Starting phenix.real_space_refine on Fri Sep 19 07:05:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kzj_62664/09_2025/9kzj_62664.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kzj_62664/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9kzj_62664/09_2025/9kzj_62664.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kzj_62664/09_2025/9kzj_62664.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kzj_62664/09_2025/9kzj_62664.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kzj_62664/09_2025/9kzj_62664.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 5.07, per 1000 atoms: 0.21 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: 1.97 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.13 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: 4.26 Time building geometry restraints manager: 2.71 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: 10.330 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: 0.040 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.040 Process input model: 21.620 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.250 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.008 0.000 ARG E 58 TYR 0.011 0.001 TYR A 237 PHE 0.012 0.001 PHE E 282 TRP 0.013 0.001 TRP H 92 HIS 0.007 0.001 HIS B 293 Details of bonding type rmsd covalent geometry : bond 0.00332 (24556) covalent geometry : angle 0.65651 (33376) hydrogen bonds : bond 0.23202 ( 743) hydrogen bonds : angle 8.50712 ( 2118) *********************** 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 : 0.965 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: symmetry clash REVERT: E 205 ARG cc_start: 0.7246 (mmt180) cc_final: 0.6732 (tpt170) REVERT: I 123 ASP cc_start: 0.8022 (OUTLIER) cc_final: 0.7770 (p0) REVERT: J 119 LYS cc_start: 0.8060 (mttm) cc_final: 0.7047 (mmtp) REVERT: K 86 MET cc_start: 0.7362 (mtm) cc_final: 0.7123 (mtm) outliers start: 29 outliers final: 2 residues processed: 612 average time/residue: 0.1899 time to fit residues: 174.2659 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 : 1.004 ------------------------------------------------------------------------------- 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 197 optimal weight: 10.0000 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.0970 chunk 207 optimal weight: 0.4980 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 10.0000 overall best weight: 2.5184 ------------------------------------------------------------------------------- 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 207 GLN 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 ** I 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.056513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2489 r_free = 0.2489 target = 0.044929 restraints weight = 82443.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2528 r_free = 0.2528 target = 0.046471 restraints weight = 33870.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2554 r_free = 0.2554 target = 0.047479 restraints weight = 18671.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2571 r_free = 0.2571 target = 0.048145 restraints weight = 12156.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.048592 restraints weight = 8878.102| |-----------------------------------------------------------------------------| r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 24556 Z= 0.188 Angle : 0.611 8.022 33376 Z= 0.330 Chirality : 0.046 0.162 3909 Planarity : 0.005 0.052 4265 Dihedral : 4.442 31.821 3341 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.46 % Favored : 96.18 % Rotamer: Outliers : 2.96 % Allowed : 19.45 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.14), residues: 3117 helix: 1.44 (0.25), residues: 528 sheet: -0.26 (0.27), residues: 381 loop : -1.65 (0.11), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 209 TYR 0.014 0.001 TYR C 237 PHE 0.013 0.001 PHE E 282 TRP 0.009 0.001 TRP H 92 HIS 0.006 0.001 HIS L 156 Details of bonding type rmsd covalent geometry : bond 0.00422 (24556) covalent geometry : angle 0.61061 (33376) hydrogen bonds : bond 0.04770 ( 743) hydrogen bonds : angle 5.86868 ( 2118) *********************** 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 552 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 474 time to evaluate : 0.971 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 232 MET cc_start: 0.9228 (mtt) cc_final: 0.8995 (mtp) REVERT: B 246 GLU cc_start: 0.8342 (mp0) cc_final: 0.7913 (mp0) REVERT: C 31 MET cc_start: 0.8953 (mtp) cc_final: 0.8748 (mtp) REVERT: C 75 TYR cc_start: 0.9456 (p90) cc_final: 0.8896 (p90) REVERT: C 241 GLN cc_start: 0.8815 (mm110) cc_final: 0.8341 (mm110) REVERT: C 272 MET cc_start: 0.9319 (tpp) cc_final: 0.9118 (tpt) REVERT: D 130 ARG cc_start: 0.9377 (ttm170) cc_final: 0.7579 (ppt170) REVERT: D 309 ARG cc_start: 0.9058 (mmp80) cc_final: 0.8783 (mmp80) REVERT: E 63 THR cc_start: 0.9721 (OUTLIER) cc_final: 0.9377 (p) REVERT: E 201 GLU cc_start: 0.9288 (tt0) cc_final: 0.8971 (tm-30) REVERT: E 230 THR cc_start: 0.9506 (OUTLIER) cc_final: 0.9259 (p) REVERT: F 47 TYR cc_start: 0.8431 (m-10) cc_final: 0.8216 (m-10) REVERT: F 207 GLN cc_start: 0.8431 (mt0) cc_final: 0.6751 (mt0) REVERT: G 64 THR cc_start: 0.9812 (OUTLIER) cc_final: 0.9523 (p) REVERT: G 100 LEU cc_start: 0.9160 (mp) cc_final: 0.8930 (mp) REVERT: G 219 MET cc_start: 0.8947 (mmt) cc_final: 0.8708 (mmm) REVERT: G 254 GLU cc_start: 0.9107 (OUTLIER) cc_final: 0.8879 (mt-10) REVERT: N 106 SER cc_start: 0.9090 (t) cc_final: 0.8876 (p) REVERT: N 119 LYS cc_start: 0.9211 (mmmm) cc_final: 0.8234 (mmmm) REVERT: I 36 GLU cc_start: 0.8153 (pm20) cc_final: 0.7439 (pm20) REVERT: I 80 VAL cc_start: 0.9123 (OUTLIER) cc_final: 0.8828 (p) REVERT: I 97 MET cc_start: 0.9628 (ttm) cc_final: 0.9329 (ttt) REVERT: K 86 MET cc_start: 0.8233 (mtm) cc_final: 0.7926 (mtm) REVERT: K 144 LYS cc_start: 0.9600 (ttpt) cc_final: 0.9368 (ttmm) REVERT: L 3 GLN cc_start: 0.8167 (mm-40) cc_final: 0.7932 (mm-40) REVERT: M 36 GLU cc_start: 0.8680 (pt0) cc_final: 0.8245 (pm20) REVERT: M 49 GLN cc_start: 0.9327 (tt0) cc_final: 0.9106 (tm-30) REVERT: M 51 GLN cc_start: 0.9142 (mt0) cc_final: 0.8509 (mt0) REVERT: M 84 ASN cc_start: 0.9027 (t0) cc_final: 0.8489 (t0) REVERT: M 107 LYS cc_start: 0.9396 (mtpt) cc_final: 0.9074 (mtpt) REVERT: M 119 LYS cc_start: 0.9347 (mttp) cc_final: 0.9054 (mttm) REVERT: M 133 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7554 (mm-30) REVERT: M 144 LYS cc_start: 0.9322 (ttmm) cc_final: 0.8878 (ttmm) outliers start: 78 outliers final: 36 residues processed: 518 average time/residue: 0.1701 time to fit residues: 137.9739 Evaluate side-chains 469 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 428 time to evaluate : 0.983 ------------------------------------------------------------------------------- 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 207 GLN Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 302 CYS 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 207 GLN 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 64 THR Chi-restraints excluded: chain G residue 254 GLU 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 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 73 ILE 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 246 optimal weight: 9.9990 chunk 228 optimal weight: 5.9990 chunk 229 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 132 optimal weight: 1.9990 chunk 191 optimal weight: 0.9980 chunk 111 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 265 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 166 ASN ** H 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 HIS K 46 GLN ** L 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.054771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2445 r_free = 0.2445 target = 0.043273 restraints weight = 83106.