Starting phenix.real_space_refine on Fri Jun 20 19:40:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kzj_62664/06_2025/9kzj_62664.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kzj_62664/06_2025/9kzj_62664.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/9kzj_62664/06_2025/9kzj_62664.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kzj_62664/06_2025/9kzj_62664.map" model { file = "/net/cci-nas-00/data/ceres_data/9kzj_62664/06_2025/9kzj_62664.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kzj_62664/06_2025/9kzj_62664.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= -0.003 sd= 0.885 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: 4 Type Number sf(0) Gaussians S 131 5.16 5 C 15240 2.51 5 N 4038 2.21 5 O 4686 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 103 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24095 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2267 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 17, 'TRANS': 275} Chain: "B" Number of atoms: 2267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2267 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 17, 'TRANS': 275} Chain: "C" Number of atoms: 2267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2267 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 17, 'TRANS': 275} Chain: "D" Number of atoms: 2267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2267 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 17, 'TRANS': 275} Chain: "E" Number of atoms: 2267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2267 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 17, 'TRANS': 275} Chain: "F" Number of atoms: 2267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2267 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 17, 'TRANS': 275} Chain: "G" Number of atoms: 2267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2267 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 17, 'TRANS': 275} Chain: "N" Number of atoms: 1184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1184 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 3, 'TRANS': 153} Chain: "H" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1122 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 7, 'TRANS': 144} Chain: "I" Number of atoms: 1184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1184 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 3, 'TRANS': 153} Chain: "J" Number of atoms: 1184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1184 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 3, 'TRANS': 153} Chain: "K" Number of atoms: 1184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1184 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 3, 'TRANS': 153} Chain: "L" Number of atoms: 1184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1184 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 3, 'TRANS': 153} Chain: "M" Number of atoms: 1184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1184 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 3, 'TRANS': 153} Time building chain proxies: 15.62, per 1000 atoms: 0.65 Number of scatterers: 24095 At special positions: 0 Unit cell: (220.32, 216.24, 137.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 131 16.00 O 4686 8.00 N 4038 7.00 C 15240 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: 5.51 Conformation dependent library (CDL) restraints added in 3.0 seconds 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5828 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 62 sheets defined 18.0% alpha, 30.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.72 Creating SS restraints... Processing helix chain 'A' and resid 55 through 60 removed outlier: 3.564A pdb=" N PHE A 60 " --> pdb=" O ALA A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 129 Processing helix chain 'A' and resid 132 through 154 removed outlier: 3.742A pdb=" N ALA A 139 " --> pdb=" O ARG A 135 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS A 140 " --> pdb=" O LYS A 136 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN A 141 " --> pdb=" O ALA A 137 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE A 153 " --> pdb=" O ASN A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 204 removed outlier: 3.575A pdb=" N ILE A 200 " --> pdb=" O ALA A 196 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLU A 201 " --> pdb=" O ILE A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 223 Processing helix chain 'A' and resid 233 through 238 removed outlier: 3.848A pdb=" N PHE A 238 " --> pdb=" O TYR A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 255 removed outlier: 3.731A pdb=" N GLU A 254 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP A 255 " --> pdb=" O GLU A 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 251 through 255' Processing helix chain 'A' and resid 309 through 311 No H-bonds generated for 'chain 'A' and resid 309 through 311' Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'B' and resid 119 through 129 Processing helix chain 'B' and resid 132 through 154 Processing helix chain 'B' and resid 163 through 167 removed outlier: 3.838A pdb=" N HIS B 167 " --> pdb=" O VAL B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 205 removed outlier: 3.630A pdb=" N ALA B 191 " --> pdb=" O GLU B 187 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE B 200 " --> pdb=" O ALA B 196 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU B 201 " --> pdb=" O ILE B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 223 Processing helix chain 'B' and resid 233 through 242 Processing helix chain 'B' and resid 252 through 255 removed outlier: 4.067A pdb=" N ASP B 255 " --> pdb=" O GLU B 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 252 through 255' Processing helix chain 'B' and resid 309 through 312 Processing helix chain 'C' and resid 55 through 60 Processing helix chain 'C' and resid 119 through 129 Processing helix chain 'C' and resid 132 through 154 Processing helix chain 'C' and resid 185 through 205 removed outlier: 4.281A pdb=" N ALA C 189 " --> pdb=" O LYS C 185 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLU C 190 " --> pdb=" O PRO C 186 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA C 191 " --> pdb=" O GLU C 187 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE C 200 " --> pdb=" O ALA C 196 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU C 201 " --> pdb=" O ILE C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 222 removed outlier: 3.743A pdb=" N LYS C 221 " --> pdb=" O SER C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 242 removed outlier: 3.527A pdb=" N TYR C 237 " --> pdb=" O SER C 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 40 removed outlier: 3.777A pdb=" N GLU D 38 " --> pdb=" O THR D 35 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N HIS D 40 " --> pdb=" O GLN D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 60 Processing helix chain 'D' and resid 119 through 129 Processing helix chain 'D' and resid 132 through 154 Processing helix chain 'D' and resid 187 through 205 removed outlier: 3.738A pdb=" N ALA D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE D 200 " --> pdb=" O ALA D 196 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU D 201 " --> pdb=" O ILE D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 223 Processing helix chain 'D' and resid 233 through 242 removed outlier: 3.539A pdb=" N TYR D 237 " --> pdb=" O SER D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 254 removed outlier: 3.520A pdb=" N GLU D 254 " --> pdb=" O ALA D 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 251 through 254' Processing helix chain 'E' and resid 36 through 38 No H-bonds generated for 'chain 'E' and resid 36 through 38' Processing helix chain 'E' and resid 55 through 60 removed outlier: 3.537A pdb=" N PHE E 60 " --> pdb=" O ALA E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 129 Processing helix chain 'E' and resid 132 through 154 Processing helix chain 'E' and resid 187 through 205 removed outlier: 3.514A pdb=" N ALA E 191 " --> pdb=" O GLU E 187 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE E 200 " --> pdb=" O ALA E 196 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU E 201 " --> pdb=" O ILE E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 223 Processing helix chain 'E' and resid 233 through 242 Processing helix chain 'E' and resid 251 through 254 removed outlier: 3.743A pdb=" N GLU E 254 " --> pdb=" O ALA E 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 251 through 254' Processing helix chain 'F' and resid 119 through 129 Processing helix chain 'F' and resid 132 through 154 Processing helix chain 'F' and resid 163 through 167 removed outlier: 3.666A pdb=" N HIS F 167 " --> pdb=" O VAL F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 205 removed outlier: 4.076A pdb=" N ALA F 189 " --> pdb=" O LYS F 185 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU F 190 " --> pdb=" O PRO F 186 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA F 191 " --> pdb=" O GLU F 187 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE F 200 " --> pdb=" O ALA F 196 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU F 201 " --> pdb=" O ILE F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 218 through 223 Processing helix chain 'F' and resid 233 through 242 Processing helix chain 'F' and resid 251 through 254 removed outlier: 4.217A pdb=" N GLU F 254 " --> pdb=" O ALA F 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 251 through 254' Processing helix chain 'G' and resid 55 through 60 Processing helix chain 'G' and resid 119 through 129 Processing helix chain 'G' and resid 132 through 154 Processing helix chain 'G' and resid 185 through 204 removed outlier: 4.159A pdb=" N ALA G 189 " --> pdb=" O LYS G 185 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLU G 190 " --> pdb=" O PRO G 186 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA G 191 " --> pdb=" O GLU G 187 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE G 200 " --> pdb=" O ALA G 196 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU G 201 " --> pdb=" O ILE G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 219 through 224 Processing helix chain 'G' and resid 233 through 242 Processing helix chain 'G' and resid 251 through 254 removed outlier: 3.525A pdb=" N GLU G 254 " --> pdb=" O ALA G 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 251 through 254' Processing sheet with id=AA1, first strand: chain 'A' and resid 72 through 81 removed outlier: 3.806A pdb=" N PHE A 73 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL A 81 " --> pdb=" O ASP A 98 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 109 through 118 Processing sheet with id=AA3, first strand: chain 'A' and resid 109 through 118 Processing sheet with id=AA4, first strand: chain 'A' and resid 171 through 174 removed outlier: 6.743A pdb=" N THR A 171 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N THR A 317 " --> pdb=" O THR A 171 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ILE A 173 " --> pdb=" O THR A 317 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 274 through 276 Processing sheet with id=AA6, first strand: chain 'B' and resid 41 through 48 removed outlier: 6.044A pdb=" N MET G 76 " --> pdb=" O LYS B 43 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N GLN B 45 " --> pdb=" O MET G 76 " (cutoff:3.500A) removed outlier: 9.093A pdb=" N PHE G 78 " --> pdb=" O GLN B 45 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N TYR B 47 " --> pdb=" O PHE G 78 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE G 73 " --> pdb=" O GLY G 106 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 98 through 107 removed outlier: 3.650A pdb=" N PHE B 73 " --> pdb=" O GLY B 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 98 through 107 removed outlier: 3.650A pdb=" N PHE B 73 " --> pdb=" O GLY B 106 " (cutoff:3.500A) removed outlier: 9.605A pdb=" N TYR C 47 " --> pdb=" O GLU B 74 