Starting phenix.real_space_refine on Sat Jul 4 00:31:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wht_32511/07_2026/7wht_32511.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wht_32511/07_2026/7wht_32511.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wht_32511/07_2026/7wht_32511.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wht_32511/07_2026/7wht_32511.map" model { file = "/net/cci-nas-00/data/ceres_data/7wht_32511/07_2026/7wht_32511.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wht_32511/07_2026/7wht_32511.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7wht_32511/07_2026/7wht_32511.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wht_32511/07_2026/7wht_32511.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.051 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 6 5.21 5 S 102 5.16 5 C 10806 2.51 5 N 2910 2.21 5 O 3144 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16980 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2790 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 21, 'TRANS': 338} Chain breaks: 3 Chain: "B" Number of atoms: 2790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2790 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 21, 'TRANS': 338} Chain breaks: 3 Chain: "C" Number of atoms: 2790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2790 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 21, 'TRANS': 338} Chain breaks: 3 Chain: "D" Number of atoms: 2790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2790 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 21, 'TRANS': 338} Chain breaks: 3 Chain: "E" Number of atoms: 2790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2790 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 21, 'TRANS': 338} Chain breaks: 3 Chain: "F" Number of atoms: 2790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2790 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 21, 'TRANS': 338} Chain breaks: 3 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {' MG': 1, 'GDD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {' MG': 1, 'GDD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {' MG': 1, 'GDD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {' MG': 1, 'GDD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {' MG': 1, 'GDD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {' MG': 1, 'GDD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.42, per 1000 atoms: 0.20 Number of scatterers: 16980 At special positions: 0 Unit cell: (120.91, 121.98, 112.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 102 16.00 P 12 15.00 Mg 6 11.99 O 3144 8.00 N 2910 7.00 C 10806 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: 1.37 Conformation dependent library (CDL) restraints added in 597.5 milliseconds 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3900 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 52 sheets defined 20.8% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 22 through 27 Processing helix chain 'A' and resid 30 through 34 Processing helix chain 'A' and resid 40 through 52 removed outlier: 3.859A pdb=" N HIS A 44 " --> pdb=" O PRO A 40 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLN A 45 " --> pdb=" O MET A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 66 No H-bonds generated for 'chain 'A' and resid 64 through 66' Processing helix chain 'A' and resid 67 through 74 Processing helix chain 'A' and resid 75 through 77 No H-bonds generated for 'chain 'A' and resid 75 through 77' Processing helix chain 'A' and resid 94 through 100 removed outlier: 3.985A pdb=" N LEU A 98 " --> pdb=" O THR A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 108 removed outlier: 3.601A pdb=" N ILE A 104 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN A 107 " --> pdb=" O ASP A 103 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP A 108 " --> pdb=" O ILE A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 192 removed outlier: 4.253A pdb=" N LEU A 191 " --> pdb=" O ASN A 187 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP A 192 " --> pdb=" O LYS A 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 187 through 192' Processing helix chain 'A' and resid 229 through 244 Proline residue: A 242 - end of helix Processing helix chain 'B' and resid 22 through 27 Processing helix chain 'B' and resid 30 through 34 Processing helix chain 'B' and resid 40 through 52 removed outlier: 3.681A pdb=" N HIS B 44 " --> pdb=" O PRO B 40 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN B 45 " --> pdb=" O MET B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 66 No H-bonds generated for 'chain 'B' and resid 64 through 66' Processing helix chain 'B' and resid 67 through 74 Processing helix chain 'B' and resid 94 through 100 removed outlier: 3.970A pdb=" N LEU B 98 " --> pdb=" O THR B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 108 removed outlier: 3.653A pdb=" N ILE B 104 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLN B 107 " --> pdb=" O ASP B 103 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASP B 108 " --> pdb=" O ILE B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 192 removed outlier: 4.133A pdb=" N LEU B 191 " --> pdb=" O ASN B 187 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP B 192 " --> pdb=" O LYS B 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 187 through 192' Processing helix chain 'B' and resid 229 through 244 Proline residue: B 242 - end of helix Processing helix chain 'C' and resid 22 through 27 Processing helix chain 'C' and resid 30 through 34 Processing helix chain 'C' and resid 40 through 52 removed outlier: 3.671A pdb=" N HIS C 44 " --> pdb=" O PRO C 40 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN C 45 " --> pdb=" O MET C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 66 No H-bonds generated for 'chain 'C' and resid 64 through 66' Processing helix chain 'C' and resid 67 through 74 Processing helix chain 'C' and resid 94 through 100 removed outlier: 3.965A pdb=" N LEU C 98 " --> pdb=" O THR C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 108 removed outlier: 3.671A pdb=" N ILE C 104 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN C 107 " --> pdb=" O ASP C 103 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP C 108 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 192 removed outlier: 4.056A pdb=" N LEU C 191 " --> pdb=" O ASN C 187 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP C 192 " --> pdb=" O LYS C 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 187 through 192' Processing helix chain 'C' and resid 229 through 244 Proline residue: C 242 - end of helix Processing helix chain 'D' and resid 22 through 27 Processing helix chain 'D' and resid 30 through 34 Processing helix chain 'D' and resid 40 through 52 removed outlier: 3.714A pdb=" N HIS D 44 " --> pdb=" O PRO D 40 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLN D 45 " --> pdb=" O MET D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 66 No H-bonds generated for 'chain 'D' and