Starting phenix.real_space_refine on Sun Jun 15 09:51:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wht_32511/06_2025/7wht_32511.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wht_32511/06_2025/7wht_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_32511/06_2025/7wht_32511.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wht_32511/06_2025/7wht_32511.map" model { file = "/net/cci-nas-00/data/ceres_data/7wht_32511/06_2025/7wht_32511.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wht_32511/06_2025/7wht_32511.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.57, per 1000 atoms: 0.56 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: 3.81 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 2.41 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: 4.82 Time building geometry restraints manager: 4.48 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 - 25.90: 9838 25.90 - 51.80: 612 51.80 - 77.70: 73 77.70 - 103.60: 25 103.60 - 129.50: 42 Dihedral angle restraints: 10590 sinusoidal: 4512 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 10587 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: 0.03 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: 1.200 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: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 36.540 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 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 : 18.722 129.497 6690 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (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 TRP 0.010 0.001 TRP D 329 HIS 0.005 0.001 HIS A 135 PHE 0.018 0.001 PHE E 223 TYR 0.019 0.001 TYR B 152 ARG 0.006 0.000 ARG C 178 Details of bonding type rmsd hydrogen bonds : bond 0.25150 ( 256) hydrogen bonds : angle 6.88640 ( 702) covalent geometry : bond 0.00587 (17340) covalent geometry : angle 0.90173 (23496) *********************** 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 : 1.977 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: 0.2534 time to fit residues: 112.2380 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 : 1.740 ------------------------------------------------------------------------------- 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 182 optimal weight: 0.9990 chunk 163 optimal weight: 1.9990 chunk 90 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 87 optimal weight: 8.9990 chunk 169 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 126 optimal weight: 7.9990 chunk 196 optimal weight: 6.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 GLN ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.188900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.146412 restraints weight = 18080.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.145823 restraints weight = 22378.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.146789 restraints weight = 20337.445| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 17340 Z= 0.206 Angle : 0.687 8.062 23496 Z= 0.344 Chirality : 0.054 0.231 2640 Planarity : 0.006 0.080 2988 Dihedral : 15.480 90.152 2632 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.84 % Favored : 89.16 % Rotamer: Outliers : 1.43 % Allowed : 10.15 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.18), residues: 2112 helix: 0.36 (0.32), residues: 276 sheet: 0.43 (0.30), residues: 276 loop : -1.64 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 329 HIS 0.006 0.001 HIS E 338 PHE 0.017 0.001 PHE B 167 TYR 0.019 0.002 TYR A 233 ARG 0.003 0.000 ARG D 178 Details of bonding type rmsd hydrogen bonds : bond 0.05008 ( 256) hydrogen bonds : angle 5.76912 ( 702) covalent geometry : bond 0.00510 (17340) covalent geometry : angle 0.68672 (23496) *********************** 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 271 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 245 time to evaluate : 1.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 321 MET cc_start: 0.7966 (ttp) cc_final: 0.7473 (ttm) REVERT: D 9 MET cc_start: 0.5981 (tpp) cc_final: 0.5483 (tpp) REVERT: F 206 PHE cc_start: 0.4514 (OUTLIER) cc_final: 0.3184 (m-80) outliers start: 26 outliers final: 16 residues processed: 270 average time/residue: 0.2742 time to fit residues: 113.3412 Evaluate side-chains 258 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 241 time to evaluate : 1.808 ------------------------------------------------------------------------------- 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 C residue 214 GLN Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain D residue 212 GLU 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 206 PHE Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain F residue 325 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 87 optimal weight: 3.9990 chunk 163 optimal weight: 0.1980 chunk 16 optimal weight: 9.9990 chunk 69 optimal weight: 0.6980 chunk 107 optimal weight: 0.1980 chunk 68 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 203 optimal weight: 20.0000 chunk 4 optimal weight: 0.9980 chunk 49 optimal weight: 10.