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N MET B 76 " --> pdb=" O TYR C 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 85 through 86 removed outlier: 3.751A pdb=" N GLN B 85 " --> pdb=" O GLY C 112 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE C 117 " --> pdb=" O PHE C 294 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 280 through 284 removed outlier: 5.560A pdb=" N ALA B 281 " --> pdb=" O LYS B 301 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N LYS B 301 " --> pdb=" O ALA B 281 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ILE B 117 " --> pdb=" O PHE B 294 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN G 85 " --> pdb=" O GLY B 112 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 171 through 174 removed outlier: 9.732A pdb=" N SER I 7 " --> pdb=" O ILE B 247 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N SER B 249 " --> pdb=" O SER I 7 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 179 through 180 Processing sheet with id=AB4, first strand: chain 'B' and resid 274 through 276 Processing sheet with id=AB5, first strand: chain 'C' and resid 98 through 107 removed outlier: 3.710A pdb=" N PHE C 73 " --> pdb=" O GLY C 106 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N LYS D 43 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLU C 74 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLN D 45 " --> pdb=" O GLU C 74 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N MET C 76 " --> pdb=" O GLN D 45 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 85 through 86 removed outlier: 3.954A pdb=" N GLN C 85 " --> pdb=" O GLY D 112 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE D 117 " --> pdb=" O PHE D 294 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 171 through 174 removed outlier: 6.545A pdb=" N THR C 171 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N THR C 317 " --> pdb=" O THR C 171 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE C 173 " --> pdb=" O THR C 317 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ILE C 213 " --> pdb=" O ASP C 248 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ILE C 250 " --> pdb=" O ILE C 213 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ILE C 215 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 9.850A pdb=" N SER N 7 " --> pdb=" O ILE C 247 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N SER C 249 " --> pdb=" O SER N 7 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 179 through 180 Processing sheet with id=AB9, first strand: chain 'C' and resid 274 through 276 removed outlier: 3.564A pdb=" N SER C 275 " --> pdb=" O THR C 306 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 98 through 107 removed outlier: 3.543A pdb=" N LEU D 100 " --> pdb=" O ASP D 79 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE D 73 " --> pdb=" O GLY D 106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 98 through 107 removed outlier: 3.543A pdb=" N LEU D 100 " --> pdb=" O ASP D 79 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE D 73 " --> pdb=" O GLY D 106 " (cutoff:3.500A) removed outlier: 9.247A pdb=" N TYR E 47 " --> pdb=" O GLU D 74 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N MET D 76 " --> pdb=" O TYR E 47 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 85 through 86 removed outlier: 3.685A pdb=" N GLN D 85 " --> pdb=" O GLY E 112 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE E 117 " --> pdb=" O PHE E 294 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 171 through 174 removed outlier: 3.639A pdb=" N THR D 171 " --> pdb=" O ILE D 313 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 179 through 180 Processing sheet with id=AC6, first strand: chain 'D' and resid 274 through 276 Processing sheet with id=AC7, first strand: chain 'E' and resid 98 through 107 removed outlier: 3.536A pdb=" N VAL E 81 " --> pdb=" O ASP E 98 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU E 100 " --> pdb=" O ASP E 79 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE E 73 " --> pdb=" O GLY E 106 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR E 72 " --> pdb=" O ARG F 41 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N LYS F 43 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N GLU E 74 " --> pdb=" O LYS F 43 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N GLN F 45 " --> pdb=" O GLU E 74 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N MET E 76 " --> pdb=" O GLN F 45 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 85 through 86 removed outlier: 3.787A pdb=" N GLN E 85 " --> pdb=" O GLY F 112 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE F 117 " --> pdb=" O PHE F 294 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 171 through 174 removed outlier: 6.568A pdb=" N THR E 171 " --> pdb=" O LEU E 315 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N THR E 317 " --> pdb=" O THR E 171 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ILE E 173 " --> pdb=" O THR E 317 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 179 through 180 Processing sheet with id=AD2, first strand: chain 'E' and resid 274 through 276 Processing sheet with id=AD3, first strand: chain 'F' and resid 98 through 107 removed outlier: 3.532A pdb=" N LEU F 100 " --> pdb=" O ASP F 79 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP F 79 " --> pdb=" O LEU F 100 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE F 73 " --> pdb=" O GLY F 106 " (cutoff:3.500A) removed outlier: 9.286A pdb=" N TYR G 47 " --> pdb=" O GLU F 74 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N MET F 76 " --> pdb=" O TYR G 47 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 85 through 86 removed outlier: 3.714A pdb=" N GLN F 85 " --> pdb=" O GLY G 112 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE G 117 " --> pdb=" O PHE G 294 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 171 through 174 removed outlier: 6.507A pdb=" N THR F 171 " --> pdb=" O LEU F 315 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N THR F 317 " --> pdb=" O THR F 171 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE F 173 " --> pdb=" O THR F 317 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 179 through 180 Processing sheet with id=AD7, first strand: chain 'F' and resid 274 through 276 Processing sheet with id=AD8, first strand: chain 'G' and resid 80 through 81 Processing sheet with id=AD9, first strand: chain 'G' and resid 171 through 174 removed outlier: 6.652A pdb=" N THR G 171 " --> pdb=" O LEU G 315 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N THR G 317 " --> pdb=" O THR G 171 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE G 173 " --> pdb=" O THR G 317 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 179 through 180 Processing sheet with id=AE2, first strand: chain 'G' and resid 274 through 275 Processing sheet with id=AE3, first strand: chain 'N' and resid 27 through 29 removed outlier: 6.685A pdb=" N ASN N 27 " --> pdb=" O THR N 98 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL N 96 " --> pdb=" O ASP N 29 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL N 71 " --> pdb=" O MET N 97 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'N' and resid 27 through 29 removed outlier: 6.685A pdb=" N ASN N 27 " --> pdb=" O THR N 98 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL N 96 " --> pdb=" O ASP N 29 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLY N 141 " --> pdb=" O GLU N 152 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLN N 154 " --> pdb=" O ALA N 139 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ALA N 139 " --> pdb=" O GLN N 154 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N THR N 134 " --> pdb=" O LEU N 120 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N LEU N 120 " --> pdb=" O THR N 134 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N TRP N 136 " --> pdb=" O VAL N 118 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 32 through 34 removed outlier: 6.186A pdb=" N VAL N 33 " --> pdb=" O VAL N 59 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N ALA N 61 " --> pdb=" O VAL N 33 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN N 49 " --> pdb=" O LEU N 58 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LYS N 60 " --> pdb=" O VAL N 47 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N VAL N 47 " --> pdb=" O LYS N 60 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 39 through 40 Processing sheet with id=AE7, first strand: chain 'H' and resid 23 through 25 removed outlier: 6.884A pdb=" N ASP H 25 " --> pdb=" O VAL H 86 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N VAL H 86 " --> pdb=" O ASP H 25 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE H 64 " --> pdb=" O VAL H 86 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY H 63 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA H 65 " --> pdb=" O SER H 38 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N SER H 38 " --> pdb=" O ALA H 65 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N VAL H 42 " --> pdb=" O THR H 53 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N THR H 53 " --> pdb=" O VAL H 42 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLY H 44 " --> pdb=" O VAL H 51 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 23 through 25 removed outlier: 6.884A pdb=" N ASP H 25 " --> pdb=" O VAL H 86 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N VAL H 86 " --> pdb=" O ASP H 25 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU H 140 " --> pdb=" O GLY H 129 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N GLY H 129 " --> pdb=" O GLU H 140 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ARG H 142 " --> pdb=" O ALA H 127 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ALA H 127 " --> pdb=" O ARG H 142 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 108 through 110 removed outlier: 3.865A pdb=" N GLY H 117 " --> pdb=" O GLN H 108 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N GLY H 110 " --> pdb=" O VAL H 115 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N VAL H 115 " --> pdb=" O GLY H 110 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 27 through 29 removed outlier: 6.284A pdb=" N ASN I 27 " --> pdb=" O THR I 98 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL I 96 " --> pdb=" O ASP I 29 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLY I 70 " --> pdb=" O VAL I 45 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LEU I 58 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 27 through 29 removed outlier: 6.284A pdb=" N ASN I 27 " --> pdb=" O THR I 98 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL I 96 " --> pdb=" O ASP I 29 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY I 100 " --> pdb=" O LEU I 155 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ILE I 148 " --> pdb=" O THR I 143 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N THR I 143 " --> pdb=" O ILE I 148 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU I 150 " --> pdb=" O GLY I 141 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N GLY I 141 " --> pdb=" O LEU I 150 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N GLU I 152 " --> pdb=" O ALA I 139 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N THR I 134 " --> pdb=" O LEU I 120 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N LEU I 120 " --> pdb=" O THR I 134 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N TRP I 136 " --> pdb=" O VAL I 118 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 39 through 40 Processing sheet with id=AF4, first strand: chain 'J' and resid 27 through 29 removed outlier: 6.317A pdb=" N ASN J 27 " --> pdb=" O THR J 98 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 27 through 29 removed outlier: 6.317A pdb=" N ASN J 27 " --> pdb=" O THR J 98 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ILE J 148 " --> pdb=" O THR J 143 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N THR J 143 " --> pdb=" O ILE J 148 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N