resid 64 through 66' Processing helix chain 'D' and resid 67 through 74 Processing helix chain 'D' and resid 75 through 77 No H-bonds generated for 'chain 'D' and resid 75 through 77' Processing helix chain 'D' and resid 94 through 100 removed outlier: 4.007A pdb=" N LEU D 98 " --> pdb=" O THR D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 108 removed outlier: 3.708A pdb=" N ILE D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN D 107 " --> pdb=" O ASP D 103 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP D 108 " --> pdb=" O ILE D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 192 removed outlier: 4.240A pdb=" N LEU D 191 " --> pdb=" O ASN D 187 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP D 192 " --> pdb=" O LYS D 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 187 through 192' Processing helix chain 'D' and resid 229 through 244 Proline residue: D 242 - end of helix Processing helix chain 'E' and resid 22 through 27 Processing helix chain 'E' and resid 30 through 34 Processing helix chain 'E' and resid 40 through 52 removed outlier: 3.604A pdb=" N HIS E 44 " --> pdb=" O PRO E 40 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLN E 45 " --> pdb=" O MET E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 74 removed outlier: 4.627A pdb=" N GLU E 70 " --> pdb=" O GLU E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 100 removed outlier: 3.967A pdb=" N LEU E 98 " --> pdb=" O THR E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 108 removed outlier: 3.772A pdb=" N ILE E 104 " --> pdb=" O LEU E 100 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN E 107 " --> pdb=" O ASP E 103 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP E 108 " --> pdb=" O ILE E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 138 removed outlier: 4.122A pdb=" N GLY E 137 " --> pdb=" O LYS E 133 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLU E 138 " --> pdb=" O ALA E 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 133 through 138' Processing helix chain 'E' and resid 187 through 192 removed outlier: 4.132A pdb=" N LEU E 191 " --> pdb=" O ASN E 187 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP E 192 " --> pdb=" O LYS E 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 187 through 192' Processing helix chain 'E' and resid 229 through 245 Proline residue: E 242 - end of helix removed outlier: 3.680A pdb=" N VAL E 245 " --> pdb=" O ILE E 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 27 Processing helix chain 'F' and resid 30 through 34 Processing helix chain 'F' and resid 40 through 52 removed outlier: 3.656A pdb=" N HIS F 44 " --> pdb=" O PRO F 40 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN F 45 " --> pdb=" O MET F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 66 No H-bonds generated for 'chain 'F' and resid 64 through 66' Processing helix chain 'F' and resid 67 through 74 Processing helix chain 'F' and resid 94 through 100 removed outlier: 3.960A pdb=" N LEU F 98 " --> pdb=" O THR F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 108 removed outlier: 3.677A pdb=" N ILE F 104 " --> pdb=" O LEU F 100 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN F 107 " --> pdb=" O ASP F 103 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP F 108 " --> pdb=" O ILE F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 192 removed outlier: 4.070A pdb=" N LEU F 191 " --> pdb=" O ASN F 187 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP F 192 " --> pdb=" O LYS F 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 187 through 192' Processing helix chain 'F' and resid 229 through 244 Proline residue: F 242 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 79 through 84 removed outlier: 6.968A pdb=" N VAL A 57 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N VAL A 84 " --> pdb=" O VAL A 57 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU A 59 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ALA A 11 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ALA A 60 " --> pdb=" O ALA A 11 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N ILE A 13 " --> pdb=" O ALA A 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 121 Processing sheet with id=AA3, first strand: chain 'A' and resid 155 through 156 removed outlier: 3.517A pdb=" N VAL A 155 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL A 168 " --> pdb=" O VAL A 155 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 268 through 269 removed outlier: 7.013A pdb=" N THR A 268 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL A 286 " --> pdb=" O ILE A 305 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 274 through 275 removed outlier: 6.865A pdb=" N LEU A 274 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N ALA A 295 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N SER A 292 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N GLU A 312 " --> pdb=" O SER A 292 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N GLY A 294 " --> pdb=" O GLU A 312 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ALA A 309 " --> pdb=" O VAL A 327 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 280 through 281 removed outlier: 6.507A pdb=" N LYS A 280 " --> pdb=" O ILE A 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 338 through 340 removed outlier: 5.914A pdb=" N HIS A 338 " --> pdb=" O LEU A 357 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 350 through 351 removed outlier: 6.758A pdb=" N GLU A 350 " --> pdb=" O VAL A 368 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 360 through 362 removed outlier: 6.593A pdb=" N LYS A 361 " --> pdb=" O ILE A 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 79 through 84 removed outlier: 7.061A pdb=" N VAL B 57 " --> pdb=" O SER B 82 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N VAL B 84 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU B 59 " --> pdb=" O VAL B 84 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ALA B 11 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ALA B 60 " --> pdb=" O ALA B 11 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ILE B 13 " --> pdb=" O ALA B 60 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 119 through 121 Processing sheet with id=AB3, first strand: chain 'B' and resid 155 through 156 removed outlier: 3.947A pdb=" N VAL B 168 " --> pdb=" O VAL B 155 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 268 through 269 removed outlier: 7.034A pdb=" N THR B 268 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N VAL B 286 " --> pdb=" O ILE B 305 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N HIS B 338 " --> pdb=" O LEU B 357 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 273 through 275 removed outlier: 6.382A pdb=" N SER B 292 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N GLU B 312 " --> pdb=" O SER B 292 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N GLY B 294 " --> pdb=" O GLU B 312 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ALA B 309 " --> pdb=" O VAL B 327 