Starting phenix.real_space_refine on Mon Jul 28 06:57:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k25_36828/07_2025/8k25_36828.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k25_36828/07_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_36828/07_2025/8k25_36828.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k25_36828/07_2025/8k25_36828.map" model { file = "/net/cci-nas-00/data/ceres_data/8k25_36828/07_2025/8k25_36828.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k25_36828/07_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-5711/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: 9.95, per 1000 atoms: 1.00 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: 2.44 Conformation dependent library (CDL) restraints added in 2.1 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: 3.18 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: 2.61 Time building geometry restraints manager: 2.88 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: 0.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 31.890 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.060 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5207 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 10156 Z= 0.255 Angle : 1.139 16.729 13841 Z= 0.602 Chirality : 0.056 0.428 1639 Planarity : 0.006 0.083 1712 Dihedral : 18.395 170.311 3631 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 7.89 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 Details of bonding type rmsd hydrogen bonds : bond 0.15878 ( 510) hydrogen bonds : angle 7.59076 ( 1485) covalent geometry : bond 0.00543 (10156) covalent geometry : angle 1.13914 (13841) *********************** 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 : 1.001 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: 0.1988 time to fit residues: 42.9845 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 : 1.078 ------------------------------------------------------------------------------- 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 = 0.4997 r_free = 0.4997 target = 0.215273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.186829 restraints weight = 53771.951| |-----------------------------------------------------------------------------| 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= 0.149 Angle : 0.633 9.224 13841 Z= 0.336 Chirality : 0.041 0.149 1639 Planarity : 0.004 0.052 1712 Dihedral : 13.941 168.954 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 Details of bonding type rmsd hydrogen bonds : bond 0.03657 ( 510) hydrogen bonds : angle 4.92210 ( 1485) covalent geometry : bond 0.00330 (10156) covalent geometry : angle 0.63298 (13841) *********************** 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 : 0.990 Fit side-chains revert: symmetry clash REVERT: A 26 GLU cc_start: 0.6974 (pm20) cc_final: 0.6713 (pm20) REVERT: A 70 ILE cc_start: 0.6656 (OUTLIER) cc_final: 0.6431 (pt) REVERT: a 31 ASN cc_start: 0.7334 (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: 0.5973 (tmm) cc_final: 0.5614 (tmm) REVERT: e 95 TYR cc_start: 0.3702 (OUTLIER) cc_final: 0.0334 (t80) REVERT: e 120 GLU cc_start: 0.6293 (tt0) cc_final: 0.5880 (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: 0.7562 (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: 0.1892 time to fit residues: 46.3179 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 : 0.989 ------------------------------------------------------------------------------- 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: 0.0020 chunk 22 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 chunk 20 optimal weight: 0.5980 chunk 120 optimal weight: 1.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- 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 = 0.5013 r_free = 0.5013 target = 0.216626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4734 r_free = 0.4734 target = 0.187940 restraints weight = 29551.365| |-----------------------------------------------------------------------------| r_work (start): 0.4704 rms_B_bonded: 4.23 r_work (final): 0.4704 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4704 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4704 r_free = 0.4704 target_work(ls_wunit_k1) = 0.187 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4704 r_free = 0.4704 target_work(ls_wunit_k1) = 0.187 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4704 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5524 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10156 