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2484 r_free = 0.2484 target = 0.044770 restraints weight = 33513.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2509 r_free = 0.2509 target = 0.045738 restraints weight = 18480.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2527 r_free = 0.2527 target = 0.046398 restraints weight = 12084.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2538 r_free = 0.2538 target = 0.046839 restraints weight = 8828.795| |-----------------------------------------------------------------------------| r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 24556 Z= 0.197 Angle : 0.591 8.691 33376 Z= 0.318 Chirality : 0.045 0.157 3909 Planarity : 0.004 0.051 4265 Dihedral : 4.364 19.820 3335 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.63 % Favored : 95.99 % Rotamer: Outliers : 3.12 % Allowed : 19.91 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.18 (0.14), residues: 3117 helix: 1.44 (0.25), residues: 535 sheet: 0.18 (0.32), residues: 279 loop : -1.59 (0.11), residues: 2303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 209 TYR 0.015 0.001 TYR C 237 PHE 0.011 0.001 PHE E 282 TRP 0.008 0.001 TRP L 103 HIS 0.005 0.001 HIS G 293 Details of bonding type rmsd covalent geometry : bond 0.00440 (24556) covalent geometry : angle 0.59099 (33376) hydrogen bonds : bond 0.04721 ( 743) hydrogen bonds : angle 5.56368 ( 2118) *********************** 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 515 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 433 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 246 GLU cc_start: 0.8316 (mp0) cc_final: 0.7833 (mp0) REVERT: C 31 MET cc_start: 0.8854 (mtp) cc_final: 0.8593 (mtp) REVERT: C 48 GLU cc_start: 0.8806 (mt-10) cc_final: 0.8576 (mm-30) REVERT: C 269 LYS cc_start: 0.9307 (OUTLIER) cc_final: 0.8678 (tttp) REVERT: D 272 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8168 (tmm) REVERT: E 63 THR cc_start: 0.9744 (OUTLIER) cc_final: 0.9314 (p) REVERT: E 201 GLU cc_start: 0.9181 (tt0) cc_final: 0.8957 (tm-30) REVERT: E 230 THR cc_start: 0.9468 (OUTLIER) cc_final: 0.9202 (p) REVERT: E 246 GLU cc_start: 0.8522 (mp0) cc_final: 0.8132 (mp0) REVERT: F 209 ARG cc_start: 0.8096 (mtt-85) cc_final: 0.7773 (mtt-85) REVERT: F 283 ASN cc_start: 0.8389 (m-40) cc_final: 0.8129 (m-40) REVERT: G 64 THR cc_start: 0.9827 (OUTLIER) cc_final: 0.9565 (p) REVERT: G 230 THR cc_start: 0.9077 (OUTLIER) cc_final: 0.8811 (p) REVERT: G 254 GLU cc_start: 0.9166 (OUTLIER) cc_final: 0.8924 (mt-10) REVERT: N 10 ARG cc_start: 0.9093 (ttt180) cc_final: 0.8744 (ttt180) REVERT: N 90 ASP cc_start: 0.9031 (t0) cc_final: 0.8319 (t70) REVERT: N 106 SER cc_start: 0.9033 (t) cc_final: 0.8755 (p) REVERT: N 119 LYS cc_start: 0.9136 (mmmm) cc_final: 0.8791 (mmmm) REVERT: N 155 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9002 (mt) REVERT: H 71 GLU cc_start: 0.7484 (mp0) cc_final: 0.7017 (mp0) REVERT: I 36 GLU cc_start: 0.8729 (pm20) cc_final: 0.8163 (pm20) REVERT: I 97 MET cc_start: 0.9637 (ttm) cc_final: 0.9345 (ttt) REVERT: J 36 GLU cc_start: 0.8794 (pt0) cc_final: 0.8325 (pp20) REVERT: J 84 ASN cc_start: 0.9054 (t0) cc_final: 0.8842 (t0) REVERT: K 5 ASN cc_start: 0.9337 (m110) cc_final: 0.8897 (m110) REVERT: K 9 GLN cc_start: 0.9241 (tm-30) cc_final: 0.8578 (tp-100) REVERT: K 144 LYS cc_start: 0.9624 (ttpt) cc_final: 0.9250 (ttpp) REVERT: L 86 MET cc_start: 0.8347 (mtm) cc_final: 0.8097 (mtm) REVERT: M 36 GLU cc_start: 0.8823 (pt0) cc_final: 0.8279 (pm20) REVERT: M 60 LYS cc_start: 0.9320 (tttt) cc_final: 0.8751 (tttp) REVERT: M 84 ASN cc_start: 0.9077 (t0) cc_final: 0.8813 (t0) REVERT: M 107 LYS cc_start: 0.9369 (mtpt) cc_final: 0.8919 (mtpt) REVERT: M 133 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7681 (mm-30) REVERT: M 144 LYS cc_start: 0.9374 (ttmm) cc_final: 0.8845 (ttmm) outliers start: 82 outliers final: 54 residues processed: 487 average time/residue: 0.1604 time to fit residues: 125.6918 Evaluate side-chains 470 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 408 time to evaluate : 1.013 ------------------------------------------------------------------------------- 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 232 MET Chi-restraints excluded: chain B residue 302 CYS 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 152 VAL 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 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 223 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 64 THR 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 155 LEU Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain I residue 16 LEU 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 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 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 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 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 102 optimal weight: 8.9990 chunk 38 optimal weight: 6.9990 chunk 162 optimal weight: 2.9990 chunk 290 optimal weight: 6.9990 chunk 230 optimal weight: 2.9990 chunk 220 optimal weight: 1.9990 chunk 59 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 283 optimal weight: 10.0000 chunk 61 optimal weight: 7.9990 chunk 159 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 241 GLN ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 241 GLN ** H 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.053466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2414 r_free = 0.2414 target = 0.042088 restraints weight = 84007.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2453 r_free = 0.2453 target = 0.043566 restraints weight = 33605.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2479 r_free = 0.2479 target = 0.044519 restraints weight = 18468.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2496 r_free = 0.2496 target = 0.045164 restraints weight = 12081.