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 280 through 281 removed outlier: 6.574A pdb=" N LYS B 280 " --> pdb=" O ILE B 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 350 through 351 removed outlier: 6.721A pdb=" N GLU B 350 " --> pdb=" O VAL B 368 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 360 through 362 removed outlier: 6.456A pdb=" N LYS B 361 " --> pdb=" O ILE B 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 79 through 84 removed outlier: 7.045A pdb=" N VAL C 57 " --> pdb=" O SER C 82 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N VAL C 84 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU C 59 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ALA C 11 " --> pdb=" O ILE C 58 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ALA C 60 " --> pdb=" O ALA C 11 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ILE C 13 " --> pdb=" O ALA C 60 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 119 through 121 Processing sheet with id=AC2, first strand: chain 'C' and resid 155 through 156 removed outlier: 3.511A pdb=" N VAL C 155 " --> pdb=" O VAL C 168 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N VAL C 168 " --> pdb=" O VAL C 155 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 268 through 269 removed outlier: 7.006A pdb=" N THR C 268 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N VAL C 286 " --> pdb=" O ILE C 305 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N HIS C 338 " --> pdb=" O LEU C 357 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 274 through 275 removed outlier: 7.013A pdb=" N LEU C 274 " --> pdb=" O ILE C 293 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N ALA C 295 " --> pdb=" O LEU C 274 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N SER C 292 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N GLU C 312 " --> pdb=" O SER C 292 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N GLY C 294 " --> pdb=" O GLU C 312 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ALA C 309 " --> pdb=" O VAL C 327 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'C' and resid 280 through 281 removed outlier: 6.519A pdb=" N LYS C 280 " --> pdb=" O ILE C 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'C' and resid 350 through 351 removed outlier: 6.769A pdb=" N GLU C 350 " --> pdb=" O VAL C 368 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 360 through 362 removed outlier: 6.484A pdb=" N LYS C 361 " --> pdb=" O ILE C 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'D' and resid 79 through 84 removed outlier: 6.973A pdb=" N VAL D 57 " --> pdb=" O SER D 82 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N VAL D 84 " --> pdb=" O VAL D 57 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU D 59 " --> pdb=" O VAL D 84 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ALA D 11 " --> pdb=" O ILE D 58 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ALA D 60 " --> pdb=" O ALA D 11 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ILE D 13 " --> pdb=" O ALA D 60 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 119 through 121 Processing sheet with id=AD1, first strand: chain 'D' and resid 155 through 156 removed outlier: 4.078A pdb=" N VAL D 168 " --> pdb=" O VAL D 155 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 268 through 269 removed outlier: 7.032A pdb=" N THR D 268 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N VAL D 286 " --> pdb=" O ILE D 305 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 274 through 275 removed outlier: 6.835A pdb=" N LEU D 274 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N ALA D 295 " --> pdb=" O LEU D 274 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N SER D 292 " --> pdb=" O ILE D 310 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N GLU D 312 " --> pdb=" O SER D 292 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N GLY D 294 " --> pdb=" O GLU D 312 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA D 309 " --> pdb=" O VAL D 327 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'D' and resid 280 through 281 removed outlier: 6.522A pdb=" N LYS D 280 " --> pdb=" O ILE D 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'D' and resid 338 through 340 Processing sheet with id=AD6, first strand: chain 'D' and resid 350 through 351 removed outlier: 6.761A pdb=" N GLU D 350 " --> pdb=" O VAL D 368 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'D' and resid 360 through 362 removed outlier: 6.594A pdb=" N LYS D 361 " --> pdb=" O ILE D 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'E' and resid 79 through 84 removed outlier: 7.035A pdb=" N VAL E 57 " --> pdb=" O SER E 82 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N VAL E 84 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU E 59 " --> pdb=" O VAL E 84 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ALA E 11 " --> pdb=" O ILE E 58 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ALA E 60 " --> pdb=" O ALA E 11 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ILE E 13 " --> pdb=" O ALA E 60 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 119 through 121 Processing sheet with id=AE1, first strand: chain 'E' and resid 155 through 156 removed outlier: 3.995A pdb=" N VAL E 168 " --> pdb=" O VAL E 155 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 268 through 269 removed outlier: 7.029A pdb=" N THR E 268 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N VAL E 286 " --> pdb=" O ILE E 305 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 273 through 275 removed outlier: 6.368A pdb=" N SER E 292 " --> pdb=" O ILE E 310 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N GLU E 312 " --> pdb=" O SER E 292 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N GLY E 294 " --> pdb=" O GLU E 312 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA E 309 " --> pdb=" O VAL E 327 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 280 through 281 removed outlier: 6.561A pdb=" N LYS E 280 " --> pdb=" O ILE E 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'E' and resid 338 through 340 Processing sheet with id=AE6, first strand: chain 'E' and resid 350 through 351 removed outlier: 6.724A pdb=" N GLU E 350 " --> pdb=" O VAL E 368 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'E' and resid 360 through 362 removed outlier: 6.478A pdb=" N LYS E 361 " --> pdb=" O ILE E 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'F' and resid 79 through 84 removed outlier: 7.029A pdb=" N VAL F 57 " --> pdb=" O SER F 82 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N VAL F 84 " --> pdb=" O VAL F 57 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU F 59 " --> pdb=" O VAL F 84 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ALA F 11 " --> pdb=" O ILE F 58 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ALA F 60 " --> pdb=" O ALA F 11 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ILE F 13 " --> pdb=" O ALA F 60 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 119 through 121 Processing sheet with