Starting phenix.real_space_refine on Fri Feb 14 10:58:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k25_36828/02_2025/8k25_36828.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k25_36828/02_2025/8k25_36828.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k25_36828/02_2025/8k25_36828.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k25_36828/02_2025/8k25_36828.map" model { file = "/net/cci-nas-00/data/ceres_data/8k25_36828/02_2025/8k25_36828.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k25_36828/02_2025/8k25_36828.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {' DG:plan': 4, ' DG:plan2': 4, ' DC:plan2': 1, ' DA:plan2': 8, ' DC:plan': 1, ' DT:plan': 4, ' DA:plan': 8} 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: {' DG:plan': 1, ' DG:plan2': 1, ' DC:plan2': 4, ' DA:plan2': 4, ' DC:plan': 4, ' DT:plan': 8, ' DA:plan': 4} 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, 'ARG:plan': 1, 'TRP: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, 'ARG:plan': 1, 'TRP: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, 'ASP:plan': 16, 'TYR:plan': 14, 'ASN:plan1': 18, 'TRP:plan': 4, 'HIS:plan': 9, 'PHE:plan': 13, 'GLU:plan': 15, 'ARG:plan': 12} 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, 'ASP:plan': 16, 'TYR:plan': 14, 'ASN:plan1': 18, 'TRP:plan': 4, 'HIS:plan': 9, 'PHE:plan': 13, 'GLU:plan': 15, 'ARG:plan': 12} 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: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP: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: 9.52, per 1000 atoms: 0.96 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: 2.63 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 3.24 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: 3.06 Time building geometry restraints manager: 2.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2701 1.34 - 1.46: 2299 1.46 - 1.58: 5012 1.58 - 1.70: 69 1.70 - 1.83: 75 Bond restraints: 10156 Sorted by residual: bond pdb=" C LEU e 252 " pdb=" N PRO e 253 " ideal model delta sigma weight residual 1.336 1.391 -0.055 1.20e-02 6.94e+03 2.13e+01 bond pdb=" CB ASN e 12 " pdb=" CG ASN e 12 " ideal model delta sigma weight residual 1.516 1.588 -0.072 2.50e-02 1.60e+03 8.20e+00 bond pdb=" CB LYS D 154 " pdb=" CG LYS D 154 " ideal model delta sigma weight residual 1.520 1.591 -0.071 3.00e-02 1.11e+03 5.58e+00 bond pdb=" CG LEU D 282 " pdb=" CD1 LEU D 282 " ideal model delta sigma weight residual 1.521 1.445 0.076 3.30e-02 9.18e+02 5.28e+00 bond pdb=" C GLN a 11 " pdb=" N PRO a 12 " ideal model delta sigma weight residual 1.334 1.387 -0.053 2.34e-02 1.83e+03 5.13e+00 ... (remaining 10151 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.35: 13558 3.35 - 6.69: 225 6.69 - 10.04: 41 10.04 - 13.38: 13 13.38 - 16.73: 4 Bond angle restraints: 13841 Sorted by residual: angle pdb=" CB LYS D 154 " pdb=" CG LYS D 154 " pdb=" CD LYS D 154 " ideal model delta sigma weight residual 111.30 126.80 -15.50 2.30e+00 1.89e-01 4.54e+01 angle pdb=" C LYS E 75 " pdb=" N GLY E 76 " pdb=" CA GLY E 76 " ideal model delta sigma weight residual 119.92 125.34 -5.42 9.60e-01 1.09e+00 3.19e+01 angle pdb=" CB MET E 61 " pdb=" CG MET E 61 " pdb=" SD MET E 61 " ideal model delta sigma weight residual 112.70 129.43 -16.73 3.00e+00 1.11e-01 3.11e+01 angle pdb=" CD1 LEU D 282 " pdb=" CG LEU D 282 " pdb=" CD2 LEU D 282 " ideal model delta sigma weight residual 110.80 98.56 12.24 2.20e+00 2.07e-01 3.09e+01 angle pdb=" C ASN E 279 " pdb=" N ASP E 280 " pdb=" CA ASP E 280 " ideal model delta sigma weight residual 122.82 129.85 -7.03 1.42e+00 4.96e-01 2.45e+01 ... (remaining 13836 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.06: 5847 34.06 - 68.12: 267 68.12 - 102.19: 14 102.19 - 136.25: 0 136.25 - 170.31: 1 Dihedral angle restraints: 6129 sinusoidal: 2250 harmonic: 3879 Sorted by residual: dihedral pdb=" CA LEU a 49 " pdb=" C LEU a 49 " pdb=" N ILE a 50 " pdb=" CA ILE a 50 " ideal model delta harmonic sigma weight residual 180.00 153.49 26.51 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA PHE a 8 " pdb=" C PHE a 8 " pdb=" N SER a 9 " pdb=" CA SER a 9 " ideal model delta harmonic sigma weight residual -180.00 -154.89 -25.11 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA ILE D 70 " pdb=" C ILE D 70 " pdb=" N VAL D 71 " pdb=" CA VAL D 71 " ideal model delta harmonic sigma weight residual 180.00 155.20 24.80 0 5.00e+00 4.00e-02 2.46e+01 ... (remaining 6126 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1442 0.086 - 0.171: 179 0.171 - 0.257: 17 0.257 - 0.342: 0 0.342 - 0.428: 1 Chirality restraints: 1639 Sorted by residual: chirality pdb=" CB VAL a 66 " pdb=" CA VAL a 66 " pdb=" CG1 VAL a 66 " pdb=" CG2 VAL a 66 " both_signs ideal model delta sigma weight residual False -2.63 -2.20 -0.43 2.00e-01 2.50e+01 4.58e+00 chirality pdb=" CB ILE a 70 " pdb=" CA ILE a 70 " pdb=" CG1 ILE a 70 " pdb=" CG2 ILE a 70 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CG LEU D 16 " pdb=" CB LEU D 16 " pdb=" CD1 LEU D 16 " pdb=" CD2 LEU D 16 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 1636 not shown) Planarity restraints: 1712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA E 213 " 0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C ALA E 213 " -0.060 2.00e-02 2.50e+03 pdb=" O ALA E 213 " 0.022 2.00e-02 2.50e+03 pdb=" N ARG E 214 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG E 96 " -0.055 5.00e-02 4.00e+02 8.31e-02 1.10e+01 pdb=" N PRO E 97 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO E 97 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO E 97 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN E 102 " -0.015 2.00e-02 