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.189527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 113)---------------| | r_work = 0.3798 r_free = 0.3798 target = 0.154136 restraints weight = 18012.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.148922 restraints weight = 25757.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.147691 restraints weight = 17196.146| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17340 Z= 0.131 Angle : 0.611 7.535 23496 Z= 0.304 Chirality : 0.052 0.202 2640 Planarity : 0.006 0.077 2988 Dihedral : 9.269 59.456 2620 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.85 % Favored : 90.15 % Rotamer: Outliers : 1.71 % Allowed : 13.58 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.18), residues: 2112 helix: 0.09 (0.31), residues: 306 sheet: 0.37 (0.31), residues: 276 loop : -1.52 (0.16), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 329 HIS 0.003 0.001 HIS E 338 PHE 0.016 0.001 PHE F 167 TYR 0.017 0.001 TYR D 152 ARG 0.003 0.000 ARG A 102 Details of bonding type rmsd hydrogen bonds : bond 0.04289 ( 256) hydrogen bonds : angle 5.55639 ( 702) covalent geometry : bond 0.00316 (17340) covalent geometry : angle 0.61116 (23496) *********************** 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 279 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 248 time to evaluate : 1.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 152 TYR cc_start: 0.7131 (p90) cc_final: 0.6874 (p90) REVERT: B 321 MET cc_start: 0.7873 (ttp) cc_final: 0.7408 (ttm) REVERT: C 142 MET cc_start: 0.4200 (mmm) cc_final: 0.3738 (mpp) REVERT: F 142 MET cc_start: 0.4261 (mmm) cc_final: 0.3790 (mmt) outliers start: 31 outliers final: 14 residues processed: 276 average time/residue: 0.2672 time to fit residues: 113.5556 Evaluate side-chains 254 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 240 time to evaluate : 1.731 ------------------------------------------------------------------------------- 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 B residue 320 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 214 GLN Chi-restraints excluded: chain D residue 212 GLU Chi-restraints excluded: chain E residue 168 VAL 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 24 optimal weight: 5.9990 chunk 52 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 chunk 70 optimal weight: 0.8980 chunk 165 optimal weight: 2.9990 chunk 191 optimal weight: 7.9990 chunk 109 optimal weight: 0.3980 chunk 51 optimal weight: 4.9990 chunk 176 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN B 148 GLN ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.184549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.153822 restraints weight = 18045.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.142561 restraints weight = 25553.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.143484 restraints weight = 21438.114| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 17340 Z= 0.205 Angle : 0.639 8.755 23496 Z= 0.325 Chirality : 0.052 0.179 2640 Planarity : 0.006 0.078 2988 Dihedral : 7.269 59.453 2620 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.84 % Favored : 88.16 % Rotamer: Outliers : 2.70 % Allowed : 15.01 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.18), residues: 2112 helix: 0.04 (0.31), residues: 306 sheet: 0.24 (0.30), residues: 276 loop : -1.62 (0.16), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 329 HIS 0.006 0.001 HIS E 338 PHE 0.020 0.001 PHE E 167 TYR 0.019 0.002 TYR A 233 ARG 0.003 0.000 ARG C 23 Details of bonding type rmsd hydrogen bonds : bond 0.04430 ( 256) hydrogen bonds : angle 5.59191 ( 702) covalent geometry : bond 0.00507 (17340) covalent geometry : angle 0.63862 (23496) *********************** 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 303 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 254 time to evaluate : 1.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 152 TYR cc_start: 0.7331 (p90) cc_final: 0.7072 (p90) REVERT: B 220 LEU cc_start: 0.7304 (OUTLIER) cc_final: 0.6965 (tt) REVERT: B 225 MET cc_start: 0.8024 (tpp) cc_final: 0.7806 (tpt) REVERT: B 321 MET cc_start: 0.8029 (ttp) cc_final: 0.7584 (ttm) REVERT: D 152 TYR cc_start: 0.7325 (p90) cc_final: 0.7010 (p90) REVERT: F 142 MET cc_start: 0.4605 (mmm) cc_final: 0.4077 (mmt) outliers start: 49 outliers final: 31 residues processed: 295 average time/residue: 0.2743 time to fit residues: 124.7361 Evaluate side-chains 281 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 249 time to evaluate : 1.