id=AF1, first strand: chain 'F' and resid 155 through 156 removed outlier: 3.972A pdb=" N VAL F 168 " --> pdb=" O VAL F 155 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 268 through 269 removed outlier: 7.004A pdb=" N THR F 268 " --> pdb=" O ILE F 287 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL F 286 " --> pdb=" O ILE F 305 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 274 through 275 removed outlier: 6.961A pdb=" N LEU F 274 " --> pdb=" O ILE F 293 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N ALA F 295 " --> pdb=" O LEU F 274 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N SER F 292 " --> pdb=" O ILE F 310 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N GLU F 312 " --> pdb=" O SER F 292 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N GLY F 294 " --> pdb=" O GLU F 312 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ALA F 309 " --> pdb=" O VAL F 327 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'F' and resid 280 through 281 removed outlier: 6.507A pdb=" N LYS F 280 " --> pdb=" O ILE F 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'F' and resid 338 through 340 removed outlier: 5.945A pdb=" N HIS F 338 " --> pdb=" O LEU F 357 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'F' and resid 350 through 351 removed outlier: 6.778A pdb=" N GLU F 350 " --> pdb=" O VAL F 368 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'F' and resid 360 through 362 removed outlier: 6.541A pdb=" N LYS F 361 " --> pdb=" O ILE F 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 256 hydrogen bonds defined for protein. 702 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: 2.52 Time building geometry restraints manager: 1.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3607 1.33 - 1.45: 3690 1.45 - 1.57: 9845 1.57 - 1.69: 24 1.69 - 1.81: 174 Bond restraints: 17340 Sorted by residual: bond pdb=" CA TRP A 224 " pdb=" C TRP A 224 " ideal model delta sigma weight residual 1.521 1.450 0.070 1.26e-02 6.30e+03 3.13e+01 bond pdb=" CA TRP D 224 " pdb=" C TRP D 224 " ideal model delta sigma weight residual 1.521 1.455 0.066 1.28e-02 6.10e+03 2.69e+01 bond pdb=" CA PHE E 223 " pdb=" C PHE E 223 " ideal model delta sigma weight residual 1.526 1.461 0.065 1.37e-02 5.33e+03 2.26e+01 bond pdb=" CA PHE B 223 " pdb=" C PHE B 223 " ideal model delta sigma weight residual 1.526 1.463 0.063 1.37e-02 5.33e+03 2.15e+01 bond pdb=" CA PHE F 223 " pdb=" C PHE F 223 " ideal model delta sigma weight residual 1.526 1.463 0.063 1.37e-02 5.33e+03 2.13e+01 ... (remaining 17335 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 23012 2.65 - 5.30: 355 5.30 - 7.96: 66 7.96 - 10.61: 54 10.61 - 13.26: 9 Bond angle restraints: 23496 Sorted by residual: angle pdb=" N ALA A 210 " pdb=" CA ALA A 210 " pdb=" C ALA A 210 " ideal model delta sigma weight residual 111.36 122.44 -11.08 1.09e+00 8.42e-01 1.03e+02 angle pdb=" N ALA A 211 " pdb=" CA ALA A 211 " pdb=" C ALA A 211 " ideal model delta sigma weight residual 108.76 122.02 -13.26 1.58e+00 4.01e-01 7.04e+01 angle pdb=" N HIS A 132 " pdb=" CA HIS A 132 " pdb=" C HIS A 132 " ideal model delta sigma weight residual 111.36 103.61 7.75 1.09e+00 8.42e-01 5.06e+01 angle pdb=" N GLU D 212 " pdb=" CA GLU D 212 " pdb=" C GLU D 212 " ideal model delta sigma weight residual 108.60 118.70 -10.10 1.46e+00 4.69e-01 4.78e+01 angle pdb=" N ALA C 208 " pdb=" CA ALA C 208 " pdb=" C ALA C 208 " ideal model delta sigma weight residual 111.28 118.74 -7.46 1.09e+00 8.42e-01 4.68e+01 ... (remaining 23491 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.97: 9026 15.97 - 31.94: 987 31.94 - 47.92: 205 47.92 - 63.89: 45 63.89 - 79.86: 15 Dihedral angle restraints: 10278 sinusoidal: 4200 harmonic: 6078 Sorted by residual: dihedral pdb=" C GLU E 212 " pdb=" N GLU E 212 " pdb=" CA GLU E 212 " pdb=" CB GLU E 212 " ideal model delta harmonic sigma weight residual -122.60 -133.79 11.19 0 2.50e+00 1.60e-01 2.00e+01 dihedral pdb=" N GLU E 212 " pdb=" C GLU E 212 " pdb=" CA GLU E 212 " pdb=" CB GLU E 212 " ideal model delta harmonic sigma weight residual 122.80 133.75 -10.95 0 2.50e+00 1.60e-01 1.92e+01 dihedral pdb=" N ALA B 211 " pdb=" C ALA B 211 " pdb=" CA ALA B 211 " pdb=" CB ALA B 211 " ideal model delta harmonic sigma weight residual 122.90 133.76 -10.86 0 2.50e+00 1.60e-01 1.89e+01 ... (remaining 10275 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 2242 0.090 - 0.180: 361 0.180 - 0.271: 23 0.271 - 0.361: 10 0.361 - 0.451: 4 Chirality restraints: 2640 Sorted by residual: chirality pdb=" CA ALA B 211 " pdb=" N ALA B 211 " pdb=" C ALA B 211 " pdb=" CB ALA B 211 " both_signs ideal model delta sigma weight residual False 2.48 2.03 0.45 2.00e-01 2.50e+01 5.08e+00 chirality pdb=" CA GLU E 212 " pdb=" N GLU E 212 " pdb=" C GLU E 212 " pdb=" CB GLU E 212 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.83e+00 chirality pdb=" CA ALA A 134 " pdb=" N ALA A 134 " pdb=" C ALA A 134 " pdb=" CB ALA A 134 " both_signs ideal model delta sigma weight residual False 2.48 2.11 0.38 2.00e-01 2.50e+01 3.53e+00 ... (remaining 2637 not shown) Planarity restraints: 2988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR D 140 " 0.023 2.00e-02 2.50e+03 4.61e-02 2.13e+01 pdb=" C THR D 140 " -0.080 2.00e-02 2.50e+03 pdb=" O THR D 140 " 0.030 2.00e-02 2.50e+03 pdb=" N ILE D 141 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE F 206 " -0.069 5.00e-02 4.00e+02 1.04e-01 1.74e+01 pdb=" N PRO F 207 " 0.180 5.00e-02 4.00e+02 pdb=" CA PRO F 207 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO F 207 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE E 206 " 0.068 5.00e-02 4.00e+02 1.03e-01 1.70e+01 pdb=" N PRO E 207 " -0.178 5.00e-02 4.00e+02 pdb=" CA PRO E 207 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO E 207 " 0.059 5.00e-02 4.00e+02 ... (remaining 2985 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.16: 19 2.16 - 2.84: 5667 2.84 - 3.53: 23261 3.53 - 4.21: 39123 4.21 - 4.90: 68482 Nonbonded interactions: 136552 Sorted by model distance: nonbonded pdb=" O PHE C 131 " pdb=" OE1 GLU C 212 " model vdw 1.473 3.040 nonbonded pdb=" NH2 ARG D 193 " pdb=" NE2 GLN D 214 " model vdw 1.629 3.200 nonbonded pdb=" SD MET A 209 " pdb=" NE2 GLN A 214 " model vdw 1.635 3.480 nonbonded pdb=" CE MET A 209 " pdb=" NE2 GLN A 214 " model vdw 1.864 3.540 nonbonded pdb=" NH2 ARG D 193 " pdb=" OE1 GLN D 214 " model vdw 1.956 3.120 ... (remaining 136547 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.010 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 17340 Z= 0.317 Angle : 0.902 13.259 23496 Z= 0.455 Chirality : 0.061 0.451 2640 Planarity : 0.007 0.104 2988 Dihedral : 14.081 79.861 6378 Min Nonbonded Distance : 1.473 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % Rotamer: Outliers : 1.38 % Allowed : 0.88 % Favored : 97.74 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.18), residues: 2112 helix: 0.73 (0.35), residues: 264 sheet: 0.12 (0.28), residues: 348 loop : -1.53 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 178 TYR 0.019 0.001 TYR B 152 PHE 0.018 