LEU J 150 " --> pdb=" O GLY J 141 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N GLY J 141 " --> pdb=" O LEU J 150 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N GLU J 152 " --> pdb=" O ALA J 139 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N VAL J 118 " --> pdb=" O THR J 134 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 32 through 34 removed outlier: 5.804A pdb=" N VAL J 33 " --> pdb=" O VAL J 59 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N ALA J 61 " --> pdb=" O VAL J 33 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN J 49 " --> pdb=" O LEU J 58 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LYS J 60 " --> pdb=" O VAL J 47 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N VAL J 47 " --> pdb=" O LYS J 60 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'J' and resid 39 through 40 Processing sheet with id=AF8, first strand: chain 'K' and resid 27 through 29 removed outlier: 6.328A pdb=" N ASN K 27 " --> pdb=" O THR K 98 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY K 70 " --> pdb=" O VAL K 45 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N VAL K 47 " --> pdb=" O LYS K 60 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LYS K 60 " --> pdb=" O VAL K 47 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N VAL K 33 " --> pdb=" O VAL K 59 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N ALA K 61 " --> pdb=" O VAL K 33 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K' and resid 27 through 29 removed outlier: 6.328A pdb=" N ASN K 27 " --> pdb=" O THR K 98 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY K 100 " --> pdb=" O LEU K 155 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ILE K 148 " --> pdb=" O THR K 143 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N THR K 143 " --> pdb=" O ILE K 148 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N LEU K 150 " --> pdb=" O GLY K 141 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N GLY K 141 " --> pdb=" O LEU K 150 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N GLU K 152 " --> pdb=" O ALA K 139 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N VAL K 118 " --> pdb=" O THR K 134 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 39 through 40 Processing sheet with id=AG2, first strand: chain 'L' and resid 45 through 50 removed outlier: 5.901A pdb=" N VAL L 47 " --> pdb=" O LYS L 60 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N LYS L 60 " --> pdb=" O VAL L 47 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN L 49 " --> pdb=" O LEU L 58 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ASN L 27 " --> pdb=" O THR L 98 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ALA L 31 " --> pdb=" O ILE L 94 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ILE L 94 " --> pdb=" O ALA L 31 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 45 through 50 removed outlier: 5.901A pdb=" N VAL L 47 " --> pdb=" O LYS L 60 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N LYS L 60 " --> pdb=" O VAL L 47 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN L 49 " --> pdb=" O LEU L 58 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ASN L 27 " --> pdb=" O THR L 98 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ALA L 31 " --> pdb=" O ILE L 94 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ILE L 94 " --> pdb=" O ALA L 31 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY L 100 " --> pdb=" O LEU L 155 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ILE L 148 " --> pdb=" O THR L 143 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N THR L 143 " --> pdb=" O ILE L 148 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N LEU L 150 " --> pdb=" O GLY L 141 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N GLY L 141 " --> pdb=" O LEU L 150 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N GLU L 152 " --> pdb=" O ALA L 139 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 39 through 40 Processing sheet with id=AG5, first strand: chain 'L' and resid 119 through 120 Processing sheet with id=AG6, first strand: chain 'M' and resid 27 through 29 removed outlier: 6.568A pdb=" N ASN M 27 " --> pdb=" O THR M 98 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY M 70 " --> pdb=" O VAL M 45 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N VAL M 47 " --> pdb=" O LYS M 60 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LYS M 60 " --> pdb=" O VAL M 47 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN M 49 " --> pdb=" O LEU M 58 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL M 33 " --> pdb=" O VAL M 59 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N ALA M 61 " --> pdb=" O VAL M 33 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'M' and resid 27 through 29 removed outlier: 6.568A pdb=" N ASN M 27 " --> pdb=" O THR M 98 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY M 100 " --> pdb=" O LEU M 155 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ILE M 148 " --> pdb=" O THR M 143 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N THR M 143 " --> pdb=" O ILE M 148 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N LEU M 150 " --> pdb=" O GLY M 141 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N GLY M 141 " --> pdb=" O LEU M 150 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N GLU M 152 " --> pdb=" O ALA M 139 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA M 139 " --> pdb=" O GLU M 152 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N VAL M 118 " --> pdb=" O THR M 134 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'M' and resid 39 through 40 792 hydrogen bonds defined for protein. 2118 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: 8.88 Time building geometry restraints manager: 6.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 4097 1.31 - 1.44: 6114 1.44 - 1.56: 14112 1.56 - 1.69: 1 1.69 - 1.81: 232 Bond restraints: 24556 Sorted by residual: bond pdb=" CA ALA G 29 " pdb=" C ALA G 29 " ideal model delta sigma weight residual 1.523 1.442 0.081 1.34e-02 5.57e+03 3.66e+01 bond pdb=" N MET G 31 " pdb=" CA MET G 31 " ideal model delta sigma weight residual 1.457 1.387 0.071 1.29e-02 6.01e+03 3.02e+01 bond pdb=" N ALA G 29 " pdb=" CA ALA G 29 " ideal model delta sigma weight residual 1.457 1.399 0.059 1.29e-02 6.01e+03 2.06e+01 bond pdb=" C MET G 31 " pdb=" O MET G 31 " ideal model delta sigma weight residual 1.235 1.187 0.048 1.26e-02 6.30e+03 1.46e+01 bond pdb=" CA MET G 31 " pdb=" CB MET G 31 " ideal model delta sigma weight residual 1.530 1.466 0.064 1.69e-02 3.50e+03 1.43e+01 ... (remaining 24551 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 32723 2.02 - 4.03: 589 4.03 - 6.05: 56 6.05 - 8.07: 6 8.07 - 10.09: 2 Bond angle restraints: 33376 Sorted by residual: angle pdb=" N PRO C 289 " pdb=" CA PRO C 289 " pdb=" C PRO C 289 " ideal model delta sigma weight residual 111.32 120.45 -9.13 1.71e+00 3.42e-01 2.85e+01 angle pdb=" C ASN G 270 " pdb=" N PRO G 271 " pdb=" CA PRO G 271 " ideal model delta sigma weight residual 119.84 113.80 6.04 1.25e+00 6.40e-01 2.34e+01 angle pdb=" N ALA G 29 " pdb=" CA ALA G 29 " pdb=" C ALA G 29 " ideal model delta sigma weight residual 110.80 100.71 10.09 2.13e+00 2.20e-01 2.24e+01 angle pdb=" N TYR B 308 " pdb=" CA TYR B 308 " pdb=" C TYR B 308 " ideal model delta sigma weight residual 113.97 107.92 6.05 1.28e+00 6.10e-01 2.23e+01 angle pdb=" C ASP A 291 " pdb=" CA ASP A 291 " pdb=" CB ASP A 291 " ideal model delta sigma weight residual 117.23 110.82 6.41 1.36e+00 5.41e-01 2.22e+01 ... (remaining 33371 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.20: 12907 16.20 - 32.40: 1354 32.40 - 48.60: 392 48.60 - 64.80: 114 64.80 - 81.00: 22 Dihedral angle restraints: 14789 sinusoidal: 5725 harmonic: 9064 Sorted by residual: dihedral pdb=" N ALA G 29 " pdb=" C ALA G 29 " pdb=" CA ALA G 29 " pdb=" CB ALA G 29 " ideal model delta harmonic sigma weight residual 122.90 113.94 8.96 0 2.50e+00 1.60e-01 1.28e+01 dihedral pdb=" CA PHE H 36 " pdb=" C PHE H 36 " pdb=" N GLY H 37 " pdb=" CA GLY H 37 " ideal model delta harmonic sigma weight residual -180.00 -162.28 -17.72 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA GLY D 258 " pdb=" C GLY D 258 " pdb=" N ALA D 259 " pdb=" CA ALA D 259 " ideal model delta harmonic sigma weight residual -180.00 -162.33 -17.67 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 14786 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 3148 0.053 - 0.106: 613 0.106 - 0.159: 147 0.159 - 0.212: 0 0.212 - 0.265: 1 Chirality restraints: 3909 Sorted by residual: chirality pdb=" CA PRO C 289 " pdb=" N PRO C 289 " pdb=" C PRO C 289 " pdb=" CB PRO C 289 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA ASP G 93 " pdb=" N ASP G 93 " pdb=" C ASP G 93 " pdb=" CB ASP G 93 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.80e-01 chirality pdb=" CA ILE E 276 " pdb=" N ILE E 276 " pdb=" C ILE E 276 " pdb=" CB ILE E 276 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.09e-01 ... (remaining 3906 not shown) Planarity restraints: 4265 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 185 " -0.052 5.00e-02 4.00e+02 7.92e-02 1.00e+01 pdb=" N PRO A 186 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO A 186 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 186 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN G 270 " -0.049 5.00e-02 4.00e+02 7.29e-02 8.50e+00 pdb=" N PRO G 271 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO G 271 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO G 271 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS F 185 " 0.041 5.00e-02 4.00e+02 6.22e-02 6.19e+00 pdb=" N PRO F 186 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO F 186 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO F 186 " 0.034 5.00e-02 4.00e+02 ... (remaining 4262 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 616 2.69 - 3.24: 21398 3.24 - 3.79: 33238 3.79 - 4.35: 44494 4.35 - 4.90: 78540 Nonbonded interactions: 178286 Sorted by model distance: nonbonded pdb=" OG1 THR E 211 " pdb=" OD1 ASN E 212 " model vdw 2.133 3.040 nonbonded pdb=" O THR G 30 " pdb=" C MET G 31 " model vdw 2.194 3.270 nonbonded pdb=" OE2 GLU I 126 " pdb=" OH TYR I 138 " model vdw 2.204 3.040 nonbonded pdb=" NZ LYS M 107 " pdb=" OD2 ASP M 121 " model vdw 2.207 3.120 nonbonded pdb=" OG SER B 249 " pdb=" O ASN I 5 " model vdw 2.207 3.040 ... (remaining 178281 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 228.460 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: 0.030 Extract box with map and model: 0.880 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 56.210 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 289.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 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 : 0.003 0.081 24556 Z= 0.196 Angle : 0.657 10.086 33376 Z= 0.399 Chirality : 0.044 0.265 3909 Planarity : 0.005 0.079 4265 Dihedral : 15.235 81.004 8961 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.71 % Allowed : 3.50 % Favored : 95.80 % Rotamer: Outliers : 1.10 % Allowed : 19.26 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.14), residues: 3117 helix: 1.33 (0.25), residues: 509 sheet: 0.54 (0.41), residues: 195 loop : -1.70 (0.11), residues: 2413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 92 HIS 0.007 0.001 HIS B 293 PHE 0.012 0.001 PHE E 282 TYR 0.011 0.001 TYR A 237 ARG 0.008 0.000 ARG E 58 Details of bonding type rmsd hydrogen bonds : bond 0.23202 ( 743) hydrogen bonds : angle 8.50712 ( 2118) covalent geometry : bond 0.00332 (24556) covalent geometry : angle 0.65651 (33376) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 598 time to evaluate : 2.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 205 ARG cc_start: 0.7246 (mmt180) cc_final: 0.6733 (tpt170) REVERT: I 123 ASP cc_start: 0.8022 (OUTLIER) cc_final: 0.7750 (p0) REVERT: J 119 LYS cc_start: 0.8060 (mttm) cc_final: 0.7046 (mmtp) REVERT: K 86 MET cc_start: 0.7362 (mtm) cc_final: 0.7123 (mtm) REVERT: M 60 LYS cc_start: 0.7840 (tttt) cc_final: 0.7213 (tttm) outliers start: 29 outliers final: 2 residues processed: 612 average time/residue: 0.3870 time to fit residues: 353.5765 Evaluate side-chains 454 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 451 time to evaluate : 2.