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2508 r_free = 0.2508 target = 0.045595 restraints weight = 8820.748| |-----------------------------------------------------------------------------| r_work (final): 0.2502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 24556 Z= 0.226 Angle : 0.616 13.088 33376 Z= 0.330 Chirality : 0.046 0.165 3909 Planarity : 0.005 0.054 4265 Dihedral : 4.473 23.407 3335 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.04 % Favored : 95.57 % Rotamer: Outliers : 3.38 % Allowed : 20.29 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.24 (0.14), residues: 3117 helix: 1.21 (0.24), residues: 558 sheet: 0.20 (0.31), residues: 287 loop : -1.62 (0.11), residues: 2272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 309 TYR 0.019 0.001 TYR C 237 PHE 0.011 0.001 PHE E 282 TRP 0.009 0.001 TRP L 103 HIS 0.006 0.001 HIS G 293 Details of bonding type rmsd covalent geometry : bond 0.00514 (24556) covalent geometry : angle 0.61565 (33376) hydrogen bonds : bond 0.04801 ( 743) hydrogen bonds : angle 5.42489 ( 2118) *********************** 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 516 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 427 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 GLN cc_start: 0.8654 (tp40) cc_final: 0.8416 (tp40) REVERT: B 98 ASP cc_start: 0.9006 (OUTLIER) cc_final: 0.8649 (t0) REVERT: B 246 GLU cc_start: 0.8387 (mp0) cc_final: 0.7798 (mp0) REVERT: C 31 MET cc_start: 0.9053 (mtp) cc_final: 0.8835 (mtp) REVERT: C 48 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8497 (mm-30) REVERT: C 269 LYS cc_start: 0.9444 (OUTLIER) cc_final: 0.8792 (tttp) REVERT: D 116 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7893 (mt) REVERT: D 130 ARG cc_start: 0.9415 (ttm170) cc_final: 0.7278 (ppt170) REVERT: D 272 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.8425 (tmm) REVERT: D 306 THR cc_start: 0.9043 (OUTLIER) cc_final: 0.8819 (p) REVERT: E 63 THR cc_start: 0.9747 (OUTLIER) cc_final: 0.9297 (p) REVERT: E 230 THR cc_start: 0.9481 (OUTLIER) cc_final: 0.9175 (p) REVERT: E 246 GLU cc_start: 0.8545 (mp0) cc_final: 0.8193 (mp0) REVERT: F 209 ARG cc_start: 0.8146 (mtt-85) cc_final: 0.7869 (mtt-85) REVERT: F 283 ASN cc_start: 0.8386 (m-40) cc_final: 0.8029 (m-40) REVERT: G 31 MET cc_start: 0.8186 (mmm) cc_final: 0.7868 (mmm) REVERT: G 64 THR cc_start: 0.9831 (OUTLIER) cc_final: 0.9604 (p) REVERT: G 241 GLN cc_start: 0.8895 (mt0) cc_final: 0.8677 (mt0) REVERT: G 254 GLU cc_start: 0.9226 (OUTLIER) cc_final: 0.8979 (mt-10) REVERT: N 62 LEU cc_start: 0.9295 (tp) cc_final: 0.9052 (tp) REVERT: N 106 SER cc_start: 0.9091 (t) cc_final: 0.8794 (p) REVERT: N 119 LYS cc_start: 0.9140 (mmmm) cc_final: 0.8809 (mmmm) REVERT: N 155 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.8973 (mt) REVERT: I 36 GLU cc_start: 0.8855 (pm20) cc_final: 0.8154 (pm20) REVERT: I 66 THR cc_start: 0.9520 (OUTLIER) cc_final: 0.9100 (p) REVERT: I 86 MET cc_start: 0.8890 (mtm) cc_final: 0.8591 (mtm) REVERT: I 90 ASP cc_start: 0.8696 (t0) cc_final: 0.8403 (m-30) REVERT: I 97 MET cc_start: 0.9645 (ttm) cc_final: 0.9364 (ttt) REVERT: I 154 GLN cc_start: 0.9265 (OUTLIER) cc_final: 0.8730 (tp40) REVERT: J 36 GLU cc_start: 0.8891 (pt0) cc_final: 0.8540 (pp20) REVERT: K 5 ASN cc_start: 0.9109 (m110) cc_final: 0.8752 (m110) REVERT: K 27 ASN cc_start: 0.9425 (OUTLIER) cc_final: 0.8906 (t0) REVERT: K 107 LYS cc_start: 0.9181 (mttt) cc_final: 0.8897 (mttt) REVERT: K 144 LYS cc_start: 0.9604 (ttpt) cc_final: 0.9209 (ttpp) REVERT: L 3 GLN cc_start: 0.8344 (mm-40) cc_final: 0.8089 (mm-40) REVERT: L 81 ASN cc_start: 0.8899 (m-40) cc_final: 0.8556 (m-40) REVERT: M 36 GLU cc_start: 0.8888 (pt0) cc_final: 0.8335 (pm20) REVERT: M 60 LYS cc_start: 0.9335 (tttt) cc_final: 0.8848 (tttp) REVERT: M 84 ASN cc_start: 0.9163 (t0) cc_final: 0.8845 (t0) REVERT: M 107 LYS cc_start: 0.9347 (mtpt) cc_final: 0.8897 (mtpt) REVERT: M 144 LYS cc_start: 0.9395 (ttmm) cc_final: 0.9093 (ttmm) outliers start: 89 outliers final: 53 residues processed: 488 average time/residue: 0.1640 time to fit residues: 127.3057 Evaluate side-chains 472 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 406 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 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 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 152 VAL Chi-restraints excluded: chain C residue 269 LYS Chi-restraints excluded: chain C residue 311 MET 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 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 223 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 64 THR Chi-restraints excluded: chain G residue 223 LEU 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 116 THR 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 94 ILE Chi-restraints excluded: chain K residue 19 MET Chi-restraints excluded: chain K residue 27 ASN 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 298 optimal weight: 9.9990 chunk 64 optimal weight: 0.0470 chunk 132 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 157 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 101 optimal weight: 0.0170 chunk 48 optimal weight: 0.5980 chunk 88 optimal weight: 9.9990 chunk 303 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 overall best weight: 1.3320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.054707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2451 r_free = 0.2451 target = 0.043352 restraints weight = 82451.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2491 r_free = 0.2491 target = 0.044860 restraints weight = 32902.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2516 r_free = 0.2516 target = 0.045840 restraints weight = 18019.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2533 r_free = 0.2533 target = 0.046488 restraints weight = 11683.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.046924 restraints weight = 8523.351| |-----------------------------------------------------------------------------| r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.2752 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= 0.134 Angle : 0.568 11.587 33376 Z= 0.302 Chirality : 0.045 0.152 3909 Planarity : 0.004 0.050 4265 Dihedral : 4.290 20.300 3335 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.37 % Favored : 96.21 % Rotamer: Outliers : 2.89 % Allowed : 20.97 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.14), residues: 3117 helix: 1.56 (0.25), residues: 528 sheet: -0.01 (0.28), residues: 324 loop : -1.50 (0.11), residues: 2265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 209 TYR 0.011 0.001 TYR A 115 PHE 0.009 0.001 PHE E 282 TRP 0.009 0.001 TRP L 103 HIS 0.008 0.001 HIS H 133 Details of bonding type rmsd covalent geometry : bond 0.00289 (24556) covalent geometry : angle 0.56775 (33376) hydrogen bonds : bond 0.03956 ( 743) hydrogen bonds : angle 5.20384 ( 2118) *********************** 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 510 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 434 time to evaluate : 1.009 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 261 THR cc_start: 0.8415 (OUTLIER) cc_final: 0.8192 (m) REVERT: B 98 ASP cc_start: 0.8949 (OUTLIER) cc_final: 0.8580 (t0) REVERT: B 212 ASN cc_start: 0.9460 (m-40) cc_final: 0.9115 (m-40) REVERT: B 246 GLU cc_start: 0.8329 (mp0) cc_final: 0.7693 (mp0) REVERT: C 47 TYR cc_start: 0.8631 (t80) cc_final: 0.8204 (t80) REVERT: C 48 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8517 (mm-30) REVERT: C 269 LYS cc_start: 0.9467 (OUTLIER) cc_final: 0.8864 (tttp) REVERT: D 45 GLN cc_start: 0.9193 (mm110) cc_final: 0.8982 (mm-40) REVERT: D 65 GLU cc_start: 0.9347 (OUTLIER) cc_final: 0.9079 (tt0) REVERT: D 272 MET cc_start: 0.8755 (OUTLIER) cc_final: 0.8408 (tmm) REVERT: E 63 THR cc_start: 0.9759 (OUTLIER) cc_final: 0.9335 (p) REVERT: E 160 LYS cc_start: 0.9536 (mtmt) cc_final: 0.9199 (mttt) REVERT: E 230 THR cc_start: 0.9435 (OUTLIER) cc_final: 0.9122 (p) REVERT: E 246 GLU cc_start: 0.8560 (mp0) cc_final: 0.8231 (mp0) REVERT: F 209 ARG cc_start: 0.8173 (mtt-85) cc_final: 0.7890 (mtt-85) REVERT: G 31 MET cc_start: 0.7510 (mmm) cc_final: 0.7191 (mmm) REVERT: G 64 THR cc_start: 0.9823 (OUTLIER) cc_final: 0.9603 (p) REVERT: G 100 LEU cc_start: 0.9139 (mp) cc_final: 0.8913 (mp) REVERT: G 230 THR cc_start: 0.9083 (OUTLIER) cc_final: 0.8880 (p) REVERT: G 241 GLN cc_start: 0.8857 (mt0) cc_final: 0.8623 (mt0) REVERT: G 254 GLU cc_start: 0.9201 (OUTLIER) cc_final: 0.8976 (mt-10) REVERT: N 36 GLU cc_start: 0.9321 (tt0) cc_final: 0.9013 (tm-30) REVERT: N 60 LYS cc_start: 0.9083 (ttmm) cc_final: 0.8283 (ttpp) REVERT: N 62 LEU cc_start: 0.9276 (tp) cc_final: 0.9010 (tp) REVERT: N 89 GLU cc_start: 0.8224 (pm20) cc_final: 0.8002 (pm20) REVERT: N 106 SER cc_start: 0.9041 (t) cc_final: 0.8783 (p) REVERT: N 119 LYS cc_start: 0.9154 (mmmm) cc_final: 0.8871 (mmmm) REVERT: N 155 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.8993 (mt) REVERT: H 71 GLU cc_start: 0.7393 (mp0) cc_final: 0.7057 (mp0) REVERT: H 81 GLU cc_start: 0.8925 (mt-10) cc_final: 0.8672 (mt-10) REVERT: I 36 GLU cc_start: 0.8844 (pm20) cc_final: 0.8121 (pm20) REVERT: I 90 ASP cc_start: 0.8699 (t0) cc_final: 0.8396 (m-30) REVERT: I 97 MET cc_start: 0.9625 (ttm) cc_final: 0.9326 (ttt) REVERT: I 154 GLN cc_start: 0.9198 (OUTLIER) cc_final: 0.8684 (tp40) REVERT: K 9 GLN cc_start: 0.9278 (tm-30) cc_final: 0.8533 (tp-100) REVERT: K 144 LYS cc_start: 0.9599 (ttpt) cc_final: 0.9260 (ttpp) REVERT: K 154 GLN cc_start: 0.9151 (OUTLIER) cc_final: 0.8500 (tp40) REVERT: L 3 GLN cc_start: 0.8360 (mm-40) cc_final: 0.8079 (mm-40) REVERT: L 81 ASN cc_start: 0.8850 (m-40) cc_final: 0.8475 (m-40) REVERT: M 36 GLU cc_start: 0.8860 (pt0) cc_final: 0.8312 (pm20) REVERT: M 49 GLN cc_start: 0.9309 (tt0) cc_final: 0.8995 (tm-30) REVERT: M 51 GLN cc_start: 0.9137 (mt0) cc_final: 0.8365 (mt0) REVERT: M 60 LYS cc_start: 0.9315 (tttt) cc_final: 0.8939 (tttp) REVERT: M 84 ASN cc_start: 0.9187 (t0) cc_final: 0.8749 (t0) REVERT: M 107 LYS cc_start: 0.9356 (mtpt) cc_final: 0.8925 (mtpt) REVERT: M 144 LYS cc_start: 0.9370 (ttmm) cc_final: 0.8805 (ttmm) outliers start: 76 outliers final: 49 residues processed: 485 average time/residue: 0.1578 time to fit residues: 122.8427 Evaluate side-chains 474 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 412 time to evaluate : 0.924 ------------------------------------------------------------------------------- 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 315 LEU Chi-restraints excluded: chain B residue 44 SER 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 C residue 311 MET Chi-restraints excluded: chain D residue 65 GLU 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 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 223 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 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 155 LEU Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 98 ASP 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 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 40 LEU 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 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 62 LEU Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 75 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 281 optimal weight: 1.9990 chunk 131 optimal weight: 7.9990 chunk 230 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 214 optimal weight: 30.0000 chunk 75 optimal weight: 0.6980 chunk 270 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 96 optimal weight: 9.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 195 GLN ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 288 GLN E 144 HIS ** H 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 85 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.052741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2398 r_free = 0.2398 target = 0.041417 restraints weight = 84468.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2438 r_free = 0.2438 target = 0.042871 restraints weight = 34000.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2464 r_free = 0.2464 target = 0.043843 restraints weight = 18853.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2481 r_free = 0.2481 target = 0.044484 restraints weight = 12257.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2493 r_free = 0.2493 target = 0.044902 restraints weight = 8958.409| |-----------------------------------------------------------------------------| r_work (final): 0.2487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 24556 Z= 0.239 Angle : 0.627 10.663 33376 Z= 0.336 Chirality : 0.046 0.171 3909 Planarity : 0.004 0.049 4265 Dihedral : 4.443 19.220 3335 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.43 % Favored : 95.16 % Rotamer: Outliers : 3.42 % Allowed : 20.90 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.14), residues: 3117 helix: 1.30 (0.24), residues: 557 sheet: -0.02 (0.29), residues: 305 loop : -1.55 (0.11), residues: 2255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 74 TYR 0.015 0.001 TYR F 47 PHE 0.011 0.001 PHE L 114 TRP 0.009 0.001 TRP L 103 HIS 0.006 0.001 HIS G 293 Details of bonding type rmsd covalent geometry : bond 0.00546 (24556) covalent geometry : angle 0.62709 (33376) hydrogen bonds : bond 0.04825 ( 743) hydrogen bonds : angle 5.25660 ( 2118) *********************** 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 494 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 404 time to evaluate : 1.012 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: 0.8752 (mmm) cc_final: 0.8423 (mmt) REVERT: A 261 THR cc_start: 0.8663 (OUTLIER) cc_final: 0.8372 (m) REVERT: B 98 ASP cc_start: 0.9030 (OUTLIER) cc_final: 0.8707 (t0) REVERT: B 246 GLU cc_start: 0.8348 (mp0) cc_final: 0.7977 (mp0) REVERT: C 31 MET cc_start: 0.8807 (mtt) cc_final: 0.8041 (mmm) REVERT: C 48 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8507 (mm-30) REVERT: C 269 LYS cc_start: 0.9499 (OUTLIER) cc_final: 0.8905 (tttp) REVERT: C 270 ASN cc_start: 0.9064 (t0) cc_final: 0.8695 (t0) REVERT: D 45 GLN cc_start: 0.9167 (mm110) cc_final: 0.8847 (mm-40) REVERT: D 65 GLU cc_start: 0.9335 (OUTLIER) cc_final: 0.9050 (tt0) REVERT: D 272 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.8267 (tmm) REVERT: D 306 THR cc_start: 0.9146 (OUTLIER) cc_final: 0.8920 (p) REVERT: E 63 THR cc_start: 0.9750 (OUTLIER) cc_final: 0.9288 (p) REVERT: E 160 LYS cc_start: 0.9570 (mtmt) cc_final: 0.9234 (mttt) REVERT: E 171 THR cc_start: 0.9581 (OUTLIER) cc_final: 0.9010 (p) REVERT: E 230 THR cc_start: 0.9440 (OUTLIER) cc_final: 0.9134 (p) REVERT: E 246 GLU cc_start: 0.8625 (mp0) cc_final: 0.8318 (mp0) REVERT: F 209 ARG cc_start: 0.8185 (mtt-85) cc_final: 0.7918 (mtt-85) REVERT: F 283 ASN cc_start: 0.8848 (t0) cc_final: 0.8510 (t0) REVERT: G 31 MET cc_start: 0.7602 (mmm) cc_final: 0.7258 (mmm) REVERT: G 64 THR cc_start: 0.9806 (OUTLIER) cc_final: 0.9606 (p) REVERT: G 207 GLN cc_start: 0.9036 (mm-40) cc_final: 0.8830 (mm-40) REVERT: G 230 THR cc_start: 0.9175 (OUTLIER) cc_final: 0.8952 (p) REVERT: G 241 GLN cc_start: 0.8866 (mt0) cc_final: 0.8602 (mt0) REVERT: G 254 GLU cc_start: 0.9240 (OUTLIER) cc_final: 0.8719 (tt0) REVERT: N 36 GLU cc_start: 0.9337 (tt0) cc_final: 0.8976 (tm-30) REVERT: N 62 LEU cc_start: 0.9334 (tp) cc_final: 0.9072 (tp) REVERT: N 106 SER cc_start: 0.9098 (t) cc_final: 0.8868 (p) REVERT: N 119 LYS cc_start: 0.9141 (mmmm) cc_final: 0.8863 (mmmm) REVERT: N 155 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8950 (mt) REVERT: H 71 GLU cc_start: 0.7500 (mp0) cc_final: 0.6979 (mp0) REVERT: I 36 GLU cc_start: 0.8872 (pm20) cc_final: 0.7912 (pm20) REVERT: I 66 THR cc_start: 0.9488 (OUTLIER) cc_final: 0.9107 (p) REVERT: I 90 ASP cc_start: 0.8564 (t0) cc_final: 0.8358 (m-30) REVERT: I 97 MET cc_start: 0.9650 (ttm) cc_final: 0.9403 (ttt) REVERT: J 97 MET cc_start: 0.9138 (ttt) cc_final: 0.8420 (ttt) REVERT: K 3 GLN cc_start: 0.8174 (pp30) cc_final: 0.7953 (pp30) REVERT: K 144 LYS cc_start: 0.9591 (ttpt) cc_final: 0.9254 (ttpp) REVERT: K 154 GLN cc_start: 0.9220 (OUTLIER) cc_final: 0.8487 (tp40) REVERT: L 154 GLN cc_start: 0.9255 (OUTLIER) cc_final: 0.8376 (tt0) REVERT: M 36 GLU cc_start: 0.8933 (pt0) cc_final: 0.8620 (pm20) REVERT: M 60 LYS cc_start: 0.9307 (tttt) cc_final: 0.9028 (tttp) REVERT: M 84 ASN cc_start: 0.9255 (t0) cc_final: 0.8899 (t0) REVERT: M 87 ILE cc_start: 0.9500 (tt) cc_final: 0.9262 (tp) REVERT: M 107 LYS cc_start: 0.9345 (mtpt) cc_final: 0.8893 (mtpt) REVERT: M 119 LYS cc_start: 0.9425 (mmtp) cc_final: 0.9082 (mmmm) REVERT: M 133 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8260 (mm-30) REVERT: M 144 LYS cc_start: 0.9378 (ttmm) cc_final: 0.9036 (ttmm) outliers start: 90 outliers final: 58 residues processed: 467 average time/residue: 0.1614 time to fit residues: 120.2260 Evaluate side-chains 470 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 396 time to evaluate : 0.962 ------------------------------------------------------------------------------- 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 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 223 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 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 155 LEU Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 98 ASP 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 158 LEU Chi-restraints excluded: chain J residue 4 ILE 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 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 36 GLU Chi-restraints excluded: chain L residue 66 THR Chi-restraints excluded: chain L residue 154 GLN Chi-restraints excluded: chain M residue 4 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 306 optimal weight: 8.9990 chunk 109 optimal weight: 7.9990 chunk 246 optimal weight: 1.9990 chunk 222 optimal weight: 2.9990 chunk 239 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 202 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 241 GLN ** H 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.053592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2422 r_free = 0.2422 target = 0.042297 restraints weight = 83457.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2461 r_free = 0.2461 target = 0.043777 restraints weight = 33219.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2486 r_free = 0.2486 target = 0.044728 restraints weight = 18194.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2504 r_free = 0.2504 target = 0.045373 restraints weight = 11856.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2515 r_free = 0.2515 target = 0.045797 restraints weight = 8643.828| |-----------------------------------------------------------------------------| r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 24556 Z= 0.165 Angle : 0.591 11.633 33376 Z= 0.315 Chirality : 0.045 0.151 3909 Planarity : 0.004 0.049 4265 Dihedral : 4.350 20.326 3335 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.50 % Favored : 96.09 % Rotamer: Outliers : 2.93 % Allowed : 22.26 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.14), residues: 3117 helix: 1.59 (0.25), residues: 528 sheet: 0.02 (0.28), residues: 315 loop : -1.48 (0.12), residues: 2274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 209 TYR 0.011 0.001 TYR G 115 PHE 0.012 0.001 PHE D 294 TRP 0.009 0.001 TRP L 103 HIS 0.004 0.001 HIS H 133 Details of bonding type rmsd covalent geometry : bond 0.00373 (24556) covalent geometry : angle 0.59099 (33376) hydrogen bonds : bond 0.04190 ( 743) hydrogen bonds : angle 5.08287 ( 2118) *********************** 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 488 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 411 time to evaluate : 0.642 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: 0.8529 (OUTLIER) cc_final: 0.8253 (m) REVERT: B 31 MET cc_start: 0.8871 (mtt) cc_final: 0.8518 (mtt) REVERT: B 98 ASP cc_start: 0.9019 (OUTLIER) cc_final: 0.8683 (t0) REVERT: B 100 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.9116 (pt) REVERT: B 246 GLU cc_start: 0.8344 (mp0) cc_final: 0.7972 (mp0) REVERT: B 309 ARG cc_start: 0.8797 (mmp80) cc_final: 0.8589 (mmp80) REVERT: C 241 GLN cc_start: 0.9240 (mm110) cc_final: 0.9008 (mm110) REVERT: C 269 LYS cc_start: 0.9493 (OUTLIER) cc_final: 0.8967 (tttp) REVERT: C 270 ASN cc_start: 0.9120 (t0) cc_final: 0.8659 (t0) REVERT: D 45 GLN cc_start: 0.9126 (mm110) cc_final: 0.8823 (mm-40) REVERT: D 65 GLU cc_start: 0.9370 (OUTLIER) cc_final: 0.9109 (tt0) REVERT: D 272 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8246 (tmm) REVERT: E 63 THR cc_start: 0.9767 (OUTLIER) cc_final: 0.9332 (p) REVERT: E 160 LYS cc_start: 0.9552 (mtmt) cc_final: 0.9197 (mttt) REVERT: E 246 GLU cc_start: 0.8597 (mp0) cc_final: 0.8298 (mp0) REVERT: F 209 ARG cc_start: 0.8182 (mtt-85) cc_final: 0.7907 (mtt-85) REVERT: F 283 ASN cc_start: 0.8844 (t0) cc_final: 0.8477 (t0) REVERT: G 31 MET cc_start: 0.7609 (mmm) cc_final: 0.7255 (mmm) REVERT: G 64 THR cc_start: 0.9799 (OUTLIER) cc_final: 0.9593 (p) REVERT: G 100 LEU cc_start: 0.9124 (mp) cc_final: 0.8886 (mp) REVERT: G 254 GLU cc_start: 0.9224 (OUTLIER) cc_final: 0.8991 (mt-10) REVERT: N 62 LEU cc_start: 0.9350 (tp) cc_final: 0.9088 (tp) REVERT: N 106 SER cc_start: 0.9099 (t) cc_final: 0.8844 (p) REVERT: N 119 LYS cc_start: 0.9170 (mmmm) cc_final: 0.8916 (mmmm) REVERT: N 155 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8981 (mt) REVERT: H 71 GLU cc_start: 0.7574 (mp0) cc_final: 0.7054 (mp0) REVERT: I 36 GLU cc_start: 0.8805 (pm20) cc_final: 0.8048 (pm20) REVERT: I 66 THR cc_start: 0.9509 (OUTLIER) cc_final: 0.9102 (p) REVERT: I 90 ASP cc_start: 0.8553 (t0) cc_final: 0.8302 (m-30) REVERT: I 97 MET cc_start: 0.9641 (ttm) cc_final: 0.9380 (ttt) REVERT: J 97 MET cc_start: 0.9037 (ttt) cc_final: 0.8359 (ttt) REVERT: K 9 GLN cc_start: 0.9401 (tm-30) cc_final: 0.8573 (tp-100) REVERT: K 144 LYS cc_start: 0.9580 (ttpt) cc_final: 0.9249 (ttpp) REVERT: K 154 GLN cc_start: 0.9203 (OUTLIER) cc_final: 0.8519 (tp40) REVERT: L 3 GLN cc_start: 0.8375 (mm-40) cc_final: 0.8075 (mm-40) REVERT: L 81 ASN cc_start: 0.8722 (m-40) cc_final: 0.8453 (m-40) REVERT: M 36 GLU cc_start: 0.8976 (pt0) cc_final: 0.8662 (pm20) REVERT: M 60 LYS cc_start: 0.9310 (tttt) cc_final: 0.9079 (tttp) REVERT: M 84 ASN cc_start: 0.9278 (t0) cc_final: 0.9050 (t0) REVERT: M 87 ILE cc_start: 0.9476 (tt) cc_final: 0.9250 (tp) REVERT: M 104 MET cc_start: 0.8951 (ttp) cc_final: 0.8689 (ttp) REVERT: M 107 LYS cc_start: 0.9393 (mtpt) cc_final: 0.8951 (mtpt) REVERT: M 119 LYS cc_start: 0.9417 (mmtp) cc_final: 0.9094 (mmmm) REVERT: M 144 LYS cc_start: 0.9369 (ttmm) cc_final: 0.9020 (ttmm) outliers start: 77 outliers final: 52 residues processed: 464 average time/residue: 0.1549 time to fit residues: 115.2632 Evaluate side-chains 460 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 396 time to evaluate : 0.965 ------------------------------------------------------------------------------- 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 315 LEU Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 232 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 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 D residue 298 CYS 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 81 VAL Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 223 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 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 254 GLU 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 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 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 73 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 120 LEU 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 36 GLU Chi-restraints excluded: chain L residue 66 THR 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 6 optimal weight: 2.9990 chunk 167 optimal weight: 3.9990 chunk 153 optimal weight: 5.9990 chunk 245 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 76 optimal weight: 8.9990 chunk 302 optimal weight: 10.0000 chunk 297 optimal weight: 5.9990 chunk 249 optimal weight: 5.9990 chunk 200 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 83 GLN ** L 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.052323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2389 r_free = 0.2389 target = 0.041008 restraints weight = 84260.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2427 r_free = 0.2427 target = 0.042452 restraints weight = 33991.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2453 r_free = 0.2453 target = 0.043397 restraints weight = 18742.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2470 r_free = 0.2470 target = 0.044027 restraints weight = 12238.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2482 r_free = 0.2482 target = 0.044448 restraints weight = 8965.247| |-----------------------------------------------------------------------------| r_work (final): 0.2495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 24556 Z= 0.261 Angle : 0.646 10.882 33376 Z= 0.345 Chirality : 0.046 0.173 3909 Planarity : 0.004 0.050 4265 Dihedral : 4.504 20.170 3335 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.81 % Favored : 94.80 % Rotamer: Outliers : 3.12 % Allowed : 22.04 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.18 (0.14), residues: 3117 helix: 1.34 (0.24), residues: 557 sheet: -0.14 (0.29), residues: 293 loop : -1.55 (0.11), residues: 2267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 74 TYR 0.017 0.001 TYR F 47 PHE 0.011 0.001 PHE L 114 TRP 0.008 0.001 TRP L 103 HIS 0.006 0.001 HIS G 293 Details of bonding type rmsd covalent geometry : bond 0.00600 (24556) covalent geometry : angle 0.64634 (33376) hydrogen bonds : bond 0.04897 ( 743) hydrogen bonds : angle 5.21166 ( 2118) *********************** 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 469 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 387 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 MET cc_start: 0.8803 (mmm) cc_final: 0.8406 (mmt) REVERT: B 31 MET cc_start: 0.8899 (mtt) cc_final: 0.8287 (mtt) REVERT: B 98 ASP cc_start: 0.9044 (OUTLIER) cc_final: 0.8724 (t0) REVERT: B 246 GLU cc_start: 0.8290 (mp0) cc_final: 0.7955 (mp0) REVERT: B 309 ARG cc_start: 0.8925 (mmp80) cc_final: 0.8666 (mmp80) REVERT: C 269 LYS cc_start: 0.9502 (OUTLIER) cc_final: 0.8908 (tttp) REVERT: C 270 ASN cc_start: 0.9232 (t0) cc_final: 0.8754 (t0) REVERT: D 45 GLN cc_start: 0.9129 (mm110) cc_final: 0.8837 (mm-40) REVERT: D 65 GLU cc_start: 0.9356 (OUTLIER) cc_final: 0.9079 (tt0) REVERT: D 272 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.8186 (tmm) REVERT: E 63 THR cc_start: 0.9763 (OUTLIER) cc_final: 0.9311 (p) REVERT: E 160 LYS cc_start: 0.9570 (mtmt) cc_final: 0.9237 (mttt) REVERT: E 230 THR cc_start: 0.9426 (OUTLIER) cc_final: 0.9121 (p) REVERT: E 246 GLU cc_start: 0.8620 (mp0) cc_final: 0.8317 (mp0) REVERT: F 209 ARG cc_start: 0.8230 (mtt-85) cc_final: 0.7959 (mtt-85) REVERT: F 283 ASN cc_start: 0.8863 (t0) cc_final: 0.8522 (t0) REVERT: G 254 GLU cc_start: 0.9269 (OUTLIER) cc_final: 0.8806 (tt0) REVERT: N 36 GLU cc_start: 0.9297 (tt0) cc_final: 0.8989 (pp20) REVERT: N 62 LEU cc_start: 0.9374 (tp) cc_final: 0.9112 (tp) REVERT: N 119 LYS cc_start: 0.9149 (mmmm) cc_final: 0.8873 (mmmm) REVERT: N 155 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8986 (mt) REVERT: I 36 GLU cc_start: 0.8845 (pm20) cc_final: 0.8090 (pm20) REVERT: I 66 THR cc_start: 0.9490 (OUTLIER) cc_final: 0.9069 (p) REVERT: I 97 MET cc_start: 0.9665 (ttm) cc_final: 0.9424 (ttt) REVERT: J 74 ARG cc_start: 0.9615 (OUTLIER) cc_final: 0.9248 (ptm-80) REVERT: J 97 MET cc_start: 0.9090 (ttt) cc_final: 0.8888 (ttt) REVERT: K 144 LYS cc_start: 0.9575 (ttpt) cc_final: 0.9249 (ttpp) REVERT: K 154 GLN cc_start: 0.9250 (OUTLIER) cc_final: 0.8506 (tp40) REVERT: L 81 ASN cc_start: 0.8791 (m-40) cc_final: 0.8560 (m-40) REVERT: L 154 GLN cc_start: 0.9276 (OUTLIER) cc_final: 0.8370 (tt0) REVERT: M 36 GLU cc_start: 0.9016 (pt0) cc_final: 0.8732 (pm20) REVERT: M 84 ASN cc_start: 0.9295 (t0) cc_final: 0.9076 (t0) REVERT: M 87 ILE cc_start: 0.9485 (tt) cc_final: 0.9261 (tp) REVERT: M 104 MET cc_start: 0.8899 (ttp) cc_final: 0.8620 (ttp) REVERT: M 107 LYS cc_start: 0.9389 (mtpt) cc_final: 0.8959 (mtpt) REVERT: M 133 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8293 (mm-30) REVERT: M 144 LYS cc_start: 0.9377 (ttmm) cc_final: 0.9023 (ttmm) outliers start: 82 outliers final: 61 residues processed: 446 average time/residue: 0.1625 time to fit residues: 115.7628 Evaluate side-chains 452 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 379 time to evaluate : 0.993 ------------------------------------------------------------------------------- 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 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 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 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 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 223 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 298 CYS Chi-restraints excluded: chain F residue 302 CYS Chi-restraints excluded: chain G residue 223 LEU 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 155 LEU Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 98 ASP 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 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 73 ILE Chi-restraints excluded: chain J residue 74 ARG Chi-restraints excluded: chain J residue 94 ILE 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 96 VAL Chi-restraints excluded: chain K residue 120 LEU 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 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 128 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 276 optimal weight: 4.9990 chunk 245 optimal weight: 3.9990 chunk 123 optimal weight: 7.9990 chunk 194 optimal weight: 0.8980 chunk 222 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 251 optimal weight: 0.9980 chunk 243 optimal weight: 3.9990 chunk 192 optimal weight: 0.9980 chunk 267 optimal weight: 10.0000 chunk 288 optimal weight: 7.