Z= 0.119 Angle : 0.584 11.275 13841 Z= 0.305 Chirality : 0.041 0.203 1639 Planarity : 0.003 0.046 1712 Dihedral : 13.703 169.339 1769 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.54 % Favored : 93.38 % Rotamer: Outliers : 3.56 % Allowed : 27.47 % 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: -1.18 (0.24), residues: 1319 helix: 0.42 (0.20), residues: 697 sheet: -2.21 (0.52), residues: 99 loop : -2.15 (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 0.015 0.002 PHE D 152 TYR 0.040 0.001 TYR e 210 ARG 0.002 0.000 ARG e 291 Details of bonding type rmsd hydrogen bonds : bond 0.03214 ( 510) hydrogen bonds : angle 4.57350 ( 1485) covalent geometry : bond 0.00257 (10156) covalent geometry : angle 0.58436 (13841) *********************** 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 183 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 152 time to evaluate : 1.099 Fit side-chains REVERT: A 26 GLU cc_start: 0.7186 (pm20) cc_final: 0.6870 (pm20) REVERT: a 31 ASN cc_start: 0.7214 (OUTLIER) cc_final: 0.6739 (t0) REVERT: D 102 GLN cc_start: 0.6467 (mm110) cc_final: 0.6205 (mm110) REVERT: D 109 LEU cc_start: 0.5546 (mm) cc_final: 0.4950 (mm) REVERT: D 111 GLU cc_start: 0.5702 (mm-30) cc_final: 0.4110 (pt0) REVERT: e 13 MET cc_start: 0.6117 (tmm) cc_final: 0.5762 (tmm) REVERT: e 95 TYR cc_start: 0.3795 (OUTLIER) cc_final: 0.0121 (t80) outliers start: 31 outliers final: 12 residues processed: 173 average time/residue: 0.2110 time to fit residues: 51.7519 Evaluate side-chains 151 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 0.994 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 15 optimal weight: 3.9990 chunk 63 optimal weight: 30.0000 chunk 18 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 69 optimal weight: 9.9990 chunk 87 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4909 r_free = 0.4909 target = 0.206865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.177693 restraints weight = 47744.587| |-----------------------------------------------------------------------------| r_work (start): 0.4589 rms_B_bonded: 8.12 r_work: 0.4209 rms_B_bonded: 8.01 restraints_weight: 2.0000 r_work (final): 0.4209 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4220 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4220 r_free = 0.4220 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4220 r_free = 0.4220 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4220 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6178 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 10156 Z= 0.258 Angle : 0.736 11.213 13841 Z= 0.396 Chirality : 0.046 0.196 1639 Planarity : 0.004 0.044 1712 Dihedral : 14.243 171.300 1769 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 20.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.37 % Favored : 91.55 % Rotamer: Outliers : 5.17 % Allowed : 26.67 % Favored : 68.16 % 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: -1.59 (0.23), residues: 1319 helix: 0.20 (0.20), residues: 702 sheet: -1.83 (0.55), residues: 95 loop : -2.69 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP E 104 HIS 0.006 0.002 HIS e 132 PHE 0.021 0.003 PHE D 152 TYR 0.020 0.002 TYR e 210 ARG 0.004 0.001 ARG D 214 Details of bonding type rmsd hydrogen bonds : bond 0.04308 ( 510) hydrogen bonds : angle 5.17364 ( 1485) covalent geometry : bond 0.00564 (10156) covalent geometry : angle 0.73595 (13841) *********************** 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 180 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 135 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7770 (pm20) REVERT: a 31 ASN cc_start: 0.7988 (OUTLIER) cc_final: 0.7655 (t0) REVERT: D 102 GLN cc_start: 0.7334 (mm110) cc_final: 0.6899 (mm110) REVERT: D 111 GLU cc_start: 0.6042 (mm-30) cc_final: 0.4520 (pt0) REVERT: E 124 MET cc_start: 0.7935 (ptp) cc_final: 0.7666 (ptp) REVERT: E 263 MET cc_start: 0.1234 (mpp) cc_final: 0.0985 (mpp) REVERT: e 95 TYR cc_start: 0.4640 (OUTLIER) cc_final: 0.0454 (t80) outliers start: 45 outliers final: 32 residues processed: 169 average time/residue: 0.2161 time to fit residues: 52.9645 Evaluate side-chains 164 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 129 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 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 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 31 LEU 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 206 ASN Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain D residue 