61065.140| |-----------------------------------------------------------------------------| r_work (start): 0.4650 rms_B_bonded: 9.91 r_work: 0.4206 rms_B_bonded: 9.79 restraints_weight: 2.0000 r_work: 0.4390 rms_B_bonded: 5.83 restraints_weight: 4.0000 r_work (final): 0.4390 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4402 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4402 r_free = 0.4402 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4402 r_free = 0.4402 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.4402 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5994 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 10156 Z= 0.158 Angle : 0.643 12.115 13841 Z= 0.334 Chirality : 0.043 0.174 1639 Planarity : 0.003 0.036 1712 Dihedral : 14.039 166.400 1767 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.23 % Favored : 92.69 % Rotamer: Outliers : 4.71 % Allowed : 26.44 % 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: -1.21 (0.24), residues: 1319 helix: 0.53 (0.20), residues: 703 sheet: -1.70 (0.54), residues: 99 loop : -2.56 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 291 TYR 0.020 0.002 TYR E 284 PHE 0.016 0.002 PHE e 152 TRP 0.025 0.002 TRP D 104 HIS 0.008 0.001 HIS e 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (10156) covalent geometry : angle 0.64272 / 0.33 (13841) hydrogen bonds : bond 0.03462 / 2.86 ( 510) hydrogen bonds : angle 4.72894 / 3.42 ( 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 179 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 138 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7427 (pm20) REVERT: D 3 LYS cc_start: 0.5512 (pttm) cc_final: 0.4596 (mtmm) REVERT: D 102 GLN cc_start: 0.7193 (mm110) cc_final: 0.6744 (mm110) REVERT: D 111 GLU cc_start: 0.5910 (mm-30) cc_final: 0.4646 (pt0) REVERT: E 106 ARG cc_start: 0.6066 (OUTLIER) cc_final: 0.5596 (mtt-85) REVERT: e 13 MET cc_start: 0.6541 (tmm) cc_final: 0.5998 (tmm) REVERT: e 18 ARG cc_start: 0.2858 (OUTLIER) cc_final: 0.1061 (mmt180) REVERT: e 95 TYR cc_start: 0.4316 (OUTLIER) cc_final: 0.0017 (t80) REVERT: e 235 ARG cc_start: 0.5415 (tpt170) cc_final: 0.4435 (tpp-160) outliers start: 41 outliers final: 28 residues processed: 170 average time/residue: 0.0760 time to fit residues: 18.7907 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 : 0.218 ------------------------------------------------------------------------------- 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 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 56 ILE Chi-restraints excluded: chain D residue 90 LEU 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 106 ARG Chi-restraints excluded: chain E residue 158 GLN Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain e residue 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 25 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 1 optimal weight: 20.0000 chunk 123 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 119 optimal weight: 20.0000 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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** ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 ASN ** e 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4946 r_free = 0.4946 target = 0.210350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.182053 restraints weight = 51672.186| |-----------------------------------------------------------------------------| r_work (start): 0.4641 rms_B_bonded: 8.58 r_work (final): 0.4641 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4642 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4642 r_free = 0.4642 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 = 0.4642 r_free = 0.4642 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.4642 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5644 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 10156 Z= 0.166 Angle : 0.649 12.244 13841 Z= 0.339 Chirality : 0.043 0.175 1639 Planarity : 0.003 0.040 1712 Dihedral : 14.055 167.198 1767 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.22 % Favored : 91.70 % Rotamer: Outliers : 4.60 % Allowed : 26.44 % 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: -1.20 (0.24), residues: 1319 helix: 0.54 (0.20), residues: 706 sheet: -1.84 (0.52), residues: 99 loop : -2.52 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG a 19 TYR 0.016 0.002 TYR E 14 PHE 0.015 0.002 PHE D 152 TRP 0.023 0.002 TRP E 104 HIS 0.006 0.001 HIS e 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (10156) covalent geometry : angle 0.64856 / 