Starting phenix.real_space_refine on Wed Mar 4 23:18:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wht_32511/03_2026/7wht_32511.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wht_32511/03_2026/7wht_32511.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wht_32511/03_2026/7wht_32511.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wht_32511/03_2026/7wht_32511.map" model { file = "/net/cci-nas-00/data/ceres_data/7wht_32511/03_2026/7wht_32511.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wht_32511/03_2026/7wht_32511.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.051 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 6 5.21 5 S 102 5.16 5 C 10806 2.51 5 N 2910 2.21 5 O 3144 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16980 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2790 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 21, 'TRANS': 338} Chain breaks: 3 Chain: "B" Number of atoms: 2790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2790 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 21, 'TRANS': 338} Chain breaks: 3 Chain: "C" Number of atoms: 2790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2790 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 21, 'TRANS': 338} Chain breaks: 3 Chain: "D" Number of atoms: 2790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2790 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 21, 'TRANS': 338} Chain breaks: 3 Chain: "E" Number of atoms: 2790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2790 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 21, 'TRANS': 338} Chain breaks: 3 Chain: "F" Number of atoms: 2790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2790 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 21, 'TRANS': 338} Chain breaks: 3 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {' MG': 1, 'GDD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {' MG': 1, 'GDD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {' MG': 1, 'GDD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {' MG': 1, 'GDD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {' MG': 1, 'GDD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {' MG': 1, 'GDD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.07, per 1000 atoms: 0.24 Number of scatterers: 16980 At special positions: 0 Unit cell: (120.91, 121.98, 112.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 102 16.00 P 12 15.00 Mg 6 11.99 O 3144 8.00 N 2910 7.00 C 10806 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.37 Conformation dependent library (CDL) restraints added in 716.9 milliseconds 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3900 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 52 sheets defined 20.8% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 22 through 27 Processing helix chain 'A' and resid 30 through 34 Processing helix chain 'A' and resid 40 through 52 removed outlier: 3.859A pdb=" N HIS A 44 " --> pdb=" O PRO A 40 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLN A 45 " --> pdb=" O MET A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 66 No H-bonds generated for 'chain 'A' and resid 64 through 66' Processing helix chain 'A' and resid 67 through 74 Processing helix chain 'A' and resid 75 through 77 No H-bonds generated for 'chain 'A' and resid 75 through 77' Processing helix chain 'A' and resid 94 through 100 removed outlier: 3.985A pdb=" N LEU A 98 " --> pdb=" O THR A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 108 removed outlier: 3.601A pdb=" N ILE A 104 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN A 107 " --> pdb=" O ASP A 103 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP A 108 " --> pdb=" O ILE A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 192 removed outlier: 4.253A pdb=" N LEU A 191 " --> pdb=" O ASN A 187 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP A 192 " --> pdb=" O LYS A 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 187 through 192' Processing helix chain 'A' and resid 229 through 244 Proline residue: A 242 - end of helix Processing helix chain 'B' and resid 22 through 27 Processing helix chain 'B' and resid 30 through 34 Processing helix chain 'B' and resid 40 through 52 removed outlier: 3.681A pdb=" N HIS B 44 " --> pdb=" O PRO B 40 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN B 45 " --> pdb=" O MET B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 66 No H-bonds generated for 'chain 'B' and resid 64 through 66' Processing helix chain 'B' and resid 67 through 74 Processing helix chain 'B' and resid 94 through 100 removed outlier: 3.970A pdb=" N LEU B 98 " --> pdb=" O THR B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 108 removed outlier: 3.653A pdb=" N ILE B 104 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLN B 107 " --> pdb=" O ASP B 103 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASP B 108 " --> pdb=" O ILE B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 192 removed outlier: 4.133A pdb=" N LEU B 191 " --> pdb=" O ASN B 187 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP B 192 " --> pdb=" O LYS B 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 187 through 192' Processing helix chain 'B' and resid 229 through 244 Proline residue: B 242 - end of helix Processing helix chain 'C' and resid 22 through 27 Processing helix chain 'C' and resid 30 through 34 Processing helix chain 'C' and resid 40 through 52 removed outlier: 3.671A pdb=" N HIS C 44 " --> pdb=" O PRO C 40 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN C 45 " --> pdb=" O MET C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 66 No H-bonds generated for 'chain 'C' and resid 64 through 66' Processing helix chain 'C' and resid 67 through 74 Processing helix chain 'C' and resid 94 through 100 removed outlier: 3.965A pdb=" N LEU C 98 " --> pdb=" O THR C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 108 removed outlier: 3.671A pdb=" N ILE C 104 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN C 107 " --> pdb=" O ASP C 103 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP C 108 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 192 removed outlier: 4.056A pdb=" N LEU C 191 " --> pdb=" O ASN C 187 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP C 192 " --> pdb=" O LYS C 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 187 through 192' Processing helix chain 'C' and resid 229 through 