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 283 ASN Chi-restraints excluded: chain I residue 123 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 260 optimal weight: 7.9990 chunk 233 optimal weight: 1.9990 chunk 129 optimal weight: 6.9990 chunk 79 optimal weight: 8.9990 chunk 157 optimal weight: 4.9990 chunk 124 optimal weight: 8.9990 chunk 241 optimal weight: 8.9990 chunk 93 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 179 optimal weight: 6.9990 chunk 279 optimal weight: 0.4980 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 HIS C 37 GLN C 144 HIS C 166 ASN C 293 HIS D 144 HIS E 241 GLN ** F 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 241 GLN G 270 ASN H 72 HIS ** H 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 108 GLN I 35 ASN ** K 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.055718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2470 r_free = 0.2470 target = 0.044196 restraints weight = 82325.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2509 r_free = 0.2509 target = 0.045694 restraints weight = 33575.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2535 r_free = 0.2535 target = 0.046688 restraints weight = 18670.414| |-----------------------------------------------------------------------------| r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 24556 Z= 0.219 Angle : 0.625 7.367 33376 Z= 0.338 Chirality : 0.046 0.160 3909 Planarity : 0.005 0.053 4265 Dihedral : 4.521 32.444 3341 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.56 % Favored : 96.09 % Rotamer: Outliers : 3.04 % Allowed : 19.57 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.14), residues: 3117 helix: 1.36 (0.25), residues: 536 sheet: -0.08 (0.29), residues: 330 loop : -1.65 (0.11), residues: 2251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 92 HIS 0.007 0.001 HIS L 156 PHE 0.013 0.001 PHE E 282 TYR 0.015 0.001 TYR C 237 ARG 0.005 0.001 ARG E 150 Details of bonding type rmsd hydrogen bonds : bond 0.04965 ( 743) hydrogen bonds : angle 5.85264 ( 2118) covalent geometry : bond 0.00493 (24556) covalent geometry : angle 0.62519 (33376) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 474 time to evaluate : 2.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 GLN cc_start: 0.8713 (tm-30) cc_final: 0.8499 (tm-30) REVERT: B 246 GLU cc_start: 0.8343 (mp0) cc_final: 0.7890 (mp0) REVERT: B 308 TYR cc_start: 0.8759 (m-10) cc_final: 0.8216 (m-80) REVERT: C 31 MET cc_start: 0.8926 (mtp) cc_final: 0.8646 (mtp) REVERT: C 75 TYR cc_start: 0.9471 (p90) cc_final: 0.8637 (p90) REVERT: C 104 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8517 (mp0) REVERT: C 241 GLN cc_start: 0.8863 (mm110) cc_final: 0.8481 (mm110) REVERT: C 272 MET cc_start: 0.9335 (tpp) cc_final: 0.9133 (tpt) REVERT: D 130 ARG cc_start: 0.9436 (ttm170) cc_final: 0.7563 (ppt170) REVERT: E 63 THR cc_start: 0.9734 (OUTLIER) cc_final: 0.9391 (p) REVERT: E 201 GLU cc_start: 0.9291 (tt0) cc_final: 0.8955 (tm-30) REVERT: E 230 THR cc_start: 0.9530 (OUTLIER) cc_final: 0.9275 (p) REVERT: F 47 TYR cc_start: 0.8451 (m-10) cc_final: 0.8235 (m-10) REVERT: G 31 MET cc_start: 0.7489 (mmm) cc_final: 0.7132 (mmm) REVERT: G 64 THR cc_start: 0.9813 (OUTLIER) cc_final: 0.9507 (p) REVERT: G 100 LEU cc_start: 0.9179 (mp) cc_final: 0.8966 (mp) REVERT: G 254 GLU cc_start: 0.9169 (OUTLIER) cc_final: 0.8932 (mt-10) REVERT: N 10 ARG cc_start: 0.9123 (ttt180) cc_final: 0.8769 (ttt180) REVERT: N 106 SER cc_start: 0.9119 (t) cc_final: 0.8918 (p) REVERT: N 119 LYS cc_start: 0.9203 (mmmm) cc_final: 0.8224 (mmmm) REVERT: H 71 GLU cc_start: 0.7403 (mp0) cc_final: 0.7165 (mp0) REVERT: I 60 LYS cc_start: 0.9191 (tttp) cc_final: 0.8650 (tttp) REVERT: I 80 VAL cc_start: 0.9143 (OUTLIER) cc_final: 0.8860 (p) REVERT: I 84 ASN cc_start: 0.8571 (t0) cc_final: 0.8251 (t0) REVERT: I 97 MET cc_start: 0.9634 (ttm) cc_final: 0.9346 (ttt) REVERT: J 84 ASN cc_start: 0.9052 (t0) cc_final: 0.8822 (t0) REVERT: K 86 MET cc_start: 0.8281 (mtm) cc_final: 0.8031 (mtm) REVERT: K 144 LYS cc_start: 0.9602 (ttpt) cc_final: 0.9232 (ttpp) REVERT: L 3 GLN cc_start: 0.8231 (mm-40) cc_final: 0.7992 (mm-40) REVERT: M 12 MET cc_start: 0.4437 (ttt) cc_final: 0.4131 (ttt) REVERT: M 36 GLU cc_start: 0.8751 (pt0) cc_final: 0.8123 (pm20) REVERT: M 49 GLN cc_start: 0.9341 (tt0) cc_final: 0.9106 (tm-30) REVERT: M 51 GLN cc_start: 0.9155 (mt0) cc_final: 0.8510 (mt0) REVERT: M 60 LYS cc_start: 0.9280 (tttt) cc_final: 0.8423 (tttt) REVERT: M 84 ASN cc_start: 0.9046 (t0) cc_final: 0.8248 (t0) REVERT: M 107 LYS cc_start: 0.9388 (mtpt) cc_final: 0.9037 (mtpt) REVERT: M 133 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7773 (mm-30) REVERT: M 144 LYS cc_start: 0.9334 (ttmm) cc_final: 0.8871 (ttmm) outliers start: 80 outliers final: 43 residues processed: 523 average time/residue: 0.3677 time to fit residues: 302.2615 Evaluate side-chains 475 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 427 time to evaluate : 2.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 207 GLN Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 311 MET Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 302 CYS Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain F residue 76 MET Chi-restraints excluded: chain F residue 184 MET Chi-restraints excluded: chain F residue 222 VAL Chi-restraints excluded: chain F residue 302 CYS Chi-restraints excluded: chain G residue 50 ASP Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain G residue 254 GLU Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain K residue 19 MET Chi-restraints excluded: chain K residue 66 THR Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 128 SER Chi-restraints excluded: chain K residue 155 LEU Chi-restraints excluded: chain L residue 36 GLU Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain M residue 19 MET Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 75 SER Chi-restraints excluded: chain M residue 81 ASN Chi-restraints excluded: chain M residue 128 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 245 optimal weight: 8.9990 chunk 150 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 257 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 270 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 137 optimal weight: 8.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 166 ASN G 207 GLN ** H 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 46 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 = 0.2724 r_free = 0.2724 target = 0.053857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2421 r_free = 0.2421 target = 0.042412 restraints weight = 82933.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2460 r_free = 0.2460 target = 0.043893 restraints weight = 33455.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2486 r_free = 0.2486 target = 0.044860 restraints weight = 18462.476| |-----------------------------------------------------------------------------| r_work (final): 0.2479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 24556 Z= 0.225 Angle : 0.608 8.146 33376 Z= 0.328 Chirality : 0.046 0.164 3909 Planarity : 0.005 0.052 4265 Dihedral : 4.460 22.569 3335 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.75 % Favored : 95.86 % Rotamer: Outliers : 3.31 % Allowed : 19.98 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.14), residues: 3117 helix: 1.22 (0.24), residues: 557 sheet: 0.01 (0.32), residues: 279 loop : -1.65 (0.11), residues: 2281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 103 HIS 0.006 0.001 HIS G 293 PHE 0.011 0.001 PHE E 282 TYR 0.016 0.001 TYR D 115 ARG 0.006 0.001 ARG D 205 Details of bonding type rmsd hydrogen bonds : bond 0.05010 ( 743) hydrogen bonds : angle 5.58270 ( 2118) covalent geometry : bond 0.00508 (24556) covalent geometry : angle 0.60750 (33376) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 433 time to evaluate : 2.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 246 GLU cc_start: 0.8321 (mp0) cc_final: 0.7818 (mp0) REVERT: C 104 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8645 (mt-10) REVERT: C 269 LYS cc_start: 0.9369 (OUTLIER) cc_final: 0.8729 (tttp) REVERT: C 272 MET cc_start: 0.9274 (tpp) cc_final: 0.9046 (tpt) REVERT: D 272 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8178 (tmm) REVERT: E 63 THR cc_start: 0.9745 (OUTLIER) cc_final: 0.9295 (p) REVERT: E 201 GLU cc_start: 0.9161 (tt0) cc_final: 0.8911 (tm-30) REVERT: E 230 THR cc_start: 0.9475 (OUTLIER) cc_final: 0.9154 (p) REVERT: E 246 GLU cc_start: 0.8261 (mp0) cc_final: 0.7966 (mp0) REVERT: F 207 GLN cc_start: 0.8385 (mt0) cc_final: 0.7650 (mt0) REVERT: F 209 ARG cc_start: 0.8142 (mtt-85) cc_final: 0.7846 (mtt-85) REVERT: F 283 ASN cc_start: 0.8391 (m-40) cc_final: 0.8127 (m-40) REVERT: G 64 THR cc_start: 0.9830 (OUTLIER) cc_final: 0.9595 (p) REVERT: G 100 LEU cc_start: 0.9253 (mp) cc_final: 0.9044 (mp) REVERT: G 230 THR cc_start: 0.9133 (OUTLIER) cc_final: 0.8837 (p) REVERT: G 254 GLU cc_start: 0.9222 (OUTLIER) cc_final: 0.8987 (mt-10) REVERT: G 306 THR cc_start: 0.8918 (OUTLIER) cc_final: 0.8708 (p) REVERT: N 106 SER cc_start: 0.9091 (t) cc_final: 0.8845 (p) REVERT: N 119 LYS cc_start: 0.9102 (mmmm) cc_final: 0.8775 (mmmm) REVERT: N 155 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.9004 (mt) REVERT: H 71 GLU cc_start: 0.7744 (mp0) cc_final: 0.7443 (mp0) REVERT: I 36 GLU cc_start: 0.8904 (pm20) cc_final: 0.7846 (pm20) REVERT: I 97 MET cc_start: 0.9647 (ttm) cc_final: 0.9373 (ttt) REVERT: J 36 GLU cc_start: 0.8901 (pt0) cc_final: 0.8429 (pp20) REVERT: J 84 ASN cc_start: 0.9171 (t0) cc_final: 0.8908 (t0) REVERT: K 9 GLN cc_start: 0.9262 (tm-30) cc_final: 0.8577 (tp-100) REVERT: K 86 MET cc_start: 0.8431 (mtm) cc_final: 0.8188 (mtm) REVERT: K 144 LYS cc_start: 0.9618 (ttpt) cc_final: 0.9256 (ttpp) REVERT: L 86 MET cc_start: 0.8368 (mtm) cc_final: 0.8151 (mtm) REVERT: M 36 GLU cc_start: 0.8903 (pt0) cc_final: 0.8308 (pm20) REVERT: M 60 LYS cc_start: 0.9341 (tttt) cc_final: 0.8874 (tttp) REVERT: M 104 MET cc_start: 0.9384 (ttp) cc_final: 0.9045 (ttp) REVERT: M 144 LYS cc_start: 0.9390 (ttmm) cc_final: 0.9105 (ttmm) outliers start: 87 outliers final: 55 residues processed: 493 average time/residue: 0.3483 time to fit residues: 273.6004 Evaluate side-chains 473 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 409 time to evaluate : 2.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 269 LYS Chi-restraints excluded: chain C residue 311 MET Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain D residue 302 CYS Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain F residue 76 MET Chi-restraints excluded: chain F residue 222 VAL Chi-restraints excluded: chain F residue 302 CYS Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 223 LEU Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 254 GLU Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain N residue 66 THR Chi-restraints excluded: chain N residue 155 LEU Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 134 THR Chi-restraints excluded: chain I residue 158 LEU Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain J residue 66 THR Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain K residue 19 MET Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 120 LEU Chi-restraints excluded: chain K residue 128 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 19 MET Chi-restraints excluded: chain L residue 36 GLU Chi-restraints excluded: chain M residue 14 ILE Chi-restraints excluded: chain M residue 19 MET Chi-restraints excluded: chain M residue 25 LYS Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 75 SER Chi-restraints excluded: chain M residue 128 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 38 optimal weight: 7.9990 chunk 227 optimal weight: 3.9990 chunk 166 optimal weight: 3.9990 chunk 215 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 chunk 255 optimal weight: 0.9990 chunk 172 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 177 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 189 optimal weight: 0.4980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 GLN C 166 ASN ** C 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 241 GLN ** H 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 ASN ** K 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.054301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2438 r_free = 0.2438 target = 0.042921 restraints weight = 83798.