2.50e+03 2.93e-02 8.61e+00 pdb=" C GLN E 102 " 0.051 2.00e-02 2.50e+03 pdb=" O GLN E 102 " -0.019 2.00e-02 2.50e+03 pdb=" N ASN E 103 " -0.017 2.00e-02 2.50e+03 ... (remaining 1709 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2476 2.80 - 3.32: 9237 3.32 - 3.85: 17505 3.85 - 4.37: 19174 4.37 - 4.90: 32408 Nonbonded interactions: 80800 Sorted by model distance: nonbonded pdb=" O ALA D 51 " pdb=" OG1 THR D 54 " model vdw 2.271 3.040 nonbonded pdb=" OG SER A 9 " pdb=" O GLY A 55 " model vdw 2.284 3.040 nonbonded pdb=" OG SER D 194 " pdb=" OD1 ASP D 196 " model vdw 2.291 3.040 nonbonded pdb=" O SER e 225 " pdb=" OG SER e 225 " model vdw 2.291 3.040 nonbonded pdb=" O ASP e 127 " pdb=" OG1 THR e 131 " model vdw 2.307 3.040 ... (remaining 80795 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 61 or (resid 62 through 64 and (nam \ e N or name CA or name C or name O or name CB )) or resid 65 through 76 or (resi \ d 77 through 78 and (name N or name CA or name C or name O or name CB )) or resi \ d 79 through 81)) selection = (chain 'a' and (resid 1 through 48 or (resid 49 and (name N or name CA or name C \ or name O or name CB )) or resid 50 through 81)) } ncs_group { reference = (chain 'D' and ((resid 1 through 25 and (name N or name CA or name C or name O o \ r name CB )) or resid 26 or (resid 27 through 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 or (resid 36 through 48 and (name N or nam \ e CA or name C or name O or name CB )) or resid 49 or (resid 50 through 52 and ( \ name N or name CA or name C or name O or name CB )) or resid 53 or (resid 54 thr \ ough 67 and (name N or name CA or name C or name O or name CB )) or resid 68 or \ (resid 69 through 105 and (name N or name CA or name C or name O or name CB )) o \ r (resid 107 through 136 and (name N or name CA or name C or name O or name CB ) \ ) or resid 137 or (resid 138 through 149 and (name N or name CA or name C or nam \ e O or name CB )) or (resid 151 through 154 and (name N or name CA or name C or \ name O or name CB )) or resid 155 or (resid 156 through 166 and (name N or name \ CA or name C or name O or name CB )) or resid 167 or (resid 168 through 169 and \ (name N or name CA or name C or name O or name CB )) or resid 170 or (resid 171 \ through 204 and (name N or name CA or name C or name O or name CB )) or resid 20 \ 5 or (resid 206 through 210 and (name N or name CA or name C or name O or name C \ B )) or resid 211 or (resid 212 through 220 and (name N or name CA or name C or \ name O or name CB )) or resid 221 or (resid 222 through 230 and (name N or name \ CA or name C or name O or name CB )) or resid 231 or (resid 232 through 235 and \ (name N or name CA or name C or name O or name CB )) or resid 236 through 237 or \ (resid 238 through 261 and (name N or name CA or name C or name O or name CB )) \ or resid 262 or (resid 263 through 286 and (name N or name CA or name C or name \ O or name CB )) or (resid 288 through 295 and (name N or name CA or name C or n \ ame O or name CB )))) selection = (chain 'E' and ((resid 1 through 25 and (name N or name CA or name C or name O o \ r name CB )) or resid 26 or (resid 27 through 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 or (resid 36 through 48 and (name N or nam \ e CA or name C or name O or name CB )) or resid 49 or (resid 50 through 52 and ( \ name N or name CA or name C or name O or name CB )) or resid 53 or (resid 54 thr \ ough 67 and (name N or name CA or name C or name O or name CB )) or resid 68 or \ (resid 69 through 75 and (name N or name CA or name C or name O or name CB )) or \ (resid 83 through 105 and (name N or name CA or name C or name O or name CB )) \ or (resid 107 through 136 and (name N or name CA or name C or name O or name CB \ )) or resid 137 or (resid 138 through 149 and (name N or name CA or name C or na \ me O or name CB )) or (resid 151 through 154 and (name N or name CA or name C or \ name O or name CB )) or resid 155 or (resid 156 through 166 and (name N or name \ CA or name C or name O or name CB )) or resid 167 or (resid 168 through 169 and \ (name N or name CA or name C or name O or name CB )) or resid 170 or (resid 171 \ through 204 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 05 or (resid 206 through 210 and (name N or name CA or name C or name O or name \ CB )) or resid 211 or (resid 212 through 220 and (name N or name CA or name C or \ name O or name CB )) or resid 221 or (resid 222 through 230 and (name N or name \ CA or name C or name O or name CB )) or resid 231 or (resid 232 through 235 and \ (name N or name CA or name C or name O or name CB )) or resid 236 through 237 o \ r (resid 238 through 261 and (name N or name CA or name C or name O or name CB ) \ ) or resid 262 or (resid 263 through 286 and (name N or name CA or name C or nam \ e O or name CB )) or (resid 288 through 295 and (name N or name CA or name C or \ name O or name CB )))) selection = (chain 'd' and (resid 1 through 105 or resid 107 through 149 or resid 151 throug \ h 286 or resid 288 through 295)) selection = (chain 'e' and ((resid 1 through 25 and (name N or name CA or name C or name O o \ r name CB )) or resid 26 or (resid 27 through 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 or (resid 36 through 48 and (name N or nam \ e CA or name C or name O or name CB )) or resid 49 or (resid 50 through 52 and ( \ name N or name CA or name C or name O or name CB )) or resid 53 or (resid 54 thr \ ough 67 and (name N or name CA or name C or name O or name CB )) or resid 68 or \ (resid 69 through 75 and (name N or name CA or name C or name O or name CB )) or \ (resid 83 through 105 and (name N or name CA or name C or