0.34 (13841) hydrogen bonds : bond 0.03494 / 2.89 ( 510) hydrogen bonds : angle 4.76724 / 3.44 ( 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 179 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 139 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6769 (pm20) REVERT: D 3 LYS cc_start: 0.5483 (pttm) cc_final: 0.4685 (mtmm) REVERT: D 102 GLN cc_start: 0.6800 (mm110) cc_final: 0.6442 (mm110) REVERT: D 111 GLU cc_start: 0.5653 (mm-30) cc_final: 0.4636 (pt0) REVERT: E 263 MET cc_start: 0.1110 (mpp) cc_final: 0.0757 (mpp) REVERT: e 13 MET cc_start: 0.6235 (tmm) cc_final: 0.5716 (tmm) REVERT: e 18 ARG cc_start: 0.3444 (OUTLIER) cc_final: 0.1411 (mmt180) REVERT: e 95 TYR cc_start: 0.4020 (OUTLIER) cc_final: 0.0374 (t80) outliers start: 40 outliers final: 27 residues processed: 169 average time/residue: 0.0747 time to fit residues: 18.2653 Evaluate side-chains 165 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 135 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain a residue 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 56 ILE 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 239 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 158 GLN Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain e residue 18 ARG Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 32 HIS Chi-restraints excluded: chain e residue 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 115 optimal weight: 0.0770 chunk 33 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 chunk 3 optimal weight: 0.3980 chunk 44 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 50 optimal weight: 9.9990 overall best weight: 0.8942 ------------------------------------------------------------------------------- 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** ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4974 r_free = 0.4974 target = 0.213156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.183905 restraints weight = 58227.518| |-----------------------------------------------------------------------------| r_work (start): 0.4661 rms_B_bonded: 9.46 r_work: 0.4255 rms_B_bonded: 9.28 restraints_weight: 2.0000 r_work: 0.4435 rms_B_bonded: 5.50 restraints_weight: 4.0000 r_work (final): 0.4435 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4449 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4449 r_free = 0.4449 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4449 r_free = 0.4449 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.4449 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5902 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10156 Z= 0.129 Angle : 0.619 12.311 13841 Z= 0.319 Chirality : 0.042 0.186 1639 Planarity : 0.003 0.037 1712 Dihedral : 13.943 165.461 1767 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 14.55 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: -0.88 (0.24), residues: 1319 helix: 0.80 (0.20), residues: 701 sheet: -1.82 (0.50), residues: 106 loop : -2.31 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 125 TYR 0.028 0.002 TYR D 177 PHE 0.020 0.002 PHE e 152 TRP 0.022 0.002 TRP D 104 HIS 0.005 0.001 HIS E 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (10156) covalent geometry : angle 0.61858 / 0.32 (13841) hydrogen bonds : bond 0.03261 / 2.68 ( 510) hydrogen bonds : angle 4.56431 / 3.30 ( 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 182 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 150 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7427 (pm20) REVERT: D 3 LYS cc_start: 0.5259 (pttm) cc_final: 0.4339 (mtmm) REVERT: D 102 GLN cc_start: 0.7110 (mm110) cc_final: 0.6734 (mm110) REVERT: D 111 GLU cc_start: 0.5667 (mm-30) cc_final: 0.4680 (pt0) REVERT: E 73 TRP cc_start: 0.6109 (m100) cc_final: 0.5740 (m100) REVERT: E 106 ARG cc_start: 0.5900 (OUTLIER) cc_final: 0.5381 (mtt-85) REVERT: e 13 MET cc_start: 0.6416 (tmm) cc_final: 0.5785 (tmm) REVERT: e 18 ARG cc_start: 0.3239 (OUTLIER) cc_final: 0.1513 (mmt180) REVERT: e 95 TYR cc_start: 0.4120 (OUTLIER) cc_final: -0.0095 (t80) outliers start: 32 outliers final: 24 residues processed: 172 average time/residue: 0.0735 time to fit residues: 18.6470 Evaluate side-chains 169 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.244 ------------------------------------------------------------------------------- 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 78 THR Chi-restraints excluded: chain a residue 73 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 239 VAL 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 