226 PHE Chi-restraints excluded: chain D residue 230 HIS 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 164 SER Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain e residue 32 HIS Chi-restraints excluded: chain e residue 48 ILE Chi-restraints excluded: chain e residue 95 TYR Chi-restraints excluded: chain e residue 108 TRP Chi-restraints excluded: chain e residue 210 TYR Chi-restraints excluded: chain e residue 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: 0.9990 chunk 85 optimal weight: 4.9990 chunk 105 optimal weight: 0.3980 chunk 111 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.3980 chunk 75 optimal weight: 10.0000 chunk 129 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 ASN e 168 HIS ** e 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4969 r_free = 0.4969 target = 0.212647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.184189 restraints weight = 58916.202| |-----------------------------------------------------------------------------| r_work (start): 0.4668 rms_B_bonded: 9.39 r_work (final): 0.4668 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4668 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4668 r_free = 0.4668 target_work(ls_wunit_k1) = 0.184 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4668 r_free = 0.4668 target_work(ls_wunit_k1) = 0.184 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4668 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5505 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10156 Z= 0.129 Angle : 0.605 11.964 13841 Z= 0.317 Chirality : 0.042 0.156 1639 Planarity : 0.003 0.032 1712 Dihedral : 13.791 168.931 1769 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.70 % Favored : 93.23 % Rotamer: Outliers : 4.02 % Allowed : 27.01 % 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: -1.21 (0.24), residues: 1319 helix: 0.55 (0.20), residues: 708 sheet: -2.52 (0.52), residues: 99 loop : -2.42 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 104 HIS 0.004 0.001 HIS e 30 PHE 0.019 0.002 PHE e 152 TYR 0.015 0.001 TYR D 42 ARG 0.003 0.000 ARG D 125 Details of bonding type rmsd hydrogen bonds : bond 0.03254 ( 510) hydrogen bonds : angle 4.56864 ( 1485) covalent geometry : bond 0.00289 (10156) covalent geometry : angle 0.60491 (13841) *********************** 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 179 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 144 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.7034 (OUTLIER) cc_final: 0.6700 (pm20) REVERT: a 31 ASN cc_start: 0.7095 (OUTLIER) cc_final: 0.6771 (t0) REVERT: D 3 LYS cc_start: 0.5429 (pttm) cc_final: 0.4629 (mtmm) REVERT: D 102 GLN cc_start: 0.6661 (mm110) cc_final: 0.6331 (mm110) REVERT: D 111 GLU cc_start: 0.5759 (mm-30) cc_final: 0.4600 (pt0) REVERT: e 18 ARG cc_start: 0.3477 (OUTLIER) cc_final: 0.1461 (mmt180) REVERT: e 86 ILE cc_start: 0.6873 (mp) cc_final: 0.6647 (mt) REVERT: e 95 TYR cc_start: 0.3674 (OUTLIER) cc_final: 0.0172 (t80) outliers start: 35 outliers final: 20 residues processed: 169 average time/residue: 0.2059 time to fit residues: 49.8941 Evaluate side-chains 163 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain a residue 31 ASN Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain a residue 81 VAL Chi-restraints excluded: chain D residue 44 ASN Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 90 LEU 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 18 ARG Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 67 ASN Chi-restraints excluded: chain e residue 95 TYR Chi-restraints excluded: chain e residue 108 TRP Chi-restraints excluded: chain e residue 263 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 97 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 chunk 96 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 127 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 26 optimal weight: 0.0970 chunk 36 optimal weight: 20.0000 overall best weight: 1.5782 ------------------------------------------------------------------------------- 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 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4946 r_free = 0.4946 target = 0.210342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.182532 restraints weight = 62062.406| |-----------------------------------------------------------------------------| r_work (start): 0.4653 rms_B_bonded: 10.50 r_work (final): 0.4653 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4653 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4653 