name O or name CB )) \ or (resid 107 through 136 and (name N or name CA or name C or name O or name CB \ )) or resid 137 or (resid 138 through 149 and (name N or name CA or name C or na \ me O or name CB )) or (resid 151 through 154 and (name N or name CA or name C or \ name O or name CB )) or resid 155 or (resid 156 through 166 and (name N or name \ CA or name C or name O or name CB )) or resid 167 or (resid 168 through 169 and \ (name N or name CA or name C or name O or name CB )) or resid 170 or (resid 171 \ through 204 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 05 or (resid 206 through 210 and (name N or name CA or name C or name O or name \ CB )) or resid 211 or (resid 212 through 220 and (name N or name CA or name C or \ name O or name CB )) or resid 221 or (resid 222 through 230 and (name N or name \ CA or name C or name O or name CB )) or resid 231 or (resid 232 through 235 and \ (name N or name CA or name C or name O or name CB )) or resid 236 through 237 o \ r (resid 238 through 261 and (name N or name CA or name C or name O or name CB ) \ ) or resid 262 or (resid 263 through 286 and (name N or name CA or name C or nam \ e O or name CB )) or (resid 288 through 295 and (name N or name CA or name C or \ name O or name CB )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.05 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 31.960 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5207 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 10156 Z= 0.344 Angle : 1.139 16.729 13841 Z= 0.602 Chirality : 0.056 0.428 1639 Planarity : 0.006 0.083 1712 Dihedral : 18.395 170.311 3631 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 7.89 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.045 0.004 TRP D 104 HIS 0.015 0.002 HIS e 30 PHE 0.029 0.003 PHE A 8 TYR 0.046 0.003 TYR e 210 ARG 0.008 0.001 ARG D 125 *********************** 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 : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 111 GLU cc_start: 0.6158 (mm-30) cc_final: 0.3807 (pm20) REVERT: e 86 ILE cc_start: 0.7395 (mp) cc_final: 0.7135 (mt) REVERT: e 284 TYR cc_start: 0.6550 (t80) cc_final: 0.5959 (t80) outliers start: 6 outliers final: 3 residues processed: 149 average time/residue: 0.2093 time to fit residues: 45.5752 Evaluate side-chains 142 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 139 time to evaluate : 1.036 ------------------------------------------------------------------------------- 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 111 optimal weight: 0.9980 chunk 100 optimal weight: 20.0000 chunk 55 optimal weight: 9.9990 chunk 34 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 103 optimal weight: 0.1980 chunk 40 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 77 optimal weight: 0.0170 chunk 119 optimal weight: 8.9990 overall best weight: 1.2420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 ASN ** E 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 HIS e 58 ASN ** e 92 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4998 r_free = 0.4998 target = 0.215272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.186831 restraints weight = 53773.278| |-----------------------------------------------------------------------------| r_work (start): 0.4692 rms_B_bonded: 9.04 r_work (final): 0.4692 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4694 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4694 r_free = 0.4694 target_work(ls_wunit_k1) = 0.186 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4694 r_free = 0.4694 target_work(ls_wunit_k1) = 0.186 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4694 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5444 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10156 Z= 0.207 Angle : 0.633 9.223 13841 Z= 0.336 Chirality : 0.041 0.149 1639 Planarity : 0.004 0.052 1712 Dihedral : 13.941 168.955 1773 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.93 % Favored : 93.00 % Rotamer: Outliers : 3.68 % Allowed : 26.78 % Favored : 69.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.22), residues: 1319 helix: -0.26 (0.19), residues: 697 sheet: -2.12 (0.53), residues: 96 loop : -2.30 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP E 104 HIS 0.010 0.001 HIS D 30 PHE 0.021 0.002 PHE D 152 TYR 0.039 0.002 TYR e 210 ARG 0.003 0.000 ARG D 125 *********************** 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 179 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 147 time to evaluate : 1.062 Fit side-chains revert: symmetry clash REVERT: A 26 GLU cc_start: 0.6978 (pm20) cc_final: 0.6717 (pm20) REVERT: A 70 ILE cc_start: 0.6657 (OUTLIER) cc_final: 0.6432 (pt) REVERT: a 31 ASN cc_start: 0.7333 (OUTLIER) cc_final: 0.6780 (t0) REVERT: a 48 LYS cc_start: 0.7263 (ptpp) cc_final: 0.6972 (ptpp) REVERT: e 13 MET cc_start: 0.5972 (tmm) cc_final: 0.5613 (tmm) REVERT: e 95 TYR cc_start: 0.3702 (OUTLIER) cc_final: 0.0333 (t80) REVERT: e 120 GLU cc_start: 0.6292 (tt0) cc_final: 0.5879 (tt0) REVERT: e 129 LEU cc_start: 0.7045 (OUTLIER) cc_final: 0.6839 (tt) REVERT: e 246 ILE cc_start: 0.7783 (mm) cc_final: 0.7563 (mm) REVERT: e 257 HIS cc_start: 0.6553 (p-80) cc_final: 0.6214 (p-80) outliers start: 32 outliers final: 17 residues processed: 168 average time/residue: 0.2059 time to fit residues: 50.2436 Evaluate side-chains 157 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain a residue 31 ASN Chi-restraints excluded: chain a residue 75 MET Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain 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 105 VAL Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain e residue 95 TYR Chi-restraints excluded: chain e residue 108 TRP Chi-restraints excluded: chain e residue 129 LEU Chi-restraints excluded: chain e residue 140 VAL Chi-restraints excluded: chain e residue 169 GLU Chi-restraints excluded: chain e residue 210 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 65 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 110 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 78 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 GLN e 134 HIS e 279 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5002 r_free = 0.5002 target = 0.215526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.190363 restraints weight = 30003.547| |-----------------------------------------------------------------------------| r_work (start): 0.4739 rms_B_bonded: 4.42 r_work (final): 0.4739 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4739 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4739 r_free = 0.4739 target_work(ls_wunit_k1) = 0.190 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4739 r_free = 0.4739 target_work(ls_wunit_k1) = 0.190 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4739 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5477 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10156 Z= 0.175 Angle : 0.592 11.249 13841 Z= 0.309 Chirality : 0.041 0.197 1639 Planarity : 0.003 0.046 1712 Dihedral : 13.731 169.462 1769 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.62 % Favored : 93.30 % Rotamer: Outliers : 3.79 % Allowed : 27.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.24), residues: 1319 helix: 0.40 (0.20), residues: 697 sheet: -2.30 (0.52), residues: 99 loop : -2.16 (0.27), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 104 HIS 0.004 0.001 HIS e 30 PHE 0.016 0.002 PHE D 152 TYR 0.041 0.001 TYR e 210 ARG 0.002 0.000 ARG e 291 *********************** 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 185 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 152 time to evaluate : 1.163 Fit side-chains REVERT: A 26 GLU cc_start: 0.7240 (pm20) cc_final: 0.6945 (pm20) REVERT: a 30 ASN cc_start: 0.5815 (m-40) cc_final: 0.5450 (m110) REVERT: a 31 ASN cc_start: 0.7237 (OUTLIER) cc_final: 0.6729 (t0) REVERT: D 101 MET cc_start: 0.5986 (ttt) cc_final: 0.5586 (ttm) REVERT: D 102 GLN cc_start: 0.6528 (mm110) cc_final: 0.6195 (mm110) REVERT: D 109 LEU cc_start: 0.5440 (mm) cc_final: 0.4926 (mm) REVERT: D 111 GLU cc_start: 0.5633 (mm-30) cc_final: 0.4143 (pt0) REVERT: e 13 MET cc_start: 0.5984 (tmm) cc_final: 0.5577 (tmm) REVERT: e 95 TYR cc_start: 0.4004 (OUTLIER) cc_final: 0.0283 (t80) outliers start: 33 outliers final: 14 residues processed: 175 average time/residue: 0.2248 time to fit residues: 55.8839 Evaluate side-chains 153 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 1.077 ------------------------------------------------------------------------------- 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 78 THR Chi-restraints excluded: chain a residue 31 ASN 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 E residue 50 LEU 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 140 VAL Chi-restraints excluded: chain e residue 210 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 15 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 41 optimal weight: 0.0980 chunk 85 optimal weight: 6.9990 chunk 77 optimal weight: 20.0000 chunk 69 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 HIS ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 224 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4973 r_free = 0.4973 target = 0.212951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.183767 restraints weight = 47301.568| |-----------------------------------------------------------------------------| r_work (start): 0.4652 rms_B_bonded: 8.29 r_work (final): 0.4652 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4652 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4652 r_free = 0.4652 target_work(ls_wunit_k1) = 0.183 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4652 r_free = 0.4652 target_work(ls_wunit_k1) = 0.183 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4652 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5571 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10156 Z= 0.211 Angle : 0.603 11.022 13841 Z= 0.320 Chirality : 0.042 0.170 1639 Planarity : 0.003 0.037 1712 Dihedral : 13.758 169.976 1769 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.15 % Favored : 92.77 % Rotamer: Outliers : 3.79 % Allowed : 27.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.24), residues: 1319 helix: 0.58 (0.20), residues: 705 sheet: -2.34 (0.53), residues: 96 loop : -2.30 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 104 HIS 0.004 0.001 HIS e 257 PHE 0.021 0.002 PHE e 152 TYR 0.044 0.002 TYR e 210 ARG 0.002 0.000 ARG D 125 *********************** 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 167 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 134 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.6854 (OUTLIER) cc_final: 0.6473 (pm20) REVERT: A 40 GLN cc_start: 0.7107 (pt0) cc_final: 0.6715 (pt0) REVERT: a 31 ASN cc_start: 0.7056 (OUTLIER) cc_final: 0.6755 (t0) REVERT: D 111 GLU cc_start: 0.5661 (mm-30) cc_final: 0.4392 (pt0) REVERT: e 95 TYR cc_start: 0.3920 (OUTLIER) cc_final: 0.0414 (t80) outliers start: 33 outliers final: 24 residues processed: 159 average time/residue: 0.2302 time to fit residues: 52.9938 Evaluate side-chains 157 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 1.048 ------------------------------------------------------------------------------- 