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 GLN ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 208 HIS ** H 88 HIS ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.053229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2415 r_free = 0.2415 target = 0.041962 restraints weight = 84246.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2454 r_free = 0.2454 target = 0.043431 restraints weight = 33426.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2480 r_free = 0.2480 target = 0.044391 restraints weight = 18294.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2497 r_free = 0.2497 target = 0.045016 restraints weight = 11875.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2509 r_free = 0.2509 target = 0.045441 restraints weight = 8688.226| |-----------------------------------------------------------------------------| r_work (final): 0.2504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 24556 Z= 0.169 Angle : 0.621 10.705 33376 Z= 0.331 Chirality : 0.045 0.156 3909 Planarity : 0.004 0.050 4265 Dihedral : 4.418 19.365 3335 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.72 % Favored : 95.93 % Rotamer: Outliers : 2.74 % Allowed : 22.23 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.14), residues: 3117 helix: 1.62 (0.25), residues: 529 sheet: -0.07 (0.29), residues: 305 loop : -1.48 (0.12), residues: 2283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 209 TYR 0.019 0.001 TYR N 26 PHE 0.012 0.001 PHE D 294 TRP 0.009 0.001 TRP L 103 HIS 0.004 0.001 HIS G 293 Details of bonding type rmsd covalent geometry : bond 0.00384 (24556) covalent geometry : angle 0.62123 (33376) hydrogen bonds : bond 0.04281 ( 743) hydrogen bonds : angle 5.06219 ( 2118) *********************** 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 466 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 394 time to evaluate : 1.071 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: 0.8640 (mmm) cc_final: 0.8373 (mmt) REVERT: B 31 MET cc_start: 0.8873 (mtt) cc_final: 0.8502 (mtt) REVERT: B 98 ASP cc_start: 0.9034 (OUTLIER) cc_final: 0.8702 (t0) REVERT: B 246 GLU cc_start: 0.8353 (mp0) cc_final: 0.7982 (mp0) REVERT: B 309 ARG cc_start: 0.8901 (mmp80) cc_final: 0.8675 (mmp80) REVERT: C 31 MET cc_start: 0.9058 (mmt) cc_final: 0.7185 (ptt) REVERT: C 227 MET cc_start: 0.8441 (tpp) cc_final: 0.8192 (tpt) REVERT: C 269 LYS cc_start: 0.9502 (OUTLIER) cc_final: 0.8904 (tttp) REVERT: C 270 ASN cc_start: 0.9224 (t0) cc_final: 0.8761 (t0) REVERT: C 309 ARG cc_start: 0.9228 (mmm-85) cc_final: 0.8953 (mmm-85) REVERT: D 45 GLN cc_start: 0.9097 (mm110) cc_final: 0.8844 (mm-40) REVERT: D 65 GLU cc_start: 0.9383 (OUTLIER) cc_final: 0.9127 (tt0) REVERT: D 272 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8157 (tmm) REVERT: E 63 THR cc_start: 0.9768 (OUTLIER) cc_final: 0.9333 (p) REVERT: E 160 LYS cc_start: 0.9595 (mtmt) cc_final: 0.9286 (mttt) REVERT: E 171 THR cc_start: 0.9588 (OUTLIER) cc_final: 0.9049 (p) REVERT: E 246 GLU cc_start: 0.8610 (mp0) cc_final: 0.8318 (mp0) REVERT: F 47 TYR cc_start: 0.7957 (m-10) cc_final: 0.7741 (m-10) REVERT: F 209 ARG cc_start: 0.8190 (mtt-85) cc_final: 0.7914 (mtt-85) REVERT: F 283 ASN cc_start: 0.8873 (t0) cc_final: 0.8640 (t0) REVERT: G 100 LEU cc_start: 0.9163 (mp) cc_final: 0.8960 (mp) REVERT: G 254 GLU cc_start: 0.9237 (OUTLIER) cc_final: 0.8986 (mt-10) REVERT: N 62 LEU cc_start: 0.9401 (tp) cc_final: 0.9141 (tp) REVERT: N 119 LYS cc_start: 0.9164 (mmmm) cc_final: 0.8917 (mmmm) REVERT: N 155 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8997 (mt) REVERT: I 36 GLU cc_start: 0.8989 (pm20) cc_final: 0.8301 (pm20) REVERT: I 66 THR cc_start: 0.9490 (OUTLIER) cc_final: 0.9104 (p) REVERT: I 97 MET cc_start: 0.9652 (ttm) cc_final: 0.9412 (ttt) REVERT: J 74 ARG cc_start: 0.9571 (OUTLIER) cc_final: 0.9194 (ptm-80) REVERT: J 97 MET cc_start: 0.9034 (ttt) cc_final: 0.8834 (ttt) REVERT: K 9 GLN cc_start: 0.9395 (tm-30) cc_final: 0.8585 (tp-100) REVERT: K 84 ASN cc_start: 0.8710 (t0) cc_final: 0.8221 (t0) REVERT: K 144 LYS cc_start: 0.9567 (ttpt) cc_final: 0.9250 (ttpp) REVERT: K 154 GLN cc_start: 0.9220 (OUTLIER) cc_final: 0.8576 (tp40) REVERT: L 81 ASN cc_start: 0.8740 (m-40) cc_final: 0.8526 (m-40) REVERT: L 123 ASP cc_start: 0.9278 (t0) cc_final: 0.9045 (t0) REVERT: L 154 GLN cc_start: 0.9220 (OUTLIER) cc_final: 0.8326 (tt0) REVERT: M 36 GLU cc_start: 0.8948 (pt0) cc_final: 0.8377 (pm20) REVERT: M 60 LYS cc_start: 0.9088 (tttp) cc_final: 0.8776 (ttmm) REVERT: M 84 ASN cc_start: 0.9291 (t0) cc_final: 0.9081 (t0) REVERT: M 87 ILE cc_start: 0.9472 (tt) cc_final: 0.9256 (tp) REVERT: M 104 MET cc_start: 0.8873 (ttp) cc_final: 0.8580 (ttp) REVERT: M 107 LYS cc_start: 0.9396 (mtpt) cc_final: 0.8961 (mtpt) REVERT: M 133 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8341 (mm-30) REVERT: M 144 LYS cc_start: 0.9375 (ttmm) cc_final: 0.9018 (ttmm) outliers start: 72 outliers final: 57 residues processed: 444 average time/residue: 0.1630 time to fit residues: 115.2052 Evaluate side-chains 455 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 386 time to evaluate : 1.028 ------------------------------------------------------------------------------- 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 285 LEU 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 98 ASP Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 55 SER 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 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 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 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 223 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 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 254 GLU Chi-restraints excluded: chain N residue 10 ARG 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 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 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 73 ILE Chi-restraints excluded: chain J residue 74 ARG Chi-restraints excluded: chain J residue 94 ILE 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 96 VAL Chi-restraints excluded: chain K residue 120 LEU 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 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 67 THR 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 255 optimal weight: 4.9990 chunk 267 optimal weight: 0.0670 chunk 179 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 211 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 70 optimal weight: 5.9990 chunk 225 optimal weight: 9.9990 chunk 231 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 overall best weight: 2.