r_free = 0.4653 target_work(ls_wunit_k1) = 0.182 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4653 r_free = 0.4653 target_work(ls_wunit_k1) = 0.182 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4653 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5568 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10156 Z= 0.162 Angle : 0.624 12.025 13841 Z= 0.329 Chirality : 0.043 0.164 1639 Planarity : 0.003 0.038 1712 Dihedral : 13.797 169.965 1769 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.99 % Favored : 91.93 % Rotamer: Outliers : 4.25 % Allowed : 26.90 % 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: -1.17 (0.24), residues: 1319 helix: 0.59 (0.20), residues: 704 sheet: -1.85 (0.51), residues: 107 loop : -2.54 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 104 HIS 0.006 0.001 HIS e 168 PHE 0.017 0.002 PHE e 152 TYR 0.014 0.002 TYR D 42 ARG 0.003 0.000 ARG D 125 Details of bonding type rmsd hydrogen bonds : bond 0.03443 ( 510) hydrogen bonds : angle 4.64537 ( 1485) covalent geometry : bond 0.00363 (10156) covalent geometry : angle 0.62375 (13841) *********************** 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 178 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 141 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.6767 (OUTLIER) cc_final: 0.6417 (pm20) REVERT: a 31 ASN cc_start: 0.7411 (OUTLIER) cc_final: 0.6929 (t0) REVERT: D 3 LYS cc_start: 0.5600 (pttm) cc_final: 0.4785 (mtmm) REVERT: D 111 GLU cc_start: 0.5684 (mm-30) cc_final: 0.4581 (pt0) REVERT: e 18 ARG cc_start: 0.3477 (OUTLIER) cc_final: 0.1470 (mmt180) REVERT: e 95 TYR cc_start: 0.3954 (OUTLIER) cc_final: 0.0416 (t80) outliers start: 37 outliers final: 26 residues processed: 169 average time/residue: 0.2252 time to fit residues: 54.4540 Evaluate side-chains 166 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 1.085 ------------------------------------------------------------------------------- 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 31 ASN Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain a residue 75 MET Chi-restraints excluded: chain a residue 81 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 44 ASN Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain 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 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 263 MET 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: 0.9980 chunk 63 optimal weight: 7.9990 chunk 84 optimal weight: 0.8980 chunk 131 optimal weight: 0.5980 chunk 55 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 chunk 48 optimal weight: 20.0000 chunk 9 optimal weight: 7.9990 chunk 119 optimal weight: 8.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4970 r_free = 0.4970 target = 0.212818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.184241 restraints weight = 50214.051| |-----------------------------------------------------------------------------| r_work (start): 0.4672 rms_B_bonded: 8.52 r_work (final): 0.4672 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4671 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4671 r_free = 0.4671 target_work(ls_wunit_k1) = 0.183 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4671 r_free = 0.4671 target_work(ls_wunit_k1) = 0.183 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4671 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5531 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10156 Z= 0.128 Angle : 0.600 12.362 13841 Z= 0.314 Chirality : 0.042 0.142 1639 Planarity : 0.003 0.034 1712 Dihedral : 13.599 169.264 1769 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.54 % Favored : 93.38 % Rotamer: Outliers : 3.79 % Allowed : 28.28 % Favored : 67.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.00 (0.24), residues: 1319 helix: 0.72 (0.20), residues: 707 sheet: -2.45 (0.51), residues: 99 loop : -2.29 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 104 HIS 0.005 0.001 HIS e 168 PHE 0.016 0.002 PHE e 152 TYR 0.018 0.001 TYR D 177 ARG 0.003 0.000 ARG D 125 Details of bonding type rmsd hydrogen bonds : bond 0.03147 ( 510) hydrogen bonds : angle 4.47153 ( 1485) covalent geometry : bond 0.00284 (10156) covalent geometry : angle 0.59952 (13841) *********************** 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 184 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 151 time to evaluate : 1.677 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6776 (pm20) REVERT: a 31 ASN cc_start: 0.7377 (OUTLIER) cc_final: 0.6731 (t0) REVERT: D 102 GLN cc_start: 0.6551 (mm110) cc_final: 0.6276 (mm110) REVERT: D 109 LEU cc_start: 0.5233 (OUTLIER) cc_final: 0.4818 (mm) REVERT: D 111 GLU cc_start: 0.5454 (mm-30) cc_final: 0.4568 (pt0) REVERT: e 18 ARG cc_start: 0.3364 (OUTLIER) cc_final: 0.1543 (mmt180) REVERT: e 95 TYR cc_start: 0.3929 (OUTLIER) cc_final: 0.0275 (t80) outliers start: 33 outliers final: 23 residues processed: 173 average time/residue: 0.2611 time to fit residues: 62.9583 Evaluate side-chains 169 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 1.082 ------------------------------------------------------------------------------- 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 31 ASN Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain a residue 81 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 44 ASN Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 158 GLN Chi-restraints excluded: chain E residue 162 PHE Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain e residue 18 ARG Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 95 TYR Chi-restraints excluded: chain e residue 108 TRP 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: 0.7980 chunk 126 optimal weight: 7.9990 chunk 8 optimal weight: 0.0470 chunk 5 optimal weight: 5.9990 chunk 111 optimal weight: 7.9990 chunk 58 optimal weight: 9.9990 chunk 121 optimal weight: 8.9990 chunk 104 optimal weight: 8.9990 chunk 103 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 88 optimal weight: 0.0570 overall best weight: 1.7800 ------------------------------------------------------------------------------- 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 ** D 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4933 r_free = 0.4933 target = 0.208899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.179965 restraints weight = 47388.020| |-----------------------------------------------------------------------------| r_work (start): 0.4618 rms_B_bonded: 8.61 r_work: 0.4210 rms_B_bonded: 8.54 restraints_weight: 2.0000 r_work: 0.4387 rms_B_bonded: 5.10 restraints_weight: 4.0000 r_work (final): 0.4387 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4398 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4398 r_free = 0.4398 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4398 r_free = 0.4398 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4398 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5964 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10156 Z= 0.170 Angle : 0.640 12.024 13841 Z= 0.337 Chirality : 0.043 0.148 1639 Planarity : 0.003 0.039 1712 Dihedral : 13.666 169.885 1769 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.30 % Favored : 91.63 % Rotamer: Outliers : 4.60 % Allowed : 28.16 % Favored : 67.24 % 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: -1.08 (0.24), residues: 1319 helix: 0.64 (0.20), residues: 705 sheet: -1.86 (0.50), residues: 106 loop : -2.46 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP E 104 HIS 0.005 0.001 HIS e 168 PHE 0.015 0.002 PHE e 152 TYR 0.018 0.002 TYR D 42 ARG 0.003 0.001 ARG D 125 Details of bonding type rmsd hydrogen bonds : bond 0.03530 ( 510) hydrogen bonds : angle 4.69566 ( 1485) covalent geometry : bond 0.00382 (10156) covalent geometry : angle 0.63966 (13841) *********************** 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 185 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 145 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7403 (pm20) REVERT: a 31 ASN cc_start: 0.7812 (OUTLIER) cc_final: 0.7124 (t0) REVERT: D 102 GLN cc_start: 0.6965 (mm110) cc_final: 0.6661 (mm110) REVERT: D 111 GLU cc_start: 0.5676 (mm-30) cc_final: 0.4843 (pm20) REVERT: E 30 HIS cc_start: 0.4474 (OUTLIER) cc_final: 0.4021 (p-80) REVERT: e 18 ARG cc_start: 0.3349 (OUTLIER) cc_final: 0.1624 (mmt180) REVERT: e 95 TYR cc_start: 0.4411 (OUTLIER) cc_final: 0.0266 (t80) outliers start: 40 outliers final: 25 residues processed: 174 average time/residue: 0.2069 time to fit residues: 51.1796 Evaluate side-chains 169 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 1.077 ------------------------------------------------------------------------------- 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 1 MET Chi-restraints excluded: chain a residue 31 ASN Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain a residue 81 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 44 ASN Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain E residue 30 HIS 