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 26 GLU Chi-restraints excluded: chain a residue 31 ASN Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain a residue 81 VAL Chi-restraints excluded: chain D residue 44 ASN Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 32 HIS Chi-restraints excluded: chain e residue 95 TYR Chi-restraints excluded: chain e residue 108 TRP Chi-restraints excluded: chain e residue 210 TYR 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 90 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 3 optimal weight: 0.1980 chunk 85 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 chunk 111 optimal weight: 4.9990 chunk 31 optimal weight: 0.1980 chunk 25 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 chunk 129 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 ASN e 168 HIS ** e 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4964 r_free = 0.4964 target = 0.211895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.183175 restraints weight = 59220.324| |-----------------------------------------------------------------------------| r_work (start): 0.4658 rms_B_bonded: 9.58 r_work: 0.4228 rms_B_bonded: 9.49 restraints_weight: 2.0000 r_work: 0.4412 rms_B_bonded: 5.64 restraints_weight: 4.0000 r_work (final): 0.4412 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4422 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4422 r_free = 0.4422 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4422 r_free = 0.4422 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4422 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5910 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10156 Z= 0.213 Angle : 0.602 11.906 13841 Z= 0.319 Chirality : 0.042 0.148 1639 Planarity : 0.003 0.035 1712 Dihedral : 13.734 169.734 1769 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.08 % Favored : 92.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.24), residues: 1319 helix: 0.68 (0.20), residues: 703 sheet: -2.35 (0.52), residues: 96 loop : -2.33 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 104 HIS 0.004 0.001 HIS e 257 PHE 0.016 0.002 PHE e 152 TYR 0.045 0.002 TYR e 210 ARG 0.003 0.000 ARG D 190 *********************** 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 176 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 136 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7389 (pm20) REVERT: A 40 GLN cc_start: 0.6951 (pt0) cc_final: 0.6625 (pt0) REVERT: a 31 ASN cc_start: 0.7591 (OUTLIER) cc_final: 0.7211 (t0) REVERT: D 3 LYS cc_start: 0.5149 (pttm) cc_final: 0.4228 (mtmm) REVERT: D 111 GLU cc_start: 0.5729 (mm-30) cc_final: 0.4480 (pt0) REVERT: D 263 MET cc_start: 0.5349 (pmm) cc_final: 0.4990 (pmm) REVERT: e 18 ARG cc_start: 0.2544 (OUTLIER) cc_final: 0.0992 (mmt180) REVERT: e 95 TYR cc_start: 0.4233 (OUTLIER) cc_final: -0.0064 (t80) outliers start: 40 outliers final: 28 residues processed: 167 average time/residue: 0.2218 time to fit residues: 52.3951 Evaluate side-chains 167 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 1.173 ------------------------------------------------------------------------------- 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 13 ILE Chi-restraints excluded: chain a residue 31 ASN Chi-restraints excluded: chain a residue 37 ILE Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain a residue 81 VAL Chi-restraints excluded: chain D residue 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 239 VAL Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain e residue 18 ARG Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 32 HIS Chi-restraints excluded: chain e residue 67 ASN Chi-restraints excluded: chain e residue 95 TYR Chi-restraints excluded: chain e residue 108 TRP Chi-restraints excluded: chain e residue 210 TYR Chi-restraints excluded: chain e residue 263 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 97 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 127 optimal weight: 0.5980 chunk 56 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 36 optimal weight: 20.0000 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 279 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4917 r_free = 0.4917 target = 0.207278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.178690 restraints weight = 62205.533| |-----------------------------------------------------------------------------| r_work (start): 0.4610 rms_B_bonded: 10.38 r_work: 0.4125 rms_B_bonded: 10.33 restraints_weight: 2.0000 r_work: 0.4310 rms_B_bonded: 6.31 restraints_weight: 4.0000 r_work (final): 0.4310 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4317 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4317 r_free = 0.4317 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4317 r_free = 0.4317 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4317 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6093 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 10156 Z= 0.309 Angle : 0.685 12.136 13841 Z= 0.364 Chirality : 0.044 0.175 1639 Planarity : 0.004 0.043 1712 Dihedral : 14.008 170.233 1769 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.37 % Favored : 91.55 % Rotamer: Outliers : 5.29 % Allowed : 26.09 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.23), residues: 1319 helix: 0.52 (0.20), residues: 702 sheet: -2.12 (0.49), residues: 105 loop : -2.60 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP E 104 HIS 0.007 0.001 HIS e 168 PHE 0.017 0.002 PHE D 152 TYR 0.047 0.002 TYR e 210 ARG 0.004 0.001 ARG D 125 *********************** 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 190 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 