244 Proline residue: C 242 - end of helix Processing helix chain 'D' and resid 22 through 27 Processing helix chain 'D' and resid 30 through 34 Processing helix chain 'D' and resid 40 through 52 removed outlier: 3.714A pdb=" N HIS D 44 " --> pdb=" O PRO D 40 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLN D 45 " --> pdb=" O MET D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 66 No H-bonds generated for 'chain 'D' and resid 64 through 66' Processing helix chain 'D' and resid 67 through 74 Processing helix chain 'D' and resid 75 through 77 No H-bonds generated for 'chain 'D' and resid 75 through 77' Processing helix chain 'D' and resid 94 through 100 removed outlier: 4.007A pdb=" N LEU D 98 " --> pdb=" O THR D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 108 removed outlier: 3.708A pdb=" N ILE D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN D 107 " --> pdb=" O ASP D 103 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP D 108 " --> pdb=" O ILE D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 192 removed outlier: 4.240A pdb=" N LEU D 191 " --> pdb=" O ASN D 187 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP D 192 " --> pdb=" O LYS D 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 187 through 192' Processing helix chain 'D' and resid 229 through 244 Proline residue: D 242 - end of helix Processing helix chain 'E' and resid 22 through 27 Processing helix chain 'E' and resid 30 through 34 Processing helix chain 'E' and resid 40 through 52 removed outlier: 3.604A pdb=" N HIS E 44 " --> pdb=" O PRO E 40 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLN E 45 " --> pdb=" O MET E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 74 removed outlier: 4.627A pdb=" N GLU E 70 " --> pdb=" O GLU E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 100 removed outlier: 3.967A pdb=" N LEU E 98 " --> pdb=" O THR E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 108 removed outlier: 3.772A pdb=" N ILE E 104 " --> pdb=" O LEU E 100 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN E 107 " --> pdb=" O ASP E 103 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP E 108 " --> pdb=" O ILE E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 138 removed outlier: 4.122A pdb=" N GLY E 137 " --> pdb=" O LYS E 133 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLU E 138 " --> pdb=" O ALA E 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 133 through 138' Processing helix chain 'E' and resid 187 through 192 removed outlier: 4.132A pdb=" N LEU E 191 " --> pdb=" O ASN E 187 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP E 192 " --> pdb=" O LYS E 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 187 through 192' Processing helix chain 'E' and resid 229 through 245 Proline residue: E 242 - end of helix removed outlier: 3.680A pdb=" N VAL E 245 " --> pdb=" O ILE E 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 27 Processing helix chain 'F' and resid 30 through 34 Processing helix chain 'F' and resid 40 through 52 removed outlier: 3.656A pdb=" N HIS F 44 " --> pdb=" O PRO F 40 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN F 45 " --> pdb=" O MET F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 66 No H-bonds generated for 'chain 'F' and resid 64 through 66' Processing helix chain 'F' and resid 67 through 74 Processing helix chain 'F' and resid 94 through 100 removed outlier: 3.960A pdb=" N LEU F 98 " --> pdb=" O THR F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 108 removed outlier: 3.677A pdb=" N ILE F 104 " --> pdb=" O LEU F 100 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN F 107 " --> pdb=" O ASP F 103 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP F 108 " --> pdb=" O ILE F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 192 removed outlier: 4.070A pdb=" N LEU F 191 " --> pdb=" O ASN F 187 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP F 192 " --> pdb=" O LYS F 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 187 through 192' Processing helix chain 'F' and resid 229 through 244 Proline residue: F 242 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 79 through 84 removed outlier: 6.968A pdb=" N VAL A 57 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N VAL A 84 " --> pdb=" O VAL A 57 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU A 59 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ALA A 11 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ALA A 60 " --> pdb=" O ALA A 11 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N ILE A 13 " --> pdb=" O ALA A 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 121 Processing sheet with id=AA3, first strand: chain 'A' and resid 155 through 156 removed outlier: 3.517A pdb=" N VAL A 155 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL A 168 " --> pdb=" O VAL A 155 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 268 through 269 removed outlier: 7.013A pdb=" N THR A 268 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL A 286 " --> pdb=" O ILE A 305 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 274 through 275 removed outlier: 6.865A pdb=" N LEU A 274 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N ALA A 295 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N SER A 292 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N GLU A 312 " --> pdb=" O SER A 292 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N GLY A 294 " --> pdb=" O GLU A 312 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ALA A 309 " --> pdb=" O VAL A 327 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 280 through 281 removed outlier: 6.507A pdb=" N LYS A 280 " --> pdb=" O ILE A 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 338 through 340 removed outlier: 5.914A pdb=" N HIS A 338 " --> pdb=" O LEU A 357 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 350 through 351 removed outlier: 6.758A pdb=" N GLU A 350 " --> pdb=" O VAL A 368 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 360 through 362 removed outlier: 6.593A pdb=" N LYS A 361 " --> pdb=" O ILE A 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 79 through 84 removed outlier: 7.061A pdb=" N VAL B 57 " --> pdb=" O SER B 82 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N VAL B 84 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU B 59 " --> pdb=" O VAL B 84 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ALA B 11 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ALA