0.001 PHE E 223 TRP 0.010 0.001 TRP D 329 HIS 0.005 0.001 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00587 / 0.32 (17340) covalent geometry : angle 0.90173 / 0.45 (23496) hydrogen bonds : bond 0.25150 / 17.91 ( 256) hydrogen bonds : angle 6.88640 / 4.71 ( 702) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 260 time to evaluate : 0.487 Fit side-chains revert: symmetry clash REVERT: A 231 LYS cc_start: 0.7630 (pttm) cc_final: 0.7295 (pttm) REVERT: A 244 LEU cc_start: 0.9023 (tp) cc_final: 0.8783 (tt) REVERT: B 231 LYS cc_start: 0.7464 (pttm) cc_final: 0.7262 (pttm) REVERT: C 132 HIS cc_start: 0.8059 (p90) cc_final: 0.7067 (p90) REVERT: D 340 LYS cc_start: 0.8246 (ptmt) cc_final: 0.8042 (ptmt) outliers start: 25 outliers final: 8 residues processed: 279 average time/residue: 0.1047 time to fit residues: 46.6843 Evaluate side-chains 240 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 232 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain D residue 180 ASN Chi-restraints excluded: chain F residue 212 GLU Chi-restraints excluded: chain F residue 220 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.2980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 1.9990 chunk 212 optimal weight: 0.7980 chunk 77 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 107 GLN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 GLN D 107 GLN D 180 ASN D 214 GLN E 148 GLN F 107 GLN F 148 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.192852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.154259 restraints weight = 18017.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.153279 restraints weight = 25928.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.153369 restraints weight = 23752.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.152220 restraints weight = 20683.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.153017 restraints weight = 17909.600| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17340 Z= 0.143 Angle : 0.616 7.927 23496 Z= 0.315 Chirality : 0.051 0.227 2640 Planarity : 0.006 0.079 2988 Dihedral : 5.604 55.039 2320 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.61 % Favored : 90.39 % Rotamer: Outliers : 1.27 % Allowed : 9.16 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.18), residues: 2112 helix: 0.53 (0.33), residues: 276 sheet: 0.49 (0.31), residues: 276 loop : -1.52 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 178 TYR 0.018 0.002 TYR A 233 PHE 0.015 0.001 PHE B 167 TRP 0.009 0.001 TRP D 329 HIS 0.003 0.001 HIS E 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.14 (17340) covalent geometry : angle 0.61613 / 0.32 (23496) hydrogen bonds : bond 0.04863 / 3.43 ( 256) hydrogen bonds : angle 5.72158 / 3.93 ( 702) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 236 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 214 GLN cc_start: 0.3575 (OUTLIER) cc_final: 0.3226 (pt0) REVERT: F 206 PHE cc_start: 0.4470 (OUTLIER) cc_final: 0.3192 (m-80) outliers start: 23 outliers final: 10 residues processed: 256 average time/residue: 0.1090 time to fit residues: 43.1535 Evaluate side-chains 241 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 229 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain D residue 214 GLN Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain E residue 148 GLN Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain F residue 148 GLN Chi-restraints excluded: chain F residue 206 PHE Chi-restraints excluded: chain F residue 238 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 136 optimal weight: 3.9990 chunk 157 optimal weight: 0.0670 chunk 16 optimal weight: 10.0000 chunk 108 optimal weight: 7.9990 chunk 95 optimal weight: 20.0000 chunk 116 optimal weight: 4.9990 chunk 175 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 74 optimal weight: 0.5980 chunk 101 optimal weight: 0.0870 overall best weight: 1.1098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 HIS E 107 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.188120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.149854 restraints weight = 18410.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.148611 restraints weight = 28588.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.149285 restraints weight = 25761.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.148278 restraints weight = 19826.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.148692 restraints weight = 19036.528| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17340 Z= 0.147 Angle : 0.599 8.226 23496 Z= 0.303 Chirality : 0.051 0.223 2640 Planarity : 0.006 0.076 2988 Dihedral : 5.231 54.065 2308 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 1.66 % Allowed : 12.58 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.18), residues: 2112 helix: 0.68 (0.33), residues: 270 sheet: 0.36 (0.30), residues: 276 loop : -1.51 (0.16), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 102 TYR 0.017 0.001 TYR A 233 PHE 0.008 0.001 PHE E 206 TRP 0.009 0.001 TRP D 329 HIS 0.003 0.001 HIS E 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 (17340) covalent geometry : angle 0.59897 / 0.30 (23496) hydrogen bonds : bond 0.04402 / 3.05 ( 256) hydrogen bonds : angle 5.62040 / 3.86 ( 702) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 241 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 152 TYR cc_start: 0.7216 (p90) cc_final: 0.7004 (p90) outliers start: 30 outliers final: 18 residues processed: 265 average time/residue: 0.1096 time to fit residues: 44.9349 Evaluate side-chains 259 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 241 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 338 HIS Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain D residue 214 GLN Chi-restraints excluded: chain D residue 231 LYS Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 325 SER Chi-restraints excluded: chain E residue 231 LYS Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 338 HIS Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain F residue 325 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 25 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 157 optimal weight: 0.0570 chunk 101 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 chunk 193 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 ASN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 HIS ** D 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.187619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.144757 restraints weight = 18208.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.144180 restraints weight = 21981.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.145411 restraints weight = 20454.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.144342 restraints weight = 17887.