106 ARG 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 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: 6.9990 chunk 114 optimal weight: 0.7980 chunk 91 optimal weight: 20.0000 chunk 6 optimal weight: 0.6980 chunk 90 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 53 optimal weight: 0.0010 chunk 42 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 49 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 overall best weight: 1.0990 ------------------------------------------------------------------------------- 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** ** E 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 32 HIS ** 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 = 0.4968 r_free = 0.4968 target = 0.212608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.184541 restraints weight = 58131.095| |-----------------------------------------------------------------------------| r_work (start): 0.4672 rms_B_bonded: 9.79 r_work: 0.4226 rms_B_bonded: 9.70 restraints_weight: 2.0000 r_work: 0.4409 rms_B_bonded: 5.80 restraints_weight: 4.0000 r_work (final): 0.4409 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4420 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4420 r_free = 0.4420 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4420 r_free = 0.4420 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.4420 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5946 moved from start: 0.3415 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= 0.139 Angle : 0.635 11.909 13841 Z= 0.327 Chirality : 0.043 0.186 1639 Planarity : 0.003 0.039 1712 Dihedral : 13.909 166.288 1767 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.69 % Favored : 92.24 % Rotamer: Outliers : 3.45 % Allowed : 28.16 % 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: -0.87 (0.24), residues: 1319 helix: 0.78 (0.20), residues: 703 sheet: -1.92 (0.50), residues: 106 loop : -2.26 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG a 19 TYR 0.025 0.002 TYR E 284 PHE 0.018 0.002 PHE e 152 TRP 0.022 0.002 TRP E 104 HIS 0.006 0.001 HIS E 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (10156) covalent geometry : angle 0.63499 / 0.33 (13841) hydrogen bonds : bond 0.03278 / 2.71 ( 510) hydrogen bonds : angle 4.61590 / 3.35 ( 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 171 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7440 (pm20) REVERT: D 3 LYS cc_start: 0.5103 (pttm) cc_final: 0.4166 (mtmm) REVERT: D 102 GLN cc_start: 0.7068 (mm110) cc_final: 0.6701 (mm110) REVERT: D 111 GLU cc_start: 0.5501 (mm-30) cc_final: 0.4301 (pm20) REVERT: E 106 ARG cc_start: 0.6086 (OUTLIER) cc_final: 0.5592 (mtt-85) REVERT: e 13 MET cc_start: 0.6457 (tmm) cc_final: 0.5853 (tmm) REVERT: e 18 ARG cc_start: 0.3144 (OUTLIER) cc_final: 0.1453 (mmt180) REVERT: e 95 TYR cc_start: 0.4275 (OUTLIER) cc_final: -0.0027 (t80) REVERT: e 206 ASN cc_start: 0.7318 (m-40) cc_final: 0.7111 (m110) REVERT: e 235 ARG cc_start: 0.5384 (tpt170) cc_final: 0.4794 (tpp80) outliers start: 30 outliers final: 26 residues processed: 161 average time/residue: 0.0765 time to fit residues: 17.8688 Evaluate side-chains 168 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 138 time to evaluate : 0.300 ------------------------------------------------------------------------------- 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 78 THR Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain a residue 81 VAL Chi-restraints excluded: chain D residue 44 ASN Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 188 PHE Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 106 ARG 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 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: 7.9990 chunk 131 optimal weight: 1.9990 chunk 105 optimal weight: 0.1980 chunk 2 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 3 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 23 optimal weight: 0.4980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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** ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4969 r_free = 0.4969 target = 0.212686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4696 r_free = 0.4696 target = 0.185604 restraints weight = 54731.471| |-----------------------------------------------------------------------------| r_work (start): 0.4687 rms_B_bonded: 8.76 r_work (final): 0.4687 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4688 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4688 