B 60 " --> pdb=" O ALA B 11 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ILE B 13 " --> pdb=" O ALA B 60 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 119 through 121 Processing sheet with id=AB3, first strand: chain 'B' and resid 155 through 156 removed outlier: 3.947A pdb=" N VAL B 168 " --> pdb=" O VAL B 155 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 268 through 269 removed outlier: 7.034A pdb=" N THR B 268 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N VAL B 286 " --> pdb=" O ILE B 305 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N HIS B 338 " --> pdb=" O LEU B 357 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 273 through 275 removed outlier: 6.382A pdb=" N SER B 292 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N GLU B 312 " --> pdb=" O SER B 292 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N GLY B 294 " --> pdb=" O GLU B 312 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ALA B 309 " --> pdb=" O VAL B 327 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 280 through 281 removed outlier: 6.574A pdb=" N LYS B 280 " --> pdb=" O ILE B 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 350 through 351 removed outlier: 6.721A pdb=" N GLU B 350 " --> pdb=" O VAL B 368 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 360 through 362 removed outlier: 6.456A pdb=" N LYS B 361 " --> pdb=" O ILE B 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 79 through 84 removed outlier: 7.045A pdb=" N VAL C 57 " --> pdb=" O SER C 82 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N VAL C 84 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU C 59 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ALA C 11 " --> pdb=" O ILE C 58 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ALA C 60 " --> pdb=" O ALA C 11 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ILE C 13 " --> pdb=" O ALA C 60 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 119 through 121 Processing sheet with id=AC2, first strand: chain 'C' and resid 155 through 156 removed outlier: 3.511A pdb=" N VAL C 155 " --> pdb=" O VAL C 168 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N VAL C 168 " --> pdb=" O VAL C 155 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 268 through 269 removed outlier: 7.006A pdb=" N THR C 268 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N VAL C 286 " --> pdb=" O ILE C 305 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N HIS C 338 " --> pdb=" O LEU C 357 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 274 through 275 removed outlier: 7.013A pdb=" N LEU C 274 " --> pdb=" O ILE C 293 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N ALA C 295 " --> pdb=" O LEU C 274 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N SER C 292 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N GLU C 312 " --> pdb=" O SER C 292 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N GLY C 294 " --> pdb=" O GLU C 312 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ALA C 309 " --> pdb=" O VAL C 327 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'C' and resid 280 through 281 removed outlier: 6.519A pdb=" N LYS C 280 " --> pdb=" O ILE C 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'C' and resid 350 through 351 removed outlier: 6.769A pdb=" N GLU C 350 " --> pdb=" O VAL C 368 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 360 through 362 removed outlier: 6.484A pdb=" N LYS C 361 " --> pdb=" O ILE C 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'D' and resid 79 through 84 removed outlier: 6.973A pdb=" N VAL D 57 " --> pdb=" O SER D 82 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N VAL D 84 " --> pdb=" O VAL D 57 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU D 59 " --> pdb=" O VAL D 84 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ALA D 11 " --> pdb=" O ILE D 58 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ALA D 60 " --> pdb=" O ALA D 11 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ILE D 13 " --> pdb=" O ALA D 60 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 119 through 121 Processing sheet with id=AD1, first strand: chain 'D' and resid 155 through 156 removed outlier: 4.078A pdb=" N VAL D 168 " --> pdb=" O VAL D 155 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 268 through 269 removed outlier: 7.032A pdb=" N THR D 268 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N VAL D 286 " --> pdb=" O ILE D 305 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 274 through 275 removed outlier: 6.835A pdb=" N LEU D 274 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N ALA D 295 " --> pdb=" O LEU D 274 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N SER D 292 " --> pdb=" O ILE D 310 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N GLU D 312 " --> pdb=" O SER D 292 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N GLY D 294 " --> pdb=" O GLU D 312 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA D 309 " --> pdb=" O VAL D 327 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'D' and resid 280 through 281 removed outlier: 6.522A pdb=" N LYS D 280 " --> pdb=" O ILE D 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'D' and resid 338 through 340 Processing sheet with id=AD6, first strand: chain 'D' and resid 350 through 351 removed outlier: 6.761A pdb=" N GLU D 350 " --> pdb=" O VAL D 368 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'D' and resid 360 through 362 removed outlier: 6.594A pdb=" N LYS D 361 " --> pdb=" O ILE D 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'E' and resid 79 through 84 removed outlier: 7.035A pdb=" N VAL E 57 " --> pdb=" O SER E 82 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N VAL E 84 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU E 59 " --> pdb=" O VAL E 84 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ALA E 11 " --> pdb=" O ILE E 58 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ALA E 60 " --> pdb=" O ALA E 11 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ILE E 13 " --> pdb=" O ALA E 60 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 119 through 121 Processing sheet with id=AE1, first strand: chain 'E' and resid 155 through 156 removed outlier: 3.995A pdb=" N VAL E 168 " --> pdb=" O VAL E 155 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 268 through 269 removed outlier: 7.029A pdb=" N THR E 268 