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2477 r_free = 0.2477 target = 0.044418 restraints weight = 33371.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2503 r_free = 0.2503 target = 0.045395 restraints weight = 18268.192| |-----------------------------------------------------------------------------| r_work (final): 0.2497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 24556 Z= 0.161 Angle : 0.578 12.815 33376 Z= 0.309 Chirality : 0.045 0.152 3909 Planarity : 0.004 0.051 4265 Dihedral : 4.377 19.447 3335 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.56 % Favored : 96.05 % Rotamer: Outliers : 3.04 % Allowed : 20.48 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.14), residues: 3117 helix: 1.50 (0.25), residues: 528 sheet: -0.00 (0.29), residues: 315 loop : -1.58 (0.11), residues: 2274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 103 HIS 0.004 0.001 HIS G 293 PHE 0.010 0.001 PHE E 282 TYR 0.013 0.001 TYR C 47 ARG 0.011 0.000 ARG B 309 Details of bonding type rmsd hydrogen bonds : bond 0.04263 ( 743) hydrogen bonds : angle 5.32920 ( 2118) covalent geometry : bond 0.00356 (24556) covalent geometry : angle 0.57816 (33376) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 433 time to evaluate : 4.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 GLN cc_start: 0.8766 (tm-30) cc_final: 0.8486 (tm-30) REVERT: B 37 GLN cc_start: 0.8629 (tp40) cc_final: 0.8376 (tp40) REVERT: B 98 ASP cc_start: 0.8957 (OUTLIER) cc_final: 0.8592 (t0) REVERT: B 246 GLU cc_start: 0.8373 (mp0) cc_final: 0.7760 (mp0) REVERT: C 104 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8572 (mt-10) REVERT: D 65 GLU cc_start: 0.9374 (OUTLIER) cc_final: 0.9097 (tt0) REVERT: D 130 ARG cc_start: 0.9399 (ttm170) cc_final: 0.7253 (ppt170) REVERT: D 272 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.8430 (tmm) REVERT: D 306 THR cc_start: 0.9083 (OUTLIER) cc_final: 0.8857 (p) REVERT: E 63 THR cc_start: 0.9756 (OUTLIER) cc_final: 0.9327 (p) REVERT: E 160 LYS cc_start: 0.9543 (mtmt) cc_final: 0.9182 (mttt) REVERT: E 201 GLU cc_start: 0.8969 (tt0) cc_final: 0.8769 (tm-30) REVERT: E 230 THR cc_start: 0.9444 (OUTLIER) cc_final: 0.9131 (p) REVERT: F 209 ARG cc_start: 0.8243 (mtt-85) cc_final: 0.7939 (mtt-85) REVERT: G 31 MET cc_start: 0.7533 (mmm) cc_final: 0.7321 (mmm) REVERT: G 64 THR cc_start: 0.9827 (OUTLIER) cc_final: 0.9577 (p) REVERT: G 254 GLU cc_start: 0.9241 (OUTLIER) cc_final: 0.9017 (mt-10) REVERT: N 36 GLU cc_start: 0.9304 (tt0) cc_final: 0.8970 (tm-30) REVERT: N 62 LEU cc_start: 0.9262 (tp) cc_final: 0.8995 (tp) REVERT: N 106 SER cc_start: 0.9073 (t) cc_final: 0.8769 (p) REVERT: N 119 LYS cc_start: 0.9114 (mmmm) cc_final: 0.8805 (mmmm) REVERT: N 155 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8915 (mt) REVERT: H 71 GLU cc_start: 0.7905 (mp0) cc_final: 0.7531 (mp0) REVERT: H 81 GLU cc_start: 0.9002 (mt-10) cc_final: 0.8736 (mt-10) REVERT: I 66 THR cc_start: 0.9515 (OUTLIER) cc_final: 0.9095 (p) REVERT: I 90 ASP cc_start: 0.8655 (t0) cc_final: 0.8297 (m-30) REVERT: I 97 MET cc_start: 0.9627 (ttm) cc_final: 0.9365 (ttt) REVERT: I 154 GLN cc_start: 0.9246 (OUTLIER) cc_final: 0.8673 (tp40) REVERT: K 3 GLN cc_start: 0.8117 (pp30) cc_final: 0.7838 (pp30) REVERT: K 85 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.8410 (pt0) REVERT: K 144 LYS cc_start: 0.9611 (ttpt) cc_final: 0.9291 (ttpp) REVERT: L 3 GLN cc_start: 0.8404 (mm-40) cc_final: 0.8136 (mm-40) REVERT: L 81 ASN cc_start: 0.8912 (m-40) cc_final: 0.8592 (m-40) REVERT: M 36 GLU cc_start: 0.8915 (pt0) cc_final: 0.8279 (pm20) REVERT: M 60 LYS cc_start: 0.9343 (tttt) cc_final: 0.8882 (tttp) REVERT: M 144 LYS cc_start: 0.9379 (ttmm) cc_final: 0.8835 (ttmm) outliers start: 80 outliers final: 44 residues processed: 487 average time/residue: 0.4186 time to fit residues: 328.2734 Evaluate side-chains 464 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 408 time to evaluate : 3.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 311 MET Chi-restraints excluded: chain D residue 65 GLU Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain D residue 302 CYS Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain F residue 76 MET Chi-restraints excluded: chain F residue 222 VAL Chi-restraints excluded: chain F residue 302 CYS Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 254 GLU Chi-restraints excluded: chain N residue 155 LEU Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 154 GLN Chi-restraints excluded: chain I residue 158 LEU Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain K residue 19 MET Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 66 THR Chi-restraints excluded: chain K residue 85 GLN Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 120 LEU Chi-restraints excluded: chain K residue 128 SER Chi-restraints excluded: chain K residue 155 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 36 GLU Chi-restraints excluded: chain M residue 4 ILE Chi-restraints excluded: chain M residue 19 MET Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 67 THR Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 75 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 122 optimal weight: 0.0870 chunk 137 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 283 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 278 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 162 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 307 optimal weight: 8.9990 overall best weight: 1.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 241 GLN ** H 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 HIS K 27 ASN ** K 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.054569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2448 r_free = 0.2448 target = 0.043208 restraints weight = 83271.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2487 r_free = 0.2487 target = 0.044708 restraints weight = 33109.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2513 r_free = 0.2513 target = 0.045693 restraints weight = 18057.761| |-----------------------------------------------------------------------------| r_work (final): 0.2506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24556 Z= 0.147 Angle : 0.568 11.110 33376 Z= 0.303 Chirality : 0.045 0.154 3909 Planarity : 0.004 0.049 4265 Dihedral : 4.287 20.910 3335 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.59 % Favored : 96.02 % Rotamer: Outliers : 3.23 % Allowed : 20.78 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.14), residues: 3117 helix: 1.61 (0.25), residues: 528 sheet: -0.15 (0.30), residues: 290 loop : -1.49 (0.11), residues: 2299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 103 HIS 0.004 0.001 HIS B 293 PHE 0.010 0.001 PHE C 109 TYR 0.011 0.001 TYR A 115 ARG 0.006 0.000 ARG D 209 Details of bonding type rmsd hydrogen bonds : bond 0.03960 ( 743) hydrogen bonds : angle 5.13307 ( 2118) covalent geometry : bond 0.00324 (24556) covalent geometry : angle 0.56783 (33376) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 423 time to evaluate : 2.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 THR cc_start: 0.8502 (OUTLIER) cc_final: 0.8277 (m) REVERT: B 98 ASP cc_start: 0.8965 (OUTLIER) cc_final: 0.8609 (t0) REVERT: B 212 ASN cc_start: 0.9471 (m-40) cc_final: 0.9128 (m-40) REVERT: B 246 GLU cc_start: 0.8334 (mp0) cc_final: 0.7690 (mp0) REVERT: C 104 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8547 (mt-10) REVERT: C 269 LYS cc_start: 0.9482 (OUTLIER) cc_final: 0.8801 (tttp) REVERT: C 272 MET cc_start: 0.9369 (tpp) cc_final: 0.8964 (tpt) REVERT: D 45 GLN cc_start: 0.9054 (mm110) cc_final: 0.8719 (mm110) REVERT: D 65 GLU cc_start: 0.9357 (OUTLIER) cc_final: 0.9091 (tt0) REVERT: D 272 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8432 (tmm) REVERT: D 306 THR cc_start: 0.9132 (OUTLIER) cc_final: 0.8909 (p) REVERT: E 63 THR cc_start: 0.9757 (OUTLIER) cc_final: 0.9323 (p) REVERT: E 160 LYS cc_start: 0.9536 (mtmt) cc_final: 0.9202 (mttt) REVERT: E 171 THR cc_start: 0.9557 (OUTLIER) cc_final: 0.9009 (p) REVERT: F 209 ARG cc_start: 0.8249 (mtt-85) cc_final: 0.7964 (mtt-85) REVERT: G 31 MET cc_start: 0.7572 (mmm) cc_final: 0.7175 (mmm) REVERT: G 64 THR cc_start: 0.9826 (OUTLIER) cc_final: 0.9595 (p) REVERT: G 230 THR cc_start: 0.9063 (OUTLIER) cc_final: 0.8852 (p) REVERT: G 254 GLU cc_start: 0.9227 (OUTLIER) cc_final: 0.9010 (mt-10) REVERT: N 36 GLU cc_start: 0.9302 (tt0) cc_final: 0.9014 (tm-30) REVERT: N 60 LYS cc_start: 0.9068 (ttmm) cc_final: 0.8288 (ttpp) REVERT: N 62 LEU cc_start: 0.9264 (tp) cc_final: 0.8995 (tp) REVERT: N 106 SER cc_start: 0.9057 (t) cc_final: 0.8802 (p) REVERT: N 119 LYS cc_start: 0.9134 (mmmm) cc_final: 0.8868 (mmmm) REVERT: H 71 GLU cc_start: 0.7886 (mp0) cc_final: 0.7452 (mp0) REVERT: I 66 THR cc_start: 0.9533 (OUTLIER) cc_final: 0.9118 (p) REVERT: I 97 MET cc_start: 0.9630 (ttm) cc_final: 0.9351 (ttt) REVERT: I 154 GLN cc_start: 0.9206 (OUTLIER) cc_final: 0.8704 (tp40) REVERT: K 9 GLN cc_start: 0.9281 (tm-30) cc_final: 0.8542 (tp-100) REVERT: K 144 LYS cc_start: 0.9600 (ttpt) cc_final: 0.9281 (ttpp) REVERT: K 154 GLN cc_start: 0.9179 (OUTLIER) cc_final: 0.8519 (tp40) REVERT: L 3 GLN cc_start: 0.8430 (mm-40) cc_final: 0.8134 (mm-40) REVERT: L 81 ASN cc_start: 0.8874 (m-40) cc_final: 0.8531 (m-40) REVERT: M 36 GLU cc_start: 0.8919 (pt0) cc_final: 0.8220 (pm20) REVERT: M 49 GLN cc_start: 0.9317 (tt0) cc_final: 0.9022 (tm-30) REVERT: M 51 GLN cc_start: 0.9134 (mt0) cc_final: 0.8359 (mt0) REVERT: M 60 LYS cc_start: 0.9321 (tttt) cc_final: 0.8763 (tttp) REVERT: M 119 LYS cc_start: 0.9413 (mmtp) cc_final: 0.9189 (mmmm) REVERT: M 144 LYS cc_start: 0.9375 (ttmm) cc_final: 0.8811 (ttmm) outliers start: 85 outliers final: 56 residues processed: 479 average time/residue: 0.3283 time to fit residues: 253.8208 Evaluate side-chains 480 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 410 time to evaluate : 2.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 269 LYS Chi-restraints excluded: chain C residue 311 MET Chi-restraints excluded: chain D residue 65 GLU Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain D residue 302 CYS Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain F residue 76 MET Chi-restraints excluded: chain F residue 222 VAL Chi-restraints excluded: chain F residue 298 CYS Chi-restraints excluded: chain F residue 302 CYS Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 223 LEU Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 254 GLU Chi-restraints excluded: chain N residue 66 THR Chi-restraints excluded: chain N residue 87 ILE Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 134 THR Chi-restraints excluded: chain I residue 154 GLN Chi-restraints excluded: chain I residue 158 LEU Chi-restraints excluded: chain J residue 4 ILE Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain J residue 66 THR Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain K residue 19 MET Chi-restraints excluded: chain K residue 66 THR Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 120 LEU Chi-restraints excluded: chain K residue 128 SER Chi-restraints excluded: chain K residue 154 GLN Chi-restraints excluded: chain K residue 155 LEU Chi-restraints excluded: chain L residue 19 MET Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 36 GLU Chi-restraints excluded: chain M residue 14 ILE Chi-restraints excluded: chain M residue 19 MET Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 75 SER Chi-restraints excluded: chain M residue 81 ASN Chi-restraints excluded: chain M residue 128 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 200 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 216 optimal weight: 0.0000 chunk 224 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 118 optimal weight: 8.9990 chunk 229 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 195 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 overall best weight: 2.