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 22 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 104 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 96 optimal weight: 0.2980 chunk 28 optimal weight: 0.3980 chunk 47 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 29 optimal weight: 0.5980 chunk 67 optimal weight: 10.0000 overall best weight: 1.4582 ------------------------------------------------------------------------------- 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 ** D 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 279 ASN ** 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 = 0.4941 r_free = 0.4941 target = 0.209731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.181312 restraints weight = 42880.798| |-----------------------------------------------------------------------------| r_work (start): 0.4633 rms_B_bonded: 7.99 r_work (final): 0.4633 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4633 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4633 r_free = 0.4633 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4633 r_free = 0.4633 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4633 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5631 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10156 Z= 0.154 Angle : 0.647 13.463 13841 Z= 0.335 Chirality : 0.043 0.178 1639 Planarity : 0.003 0.042 1712 Dihedral : 13.644 169.754 1769 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.23 % Favored : 92.69 % Rotamer: Outliers : 4.37 % Allowed : 28.39 % Favored : 67.24 % 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: -1.06 (0.24), residues: 1319 helix: 0.64 (0.20), residues: 707 sheet: -2.20 (0.47), residues: 113 loop : -2.33 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 104 HIS 0.006 0.001 HIS e 168 PHE 0.023 0.002 PHE e 152 TYR 0.022 0.002 TYR E 284 ARG 0.003 0.000 ARG D 125 Details of bonding type rmsd hydrogen bonds : bond 0.03457 ( 510) hydrogen bonds : angle 4.68137 ( 1485) covalent geometry : bond 0.00347 (10156) covalent geometry : angle 0.64732 (13841) *********************** 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 178 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 140 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.7068 (OUTLIER) cc_final: 0.6708 (pm20) REVERT: a 31 ASN cc_start: 0.7428 (OUTLIER) cc_final: 0.6805 (t0) REVERT: D 1 MET cc_start: -0.0377 (ptp) cc_final: -0.1226 (ptp) REVERT: D 102 GLN cc_start: 0.6686 (mm110) cc_final: 0.6389 (mm110) REVERT: D 111 GLU cc_start: 0.5413 (mm-30) cc_final: 0.4582 (pm20) REVERT: D 261 GLN cc_start: 0.7405 (OUTLIER) cc_final: 0.6535 (mp10) REVERT: E 30 HIS cc_start: 0.3663 (OUTLIER) cc_final: 0.3410 (p-80) REVERT: e 1 MET cc_start: 0.4028 (tmm) cc_final: 0.3774 (tpp) REVERT: e 18 ARG cc_start: 0.3519 (OUTLIER) cc_final: 0.1598 (mmt180) REVERT: e 95 TYR cc_start: 0.4650 (OUTLIER) cc_final: 0.1231 (t80) outliers start: 38 outliers final: 27 residues processed: 167 average time/residue: 0.2098 time to fit residues: 50.2018 Evaluate side-chains 170 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 137 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 1 MET Chi-restraints excluded: chain a residue 31 ASN Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain a residue 81 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 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 D residue 239 VAL Chi-restraints excluded: chain D residue 261 GLN Chi-restraints excluded: chain E residue 30 HIS 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 210 TYR Chi-restraints excluded: chain e residue 263 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 58 optimal weight: 0.0570 chunk 28 optimal weight: 4.9990 chunk 88 optimal weight: 0.1980 chunk 85 optimal weight: 0.9980 chunk 100 optimal weight: 9.9990 chunk 110 optimal weight: 0.9990 chunk 71 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- 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 ** D 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 HIS ** E 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 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 = 0.4968 r_free = 0.4968 target = 0.212364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4696 r_free = 0.4696 target = 0.185979 restraints weight = 52407.381| |-----------------------------------------------------------------------------| r_work (start): 0.4691 rms_B_bonded: 8.53 r_work (final): 0.4691 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4691 