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.145202 restraints weight = 15504.746| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17340 Z= 0.153 Angle : 0.607 8.587 23496 Z= 0.307 Chirality : 0.051 0.183 2640 Planarity : 0.006 0.075 2988 Dihedral : 5.224 54.040 2308 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.46 % Favored : 89.54 % Rotamer: Outliers : 2.26 % Allowed : 14.02 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.18), residues: 2112 helix: 0.16 (0.31), residues: 306 sheet: 0.31 (0.30), residues: 276 loop : -1.53 (0.16), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 102 TYR 0.017 0.001 TYR A 233 PHE 0.016 0.001 PHE E 206 TRP 0.009 0.001 TRP D 329 HIS 0.009 0.001 HIS B 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.15 (17340) covalent geometry : angle 0.60732 / 0.31 (23496) hydrogen bonds : bond 0.04170 / 2.88 ( 256) hydrogen bonds : angle 5.50415 / 3.78 ( 702) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 252 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 152 TYR cc_start: 0.7237 (p90) cc_final: 0.7012 (p90) REVERT: D 152 TYR cc_start: 0.7173 (p90) cc_final: 0.6934 (p90) REVERT: F 66 GLU cc_start: 0.7110 (mm-30) cc_final: 0.6832 (mp0) REVERT: F 142 MET cc_start: 0.4212 (mmm) cc_final: 0.3739 (mmt) outliers start: 41 outliers final: 21 residues processed: 284 average time/residue: 0.1097 time to fit residues: 49.1120 Evaluate side-chains 265 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 244 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 338 HIS Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 325 SER Chi-restraints excluded: chain E residue 231 LYS Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain F residue 325 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 48 optimal weight: 20.0000 chunk 63 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 174 optimal weight: 0.5980 chunk 208 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 120 optimal weight: 9.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 107 GLN B 148 GLN D 148 GLN ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 338 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.185746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.143077 restraints weight = 18182.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.142748 restraints weight = 21318.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.144657 restraints weight = 19855.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.143756 restraints weight = 15609.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.144259 restraints weight = 15029.389| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17340 Z= 0.176 Angle : 0.618 9.277 23496 Z= 0.312 Chirality : 0.051 0.189 2640 Planarity : 0.006 0.077 2988 Dihedral : 5.296 53.315 2308 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.08 % Favored : 88.92 % Rotamer: Outliers : 2.48 % Allowed : 14.85 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.18), residues: 2112 helix: 0.14 (0.31), residues: 306 sheet: 0.26 (0.30), residues: 276 loop : -1.56 (0.16), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 23 TYR 0.017 0.001 TYR B 233 PHE 0.010 0.001 PHE D 123 TRP 0.009 0.001 TRP D 329 HIS 0.008 0.001 HIS B 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.18 (17340) covalent geometry : angle 0.61770 / 0.31 (23496) hydrogen bonds : bond 0.04196 / 2.88 ( 256) hydrogen bonds : angle 5.52563 / 3.80 ( 702) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 255 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 142 MET cc_start: 0.4448 (mmt) cc_final: 0.4060 (mmt) REVERT: B 152 TYR cc_start: 0.7162 (p90) cc_final: 0.6960 (p90) REVERT: B 220 LEU cc_start: 0.6839 (OUTLIER) cc_final: 0.6637 (tt) REVERT: C 142 MET cc_start: 0.4348 (mmm) cc_final: 0.3929 (mpp) REVERT: C 220 LEU cc_start: 0.6506 (OUTLIER) cc_final: 0.6242 (mm) REVERT: D 152 TYR cc_start: 0.7157 (p90) cc_final: 0.6891 (p90) REVERT: E 66 GLU cc_start: 0.7335 (mm-30) cc_final: 0.6899 (mp0) REVERT: F 142 MET cc_start: 0.4344 (mmm) cc_final: 0.3903 (mmt) outliers start: 45 outliers final: 30 residues processed: 289 average time/residue: 0.1219 time to fit residues: 55.0116 Evaluate side-chains 279 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 247 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain B residue 148 GLN Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 148 GLN Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 231 LYS Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 325 SER Chi-restraints excluded: chain E residue 231 LYS Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 338 HIS Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 325 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 125 optimal weight: 8.9990 chunk 114 optimal weight: 6.9990 chunk 179 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 101 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 199 optimal weight: 1.9990 chunk 214 optimal weight: 1.9990 chunk 187 optimal weight: 0.8980 chunk 108 optimal weight: 7.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 148 GLN ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 214 GLN E 338 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.187478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.145272 restraints weight = 18132.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.144824 restraints weight = 21950.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.145953 restraints weight = 19698.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.145310 restraints weight = 15747.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.146027 restraints weight = 14446.678| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17340 Z= 0.141 Angle : 0.606 8.328 23496 Z= 0.307 Chirality : 0.050 0.192 2640 Planarity : 0.006 0.078 2988 Dihedral : 5.187 52.012 2307 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.99 % Favored : 90.01 % Rotamer: Outliers : 3.04 % Allowed : 15.34 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.18), residues: 2112 helix: 0.04 (0.31), residues: 312 sheet: 0.29 (0.31), residues: 276 loop : -1.52 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 102 TYR 0.019 0.001 TYR E 152 PHE 0.025 0.001 PHE E 167 TRP 0.009 0.001 TRP D 329 HIS 0.009 0.001 HIS E 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.14 (17340) covalent geometry : angle 0.60633 / 0.31 (23496) hydrogen bonds : bond 0.04006 / 2.74 ( 256) hydrogen bonds : angle 5.41640 / 3.72 ( 702) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 255 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 142 MET cc_start: 0.4486 (mmt) cc_final: 0.4061 (mmt) REVERT: B 220 LEU cc_start: 0.6839 (OUTLIER) cc_final: 0.6604 (tt) REVERT: B 305 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8708 (mm) REVERT: C 142 MET cc_start: 0.4328 (mmm) cc_final: 0.3949 (mpp) REVERT: C 220 LEU cc_start: 0.6272 (OUTLIER) cc_final: 0.5928 (mm) REVERT: E 66 GLU cc_start: 0.7270 (mm-30) cc_final: 0.6917 (mp0) REVERT: E 214 GLN cc_start: 0.7739 (mp10) cc_final: 0.7434 (mp10) REVERT: E 305 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8676 (mm) REVERT: F 142 MET cc_start: 0.4278 (mmm) cc_final: 0.3868 (mmt) outliers start: 55 outliers final: 34 residues processed: 294 average time/residue: 0.1202 time to fit residues: 55.2318 Evaluate side-chains 288 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 250 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 148 GLN Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 325 SER Chi-restraints excluded: chain D residue 338 HIS Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain E residue 305 ILE Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 338 HIS Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 325 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 74 optimal weight: 0.5980 chunk 87 optimal weight: 4.9990 chunk 198 optimal weight: 0.9980 chunk 120 optimal weight: 10.0000 chunk 175 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 129 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 GLN ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 338 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.187515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.145601 restraints weight = 18090.