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 241 GLN D 288 GLN F 241 GLN ** H 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 ASN ** K 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 85 GLN M 84 ASN M 85 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.053639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2422 r_free = 0.2422 target = 0.042294 restraints weight = 83166.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2462 r_free = 0.2462 target = 0.043773 restraints weight = 33311.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2488 r_free = 0.2488 target = 0.044741 restraints weight = 18295.133| |-----------------------------------------------------------------------------| r_work (final): 0.2484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 24556 Z= 0.185 Angle : 0.588 10.850 33376 Z= 0.314 Chirality : 0.045 0.158 3909 Planarity : 0.004 0.048 4265 Dihedral : 4.300 19.640 3335 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.85 % Favored : 95.77 % Rotamer: Outliers : 3.69 % Allowed : 20.63 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.14), residues: 3117 helix: 1.60 (0.25), residues: 535 sheet: 0.07 (0.29), residues: 305 loop : -1.50 (0.11), residues: 2277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 103 HIS 0.005 0.001 HIS H 133 PHE 0.011 0.001 PHE C 109 TYR 0.013 0.001 TYR F 47 ARG 0.009 0.000 ARG B 309 Details of bonding type rmsd hydrogen bonds : bond 0.04293 ( 743) hydrogen bonds : angle 5.09101 ( 2118) covalent geometry : bond 0.00418 (24556) covalent geometry : angle 0.58773 (33376) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 409 time to evaluate : 3.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 THR cc_start: 0.8567 (OUTLIER) cc_final: 0.8313 (m) REVERT: B 98 ASP cc_start: 0.9028 (OUTLIER) cc_final: 0.8697 (t0) REVERT: B 246 GLU cc_start: 0.8332 (mp0) cc_final: 0.7995 (mp0) REVERT: B 309 ARG cc_start: 0.8894 (mmp80) cc_final: 0.8660 (mmp80) REVERT: C 104 GLU cc_start: 0.8847 (mt-10) cc_final: 0.8526 (mt-10) REVERT: C 241 GLN cc_start: 0.9030 (mm-40) cc_final: 0.8801 (mm110) REVERT: C 269 LYS cc_start: 0.9496 (OUTLIER) cc_final: 0.8978 (tttp) REVERT: C 270 ASN cc_start: 0.8944 (t0) cc_final: 0.8710 (t0) REVERT: D 65 GLU cc_start: 0.9366 (OUTLIER) cc_final: 0.9102 (tt0) REVERT: D 272 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.8286 (tmm) REVERT: D 306 THR cc_start: 0.9121 (OUTLIER) cc_final: 0.8892 (p) REVERT: E 63 THR cc_start: 0.9758 (OUTLIER) cc_final: 0.9309 (p) REVERT: E 160 LYS cc_start: 0.9550 (mtmt) cc_final: 0.9191 (mttt) REVERT: E 171 THR cc_start: 0.9569 (OUTLIER) cc_final: 0.9019 (p) REVERT: F 209 ARG cc_start: 0.8271 (mtt-85) cc_final: 0.7987 (mtt-85) REVERT: F 283 ASN cc_start: 0.8728 (t0) cc_final: 0.8521 (t0) REVERT: G 31 MET cc_start: 0.7578 (mmm) cc_final: 0.7362 (mmm) REVERT: G 64 THR cc_start: 0.9807 (OUTLIER) cc_final: 0.9585 (p) REVERT: G 230 THR cc_start: 0.9098 (OUTLIER) cc_final: 0.8888 (p) REVERT: G 254 GLU cc_start: 0.9245 (OUTLIER) cc_final: 0.9018 (mt-10) REVERT: N 36 GLU cc_start: 0.9319 (tt0) cc_final: 0.8943 (tm-30) REVERT: N 62 LEU cc_start: 0.9311 (tp) cc_final: 0.9054 (tp) REVERT: N 106 SER cc_start: 0.9071 (t) cc_final: 0.8819 (p) REVERT: N 119 LYS cc_start: 0.9128 (mmmm) cc_final: 0.8858 (mmmm) REVERT: H 71 GLU cc_start: 0.7626 (mp0) cc_final: 0.7110 (mp0) REVERT: H 81 GLU cc_start: 0.8962 (mt-10) cc_final: 0.8742 (mt-10) REVERT: I 60 LYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8697 (ttmm) REVERT: I 66 THR cc_start: 0.9507 (OUTLIER) cc_final: 0.9099 (p) REVERT: I 90 ASP cc_start: 0.8677 (t0) cc_final: 0.8237 (m-30) REVERT: I 97 MET cc_start: 0.9642 (ttm) cc_final: 0.9385 (ttt) REVERT: I 154 GLN cc_start: 0.9225 (OUTLIER) cc_final: 0.8762 (tp40) REVERT: K 3 GLN cc_start: 0.8177 (pp30) cc_final: 0.7950 (pp30) REVERT: K 27 ASN cc_start: 0.9410 (OUTLIER) cc_final: 0.8857 (t0) REVERT: K 85 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.8370 (pt0) REVERT: K 154 GLN cc_start: 0.9207 (OUTLIER) cc_final: 0.8527 (tp40) REVERT: L 154 GLN cc_start: 0.9234 (OUTLIER) cc_final: 0.8388 (tt0) REVERT: M 36 GLU cc_start: 0.8913 (pt0) cc_final: 0.8498 (pm20) REVERT: M 49 GLN cc_start: 0.9360 (tt0) cc_final: 0.8900 (tm-30) REVERT: M 51 GLN cc_start: 0.9153 (mt0) cc_final: 0.8385 (mt0) REVERT: M 60 LYS cc_start: 0.9307 (tttt) cc_final: 0.9016 (tttp) REVERT: M 84 ASN cc_start: 0.9304 (t0) cc_final: 0.9004 (t0) REVERT: M 85 GLN cc_start: 0.7672 (OUTLIER) cc_final: 0.7074 (mm-40) REVERT: M 107 LYS cc_start: 0.9244 (mtpt) cc_final: 0.8886 (mtpt) REVERT: M 144 LYS cc_start: 0.9377 (ttmm) cc_final: 0.9036 (ttmm) outliers start: 97 outliers final: 61 residues processed: 474 average time/residue: 0.3904 time to fit residues: 298.0086 Evaluate side-chains 480 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 400 time to evaluate : 2.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 269 LYS Chi-restraints excluded: chain C residue 311 MET Chi-restraints excluded: chain D residue 65 GLU Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain D residue 302 CYS Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain F residue 76 MET Chi-restraints excluded: chain F residue 222 VAL Chi-restraints excluded: chain F residue 298 CYS Chi-restraints excluded: chain F residue 302 CYS Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 223 LEU Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 254 GLU Chi-restraints excluded: chain N residue 10 ARG Chi-restraints excluded: chain N residue 66 THR Chi-restraints excluded: chain N residue 87 ILE Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 134 THR Chi-restraints excluded: chain I residue 154 GLN Chi-restraints excluded: chain I residue 158 LEU Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain J residue 66 THR Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain K residue 19 MET Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 66 THR Chi-restraints excluded: chain K residue 85 GLN Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 128 SER Chi-restraints excluded: chain K residue 154 GLN Chi-restraints excluded: chain K residue 155 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 19 MET Chi-restraints excluded: chain L residue 36 GLU Chi-restraints excluded: chain L residue 113 THR Chi-restraints excluded: chain L residue 154 GLN Chi-restraints excluded: chain M residue 14 ILE Chi-restraints excluded: chain M residue 19 MET Chi-restraints excluded: chain M residue 67 THR Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 75 SER Chi-restraints excluded: chain M residue 85 GLN Chi-restraints excluded: chain M residue 128 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 87 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 222 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 244 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 283 optimal weight: 1.9990 chunk 281 optimal weight: 6.9990 chunk 92 optimal weight: 9.9990 chunk 58 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 144 HIS F 207 GLN ** H 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 ASN ** K 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 81 ASN ** L 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.052816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2400 r_free = 0.2400 target = 0.041473 restraints weight = 84483.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2439 r_free = 0.2439 target = 0.042932 restraints weight = 33960.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2465 r_free = 0.2465 target = 0.043885 restraints weight = 18729.826| |-----------------------------------------------------------------------------| r_work (final): 0.2460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8965 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 24556 Z= 0.246 Angle : 0.626 11.027 33376 Z= 0.334 Chirality : 0.046 0.168 3909 Planarity : 0.004 0.048 4265 Dihedral : 4.411 19.811 3335 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.27 % Favored : 95.35 % Rotamer: Outliers : 3.69 % Allowed : 21.16 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.14), residues: 3117 helix: 1.56 (0.25), residues: 536 sheet: -0.03 (0.29), residues: 305 loop : -1.51 (0.12), residues: 2276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 103 HIS 0.006 0.001 HIS G 293 PHE 0.012 0.001 PHE C 109 TYR 0.012 0.001 TYR G 90 ARG 0.006 0.000 ARG B 309 Details of bonding type rmsd hydrogen bonds : bond 0.04652 ( 743) hydrogen bonds : angle 5.16225 ( 2118) covalent geometry : bond 0.00566 (24556) covalent geometry : angle 0.62638 (33376) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 400 time to evaluate : 3.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 MET cc_start: 0.8781 (mmm) cc_final: 0.8405 (mmt) REVERT: A 261 THR cc_start: 0.8656 (OUTLIER) cc_final: 0.8411 (m) REVERT: B 31 MET cc_start: 0.8941 (mtt) cc_final: 0.8601 (mtt) REVERT: B 246 GLU cc_start: 0.8386 (mp0) cc_final: 0.7986 (mp0) REVERT: C 31 MET cc_start: 0.9024 (mmt) cc_final: 0.7072 (ptt) REVERT: C 104 GLU cc_start: 0.8863 (mt-10) cc_final: 0.8525 (mt-10) REVERT: C 241 GLN cc_start: 0.9159 (mm-40) cc_final: 0.8874 (mm110) REVERT: C 269 LYS cc_start: 0.9502 (OUTLIER) cc_final: 0.8896 (tttp) REVERT: C 270 ASN cc_start: 0.9074 (t0) cc_final: 0.8761 (t0) REVERT: C 272 MET cc_start: 0.9447 (tpt) cc_final: 0.9006 (mmm) REVERT: D 65 GLU cc_start: 0.9375 (OUTLIER) cc_final: 0.9111 (tt0) REVERT: D 272 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.8283 (tmm) REVERT: D 306 THR cc_start: 0.9145 (OUTLIER) cc_final: 0.8920 (p) REVERT: E 63 THR cc_start: 0.9756 (OUTLIER) cc_final: 0.9301 (p) REVERT: E 160 LYS cc_start: 0.9565 (mtmt) cc_final: 0.9235 (mttt) REVERT: E 171 THR cc_start: 0.9586 (OUTLIER) cc_final: 0.9040 (p) REVERT: E 230 THR cc_start: 0.9420 (OUTLIER) cc_final: 0.9113 (p) REVERT: F 209 ARG cc_start: 0.8273 (mtt-85) cc_final: 0.7998 (mtt-85) REVERT: F 283 ASN cc_start: 0.8768 (t0) cc_final: 0.8498 (t0) REVERT: G 31 MET cc_start: 0.7610 (mmm) cc_final: 0.7390 (mmm) REVERT: G 230 THR cc_start: 0.9139 (OUTLIER) cc_final: 0.8923 (p) REVERT: G 254 GLU cc_start: 0.9261 (OUTLIER) cc_final: 0.8740 (tt0) REVERT: N 36 GLU cc_start: 0.9306 (tt0) cc_final: 0.8950 (tm-30) REVERT: N 62 LEU cc_start: 0.9338 (tp) cc_final: 0.9079 (tp) REVERT: N 119 LYS cc_start: 0.9130 (mmmm) cc_final: 0.8852 (mmmm) REVERT: N 155 LEU cc_start: 0.9202 (mt) cc_final: 0.8976 (mt) REVERT: H 71 GLU cc_start: 0.7640 (mp0) cc_final: 0.7104 (mp0) REVERT: I 60 LYS cc_start: 0.9148 (OUTLIER) cc_final: 0.8738 (ttmm) REVERT: I 66 THR cc_start: 0.9504 (OUTLIER) cc_final: 0.9094 (p) REVERT: I 90 ASP cc_start: 0.8590 (t0) cc_final: 0.8218 (m-30) REVERT: I 97 MET cc_start: 0.9658 (ttm) cc_final: 0.9422 (ttt) REVERT: K 9 GLN cc_start: 0.9285 (tm-30) cc_final: 0.8532 (tp-100) REVERT: K 27 ASN cc_start: 0.9445 (OUTLIER) cc_final: 0.8790 (t0) REVERT: K 84 ASN cc_start: 0.8845 (t0) cc_final: 0.8276 (t0) REVERT: K 154 GLN cc_start: 0.9239 (OUTLIER) cc_final: 0.8497 (tp40) REVERT: L 3 GLN cc_start: 0.8433 (mm-40) cc_final: 0.8119 (mm-40) REVERT: L 81 ASN cc_start: 0.8719 (m-40) cc_final: 0.8399 (m-40) REVERT: L 154 GLN cc_start: 0.9275 (OUTLIER) cc_final: 0.8390 (tt0) REVERT: M 36 GLU cc_start: 0.9012 (pt0) cc_final: 0.8530 (pm20) REVERT: M 60 LYS cc_start: 0.9316 (tttt) cc_final: 0.9017 (tttp) REVERT: M 84 ASN cc_start: 0.9372 (t0) cc_final: 0.9118 (t0) REVERT: M 87 ILE cc_start: 0.9459 (OUTLIER) cc_final: 0.9225 (tp) REVERT: M 104 MET cc_start: 0.8979 (ttp) cc_final: 0.8722 (ttp) REVERT: M 107 LYS cc_start: 0.9300 (mtpt) cc_final: 0.8973 (mtpt) REVERT: M 144 LYS cc_start: 0.9373 (ttmm) cc_final: 0.9025 (ttmm) outliers start: 97 outliers final: 70 residues processed: 468 average time/residue: 0.3818 time to fit residues: 287.0813 Evaluate side-chains 477 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 391 time to evaluate : 2.