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N VAL E 286 " --> pdb=" O ILE E 305 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 273 through 275 removed outlier: 6.368A pdb=" N SER E 292 " --> pdb=" O ILE E 310 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N GLU E 312 " --> pdb=" O SER E 292 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N GLY E 294 " --> pdb=" O GLU E 312 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA E 309 " --> pdb=" O VAL E 327 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 280 through 281 removed outlier: 6.561A pdb=" N LYS E 280 " --> pdb=" O ILE E 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'E' and resid 338 through 340 Processing sheet with id=AE6, first strand: chain 'E' and resid 350 through 351 removed outlier: 6.724A pdb=" N GLU E 350 " --> pdb=" O VAL E 368 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'E' and resid 360 through 362 removed outlier: 6.478A pdb=" N LYS E 361 " --> pdb=" O ILE E 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'F' and resid 79 through 84 removed outlier: 7.029A pdb=" N VAL F 57 " --> pdb=" O SER F 82 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N VAL F 84 " --> pdb=" O VAL F 57 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU F 59 " --> pdb=" O VAL F 84 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ALA F 11 " --> pdb=" O ILE F 58 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ALA F 60 " --> pdb=" O ALA F 11 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ILE F 13 " --> pdb=" O ALA F 60 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 119 through 121 Processing sheet with id=AF1, first strand: chain 'F' and resid 155 through 156 removed outlier: 3.972A pdb=" N VAL F 168 " --> pdb=" O VAL F 155 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 268 through 269 removed outlier: 7.004A pdb=" N THR F 268 " --> pdb=" O ILE F 287 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL F 286 " --> pdb=" O ILE F 305 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 274 through 275 removed outlier: 6.961A pdb=" N LEU F 274 " --> pdb=" O ILE F 293 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N ALA F 295 " --> pdb=" O LEU F 274 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N SER F 292 " --> pdb=" O ILE F 310 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N GLU F 312 " --> pdb=" O SER F 292 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N GLY F 294 " --> pdb=" O GLU F 312 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ALA F 309 " --> pdb=" O VAL F 327 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'F' and resid 280 through 281 removed outlier: 6.507A pdb=" N LYS F 280 " --> pdb=" O ILE F 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'F' and resid 338 through 340 removed outlier: 5.945A pdb=" N HIS F 338 " --> pdb=" O LEU F 357 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'F' and resid 350 through 351 removed outlier: 6.778A pdb=" N GLU F 350 " --> pdb=" O VAL F 368 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'F' and resid 360 through 362 removed outlier: 6.541A pdb=" N LYS F 361 " --> pdb=" O ILE F 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 256 hydrogen bonds defined for protein. 702 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.20 Time building geometry restraints manager: 1.77 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 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: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.940 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.010 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.18), residues: 2112 helix: 0.73 (0.35), residues: 264 sheet: 0.12 (0.28), residues: 348 loop : -1.53 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 178 TYR 0.019 0.001 TYR B 152 PHE 0.018 0.001 PHE E 223 TRP 0.010 0.001 TRP D 329 HIS 0.005 0.001 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00587 (17340) covalent geometry : angle 0.90173 (23496) hydrogen bonds : bond 0.25150 ( 256) hydrogen bonds : angle 6.88640 ( 702) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 260 time to evaluate : 0.548 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: 0.1068 time to fit residues: 48.0958 Evaluate side-chains 240 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 232 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain D residue 180 ASN Chi-restraints excluded: chain F residue 212 GLU Chi-restraints excluded: chain F residue 220 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.2980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 1.9990 chunk 212 optimal weight: 0.7980 chunk 77 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 D 214 GLN E 148 GLN F 107 GLN F 148 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.193121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.151354 restraints weight = 17920.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.151582 restraints weight = 22042.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.151270 restraints weight = 16921.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.150994 restraints weight = 14870.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.151535 restraints weight = 13034.413| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17340 Z= 0.146 Angle : 0.643 7.960 23496 Z= 0.322 Chirality : 0.052 0.233 2640 Planarity : 0.006 0.078 2988 Dihedral : 15.750 92.641 2632 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.61 % Favored : 90.39 % Rotamer: Outliers : 1.38 % Allowed : 9.11 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.18), residues: 2112 helix: 0.53 (0.33), residues: 276 sheet: 0.49 (0.31), residues: 276 loop : -1.52 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 178 TYR 0.018 0.002 TYR A 233 PHE 0.015 0.001 PHE B 167 TRP 0.009 0.001 TRP D 329 HIS 0.003 0.001 HIS E 338 Details of bonding type rmsd covalent geometry : bond 0.00354 (17340) covalent geometry : angle 0.64279 (23496) hydrogen bonds : bond 0.04858 ( 256) hydrogen bonds : angle 5.74039 ( 702) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 236 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 244 LEU cc_start: 0.8785 (tp) cc_final: 0.8567 (tp) REVERT: D 168 VAL cc_start: 0.7355 (p) cc_final: 0.7076 (p) REVERT: D 214 GLN cc_start: 0.3668 (OUTLIER) cc_final: 0.3052 (pt0) REVERT: F 206 PHE cc_start: 0.4448 (OUTLIER) cc_final: 0.3196 (m-80) outliers start: 25 outliers final: 11 residues processed: 