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4691 r_free = 0.4691 target_work(ls_wunit_k1) = 0.186 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4691 r_free = 0.4691 target_work(ls_wunit_k1) = 0.186 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4691 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5454 moved from start: 0.3696 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= 0.128 Angle : 0.644 14.058 13841 Z= 0.328 Chirality : 0.043 0.196 1639 Planarity : 0.003 0.037 1712 Dihedral : 13.524 169.068 1769 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.61 % Favored : 92.31 % Rotamer: Outliers : 3.45 % Allowed : 29.31 % Favored : 67.24 % 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: -0.84 (0.24), residues: 1319 helix: 0.79 (0.20), residues: 705 sheet: -1.96 (0.49), residues: 113 loop : -2.19 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP E 73 HIS 0.005 0.001 HIS e 168 PHE 0.023 0.002 PHE e 152 TYR 0.016 0.001 TYR e 210 ARG 0.003 0.000 ARG D 125 Details of bonding type rmsd hydrogen bonds : bond 0.03294 ( 510) hydrogen bonds : angle 4.55818 ( 1485) covalent geometry : bond 0.00285 (10156) covalent geometry : angle 0.64353 (13841) ********************** 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 174 residues out of total 1143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 144 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6723 (pm20) REVERT: a 31 ASN cc_start: 0.7496 (OUTLIER) cc_final: 0.6748 (t0) REVERT: D 1 MET cc_start: -0.0376 (ptp) cc_final: -0.1134 (ptp) REVERT: D 102 GLN cc_start: 0.6469 (mm110) cc_final: 0.6189 (mm110) REVERT: D 111 GLU cc_start: 0.5137 (mm-30) cc_final: 0.4278 (pm20) REVERT: e 1 MET cc_start: 0.4117 (tmm) cc_final: 0.3870 (tpp) REVERT: e 18 ARG cc_start: 0.3643 (OUTLIER) cc_final: 0.1693 (mmt180) REVERT: e 95 TYR cc_start: 0.4252 (OUTLIER) cc_final: 0.0699 (t80) REVERT: e 235 ARG cc_start: 0.4957 (tpt170) cc_final: 0.4468 (tpp-160) outliers start: 30 outliers final: 25 residues processed: 162 average time/residue: 0.2999 time to fit residues: 68.3001 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 : 2.522 ------------------------------------------------------------------------------- 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 31 ASN Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain a residue 81 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 64 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 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: 7.9990 chunk 23 optimal weight: 0.0980 chunk 1 optimal weight: 7.9990 chunk 114 optimal weight: 8.9990 chunk 82 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 33 optimal weight: 0.3980 chunk 44 optimal weight: 0.9990 chunk 53 optimal weight: 7.9990 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** ** D 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4960 r_free = 0.4960 target = 0.211624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.178906 restraints weight = 56752.708| |-----------------------------------------------------------------------------| r_work (start): 0.4588 rms_B_bonded: 7.88 r_work: 0.4285 rms_B_bonded: 7.62 restraints_weight: 2.0000 r_work (final): 0.4285 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4296 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4296 r_free = 0.4296 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4296 r_free = 0.4296 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4296 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5988 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10156 Z= 0.137 Angle : 0.631 13.453 13841 Z= 0.325 Chirality : 0.043 0.188 1639 Planarity : 0.003 0.059 1712 Dihedral : 13.523 169.818 1769 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.31 % Favored : 92.62 % Rotamer: Outliers : 3.56 % Allowed : 29.20 % Favored : 67.24 % 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: -0.81 (0.24), residues: 1319 helix: 0.82 (0.20), residues: 705 sheet: -2.11 (0.46), residues: 123 loop : -2.14 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 104 HIS 0.005 0.001 HIS e 168 PHE 0.021 0.002 PHE e 152 TYR 0.029 0.002 TYR D 177 ARG 0.003 0.000 ARG D 125 Details of bonding type rmsd hydrogen bonds : bond 0.03281 ( 510) hydrogen bonds : angle 4.57448 ( 1485) covalent geometry : bond 0.00307 (10156) covalent geometry : angle 0.63105 (13841) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5788.20 seconds wall clock time: 106 minutes 34.26 seconds (6394.26 seconds total)