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 237 MET 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 238 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 338 HIS 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 78 LYS Chi-restraints excluded: chain D residue 148 GLN Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 212 GLU 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 168 VAL 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 69 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 144 optimal weight: 7.9990 chunk 132 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 138 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 125 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 GLN D 148 GLN ** E 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.188088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 131)---------------| | r_work = 0.3826 r_free = 0.3826 target = 0.156860 restraints weight = 18089.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.145028 restraints weight = 26611.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.146011 restraints weight = 21216.868| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1825 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= 0.131 Angle : 0.587 7.426 23496 Z= 0.301 Chirality : 0.050 0.185 2640 Planarity : 0.006 0.077 2988 Dihedral : 6.944 58.974 2619 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.18 % Favored : 89.82 % Rotamer: Outliers : 2.81 % Allowed : 16.17 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.18), residues: 2112 helix: 0.08 (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 TRP 0.010 0.001 TRP B 149 HIS 0.004 0.001 HIS E 338 PHE 0.019 0.001 PHE B 167 TYR 0.015 0.001 TYR B 233 ARG 0.002 0.000 ARG A 102 Details of bonding type rmsd hydrogen bonds : bond 0.04017 ( 256) hydrogen bonds : angle 5.47344 ( 702) covalent geometry : bond 0.00323 (17340) covalent geometry : angle 0.58692 (23496) *********************** 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 305 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 254 time to evaluate : 1.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 142 MET cc_start: 0.4752 (mmt) cc_final: 0.4192 (mmt) REVERT: B 220 LEU cc_start: 0.7122 (OUTLIER) cc_final: 0.6919 (tt) REVERT: B 225 MET cc_start: 0.8012 (tpp) cc_final: 0.7783 (tpt) REVERT: B 305 ILE cc_start: 0.8889 (OUTLIER) cc_final: 0.8663 (mm) REVERT: B 321 MET cc_start: 0.7934 (ttp) cc_final: 0.7445 (ttm) REVERT: B 338 HIS cc_start: 0.8247 (OUTLIER) cc_final: 0.7695 (t-90) REVERT: C 142 MET cc_start: 0.4534 (mmm) cc_final: 0.4047 (mpp) REVERT: D 142 MET cc_start: 0.4681 (mmt) cc_final: 0.4468 (mmt) REVERT: F 142 MET cc_start: 0.4614 (mmm) cc_final: 0.4236 (mmt) outliers start: 51 outliers final: 33 residues processed: 293 average time/residue: 0.2776 time to fit residues: 125.0751 Evaluate side-chains 286 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 250 time to evaluate : 1.768 ------------------------------------------------------------------------------- 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 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 320 THR 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 106 optimal weight: 0.7980 chunk 155 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 chunk 94 optimal weight: 0.3980 chunk 50 optimal weight: 9.9990 chunk 117 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 213 optimal weight: 0.4980 chunk 56 optimal weight: 0.4980 chunk 63 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 338 HIS E 338 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.189821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.146879 restraints weight = 18159.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.146191 restraints weight = 22512.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.147818 restraints weight = 19875.196| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17340 Z= 0.116 Angle : 0.574 9.917 23496 Z= 0.295 Chirality : 0.050 0.191 2640 Planarity : 0.006 0.078 2988 Dihedral : 6.751 57.073 2619 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer: Outliers : 2.92 % Allowed : 16.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.18), residues: 2112 helix: 0.00 (0.31), residues: 312 sheet: 0.32 (0.31), residues: 276 loop : -1.48 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 329 HIS 0.004 0.000 HIS E 338 PHE 0.017 0.001 PHE E 167 TYR 0.021 0.001 TYR D 152 ARG 0.005 0.000 ARG E 102 Details of bonding type rmsd hydrogen bonds : bond 0.03849 ( 256) hydrogen bonds : angle 5.39053 ( 702) covalent geometry : bond 0.00286 (17340) covalent geometry : angle 0.57444 (23496) *********************** 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 318 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 265 time to evaluate : 1.