258 average time/residue: 0.1229 time to fit residues: 49.1539 Evaluate side-chains 242 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 229 time to evaluate : 0.665 ------------------------------------------------------------------------------- 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 325 SER Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain D residue 214 GLN Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain E residue 148 GLN Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain F residue 148 GLN Chi-restraints excluded: chain F residue 206 PHE Chi-restraints excluded: chain F residue 238 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 136 optimal weight: 3.9990 chunk 157 optimal weight: 0.0170 chunk 16 optimal weight: 10.0000 chunk 108 optimal weight: 7.9990 chunk 95 optimal weight: 20.0000 chunk 116 optimal weight: 3.9990 chunk 175 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 101 optimal weight: 0.9990 overall best weight: 1.3424 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 HIS D 214 GLN E 107 GLN E 148 GLN F 148 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.187279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 109)---------------| | r_work = 0.3827 r_free = 0.3827 target = 0.156627 restraints weight = 18373.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.145415 restraints weight = 26641.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.145506 restraints weight = 21009.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.144977 restraints weight = 18880.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.145186 restraints weight = 17774.943| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17340 Z= 0.167 Angle : 0.643 8.146 23496 Z= 0.317 Chirality : 0.053 0.202 2640 Planarity : 0.006 0.076 2988 Dihedral : 10.859 59.701 2620 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.13 % Favored : 89.87 % Rotamer: Outliers : 2.04 % Allowed : 12.36 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.18), residues: 2112 helix: 0.64 (0.33), residues: 270 sheet: 0.36 (0.30), residues: 276 loop : -1.55 (0.15), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 178 TYR 0.018 0.001 TYR A 233 PHE 0.009 0.001 PHE D 123 TRP 0.009 0.001 TRP D 329 HIS 0.004 0.001 HIS E 338 Details of bonding type rmsd covalent geometry : bond 0.00413 (17340) covalent geometry : angle 0.64295 (23496) hydrogen bonds : bond 0.04518 ( 256) hydrogen bonds : angle 5.63859 ( 702) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 246 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 152 TYR cc_start: 0.7354 (p90) cc_final: 0.7053 (p90) REVERT: F 142 MET cc_start: 0.4546 (mmm) cc_final: 0.4106 (mmt) outliers start: 37 outliers final: 19 residues processed: 276 average time/residue: 0.1163 time to fit residues: 50.1948 Evaluate side-chains 261 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 242 time to evaluate : 0.526 ------------------------------------------------------------------------------- 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 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 C residue 325 SER Chi-restraints excluded: chain D residue 231 LYS Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 325 SER Chi-restraints excluded: chain E residue 231 LYS Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain F residue 148 GLN Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain F residue 325 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 25 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 157 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 134 optimal weight: 0.8980 chunk 193 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 GLN E 338 HIS ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.187626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.157098 restraints weight = 18225.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.144154 restraints weight = 25116.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.144868 restraints weight = 21669.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.145140 restraints weight = 17547.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.145216 restraints weight = 17148.461| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17340 Z= 0.148 Angle : 0.605 8.462 23496 Z= 0.307 Chirality : 0.051 0.183 2640 Planarity : 0.006 0.076 2988 Dihedral : 7.310 59.158 2620 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.42 % Favored : 89.58 % Rotamer: Outliers : 2.32 % Allowed : 14.18 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.18), residues: 2112 helix: 0.16 (0.31), residues: 306 sheet: 0.34 (0.30), residues: 276 loop : -1.53 (0.16), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 102 TYR 0.017 0.001 TYR F 152 PHE 0.008 0.001 PHE D 123 TRP 0.009 0.001 TRP D 329 HIS 0.012 0.001 HIS B 338 Details of bonding type rmsd covalent geometry : bond 0.00366 (17340) covalent geometry : angle 0.60543 (23496) hydrogen bonds : bond 0.04143 ( 256) hydrogen bonds : angle 5.51475 ( 702) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 253 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 152 TYR cc_start: 0.7256 (p90) cc_final: 0.7034 (p90) REVERT: D 152 TYR cc_start: 0.7208 (p90) cc_final: 0.6964 (p90) REVERT: F 142 MET cc_start: 0.4746 (mmm) cc_final: 0.4247 (mmt) outliers start: 42 outliers final: 25 residues processed: 284 average time/residue: 0.1178 time to fit residues: 52.3767 Evaluate side-chains 269 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 244 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 231 LYS Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 148 GLN Chi-restraints excluded: chain B residue 185 ILE 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 185 ILE Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 325 SER Chi-restraints excluded: chain E residue 92 LEU 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 185 ILE Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain F residue 325 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 48 optimal weight: 9.9990 chunk 63 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 174 optimal weight: 0.6980 chunk 208 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 120 optimal weight: 9.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 GLN B 338 HIS D 148 GLN E 148 GLN E 338 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.185022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.154775 restraints weight = 18158.