144 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7503 (pm20) REVERT: a 31 ASN cc_start: 0.7841 (OUTLIER) cc_final: 0.7405 (t0) REVERT: D 3 LYS cc_start: 0.5642 (pttm) cc_final: 0.4727 (mtmm) REVERT: D 111 GLU cc_start: 0.5929 (mm-30) cc_final: 0.4925 (pm20) REVERT: e 18 ARG cc_start: 0.2886 (OUTLIER) cc_final: 0.1244 (mmt180) REVERT: e 86 ILE cc_start: 0.7250 (mp) cc_final: 0.6976 (mt) REVERT: e 95 TYR cc_start: 0.4624 (OUTLIER) cc_final: 0.0271 (t80) REVERT: e 245 ILE cc_start: 0.7324 (OUTLIER) cc_final: 0.6977 (mm) REVERT: e 256 PHE cc_start: 0.7397 (OUTLIER) cc_final: 0.7126 (t80) outliers start: 46 outliers final: 27 residues processed: 180 average time/residue: 0.2226 time to fit residues: 56.1442 Evaluate side-chains 171 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain a residue 13 ILE Chi-restraints excluded: chain a residue 26 GLU Chi-restraints excluded: chain a residue 31 ASN Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain a residue 81 VAL Chi-restraints excluded: chain D residue 40 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 188 PHE 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 165 LEU Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain e residue 18 ARG Chi-restraints excluded: chain e residue 32 HIS Chi-restraints excluded: chain e residue 67 ASN Chi-restraints excluded: chain e residue 95 TYR Chi-restraints excluded: chain e residue 108 TRP Chi-restraints excluded: chain e residue 210 TYR Chi-restraints excluded: chain e residue 245 ILE Chi-restraints excluded: chain e residue 256 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 113 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 63 optimal weight: 30.0000 chunk 84 optimal weight: 5.9990 chunk 131 optimal weight: 0.8980 chunk 55 optimal weight: 7.9990 chunk 27 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 119 optimal weight: 9.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4923 r_free = 0.4923 target = 0.207993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.179650 restraints weight = 49915.597| |-----------------------------------------------------------------------------| r_work (start): 0.4618 rms_B_bonded: 8.68 r_work (final): 0.4618 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4616 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4616 r_free = 0.4616 target_work(ls_wunit_k1) = 0.179 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4616 r_free = 0.4616 target_work(ls_wunit_k1) = 0.179 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4616 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5638 moved from start: 0.3663 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= 0.244 Angle : 0.652 12.418 13841 Z= 0.341 Chirality : 0.043 0.156 1639 Planarity : 0.003 0.038 1712 Dihedral : 13.830 169.364 1769 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.23 % Favored : 92.69 % Rotamer: Outliers : 4.94 % Allowed : 27.24 % Favored : 67.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.24), residues: 1319 helix: 0.58 (0.20), residues: 702 sheet: -2.34 (0.47), residues: 113 loop : -2.49 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP E 104 HIS 0.006 0.001 HIS E 30 PHE 0.015 0.002 PHE a 68 TYR 0.046 0.002 TYR e 210 ARG 0.004 0.000 ARG D 125 *********************** 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 191 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 148 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.7037 (OUTLIER) cc_final: 0.6665 (pm20) REVERT: a 31 ASN cc_start: 0.7282 (OUTLIER) cc_final: 0.6942 (t0) REVERT: D 3 LYS cc_start: 0.5522 (pttm) cc_final: 0.4749 (mtmm) REVERT: D 109 LEU cc_start: 0.5287 (OUTLIER) cc_final: 0.4877 (mm) REVERT: D 111 GLU cc_start: 0.5646 (mm-30) cc_final: 0.4934 (pm20) REVERT: D 226 PHE cc_start: 0.7994 (OUTLIER) cc_final: 0.7701 (m-80) REVERT: e 18 ARG cc_start: 0.3374 (OUTLIER) cc_final: 0.1507 (mmt180) REVERT: e 86 ILE cc_start: 0.7109 (mp) cc_final: 0.6835 (mt) REVERT: e 95 TYR cc_start: 0.4107 (OUTLIER) cc_final: 0.0585 (t80) outliers start: 43 outliers final: 26 residues processed: 179 average time/residue: 0.2241 time to fit residues: 56.5783 Evaluate side-chains 171 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain a residue 13 ILE Chi-restraints excluded: chain a residue 31 ASN Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain a residue 81 VAL Chi-restraints excluded: chain D residue 44 ASN Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 109 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 56 ILE 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 67 ASN Chi-restraints excluded: chain e residue 81 MET Chi-restraints excluded: chain e residue 95 TYR Chi-restraints excluded: chain e residue 108 TRP Chi-restraints excluded: chain e residue 210 TYR Chi-restraints excluded: chain e residue 263 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 11 optimal weight: 1.9990 chunk 126 optimal weight: 9.9990 chunk 8 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 111 optimal weight: 7.9990 chunk 58 optimal weight: 0.0980 chunk 121 optimal weight: 10.0000 chunk 104 optimal weight: 7.9990 chunk 103 optimal weight: 0.9980 chunk 51 optimal weight: 9.9990 chunk 88 optimal weight: 30.0000 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4906 r_free = 0.4906 target = 0.206507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.177585 restraints weight = 47307.874| |-----------------------------------------------------------------------------| r_work (start): 0.4590 rms_B_bonded: 8.57 r_work: 0.4191 rms_B_bonded: 8.28 restraints_weight: 2.0000 r_work: 0.4362 rms_B_bonded: 5.01 restraints_weight: 4.0000 r_work (final): 0.4362 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4371 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4371 r_free = 0.4371 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4371 r_free = 0.4371 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4371 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6008 moved from start: 0.3958 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= 0.268 Angle : 0.671 12.281 13841 Z= 0.352 Chirality : 0.043 0.157 1639 Planarity : 0.003 0.038 1712 Dihedral : 13.817 169.627 1769 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.60 % Favored : 91.32 % Rotamer: Outliers : 4.48 % Allowed : 27.93 % Favored : 67.