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 220 LEU cc_start: 0.6643 (OUTLIER) cc_final: 0.6362 (tt) REVERT: B 225 MET cc_start: 0.8081 (tpp) cc_final: 0.7879 (tpt) REVERT: B 305 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8674 (mm) REVERT: B 321 MET cc_start: 0.7941 (ttp) cc_final: 0.7510 (ttm) REVERT: C 142 MET cc_start: 0.4074 (mmm) cc_final: 0.3740 (mpp) REVERT: D 167 PHE cc_start: 0.7345 (t80) cc_final: 0.6978 (t80) REVERT: D 209 MET cc_start: 0.6358 (ppp) cc_final: 0.5950 (ptm) REVERT: E 66 GLU cc_start: 0.7358 (mm-30) cc_final: 0.6932 (mp0) REVERT: E 209 MET cc_start: 0.7106 (OUTLIER) cc_final: 0.6141 (ppp) outliers start: 53 outliers final: 34 residues processed: 297 average time/residue: 0.2973 time to fit residues: 135.1382 Evaluate side-chains 288 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 251 time to evaluate : 1.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL 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 320 THR 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 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 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 92 LEU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 196 optimal weight: 10.0000 chunk 126 optimal weight: 0.9990 chunk 204 optimal weight: 0.0270 chunk 51 optimal weight: 5.9990 chunk 154 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 121 optimal weight: 7.9990 chunk 172 optimal weight: 0.9990 chunk 23 optimal weight: 20.0000 chunk 64 optimal weight: 0.9990 overall best weight: 1.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 338 HIS ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 GLN E 107 GLN E 338 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.187646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.157077 restraints weight = 18073.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.155261 restraints weight = 33820.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.154314 restraints weight = 34513.750| |-----------------------------------------------------------------------------| r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2000 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 : 0.610 10.905 23496 Z= 0.311 Chirality : 0.051 0.192 2640 Planarity : 0.006 0.078 2988 Dihedral : 6.747 57.060 2619 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.89 % Favored : 89.11 % Rotamer: Outliers : 2.76 % Allowed : 16.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.18), residues: 2112 helix: 0.10 (0.32), residues: 300 sheet: 0.29 (0.31), residues: 276 loop : -1.57 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 329 HIS 0.017 0.001 HIS E 338 PHE 0.025 0.001 PHE F 167 TYR 0.016 0.001 TYR A 233 ARG 0.007 0.000 ARG E 102 Details of bonding type rmsd hydrogen bonds : bond 0.04018 ( 256) hydrogen bonds : angle 5.42522 ( 702) covalent geometry : bond 0.00384 (17340) covalent geometry : angle 0.61029 (23496) *********************** 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 311 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 261 time to evaluate : 1.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 220 LEU cc_start: 0.6328 (OUTLIER) cc_final: 0.6070 (tt) REVERT: B 225 MET cc_start: 0.7993 (tpp) cc_final: 0.7732 (tpt) REVERT: B 321 MET cc_start: 0.7942 (ttp) cc_final: 0.7496 (ttm) REVERT: D 209 MET cc_start: 0.6666 (ppp) cc_final: 0.6164 (ptm) REVERT: E 66 GLU cc_start: 0.6880 (mm-30) cc_final: 0.6665 (mp0) REVERT: E 209 MET cc_start: 0.7330 (OUTLIER) cc_final: 0.6260 (ppp) outliers start: 50 outliers final: 36 residues processed: 294 average time/residue: 0.2677 time to fit residues: 120.9412 Evaluate side-chains 293 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 255 time to evaluate : 1.674 ------------------------------------------------------------------------------- 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 320 THR Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 78 LYS 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 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 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 Chi-restraints excluded: chain F residue 338 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 149 optimal weight: 5.9990 chunk 104 optimal weight: 0.5980 chunk 189 optimal weight: 0.8980 chunk 170 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 141 optimal weight: 3.9990 chunk 147 optimal weight: 0.9990 chunk 106 optimal weight: 0.5980 chunk 11 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 136 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 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 = 0.4171 r_free = 0.4171 target = 0.190052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 129)---------------| | r_work = 0.3859 r_free = 0.3859 target = 0.160015 restraints weight = 17998.