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.143056 restraints weight = 24484.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.142943 restraints weight = 21669.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.142450 restraints weight = 19134.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.142719 restraints weight = 17071.945| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1829 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= 0.192 Angle : 0.625 9.010 23496 Z= 0.319 Chirality : 0.052 0.188 2640 Planarity : 0.006 0.078 2988 Dihedral : 7.140 59.610 2620 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.13 % Favored : 88.87 % Rotamer: Outliers : 2.81 % Allowed : 15.07 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.18), residues: 2112 helix: 0.12 (0.31), residues: 306 sheet: 0.26 (0.30), residues: 276 loop : -1.60 (0.16), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 23 TYR 0.017 0.001 TYR B 233 PHE 0.011 0.001 PHE D 123 TRP 0.011 0.001 TRP B 149 HIS 0.010 0.001 HIS E 338 Details of bonding type rmsd covalent geometry : bond 0.00478 (17340) covalent geometry : angle 0.62533 (23496) hydrogen bonds : bond 0.04296 ( 256) hydrogen bonds : angle 5.56478 ( 702) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 254 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 142 MET cc_start: 0.4724 (mmt) cc_final: 0.4240 (mmt) REVERT: B 220 LEU cc_start: 0.7181 (OUTLIER) cc_final: 0.6942 (tt) REVERT: B 377 ILE cc_start: 0.8516 (OUTLIER) cc_final: 0.8308 (mm) REVERT: C 142 MET cc_start: 0.4628 (mmm) cc_final: 0.4101 (mpp) REVERT: C 220 LEU cc_start: 0.6629 (OUTLIER) cc_final: 0.6143 (mm) REVERT: D 152 TYR cc_start: 0.7277 (p90) cc_final: 0.6996 (p90) REVERT: D 209 MET cc_start: 0.5521 (ppp) cc_final: 0.5261 (ptp) REVERT: E 66 GLU cc_start: 0.7384 (mm-30) cc_final: 0.6919 (mp0) REVERT: E 209 MET cc_start: 0.6969 (OUTLIER) cc_final: 0.6180 (ppp) REVERT: E 283 ASP cc_start: 0.7611 (m-30) cc_final: 0.7409 (m-30) REVERT: F 142 MET cc_start: 0.4577 (mmm) cc_final: 0.4140 (mmt) outliers start: 51 outliers final: 34 residues processed: 292 average time/residue: 0.1190 time to fit residues: 54.1944 Evaluate side-chains 291 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 253 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 231 LYS 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 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 325 SER Chi-restraints excluded: chain B residue 338 HIS Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 148 GLN Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 231 LYS Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 325 SER Chi-restraints excluded: chain E residue 209 MET Chi-restraints excluded: chain E residue 231 LYS Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 338 HIS Chi-restraints excluded: chain F residue 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 125 optimal weight: 8.9990 chunk 114 optimal weight: 5.9990 chunk 179 optimal weight: 0.2980 chunk 120 optimal weight: 7.9990 chunk 7 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 199 optimal weight: 3.9990 chunk 214 optimal weight: 0.7980 chunk 187 optimal weight: 0.9990 chunk 108 optimal weight: 7.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 338 HIS E 214 GLN E 338 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.187159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.3827 r_free = 0.3827 target = 0.156844 restraints weight = 18162.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 75)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.145457 restraints weight = 24925.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.145284 restraints weight = 19611.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.145262 restraints weight = 19040.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.145323 restraints weight = 16100.867| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17340 Z= 0.142 Angle : 0.601 8.057 23496 Z= 0.306 Chirality : 0.050 0.191 2640 Planarity : 0.006 0.078 2988 Dihedral : 6.948 58.998 2619 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.18 % Favored : 89.82 % Rotamer: Outliers : 2.87 % Allowed : 15.89 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.18), residues: 2112 helix: 0.03 (0.31), residues: 312 sheet: 0.29 (0.31), residues: 276 loop : -1.56 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 102 TYR 0.018 0.001 TYR C 152 PHE 0.009 0.001 PHE D 123 TRP 0.010 0.001 TRP D 329 HIS 0.004 0.001 HIS E 338 Details of bonding type rmsd covalent geometry : bond 0.00353 (17340) covalent geometry : angle 0.60062 (23496) hydrogen bonds : bond 0.04033 ( 256) hydrogen bonds : angle 5.45118 ( 702) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 260 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 220 LEU cc_start: 0.7014 (OUTLIER) cc_final: 0.6738 (tt) REVERT: C 142 MET cc_start: 0.4550 (mmm) cc_final: 0.4095 (mpp) REVERT: C 220 LEU cc_start: 0.6520 (OUTLIER) cc_final: 0.6082 (mm) REVERT: D 209 MET cc_start: 0.5825 (ppp) cc_final: 0.5534 (ptp) REVERT: E 66 GLU cc_start: 0.7311 (mm-30) cc_final: 0.6942 (mp0) REVERT: E 209 MET cc_start: 0.7027 (OUTLIER) cc_final: 0.5777 (ppp) REVERT: E 305 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8663 (mm) REVERT: F 142 MET cc_start: 0.4619 (mmm) cc_final: 0.4252 (mmt) outliers start: 52 outliers final: 31 residues processed: 295 average time/residue: 0.1165 time to fit residues: 53.9810 Evaluate side-chains 288 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 253 time to evaluate : 0.683 ------------------------------------------------------------------------------- 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 185 ILE Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 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 305 ILE Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 338 HIS Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 325 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 74 optimal weight: 0.3980 chunk 87 optimal weight: 10.0000 chunk 198 optimal weight: 0.0770 chunk 120 optimal weight: 9.9990 chunk 175 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 129 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 178 optimal weight: 0.4980 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 338 HIS E 71 GLN E 338 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.190634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.148730 restraints weight = 18035.