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.145289 restraints weight = 21183.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.146470 restraints weight = 20407.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.145534 restraints weight = 17014.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.146245 restraints weight = 15588.900| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17340 Z= 0.140 Angle : 0.602 10.949 23496 Z= 0.303 Chirality : 0.050 0.194 2640 Planarity : 0.006 0.078 2988 Dihedral : 5.155 50.607 2307 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Rotamer: Outliers : 2.65 % Allowed : 16.39 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.18), residues: 2112 helix: 0.06 (0.31), residues: 312 sheet: 0.31 (0.31), residues: 276 loop : -1.53 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 102 TYR 0.018 0.001 TYR D 152 PHE 0.022 0.001 PHE E 167 TRP 0.009 0.001 TRP D 329 HIS 0.010 0.001 HIS E 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.14 (17340) covalent geometry : angle 0.60165 / 0.30 (23496) hydrogen bonds : bond 0.04000 / 2.73 ( 256) hydrogen bonds : angle 5.38850 / 3.69 ( 702) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 256 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 220 LEU cc_start: 0.6683 (OUTLIER) cc_final: 0.6407 (tt) REVERT: B 225 MET cc_start: 0.8049 (tpp) cc_final: 0.7810 (tpt) REVERT: B 305 ILE cc_start: 0.8911 (OUTLIER) cc_final: 0.8709 (mm) REVERT: C 142 MET cc_start: 0.4299 (OUTLIER) cc_final: 0.3951 (mpp) REVERT: C 220 LEU cc_start: 0.6154 (OUTLIER) cc_final: 0.5827 (mm) REVERT: D 167 PHE cc_start: 0.7338 (t80) cc_final: 0.7057 (t80) REVERT: E 66 GLU cc_start: 0.7177 (mm-30) cc_final: 0.6897 (mp0) REVERT: E 214 GLN cc_start: 0.7708 (mp10) cc_final: 0.7375 (mp10) REVERT: F 142 MET cc_start: 0.4261 (mmm) cc_final: 0.3857 (mmt) outliers start: 48 outliers final: 33 residues processed: 290 average time/residue: 0.1207 time to fit residues: 54.4384 Evaluate side-chains 287 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 250 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 338 HIS Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 325 SER Chi-restraints excluded: chain D residue 338 HIS Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 338 HIS Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 325 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 93 optimal weight: 0.6980 chunk 163 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 152 optimal weight: 0.0040 chunk 100 optimal weight: 0.6980 chunk 147 optimal weight: 0.8980 chunk 5 optimal weight: 0.4980 chunk 199 optimal weight: 5.9990 chunk 51 optimal weight: 0.6980 chunk 212 optimal weight: 0.7980 chunk 211 optimal weight: 2.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 338 HIS ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 338 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.190334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.147120 restraints weight = 18121.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.146401 restraints weight = 22822.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.147234 restraints weight = 20511.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.147421 restraints weight = 17550.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.147622 restraints weight = 14861.684| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17340 Z= 0.113 Angle : 0.595 11.076 23496 Z= 0.300 Chirality : 0.050 0.198 2640 Planarity : 0.006 0.078 2988 Dihedral : 5.006 49.610 2307 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.61 % Favored : 90.39 % Rotamer: Outliers : 2.15 % Allowed : 17.05 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.18), residues: 2112 helix: 0.09 (0.31), residues: 312 sheet: 0.40 (0.31), residues: 276 loop : -1.45 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 102 TYR 0.022 0.001 TYR E 152 PHE 0.019 0.001 PHE B 167 TRP 0.009 0.001 TRP A 329 HIS 0.016 0.001 HIS E 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.11 (17340) covalent geometry : angle 0.59491 / 0.30 (23496) hydrogen bonds : bond 0.03792 / 2.57 ( 256) hydrogen bonds : angle 5.30262 / 3.63 ( 702) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 256 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 220 LEU cc_start: 0.6513 (OUTLIER) cc_final: 0.6201 (tt) REVERT: B 305 ILE cc_start: 0.8895 (OUTLIER) cc_final: 0.8684 (mm) REVERT: C 102 ARG cc_start: 0.7167 (ptt-90) cc_final: 0.6881 (ptp90) REVERT: C 142 MET cc_start: 0.4204 (OUTLIER) cc_final: 0.3901 (mpp) REVERT: D 66 GLU cc_start: 0.7513 (mm-30) cc_final: 0.7062 (mp0) REVERT: D 167 PHE cc_start: 0.7320 (t80) cc_final: 0.6901 (t80) REVERT: E 66 GLU cc_start: 0.7309 (mm-30) cc_final: 0.7059 (mp0) REVERT: F 102 ARG cc_start: 0.7268 (ptt-90) cc_final: 0.7007 (ptp90) REVERT: F 142 MET cc_start: 0.4276 (mmm) cc_final: 0.3973 (mmt) outliers start: 39 outliers final: 29 residues processed: 279 average time/residue: 0.1257 time to fit residues: 54.0128 Evaluate side-chains 274 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 242 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 338 HIS Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 325 SER Chi-restraints excluded: chain D residue 338 HIS Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 338 HIS Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 325 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 196 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 198 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 181 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 202 optimal weight: 0.2980 chunk 105 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 338 HIS F 148 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.188584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.146057 restraints weight = 18102.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.145348 restraints weight = 23599.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.146362 restraints weight = 21414.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.146484 restraints weight = 16297.