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.150217 restraints weight = 26196.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.149314 restraints weight = 18933.107| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2101 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= 0.128 Angle : 0.603 11.515 23496 Z= 0.307 Chirality : 0.050 0.195 2640 Planarity : 0.006 0.077 2988 Dihedral : 6.629 57.553 2619 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.18 % Favored : 89.82 % Rotamer: Outliers : 2.43 % Allowed : 17.33 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.18), residues: 2112 helix: -0.06 (0.31), residues: 312 sheet: 0.31 (0.31), residues: 276 loop : -1.52 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 329 HIS 0.023 0.001 HIS E 338 PHE 0.021 0.001 PHE F 167 TYR 0.021 0.002 TYR E 152 ARG 0.011 0.000 ARG A 102 Details of bonding type rmsd hydrogen bonds : bond 0.03861 ( 256) hydrogen bonds : angle 5.37586 ( 702) covalent geometry : bond 0.00317 (17340) covalent geometry : angle 0.60330 (23496) *********************** 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 300 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 256 time to evaluate : 1.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.3637 (mmt) cc_final: 0.3167 (mtt) REVERT: B 142 MET cc_start: 0.4362 (mmt) cc_final: 0.4082 (mmt) REVERT: B 220 LEU cc_start: 0.6610 (OUTLIER) cc_final: 0.6355 (tt) REVERT: B 321 MET cc_start: 0.7904 (ttp) cc_final: 0.7485 (ttm) REVERT: C 9 MET cc_start: 0.6071 (tpp) cc_final: 0.5402 (tpp) REVERT: C 102 ARG cc_start: 0.7321 (ptt-90) cc_final: 0.7004 (ptp90) REVERT: D 209 MET cc_start: 0.6285 (ppp) cc_final: 0.5943 (ptm) REVERT: E 66 GLU cc_start: 0.7140 (mm-30) cc_final: 0.6847 (mp0) REVERT: E 209 MET cc_start: 0.6903 (OUTLIER) cc_final: 0.5775 (ppp) REVERT: F 102 ARG cc_start: 0.7265 (ptt-90) cc_final: 0.6950 (ptp90) outliers start: 44 outliers final: 36 residues processed: 285 average time/residue: 0.2737 time to fit residues: 119.6455 Evaluate side-chains 287 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 249 time to evaluate : 1.945 ------------------------------------------------------------------------------- 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 320 THR 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 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 C residue 338 HIS 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 238 THR Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 325 SER 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 Chi-restraints excluded: chain F residue 338 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 33 optimal weight: 0.6980 chunk 133 optimal weight: 0.0670 chunk 182 optimal weight: 0.9980 chunk 155 optimal weight: 5.9990 chunk 152 optimal weight: 0.0870 chunk 172 optimal weight: 3.9990 chunk 214 optimal weight: 0.0020 chunk 13 optimal weight: 3.9990 chunk 127 optimal weight: 7.9990 chunk 15 optimal weight: 8.9990 chunk 5 optimal weight: 9.9990 overall best weight: 0.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 GLN E 338 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.196697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.159148 restraints weight = 18179.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.158012 restraints weight = 24897.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.158058 restraints weight = 22683.555| |-----------------------------------------------------------------------------| r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2185 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= 0.108 Angle : 0.592 11.572 23496 Z= 0.300 Chirality : 0.049 0.208 2640 Planarity : 0.006 0.078 2988 Dihedral : 6.457 59.904 2619 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Rotamer: Outliers : 2.04 % Allowed : 18.32 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.18), residues: 2112 helix: -0.02 (0.31), residues: 312 sheet: 0.37 (0.31), residues: 276 loop : -1.45 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 329 HIS 0.005 0.000 HIS E 338 PHE 0.018 0.001 PHE F 167 TYR 0.015 0.001 TYR A 233 ARG 0.007 0.000 ARG A 102 Details of bonding type rmsd hydrogen bonds : bond 0.03604 ( 256) hydrogen bonds : angle 5.31006 ( 702) covalent geometry : bond 0.00266 (17340) covalent geometry : angle 0.59235 (23496) *********************** 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 282 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 245 time to evaluate : 1.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 220 LEU cc_start: 0.6246 (OUTLIER) cc_final: 0.5951 (tt) REVERT: D 66 GLU cc_start: 0.7144 (mm-30) cc_final: 0.6764 (mp0) REVERT: D 209 MET cc_start: 0.6594 (ppp) cc_final: 0.6167 (ptm) REVERT: E 209 MET cc_start: 0.7008 (OUTLIER) cc_final: 0.5962 (ppp) outliers start: 37 outliers final: 30 residues processed: 263 average time/residue: 0.2942 time to fit residues: 119.4537 Evaluate side-chains 275 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 243 time to evaluate : 1.