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.148427 restraints weight = 20902.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.149659 restraints weight = 19489.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.149299 restraints weight = 14792.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.149778 restraints weight = 14455.743| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 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 0.040 17340 Z= 0.109 Angle : 0.579 10.577 23496 Z= 0.295 Chirality : 0.049 0.195 2640 Planarity : 0.006 0.078 2988 Dihedral : 6.717 59.329 2619 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % Rotamer: Outliers : 2.26 % Allowed : 16.89 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.18), residues: 2112 helix: 0.11 (0.31), residues: 312 sheet: 0.39 (0.31), residues: 276 loop : -1.47 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 102 TYR 0.014 0.001 TYR A 233 PHE 0.021 0.001 PHE E 167 TRP 0.009 0.001 TRP D 329 HIS 0.015 0.000 HIS E 338 Details of bonding type rmsd covalent geometry : bond 0.00266 (17340) covalent geometry : angle 0.57866 (23496) hydrogen bonds : bond 0.03790 ( 256) hydrogen bonds : angle 5.35357 ( 702) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 256 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 220 LEU cc_start: 0.6538 (OUTLIER) cc_final: 0.6230 (tt) REVERT: C 142 MET cc_start: 0.3949 (OUTLIER) cc_final: 0.3668 (mpp) REVERT: C 220 LEU cc_start: 0.6171 (OUTLIER) cc_final: 0.5858 (mm) REVERT: E 66 GLU cc_start: 0.7228 (mm-30) cc_final: 0.6920 (mp0) REVERT: E 305 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8658 (mm) REVERT: F 102 ARG cc_start: 0.7210 (ptt-90) cc_final: 0.6961 (ptp90) outliers start: 41 outliers final: 26 residues processed: 280 average time/residue: 0.1250 time to fit residues: 54.0861 Evaluate side-chains 276 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 246 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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 C residue 92 LEU Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 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 305 ILE Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 338 HIS Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 325 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 93 optimal weight: 0.7980 chunk 163 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 152 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 147 optimal weight: 0.6980 chunk 5 optimal weight: 0.3980 chunk 199 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 212 optimal weight: 1.9990 chunk 211 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 338 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.190446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 106)---------------| | r_work = 0.3866 r_free = 0.3866 target = 0.160425 restraints weight = 18132.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.151934 restraints weight = 24588.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.150390 restraints weight = 16962.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.149717 restraints weight = 17825.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.149804 restraints weight = 15872.078| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17340 Z= 0.120 Angle : 0.597 11.655 23496 Z= 0.302 Chirality : 0.050 0.198 2640 Planarity : 0.006 0.078 2988 Dihedral : 6.648 59.687 2619 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.71 % Favored : 90.29 % Rotamer: Outliers : 2.32 % Allowed : 17.27 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.18), residues: 2112 helix: 0.11 (0.31), residues: 312 sheet: 0.41 (0.31), residues: 276 loop : -1.48 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 102 TYR 0.020 0.001 TYR F 152 PHE 0.021 0.001 PHE E 167 TRP 0.009 0.001 TRP D 329 HIS 0.008 0.001 HIS E 338 Details of bonding type rmsd covalent geometry : bond 0.00300 (17340) covalent geometry : angle 0.59724 (23496) hydrogen bonds : bond 0.03790 ( 256) hydrogen bonds : angle 5.30432 ( 702) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 246 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 220 LEU cc_start: 0.6681 (OUTLIER) cc_final: 0.6314 (tt) REVERT: C 102 ARG cc_start: 0.7328 (ptt-90) cc_final: 0.7007 (ptp90) REVERT: C 220 LEU cc_start: 0.6216 (OUTLIER) cc_final: 0.5889 (mm) REVERT: E 209 MET cc_start: 0.6993 (OUTLIER) cc_final: 0.5739 (ppp) REVERT: E 305 ILE cc_start: 0.8894 (OUTLIER) cc_final: 0.8688 (mm) REVERT: F 102 ARG cc_start: 0.7379 (ptt-90) cc_final: 0.7110 (ptp90) outliers start: 42 outliers final: 30 residues processed: 270 average time/residue: 0.1247 time to fit residues: 51.8637 Evaluate side-chains 277 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 243 time to evaluate : 0.853 ------------------------------------------------------------------------------- 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 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 220 LEU Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 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 231 LYS Chi-restraints excluded: chain E residue 305 ILE Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 325 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 196 optimal weight: 9.9990 chunk 74 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 198 optimal weight: 7.9990 chunk 88 optimal weight: 0.4980 chunk 181 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 202 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.192578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.150677 restraints weight = 18172.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.150374 restraints weight = 21659.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.150888 restraints weight = 19600.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.149900 restraints weight = 18247.