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 269 LYS Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 311 MET Chi-restraints excluded: chain D residue 65 GLU Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain D residue 298 CYS Chi-restraints excluded: chain D residue 302 CYS Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 184 MET Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain F residue 76 MET Chi-restraints excluded: chain F residue 207 GLN Chi-restraints excluded: chain F residue 222 VAL Chi-restraints excluded: chain F residue 298 CYS Chi-restraints excluded: chain F residue 302 CYS Chi-restraints excluded: chain G residue 223 LEU Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 254 GLU Chi-restraints excluded: chain N residue 10 ARG Chi-restraints excluded: chain N residue 66 THR Chi-restraints excluded: chain N residue 87 ILE Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 134 THR Chi-restraints excluded: chain I residue 158 LEU Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain J residue 66 THR Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain K residue 19 MET Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 66 THR Chi-restraints excluded: chain K residue 81 ASN Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 120 LEU Chi-restraints excluded: chain K residue 128 SER Chi-restraints excluded: chain K residue 154 GLN Chi-restraints excluded: chain K residue 155 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 19 MET Chi-restraints excluded: chain L residue 36 GLU Chi-restraints excluded: chain L residue 66 THR Chi-restraints excluded: chain L residue 113 THR Chi-restraints excluded: chain L residue 154 GLN Chi-restraints excluded: chain M residue 14 ILE Chi-restraints excluded: chain M residue 19 MET Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 67 THR Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 75 SER Chi-restraints excluded: chain M residue 87 ILE Chi-restraints excluded: chain M residue 128 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 4 optimal weight: 0.0570 chunk 286 optimal weight: 8.9990 chunk 150 optimal weight: 4.9990 chunk 266 optimal weight: 0.2980 chunk 50 optimal weight: 0.0970 chunk 229 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 186 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 chunk 283 optimal weight: 7.9990 overall best weight: 1.0900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 207 GLN F 208 HIS ** H 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 ASN K 46 GLN K 81 ASN ** L 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.054393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2446 r_free = 0.2446 target = 0.043092 restraints weight = 82794.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2485 r_free = 0.2485 target = 0.044584 restraints weight = 32900.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2511 r_free = 0.2511 target = 0.045556 restraints weight = 17953.383| |-----------------------------------------------------------------------------| r_work (final): 0.2507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24556 Z= 0.131 Angle : 0.587 11.714 33376 Z= 0.310 Chirality : 0.045 0.151 3909 Planarity : 0.004 0.048 4265 Dihedral : 4.273 20.149 3335 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.46 % Favored : 96.18 % Rotamer: Outliers : 2.74 % Allowed : 22.42 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.14), residues: 3117 helix: 1.73 (0.25), residues: 527 sheet: -0.13 (0.28), residues: 314 loop : -1.44 (0.12), residues: 2276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 103 HIS 0.004 0.001 HIS B 293 PHE 0.013 0.001 PHE C 109 TYR 0.011 0.001 TYR A 115 ARG 0.005 0.000 ARG B 309 Details of bonding type rmsd hydrogen bonds : bond 0.03771 ( 743) hydrogen bonds : angle 4.94174 ( 2118) covalent geometry : bond 0.00286 (24556) covalent geometry : angle 0.58654 (33376) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 417 time to evaluate : 2.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 98 ASP cc_start: 0.8972 (OUTLIER) cc_final: 0.8637 (t0) REVERT: B 246 GLU cc_start: 0.8372 (mp0) cc_final: 0.7975 (mp0) REVERT: C 31 MET cc_start: 0.9151 (mmt) cc_final: 0.7331 (ptt) REVERT: C 104 GLU cc_start: 0.8853 (mt-10) cc_final: 0.8518 (mt-10) REVERT: C 269 LYS cc_start: 0.9514 (OUTLIER) cc_final: 0.9018 (tttp) REVERT: C 270 ASN cc_start: 0.9022 (t0) cc_final: 0.8617 (t0) REVERT: C 309 ARG cc_start: 0.9180 (mmm-85) cc_final: 0.8860 (mmm-85) REVERT: D 45 GLN cc_start: 0.9173 (mm-40) cc_final: 0.8945 (mm-40) REVERT: D 65 GLU cc_start: 0.9379 (OUTLIER) cc_final: 0.9127 (tt0) REVERT: D 116 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.8020 (pp) REVERT: D 272 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.8196 (tmm) REVERT: E 160 LYS cc_start: 0.9568 (mtmt) cc_final: 0.9277 (mttt) REVERT: F 207 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.8408 (mt0) REVERT: F 209 ARG cc_start: 0.8148 (mtt-85) cc_final: 0.7876 (mtt-85) REVERT: F 283 ASN cc_start: 0.8750 (t0) cc_final: 0.8468 (t0) REVERT: G 31 MET cc_start: 0.7605 (mmm) cc_final: 0.7369 (mmm) REVERT: G 100 LEU cc_start: 0.9119 (mp) cc_final: 0.8882 (mp) REVERT: G 230 THR cc_start: 0.9089 (OUTLIER) cc_final: 0.8872 (p) REVERT: G 254 GLU cc_start: 0.9248 (OUTLIER) cc_final: 0.8804 (mm-30) REVERT: N 36 GLU cc_start: 0.9307 (tt0) cc_final: 0.8958 (tm-30) REVERT: N 62 LEU cc_start: 0.9364 (tp) cc_final: 0.9112 (tp) REVERT: N 119 LYS cc_start: 0.9151 (mmmm) cc_final: 0.8896 (mmmm) REVERT: N 155 LEU cc_start: 0.9137 (mt) cc_final: 0.8915 (mt) REVERT: H 71 GLU cc_start: 0.7649 (mp0) cc_final: 0.7124 (mp0) REVERT: I 60 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8732 (ttmm) REVERT: I 66 THR cc_start: 0.9513 (OUTLIER) cc_final: 0.9128 (p) REVERT: I 90 ASP cc_start: 0.8676 (t0) cc_final: 0.8268 (m-30) REVERT: I 97 MET cc_start: 0.9626 (ttm) cc_final: 0.9363 (ttt) REVERT: J 123 ASP cc_start: 0.9306 (t0) cc_final: 0.9048 (t70) REVERT: K 9 GLN cc_start: 0.9397 (tm-30) cc_final: 0.8580 (tp-100) REVERT: K 27 ASN cc_start: 0.9247 (OUTLIER) cc_final: 0.8537 (t0) REVERT: K 84 ASN cc_start: 0.8834 (t0) cc_final: 0.8428 (t0) REVERT: K 154 GLN cc_start: 0.9196 (OUTLIER) cc_final: 0.8564 (tp40) REVERT: L 3 GLN cc_start: 0.8430 (mm-40) cc_final: 0.8115 (mm-40) REVERT: L 22 ASP cc_start: 0.7681 (m-30) cc_final: 0.7346 (t0) REVERT: L 81 ASN cc_start: 0.8651 (m-40) cc_final: 0.8369 (m-40) REVERT: L 154 GLN cc_start: 0.9208 (OUTLIER) cc_final: 0.8310 (tt0) REVERT: M 36 GLU cc_start: 0.9028 (pt0) cc_final: 0.8629 (pm20) REVERT: M 60 LYS cc_start: 0.9288 (tttt) cc_final: 0.9011 (tttp) REVERT: M 84 ASN cc_start: 0.9352 (t0) cc_final: 0.9053 (t0) REVERT: M 104 MET cc_start: 0.8830 (ttp) cc_final: 0.8572 (ttp) REVERT: M 107 LYS cc_start: 0.9365 (mtpt) cc_final: 0.9037 (mtpt) REVERT: M 144 LYS cc_start: 0.9360 (ttmm) cc_final: 0.9008 (ttmm) outliers start: 72 outliers final: 46 residues processed: 465 average time/residue: 0.3461 time to fit residues: 256.7383 Evaluate side-chains 462 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 403 time to evaluate : 2.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 269 LYS Chi-restraints excluded: chain D residue 65 GLU Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 184 MET Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain F residue 207 GLN Chi-restraints excluded: chain F residue 227 MET Chi-restraints excluded: chain F residue 298 CYS Chi-restraints excluded: chain F residue 302 CYS Chi-restraints excluded: chain G residue 223 LEU Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 254 GLU Chi-restraints excluded: chain N residue 10 ARG Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 158 LEU Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 66 THR Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain K residue 19 MET Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 66 THR Chi-restraints excluded: chain K residue 81 ASN Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 120 LEU Chi-restraints excluded: chain K residue 128 SER Chi-restraints excluded: chain K residue 154 GLN Chi-restraints excluded: chain K residue 155 LEU Chi-restraints excluded: chain L residue 36 GLU Chi-restraints excluded: chain L residue 66 THR Chi-restraints excluded: chain L residue 154 GLN Chi-restraints excluded: chain M residue 14 ILE Chi-restraints excluded: chain M residue 19 MET Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 75 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 60 optimal weight: 8.9990 chunk 273 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 255 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 chunk 138 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 199 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 195 GLN C 241 GLN F 207 GLN ** H 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 ASN K 81 ASN K 83 GLN ** L 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.053345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2418 r_free = 0.2418 target = 0.042040 restraints weight = 84147.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2457 r_free = 0.2457 target = 0.043498 restraints weight = 33501.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2483 r_free = 0.2483 target = 0.044458 restraints weight = 18406.809| |-----------------------------------------------------------------------------| r_work (final): 0.2478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 24556 Z= 0.201 Angle : 0.623 12.159 33376 Z= 0.329 Chirality : 0.045 0.176 3909 Planarity : 0.004 0.047 4265 Dihedral : 4.324 21.334 3335 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.27 % Favored : 95.38 % Rotamer: Outliers : 3.04 % Allowed : 22.34 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.14), residues: 3117 helix: 1.70 (0.25), residues: 529 sheet: -0.08 (0.29), residues: 299 loop : -1.48 (0.11), residues: 2289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 103 HIS 0.007 0.001 HIS B 159 PHE 0.014 0.001 PHE C 109 TYR 0.019 0.001 TYR C 237 ARG 0.009 0.000 ARG B 309 Details of bonding type rmsd hydrogen bonds : bond 0.04258 ( 743) hydrogen bonds : angle 5.01002 ( 2118) covalent geometry : bond 0.00461 (24556) covalent geometry : angle 0.62290 (33376) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 390 time to evaluate : 2.