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE 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 320 THR 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 167 PHE 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 C residue 338 HIS 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 322 VAL Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 338 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 105 optimal weight: 1.9990 chunk 168 optimal weight: 7.9990 chunk 190 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 88 optimal weight: 0.0670 chunk 120 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 164 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 192 optimal weight: 9.9990 overall best weight: 1.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.183312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.153529 restraints weight = 18330.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.152279 restraints weight = 32810.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.143863 restraints weight = 32102.025| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 17340 Z= 0.189 Angle : 0.656 12.201 23496 Z= 0.331 Chirality : 0.052 0.204 2640 Planarity : 0.006 0.078 2988 Dihedral : 6.652 59.428 2619 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.17 % Favored : 88.83 % Rotamer: Outliers : 1.82 % Allowed : 18.43 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.18), residues: 2112 helix: -0.03 (0.32), residues: 300 sheet: 0.32 (0.31), residues: 276 loop : -1.58 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 336 HIS 0.004 0.001 HIS A 338 PHE 0.024 0.001 PHE F 167 TYR 0.020 0.002 TYR E 152 ARG 0.015 0.000 ARG F 102 Details of bonding type rmsd hydrogen bonds : bond 0.04129 ( 256) hydrogen bonds : angle 5.38626 ( 702) covalent geometry : bond 0.00476 (17340) covalent geometry : angle 0.65643 (23496) ********************** 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: 33 poor density : 255 time to evaluate : 1.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.3613 (mtt) cc_final: 0.3371 (mtt) REVERT: B 220 LEU cc_start: 0.6604 (OUTLIER) cc_final: 0.6295 (tt) REVERT: B 225 MET cc_start: 0.8044 (tpp) cc_final: 0.7753 (tpt) REVERT: B 321 MET cc_start: 0.7713 (ttp) cc_final: 0.7244 (ttm) REVERT: C 102 ARG cc_start: 0.7291 (ptt-90) cc_final: 0.6999 (ptp90) REVERT: D 66 GLU cc_start: 0.7267 (mm-30) cc_final: 0.6859 (mp0) REVERT: E 66 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6952 (mp0) outliers start: 33 outliers final: 29 residues processed: 275 average time/residue: 0.3084 time to fit residues: 128.1461 Evaluate side-chains 281 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 251 time to evaluate : 1.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE 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 320 THR 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 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 C residue 338 HIS 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 322 VAL Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 338 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 64 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 7 optimal weight: 0.0010 chunk 76 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 181 optimal weight: 1.9990 overall best weight: 0.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.191603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.154573 restraints weight = 18080.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.153388 restraints weight = 28123.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.153357 restraints weight = 25267.458| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17340 Z= 0.134 Angle : 0.634 12.422 23496 Z= 0.319 Chirality : 0.050 0.211 2640 Planarity : 0.006 0.077 2988 Dihedral : 6.534 59.935 2619 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.09 % Favored : 89.91 % Rotamer: Outliers : 1.82 % Allowed : 18.71 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.18), residues: 2112 helix: 0.01 (0.32), residues: 300 sheet: 0.35 (0.31), residues: 276 loop : -1.57 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 329 HIS 0.002 0.000 HIS F 371 PHE 0.020 0.001 PHE F 167 TYR 0.016 0.001 TYR A 233 ARG 0.013 0.000 ARG F 197 Details of bonding type rmsd hydrogen bonds : bond 0.03859 ( 256) hydrogen bonds : angle 5.33463 ( 702) covalent geometry : bond 0.00337 (17340) covalent geometry : angle 0.63398 (23496) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5411.69 seconds wall clock time: 95 minutes 36.73 seconds (5736.73 seconds total)