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.23), residues: 1319 helix: 0.53 (0.20), residues: 704 sheet: -2.07 (0.52), residues: 95 loop : -2.61 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP E 104 HIS 0.006 0.001 HIS E 30 PHE 0.018 0.002 PHE D 226 TYR 0.047 0.002 TYR e 210 ARG 0.004 0.000 ARG D 125 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 145 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7452 (pm20) REVERT: a 31 ASN cc_start: 0.7733 (OUTLIER) cc_final: 0.7260 (t0) REVERT: D 3 LYS cc_start: 0.5483 (pttm) cc_final: 0.4634 (mtmm) REVERT: D 111 GLU cc_start: 0.5756 (mm-30) cc_final: 0.4927 (pm20) REVERT: D 226 PHE cc_start: 0.8631 (OUTLIER) cc_final: 0.8370 (m-80) REVERT: D 261 GLN cc_start: 0.7244 (OUTLIER) cc_final: 0.6173 (mp10) REVERT: e 13 MET cc_start: 0.6564 (tmm) cc_final: 0.6157 (tmm) REVERT: e 18 ARG cc_start: 0.3330 (OUTLIER) cc_final: 0.1657 (mmt180) REVERT: e 86 ILE cc_start: 0.7212 (mp) cc_final: 0.6920 (mt) REVERT: e 95 TYR cc_start: 0.4787 (OUTLIER) cc_final: 0.0802 (t80) outliers start: 39 outliers final: 27 residues processed: 171 average time/residue: 0.2175 time to fit residues: 52.4488 Evaluate side-chains 173 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 140 time to evaluate : 1.015 ------------------------------------------------------------------------------- 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 13 ILE Chi-restraints excluded: chain a residue 31 ASN Chi-restraints excluded: chain a residue 49 LEU 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 37 VAL Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 129 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 D residue 261 GLN Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 158 GLN Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain e residue 18 ARG Chi-restraints excluded: chain e residue 67 ASN Chi-restraints excluded: chain e residue 81 MET Chi-restraints excluded: chain e residue 95 TYR Chi-restraints excluded: chain e residue 108 TRP Chi-restraints excluded: chain e residue 210 TYR Chi-restraints excluded: chain e residue 263 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 104 optimal weight: 6.9990 chunk 16 optimal weight: 0.0980 chunk 32 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 28 optimal weight: 0.0980 chunk 47 optimal weight: 10.0000 chunk 85 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 67 optimal weight: 9.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 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 = 0.4932 r_free = 0.4932 target = 0.208950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.181149 restraints weight = 42705.852| |-----------------------------------------------------------------------------| r_work (start): 0.4635 rms_B_bonded: 7.26 r_work (final): 0.4635 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4637 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4637 r_free = 0.4637 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4637 r_free = 0.4637 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4637 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5620 moved from start: 0.3885 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= 0.209 Angle : 0.633 12.477 13841 Z= 0.328 Chirality : 0.043 0.199 1639 Planarity : 0.003 0.029 1712 Dihedral : 13.640 169.685 1769 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.08 % Favored : 92.85 % Rotamer: Outliers : 3.91 % Allowed : 28.39 % Favored : 67.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.24), residues: 1319 helix: 0.69 (0.20), residues: 705 sheet: -2.32 (0.49), residues: 104 loop : -2.44 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 73 HIS 0.005 0.001 HIS E 30 PHE 0.021 0.002 PHE e 152 TYR 0.045 0.002 TYR e 210 ARG 0.003 0.000 ARG D 125 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 143 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.6703 (pm20) REVERT: a 31 ASN cc_start: 0.7419 (OUTLIER) cc_final: 0.6764 (t0) REVERT: D 3 LYS cc_start: 0.5450 (pttm) cc_final: 0.4635 (mtmm) REVERT: D 111 GLU cc_start: 0.5462 (mm-30) cc_final: 0.4444 (pm20) REVERT: D 226 PHE cc_start: 0.7989 (OUTLIER) cc_final: 0.7665 (m-80) REVERT: D 261 GLN cc_start: 0.7380 (OUTLIER) cc_final: 0.6451 (mp10) REVERT: E 124 MET cc_start: 0.7105 (ptp) cc_final: 0.6782 (ptp) REVERT: e 18 ARG cc_start: 0.3507 (OUTLIER) cc_final: 0.1768 (mmt180) REVERT: e 86 ILE cc_start: 0.6931 (mp) cc_final: 0.6648 (mt) REVERT: e 95 TYR cc_start: 0.4707 (OUTLIER) cc_final: 0.1211 (t80) outliers start: 34 outliers final: 23 residues processed: 170 average time/residue: 0.2187 time to fit residues: 52.6635 Evaluate side-chains 167 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 1.076 ------------------------------------------------------------------------------- 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 26 GLU Chi-restraints excluded: chain a residue 31 ASN Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain a residue 81 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 44 ASN Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 188 PHE Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain D residue 226 PHE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 261 GLN Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 158 GLN Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain e residue 18 ARG Chi-restraints excluded: chain e residue 81 MET Chi-restraints excluded: chain e residue 95 TYR Chi-restraints excluded: chain e residue 108 TRP Chi-restraints excluded: chain e residue 263 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 58 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 85 optimal weight: 8.9990 chunk 100 optimal weight: 9.9990 chunk 110 optimal weight: 0.9980 chunk 71 optimal weight: 20.0000 chunk 49 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 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 = 0.4936 r_free = 0.4936 target = 0.209116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.180977 restraints weight = 52383.501| |-----------------------------------------------------------------------------| r_work (start): 0.4637 rms_B_bonded: 8.77 r_work (final): 0.4637 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4637 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4637 r_free = 0.4637 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4637 r_free = 0.4637 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4637 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5591 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10156 Z= 0.207 Angle : 0.636 12.412 13841 Z= 0.330 Chirality : 0.043 0.180 1639 Planarity : 0.003 0.042 1712 Dihedral : 13.605 169.580 1769 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.99 % Favored : 91.93 % Rotamer: Outliers : 3.68 % Allowed : 28.85 % Favored : 67.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.24), residues: 1319 helix: 0.75 (0.20), residues: 704 sheet: -2.53 (0.45), residues: 118 loop : -2.28 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP E 104 HIS 0.005 0.001 HIS E 30 PHE 0.021 0.002 PHE e 152 TYR 0.054 0.002 TYR e 210 ARG 0.004 0.000 ARG D 125 ********************** 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 171 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.6688 (pm20) REVERT: a 31 ASN cc_start: 0.7431 (OUTLIER) cc_final: 0.6810 (t0) REVERT: D 1 MET cc_start: -0.0226 (ptp) cc_final: -0.1255 (ptp) REVERT: D 111 GLU cc_start: 0.5420 (mm-30) cc_final: 0.4446 (pm20) REVERT: D 261 GLN cc_start: 0.7387 (OUTLIER) cc_final: 0.6489 (mp10) REVERT: E 124 MET cc_start: 0.7264 (ptp) cc_final: 0.6959 (ptp) REVERT: e 18 ARG cc_start: 0.3433 (OUTLIER) cc_final: 0.1701 (mmt180) REVERT: e 86 ILE cc_start: 0.6843 (mp) cc_final: 0.6551 (mt) REVERT: e 95 TYR cc_start: 0.4770 (OUTLIER) cc_final: 0.1264 (t80) REVERT: e 201 PHE cc_start: 0.5903 (OUTLIER) cc_final: 0.5488 (t80) outliers start: 32 outliers final: 23 residues processed: 163 average time/residue: 0.2224 time to fit residues: 50.9754 Evaluate side-chains 165 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 136 time to evaluate : 1.050 ------------------------------------------------------------------------------- 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 31 ASN Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain a residue 81 VAL Chi-restraints excluded: chain D residue 37 VAL 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 D residue 261 GLN Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 158 GLN Chi-restraints excluded: chain E residue 162 PHE Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain e residue 18 ARG Chi-restraints excluded: chain e residue 81 MET Chi-restraints excluded: chain e residue 95 TYR Chi-restraints excluded: chain e residue 108 TRP Chi-restraints excluded: chain e residue 201 PHE 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 103 optimal weight: 9.9990 chunk 23 optimal weight: 0.6980 chunk 1 optimal weight: 10.0000 chunk 114 optimal weight: 8.9990 chunk 82 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 53 optimal weight: 9.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 HIS ** 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 = 0.4943 r_free = 0.4943 target = 0.209883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.181391 restraints weight = 56819.851| |-----------------------------------------------------------------------------| r_work (start): 0.4638 rms_B_bonded: 9.85 r_work (final): 0.4638 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4638 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4638 r_free = 0.4638 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4638 r_free = 0.4638 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4638 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5570 moved from start: 0.3953 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= 0.197 Angle : 0.625 12.307 13841 Z= 0.325 Chirality : 0.043 0.185 1639 Planarity : 0.003 0.030 1712 Dihedral : 13.541 169.621 1769 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.53 % Favored : 92.39 % Rotamer: Outliers : 3.56 % Allowed : 28.85 % Favored : 67.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.24), residues: 1319 helix: 0.82 (0.20), residues: 704 sheet: -2.39 (0.47), residues: 114 loop : -2.25 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP E 104 HIS 0.005 0.001 HIS E 30 PHE 0.020 0.002 PHE e 152 TYR 0.053 0.002 TYR e 210 ARG 0.004 0.000 ARG D 125 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4906.15 seconds wall clock time: 88 minutes 5.80 seconds (5285.80 seconds total)