r_free = 0.4688 target_work(ls_wunit_k1) = 0.185 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4688 r_free = 0.4688 target_work(ls_wunit_k1) = 0.185 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4688 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5532 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10156 Z= 0.140 Angle : 0.634 12.001 13841 Z= 0.327 Chirality : 0.043 0.189 1639 Planarity : 0.003 0.036 1712 Dihedral : 13.889 166.239 1767 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.61 % Favored : 92.31 % 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: -0.83 (0.24), residues: 1319 helix: 0.80 (0.20), residues: 701 sheet: -1.93 (0.49), residues: 110 loop : -2.19 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG a 19 TYR 0.025 0.002 TYR e 284 PHE 0.018 0.002 PHE e 152 TRP 0.022 0.002 TRP E 104 HIS 0.006 0.001 HIS E 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (10156) covalent geometry : angle 0.63402 / 0.33 (13841) hydrogen bonds : bond 0.03258 / 2.68 ( 510) hydrogen bonds : angle 4.62203 / 3.34 ( 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: 32 poor density : 138 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.6922 (pm20) REVERT: D 3 LYS cc_start: 0.5150 (pttm) cc_final: 0.4283 (mtmm) REVERT: D 102 GLN cc_start: 0.6416 (mm110) cc_final: 0.6109 (mm110) REVERT: D 111 GLU cc_start: 0.5213 (mm-30) cc_final: 0.4261 (pm20) REVERT: D 226 PHE cc_start: 0.7624 (OUTLIER) cc_final: 0.7399 (m-80) REVERT: e 13 MET cc_start: 0.6011 (tmm) cc_final: 0.5493 (tmm) REVERT: e 18 ARG cc_start: 0.3245 (OUTLIER) cc_final: 0.1446 (mmt180) REVERT: e 95 TYR cc_start: 0.4217 (OUTLIER) cc_final: 0.0622 (t80) outliers start: 32 outliers final: 27 residues processed: 159 average time/residue: 0.0824 time to fit residues: 19.2077 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 : 0.357 ------------------------------------------------------------------------------- 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 78 THR Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain a residue 81 VAL Chi-restraints excluded: chain D residue 44 ASN Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 188 PHE Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain D residue 226 PHE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 106 ARG 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 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 86 optimal weight: 6.9990 chunk 53 optimal weight: 9.9990 chunk 114 optimal weight: 0.8980 chunk 58 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 45 optimal weight: 0.0770 chunk 126 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 overall best weight: 1.7942 ------------------------------------------------------------------------------- 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 67 ASN ** E 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4937 r_free = 0.4937 target = 0.209291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.180460 restraints weight = 43583.834| |-----------------------------------------------------------------------------| r_work (start): 0.4619 rms_B_bonded: 8.08 r_work (final): 0.4619 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4619 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4619 r_free = 0.4619 target_work(ls_wunit_k1) = 0.179 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4619 r_free = 0.4619 target_work(ls_wunit_k1) = 0.179 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.4619 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5693 moved from start: 0.3755 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= 0.174 Angle : 0.671 12.317 13841 Z= 0.347 Chirality : 0.044 0.188 1639 Planarity : 0.003 0.043 1712 Dihedral : 13.989 167.293 1767 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.52 % Favored : 91.40 % Rotamer: Outliers : 3.56 % Allowed : 28.16 % 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: -1.03 (0.24), residues: 1319 helix: 0.67 (0.20), residues: 703 sheet: -2.07 (0.48), residues: 110 loop : -2.32 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG e 235 TYR 0.025 0.002 TYR e 284 PHE 0.016 0.002 PHE e 152 TRP 0.027 0.002 TRP E 104 HIS 0.006 0.001 HIS E 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (10156) covalent geometry : angle 0.67147 / 0.35 (13841) hydrogen bonds : bond 0.03502 / 2.89 ( 510) hydrogen bonds : angle 4.79566 / 3.48 ( 1485) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2390.43 seconds wall clock time: 41 minutes 42.99 seconds (2502.99 seconds total)