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.150906 restraints weight = 15312.034| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17340 Z= 0.137 Angle : 0.614 11.910 23496 Z= 0.309 Chirality : 0.050 0.199 2640 Planarity : 0.006 0.097 2988 Dihedral : 6.621 60.329 2619 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.13 % Favored : 89.87 % Rotamer: Outliers : 2.43 % Allowed : 17.22 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.18), residues: 2112 helix: 0.26 (0.32), residues: 300 sheet: 0.39 (0.31), residues: 276 loop : -1.52 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 178 TYR 0.016 0.001 TYR A 233 PHE 0.022 0.001 PHE E 167 TRP 0.008 0.001 TRP D 329 HIS 0.002 0.001 HIS E 338 Details of bonding type rmsd covalent geometry : bond 0.00343 (17340) covalent geometry : angle 0.61417 (23496) hydrogen bonds : bond 0.03874 ( 256) hydrogen bonds : angle 5.31870 ( 702) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 253 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 220 LEU cc_start: 0.6360 (OUTLIER) cc_final: 0.6058 (tt) REVERT: B 225 MET cc_start: 0.8093 (tpp) cc_final: 0.7833 (tpt) REVERT: B 321 MET cc_start: 0.7998 (ttp) cc_final: 0.7687 (ttm) REVERT: B 377 ILE cc_start: 0.8287 (OUTLIER) cc_final: 0.8077 (mm) REVERT: C 102 ARG cc_start: 0.6999 (ptt-90) cc_final: 0.6762 (ptp90) REVERT: C 220 LEU cc_start: 0.6252 (OUTLIER) cc_final: 0.5733 (mm) REVERT: E 209 MET cc_start: 0.7131 (OUTLIER) cc_final: 0.5901 (ppp) outliers start: 44 outliers final: 34 residues processed: 278 average time/residue: 0.1173 time to fit residues: 51.0317 Evaluate side-chains 288 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 250 time to evaluate : 0.605 ------------------------------------------------------------------------------- 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 B residue 338 HIS Chi-restraints excluded: chain B residue 377 ILE 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 220 LEU Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 231 LYS 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 231 LYS Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 338 HIS Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 325 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 20 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 chunk 149 optimal weight: 0.0060 chunk 172 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 132 optimal weight: 0.6980 chunk 137 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 55 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 49 optimal weight: 8.9990 overall best weight: 1.0800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.188333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.157974 restraints weight = 18135.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.147206 restraints weight = 26055.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.145316 restraints weight = 20146.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.145100 restraints weight = 19611.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.145390 restraints weight = 17191.251| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17340 Z= 0.146 Angle : 0.632 13.018 23496 Z= 0.316 Chirality : 0.051 0.201 2640 Planarity : 0.006 0.084 2988 Dihedral : 6.612 62.146 2619 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.56 % Favored : 89.44 % Rotamer: Outliers : 2.26 % Allowed : 17.60 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.18), residues: 2112 helix: 0.25 (0.32), residues: 300 sheet: 0.41 (0.31), residues: 276 loop : -1.55 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 178 TYR 0.021 0.002 TYR F 152 PHE 0.021 0.001 PHE E 167 TRP 0.008 0.001 TRP A 329 HIS 0.003 0.001 HIS B 338 Details of bonding type rmsd covalent geometry : bond 0.00367 (17340) covalent geometry : angle 0.63150 (23496) hydrogen bonds : bond 0.03900 ( 256) hydrogen bonds : angle 5.35421 ( 702) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 255 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 220 LEU cc_start: 0.6508 (OUTLIER) cc_final: 0.6151 (tt) REVERT: C 220 LEU cc_start: 0.6290 (OUTLIER) cc_final: 0.5905 (mm) REVERT: E 209 MET cc_start: 0.6713 (OUTLIER) cc_final: 0.5270 (ppp) REVERT: E 283 ASP cc_start: 0.7553 (m-30) cc_final: 0.7351 (m-30) outliers start: 41 outliers final: 37 residues processed: 277 average time/residue: 0.1200 time to fit residues: 51.8229 Evaluate side-chains 290 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 250 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 B residue 338 HIS Chi-restraints excluded: chain C residue 78 LYS 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 220 LEU Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 231 LYS Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 325 SER Chi-restraints excluded: chain 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 231 LYS Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 338 HIS Chi-restraints excluded: chain F residue 185 ILE Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 325 SER 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 21 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 118 optimal weight: 0.9990 chunk 177 optimal weight: 3.9990 chunk 131 optimal weight: 20.0000 chunk 112 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 140 optimal weight: 0.1980 chunk 146 optimal weight: 0.1980 chunk 81 optimal weight: 1.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.190502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.160263 restraints weight = 18132.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.158131 restraints weight = 24910.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.157050 restraints weight = 27255.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.155808 restraints weight = 24676.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.155545 restraints weight = 24771.612| |-----------------------------------------------------------------------------| r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2243 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= 0.119 Angle : 0.604 12.214 23496 Z= 0.305 Chirality : 0.050 0.204 2640 Planarity : 0.006 0.078 2988 Dihedral : 6.461 65.637 2619 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 2.21 % Allowed : 17.72 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.18), residues: 2112 helix: 0.28 (0.32), residues: 300 sheet: 0.44 (0.31), residues: 276 loop : -1.50 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 102 TYR 0.015 0.001 TYR A 233 PHE 0.020 0.001 PHE E 167 TRP 0.009 0.001 TRP B 329 HIS 0.002 0.000 HIS E 338 Details of bonding type rmsd covalent geometry : bond 0.00298 (17340) covalent geometry : angle 0.60436 (23496) hydrogen bonds : bond 0.03682 ( 256) hydrogen bonds : angle 5.27789 ( 702) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2664.58 seconds wall clock time: 46 minutes 51.30 seconds (2811.30 seconds total)