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 98 ASP cc_start: 0.9032 (OUTLIER) cc_final: 0.8715 (t0) REVERT: B 246 GLU cc_start: 0.8396 (mp0) cc_final: 0.8023 (mp0) REVERT: C 31 MET cc_start: 0.9135 (mmt) cc_final: 0.7457 (ptt) REVERT: C 104 GLU cc_start: 0.8871 (mt-10) cc_final: 0.8527 (mt-10) REVERT: C 241 GLN cc_start: 0.9553 (mm110) cc_final: 0.9159 (mm110) REVERT: C 270 ASN cc_start: 0.9104 (t0) cc_final: 0.8699 (t0) REVERT: D 65 GLU cc_start: 0.9382 (OUTLIER) cc_final: 0.9130 (tt0) REVERT: D 272 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8208 (tmm) REVERT: D 306 THR cc_start: 0.9122 (OUTLIER) cc_final: 0.8888 (p) REVERT: E 63 THR cc_start: 0.9764 (OUTLIER) cc_final: 0.9318 (p) REVERT: E 160 LYS cc_start: 0.9553 (mtmt) cc_final: 0.9246 (mttt) REVERT: E 171 THR cc_start: 0.9581 (OUTLIER) cc_final: 0.9045 (p) REVERT: F 207 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.8526 (mt0) REVERT: F 209 ARG cc_start: 0.8189 (mtt-85) cc_final: 0.7915 (mtt-85) REVERT: F 283 ASN cc_start: 0.8794 (t0) cc_final: 0.8486 (t0) REVERT: G 31 MET cc_start: 0.7649 (mmm) cc_final: 0.7411 (mmm) REVERT: G 100 LEU cc_start: 0.9105 (mp) cc_final: 0.8895 (mp) REVERT: G 230 THR cc_start: 0.9127 (OUTLIER) cc_final: 0.8904 (p) REVERT: G 254 GLU cc_start: 0.9250 (OUTLIER) cc_final: 0.8762 (tt0) REVERT: N 36 GLU cc_start: 0.9303 (tt0) cc_final: 0.8944 (tm-30) REVERT: N 62 LEU cc_start: 0.9357 (tp) cc_final: 0.9093 (tp) REVERT: N 119 LYS cc_start: 0.9145 (mmmm) cc_final: 0.8897 (mmmm) REVERT: H 71 GLU cc_start: 0.7670 (mp0) cc_final: 0.7097 (mp0) REVERT: I 60 LYS cc_start: 0.9146 (OUTLIER) cc_final: 0.8747 (ttmm) REVERT: I 66 THR cc_start: 0.9509 (OUTLIER) cc_final: 0.9101 (p) REVERT: I 90 ASP cc_start: 0.8666 (t0) cc_final: 0.8313 (m-30) REVERT: I 97 MET cc_start: 0.9641 (ttm) cc_final: 0.9387 (ttt) REVERT: K 27 ASN cc_start: 0.9163 (OUTLIER) cc_final: 0.8496 (t0) REVERT: K 83 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.8213 (tm-30) REVERT: K 84 ASN cc_start: 0.8833 (t0) cc_final: 0.8409 (t0) REVERT: K 154 GLN cc_start: 0.9226 (OUTLIER) cc_final: 0.8592 (tp40) REVERT: L 81 ASN cc_start: 0.8689 (m-40) cc_final: 0.8437 (m-40) REVERT: L 154 GLN cc_start: 0.9228 (OUTLIER) cc_final: 0.8357 (tt0) REVERT: M 36 GLU cc_start: 0.9051 (pt0) cc_final: 0.8633 (pm20) REVERT: M 60 LYS cc_start: 0.9295 (tttt) cc_final: 0.9075 (tttp) REVERT: M 84 ASN cc_start: 0.9358 (t0) cc_final: 0.9061 (t0) REVERT: M 89 GLU cc_start: 0.8809 (tt0) cc_final: 0.8585 (tm-30) REVERT: M 104 MET cc_start: 0.8875 (ttp) cc_final: 0.8612 (ttp) REVERT: M 107 LYS cc_start: 0.9359 (mtpt) cc_final: 0.9035 (mtpt) REVERT: M 144 LYS cc_start: 0.9380 (ttmm) cc_final: 0.9032 (ttmm) outliers start: 80 outliers final: 59 residues processed: 444 average time/residue: 0.3212 time to fit residues: 228.3519 Evaluate side-chains 464 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 390 time to evaluate : 3.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 184 MET Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain D residue 65 GLU Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain D residue 298 CYS Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 184 MET Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain F residue 207 GLN Chi-restraints excluded: chain F residue 227 MET Chi-restraints excluded: chain F residue 298 CYS Chi-restraints excluded: chain F residue 302 CYS Chi-restraints excluded: chain G residue 223 LEU Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 254 GLU Chi-restraints excluded: chain N residue 10 ARG Chi-restraints excluded: chain N residue 66 THR Chi-restraints excluded: chain N residue 87 ILE Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 158 LEU Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 62 LEU Chi-restraints excluded: chain J residue 66 THR Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain K residue 19 MET Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 66 THR Chi-restraints excluded: chain K residue 81 ASN Chi-restraints excluded: chain K residue 83 GLN Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 120 LEU Chi-restraints excluded: chain K residue 128 SER Chi-restraints excluded: chain K residue 144 LYS Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain K residue 154 GLN Chi-restraints excluded: chain K residue 155 LEU Chi-restraints excluded: chain L residue 36 GLU Chi-restraints excluded: chain L residue 66 THR Chi-restraints excluded: chain L residue 113 THR Chi-restraints excluded: chain L residue 154 GLN Chi-restraints excluded: chain M residue 14 ILE Chi-restraints excluded: chain M residue 19 MET Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 75 SER Chi-restraints excluded: chain M residue 128 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 306 optimal weight: 4.9990 chunk 165 optimal weight: 0.3980 chunk 252 optimal weight: 1.9990 chunk 245 optimal weight: 1.9990 chunk 233 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 193 optimal weight: 4.9990 chunk 289 optimal weight: 0.9990 chunk 241 optimal weight: 0.2980 chunk 104 optimal weight: 1.9990 chunk 180 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 195 GLN E 207 GLN F 207 GLN ** H 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 ASN K 81 ASN K 83 GLN ** L 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.054506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2450 r_free = 0.2450 target = 0.043218 restraints weight = 82881.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2489 r_free = 0.2489 target = 0.044709 restraints weight = 32851.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2515 r_free = 0.2515 target = 0.045675 restraints weight = 17925.851| |-----------------------------------------------------------------------------| r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24556 Z= 0.130 Angle : 0.610 12.883 33376 Z= 0.321 Chirality : 0.045 0.172 3909 Planarity : 0.004 0.047 4265 Dihedral : 4.239 21.146 3335 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.85 % Favored : 95.80 % Rotamer: Outliers : 2.47 % Allowed : 23.06 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.14), residues: 3117 helix: 1.79 (0.25), residues: 527 sheet: -0.10 (0.28), residues: 314 loop : -1.44 (0.12), residues: 2276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 103 HIS 0.006 0.001 HIS B 159 PHE 0.013 0.001 PHE C 109 TYR 0.020 0.001 TYR C 237 ARG 0.009 0.000 ARG B 309 Details of bonding type rmsd hydrogen bonds : bond 0.03713 ( 743) hydrogen bonds : angle 4.88704 ( 2118) covalent geometry : bond 0.00288 (24556) covalent geometry : angle 0.60987 (33376) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6234 Ramachandran restraints generated. 3117 Oldfield, 0 Emsley, 3117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 410 time to evaluate : 2.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 TYR cc_start: 0.8818 (m-10) cc_final: 0.8600 (m-10) REVERT: B 98 ASP cc_start: 0.8971 (OUTLIER) cc_final: 0.8630 (t0) REVERT: B 246 GLU cc_start: 0.8373 (mp0) cc_final: 0.7985 (mp0) REVERT: B 311 MET cc_start: 0.9340 (mmm) cc_final: 0.8986 (mtt) REVERT: C 31 MET cc_start: 0.9069 (mmt) cc_final: 0.7403 (ptt) REVERT: C 104 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8507 (mt-10) REVERT: C 241 GLN cc_start: 0.9575 (mm110) cc_final: 0.9239 (mm110) REVERT: C 270 ASN cc_start: 0.9065 (t0) cc_final: 0.8349 (t0) REVERT: D 65 GLU cc_start: 0.9379 (OUTLIER) cc_final: 0.8928 (tt0) REVERT: D 272 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.8101 (tmm) REVERT: E 63 THR cc_start: 0.9759 (OUTLIER) cc_final: 0.9320 (p) REVERT: E 160 LYS cc_start: 0.9557 (mtmt) cc_final: 0.9329 (mtmt) REVERT: F 207 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.8610 (mt0) REVERT: F 209 ARG cc_start: 0.8114 (mtt-85) cc_final: 0.7861 (mtt-85) REVERT: F 283 ASN cc_start: 0.8780 (t0) cc_final: 0.8482 (t0) REVERT: G 31 MET cc_start: 0.7581 (mmm) cc_final: 0.7309 (mmm) REVERT: G 100 LEU cc_start: 0.9092 (mp) cc_final: 0.8867 (mp) REVERT: G 230 THR cc_start: 0.9113 (OUTLIER) cc_final: 0.8863 (p) REVERT: G 254 GLU cc_start: 0.9250 (OUTLIER) cc_final: 0.8810 (mm-30) REVERT: N 36 GLU cc_start: 0.9306 (tt0) cc_final: 0.8952 (tm-30) REVERT: N 62 LEU cc_start: 0.9378 (tp) cc_final: 0.9124 (tp) REVERT: N 119 LYS cc_start: 0.9156 (mmmm) cc_final: 0.8915 (mmmm) REVERT: H 71 GLU cc_start: 0.7662 (mp0) cc_final: 0.7090 (mp0) REVERT: I 66 THR cc_start: 0.9522 (OUTLIER) cc_final: 0.9101 (p) REVERT: I 90 ASP cc_start: 0.8676 (t0) cc_final: 0.8360 (m-30) REVERT: I 97 MET cc_start: 0.9622 (ttm) cc_final: 0.9370 (ttt) REVERT: K 27 ASN cc_start: 0.9026 (OUTLIER) cc_final: 0.8587 (t0) REVERT: K 29 ASP cc_start: 0.8837 (m-30) cc_final: 0.8604 (m-30) REVERT: K 36 GLU cc_start: 0.9317 (pt0) cc_final: 0.8964 (pm20) REVERT: K 66 THR cc_start: 0.9342 (OUTLIER) cc_final: 0.8729 (p) REVERT: K 154 GLN cc_start: 0.9202 (OUTLIER) cc_final: 0.8571 (tp40) REVERT: L 22 ASP cc_start: 0.7692 (m-30) cc_final: 0.7337 (t0) REVERT: L 81 ASN cc_start: 0.8637 (m-40) cc_final: 0.8398 (m-40) REVERT: L 123 ASP cc_start: 0.9305 (t0) cc_final: 0.9047 (t0) REVERT: L 154 GLN cc_start: 0.9180 (OUTLIER) cc_final: 0.8222 (tt0) REVERT: M 36 GLU cc_start: 0.9037 (pt0) cc_final: 0.8607 (pm20) REVERT: M 60 LYS cc_start: 0.9315 (tttt) cc_final: 0.9099 (tttp) REVERT: M 84 ASN cc_start: 0.9362 (t0) cc_final: 0.9118 (t0) REVERT: M 89 GLU cc_start: 0.8801 (tt0) cc_final: 0.8558 (tm-30) REVERT: M 104 MET cc_start: 0.8820 (ttp) cc_final: 0.8549 (ttp) REVERT: M 107 LYS cc_start: 0.9365 (mtpt) cc_final: 0.9036 (mtpt) outliers start: 65 outliers final: 48 residues processed: 452 average time/residue: 0.3250 time to fit residues: 235.5486 Evaluate side-chains 461 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 401 time to evaluate : 2.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 105 PHE Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain D residue 65 GLU Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain D residue 298 CYS Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 184 MET Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain F residue 207 GLN Chi-restraints excluded: chain F residue 227 MET Chi-restraints excluded: chain F residue 298 CYS Chi-restraints excluded: chain F residue 302 CYS Chi-restraints excluded: chain G residue 223 LEU Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 254 GLU Chi-restraints excluded: chain N residue 10 ARG Chi-restraints excluded: chain N residue 66 THR Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 158 LEU Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 66 THR Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain K residue 19 MET Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 66 THR Chi-restraints excluded: chain K residue 81 ASN Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 120 LEU Chi-restraints excluded: chain K residue 128 SER Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain K residue 154 GLN Chi-restraints excluded: chain K residue 155 LEU Chi-restraints excluded: chain L residue 36 GLU Chi-restraints excluded: chain L residue 66 THR Chi-restraints excluded: chain L residue 113 THR Chi-restraints excluded: chain L residue 154 GLN Chi-restraints excluded: chain M residue 14 ILE Chi-restraints excluded: chain M residue 19 MET Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 128 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 56 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 173 optimal weight: 0.5980 chunk 29 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 chunk 219 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 208 optimal weight: 6.9990 chunk 90 optimal weight: 0.2980 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 195 GLN F 207 GLN ** H 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 ASN K 81 ASN K 83 GLN ** L 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.052663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2407 r_free = 0.2407 target = 0.041491 restraints weight = 84531.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2445 r_free = 0.2445 target = 0.042891 restraints weight = 34840.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2469 r_free = 0.2469 target = 0.043802 restraints weight = 19423.649| |-----------------------------------------------------------------------------| r_work (final): 0.2468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8994 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 24556 Z= 0.259 Angle : 0.666 11.989 33376 Z= 0.352 Chirality : 0.046 0.207 3909 Planarity : 0.004 0.047 4265 Dihedral : 4.429 20.370 3335 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.65 % Favored : 95.00 % Rotamer: Outliers : 2.74 % Allowed : 23.06 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.14), residues: 3117 helix: 1.70 (0.25), residues: 536 sheet: -0.13 (0.29), residues: 299 loop : -1.54 (0.11), residues: 2282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 136 HIS 0.006 0.001 HIS B 159 PHE 0.012 0.001 PHE C 109 TYR 0.026 0.001 TYR F 47 ARG 0.009 0.001 ARG B 309 Details of bonding type rmsd hydrogen bonds : bond 0.04735 ( 743) hydrogen bonds : angle 5.09759 ( 2118) covalent geometry : bond 0.00598 (24556) covalent geometry : angle 0.66623 (33376) =============================================================================== Job complete usr+sys time: 9647.63 seconds wall clock time: 170 minutes 48.36 seconds (10248.36 seconds total)