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.146573 restraints weight = 16585.436| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17340 Z= 0.154 Angle : 0.621 11.845 23496 Z= 0.312 Chirality : 0.051 0.197 2640 Planarity : 0.006 0.079 2988 Dihedral : 5.131 48.604 2307 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.61 % Favored : 89.39 % Rotamer: Outliers : 2.32 % Allowed : 17.22 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.18), residues: 2112 helix: 0.27 (0.32), residues: 300 sheet: 0.38 (0.31), residues: 276 loop : -1.54 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 102 TYR 0.018 0.001 TYR D 152 PHE 0.020 0.001 PHE B 167 TRP 0.008 0.001 TRP D 329 HIS 0.009 0.001 HIS B 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.15 (17340) covalent geometry : angle 0.62148 / 0.31 (23496) hydrogen bonds : bond 0.03940 / 2.69 ( 256) hydrogen bonds : angle 5.30734 / 3.64 ( 702) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 251 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 ASP cc_start: 0.7591 (t0) cc_final: 0.7348 (t0) REVERT: B 220 LEU cc_start: 0.6521 (OUTLIER) cc_final: 0.6228 (tt) REVERT: B 225 MET cc_start: 0.8131 (tpp) cc_final: 0.7880 (tpt) REVERT: B 305 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8696 (mm) REVERT: C 102 ARG cc_start: 0.7137 (ptt-90) cc_final: 0.6857 (ptp90) REVERT: C 142 MET cc_start: 0.4056 (OUTLIER) cc_final: 0.3817 (mpp) REVERT: D 66 GLU cc_start: 0.7388 (mm-30) cc_final: 0.6947 (mp0) REVERT: D 209 MET cc_start: 0.6128 (ppp) cc_final: 0.5818 (ptt) REVERT: E 209 MET cc_start: 0.7102 (OUTLIER) cc_final: 0.5754 (ppp) REVERT: F 102 ARG cc_start: 0.7175 (ptt-90) cc_final: 0.6962 (ptp90) REVERT: F 142 MET cc_start: 0.4229 (mmm) cc_final: 0.3932 (mmt) outliers start: 42 outliers final: 31 residues processed: 275 average time/residue: 0.1179 time to fit residues: 50.4502 Evaluate side-chains 281 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 246 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 325 SER Chi-restraints excluded: chain D residue 338 HIS Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 209 MET Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 338 HIS Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 325 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 20 optimal weight: 0.8980 chunk 48 optimal weight: 10.0000 chunk 149 optimal weight: 5.9990 chunk 172 optimal weight: 0.9990 chunk 108 optimal weight: 7.9990 chunk 132 optimal weight: 2.9990 chunk 137 optimal weight: 0.4980 chunk 80 optimal weight: 0.0040 chunk 55 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 overall best weight: 0.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 338 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.189048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.158731 restraints weight = 18037.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.156818 restraints weight = 25519.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.155822 restraints weight = 25762.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.154700 restraints weight = 23096.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.154411 restraints weight = 23769.739| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17340 Z= 0.133 Angle : 0.622 11.194 23496 Z= 0.311 Chirality : 0.050 0.201 2640 Planarity : 0.006 0.078 2988 Dihedral : 5.076 48.010 2307 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.13 % Favored : 89.87 % Rotamer: Outliers : 2.10 % Allowed : 17.60 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.18), residues: 2112 helix: 0.26 (0.32), residues: 300 sheet: 0.40 (0.31), residues: 276 loop : -1.53 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 102 TYR 0.022 0.001 TYR E 152 PHE 0.019 0.001 PHE B 167 TRP 0.009 0.001 TRP D 329 HIS 0.008 0.001 HIS E 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.13 (17340) covalent geometry : angle 0.62206 / 0.31 (23496) hydrogen bonds : bond 0.03852 / 2.63 ( 256) hydrogen bonds : angle 5.28515 / 3.63 ( 702) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 250 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 220 LEU cc_start: 0.6220 (OUTLIER) cc_final: 0.5952 (tt) REVERT: B 305 ILE cc_start: 0.8875 (OUTLIER) cc_final: 0.8664 (mm) REVERT: B 321 MET cc_start: 0.7818 (ttp) cc_final: 0.7576 (ttm) REVERT: C 102 ARG cc_start: 0.6787 (ptt-90) cc_final: 0.6568 (ptp90) REVERT: D 66 GLU cc_start: 0.7029 (mm-30) cc_final: 0.6671 (mp0) REVERT: D 209 MET cc_start: 0.6512 (ppp) cc_final: 0.6090 (ptt) REVERT: E 142 MET cc_start: 0.3864 (mtp) cc_final: 0.3639 (mmt) REVERT: E 209 MET cc_start: 0.7193 (OUTLIER) cc_final: 0.6060 (ppp) REVERT: F 142 MET cc_start: 0.4096 (mmm) cc_final: 0.3750 (mmt) outliers start: 38 outliers final: 31 residues processed: 271 average time/residue: 0.1248 time to fit residues: 52.8920 Evaluate side-chains 281 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 247 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 325 SER Chi-restraints excluded: chain D residue 338 HIS Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 209 MET Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 338 HIS Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 325 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 21 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 64 optimal weight: 0.6980 chunk 118 optimal weight: 0.8980 chunk 177 optimal weight: 0.0870 chunk 131 optimal weight: 20.0000 chunk 112 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 140 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 chunk 81 optimal weight: 7.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.190260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.159771 restraints weight = 18089.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.151338 restraints weight = 25579.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.150119 restraints weight = 18818.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.149821 restraints weight = 18089.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.149913 restraints weight = 15503.216| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17340 Z= 0.119 Angle : 0.609 12.951 23496 Z= 0.306 Chirality : 0.050 0.201 2640 Planarity : 0.006 0.078 2988 Dihedral : 5.000 47.464 2307 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.18 % Favored : 89.82 % Rotamer: Outliers : 2.10 % Allowed : 17.49 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.18), residues: 2112 helix: 0.28 (0.32), residues: 300 sheet: 0.42 (0.31), residues: 276 loop : -1.50 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 102 TYR 0.019 0.001 TYR B 152 PHE 0.018 0.001 PHE B 167 TRP 0.009 0.001 TRP D 329 HIS 0.005 0.000 HIS E 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.12 (17340) covalent geometry : angle 0.60932 / 0.31 (23496) hydrogen bonds : bond 0.03786 / 2.58 ( 256) hydrogen bonds : angle 5.27267 / 3.62 ( 702) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2474.34 seconds wall clock time: 43 minutes 49.65 seconds (2629.65 seconds total)