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 GLN ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 83 GLN ** 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 = 0.2718 r_free = 0.2718 target = 0.053340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2420 r_free = 0.2420 target = 0.042096 restraints weight = 84166.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2459 r_free = 0.2459 target = 0.043562 restraints weight = 33433.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2484 r_free = 0.2484 target = 0.044522 restraints weight = 18297.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2501 r_free = 0.2501 target = 0.045135 restraints weight = 11872.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2512 r_free = 0.2512 target = 0.045559 restraints weight = 8701.279| |-----------------------------------------------------------------------------| r_work (final): 0.2508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24556 Z= 0.169 Angle : 0.620 10.972 33376 Z= 0.329 Chirality : 0.045 0.183 3909 Planarity : 0.004 0.050 4265 Dihedral : 4.387 19.162 3335 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.46 % Favored : 95.19 % Rotamer: Outliers : 2.74 % Allowed : 22.19 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.14), residues: 3117 helix: 1.73 (0.25), residues: 528 sheet: -0.04 (0.29), residues: 303 loop : -1.48 (0.11), residues: 2286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 58 TYR 0.012 0.001 TYR M 88 PHE 0.008 0.001 PHE E 282 TRP 0.009 0.001 TRP L 103 HIS 0.005 0.001 HIS B 159 Details of bonding type rmsd covalent geometry : bond 0.00384 (24556) covalent geometry : angle 0.62048 (33376) hydrogen bonds : bond 0.04164 ( 743) hydrogen bonds : angle 5.00580 ( 2118) ********************** 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 460 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 388 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 MET cc_start: 0.8882 (mtt) cc_final: 0.8500 (mtt) REVERT: B 98 ASP cc_start: 0.9022 (OUTLIER) cc_final: 0.8701 (t0) REVERT: B 246 GLU cc_start: 0.8358 (mp0) cc_final: 0.7999 (mp0) REVERT: C 31 MET cc_start: 0.9103 (mmt) cc_final: 0.7424 (ptt) REVERT: C 227 MET cc_start: 0.8421 (tpp) cc_final: 0.8191 (tpt) REVERT: C 270 ASN cc_start: 0.9241 (t0) cc_final: 0.8490 (t0) REVERT: D 65 GLU cc_start: 0.9382 (OUTLIER) cc_final: 0.9132 (tt0) REVERT: D 242 ASN cc_start: 0.9019 (m-40) cc_final: 0.8498 (m-40) REVERT: D 272 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.8131 (tmm) REVERT: E 63 THR cc_start: 0.9767 (OUTLIER) cc_final: 0.9328 (p) REVERT: E 160 LYS cc_start: 0.9587 (mtmt) cc_final: 0.9289 (mttt) REVERT: E 171 THR cc_start: 0.9591 (OUTLIER) cc_final: 0.9058 (p) REVERT: E 246 GLU cc_start: 0.8610 (mp0) cc_final: 0.8321 (mp0) REVERT: F 47 TYR cc_start: 0.7832 (m-10) cc_final: 0.7618 (m-10) REVERT: F 209 ARG cc_start: 0.8193 (mtt-85) cc_final: 0.7920 (mtt-85) REVERT: F 272 MET cc_start: 0.8842 (mmt) cc_final: 0.8444 (mmm) REVERT: F 283 ASN cc_start: 0.8839 (t0) cc_final: 0.8598 (t0) REVERT: G 100 LEU cc_start: 0.9162 (mp) cc_final: 0.8944 (mp) REVERT: G 254 GLU cc_start: 0.9236 (OUTLIER) cc_final: 0.8790 (mm-30) REVERT: N 36 GLU cc_start: 0.9344 (tt0) cc_final: 0.9035 (pp20) REVERT: N 62 LEU cc_start: 0.9408 (tp) cc_final: 0.9202 (tp) REVERT: N 119 LYS cc_start: 0.9177 (mmmm) cc_final: 0.8932 (mmmm) REVERT: N 155 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8970 (mt) REVERT: I 36 GLU cc_start: 0.8947 (pm20) cc_final: 0.8153 (pm20) REVERT: I 66 THR cc_start: 0.9492 (OUTLIER) cc_final: 0.9110 (p) REVERT: I 97 MET cc_start: 0.9636 (ttm) cc_final: 0.9393 (ttt) REVERT: J 74 ARG cc_start: 0.9568 (OUTLIER) cc_final: 0.9195 (ptm-80) REVERT: J 123 ASP cc_start: 0.9317 (t0) cc_final: 0.9084 (t70) REVERT: K 9 GLN cc_start: 0.9395 (tm-30) cc_final: 0.8586 (tp-100) REVERT: K 84 ASN cc_start: 0.8668 (t0) cc_final: 0.8455 (t0) REVERT: K 144 LYS cc_start: 0.9566 (ttpt) cc_final: 0.9246 (ttpp) REVERT: K 154 GLN cc_start: 0.9219 (OUTLIER) cc_final: 0.8575 (tp40) REVERT: L 22 ASP cc_start: 0.7725 (m-30) cc_final: 0.7346 (t0) REVERT: L 81 ASN cc_start: 0.8786 (m-40) cc_final: 0.8566 (m-40) REVERT: L 123 ASP cc_start: 0.9285 (t0) cc_final: 0.9056 (t0) REVERT: L 154 GLN cc_start: 0.9202 (OUTLIER) cc_final: 0.8318 (tt0) REVERT: M 36 GLU cc_start: 0.8952 (pt0) cc_final: 0.8488 (pm20) REVERT: M 60 LYS cc_start: 0.9098 (tttp) cc_final: 0.8779 (ttmm) REVERT: M 84 ASN cc_start: 0.9299 (t0) cc_final: 0.8999 (t0) REVERT: M 87 ILE cc_start: 0.9468 (tt) cc_final: 0.9249 (tp) REVERT: M 104 MET cc_start: 0.8873 (ttp) cc_final: 0.8576 (ttp) REVERT: M 107 LYS cc_start: 0.9427 (mtpt) cc_final: 0.9033 (mtpt) REVERT: M 144 LYS cc_start: 0.9377 (ttmm) cc_final: 0.9020 (ttmm) outliers start: 72 outliers final: 57 residues processed: 437 average time/residue: 0.1546 time to fit residues: 108.5944 Evaluate side-chains 453 residues out of total 2632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 385 time to evaluate : 0.974 ------------------------------------------------------------------------------- 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 76 MET 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 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 272 MET Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 298 CYS 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 81 VAL Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 223 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 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 254 GLU Chi-restraints excluded: chain N residue 10 ARG 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 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 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 73 ILE Chi-restraints excluded: chain J residue 74 ARG Chi-restraints excluded: chain J residue 94 ILE 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 96 VAL Chi-restraints excluded: chain K residue 120 LEU 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 19 MET 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 67 THR 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 293 optimal weight: 10.0000 chunk 110 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 150 optimal weight: 7.9990 chunk 120 optimal weight: 0.0050 chunk 167 optimal weight: 2.9990 chunk 71 optimal weight: 0.2980 chunk 195 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 226 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 overall best weight: 1.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 GLN ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 83 GLN ** 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 = 0.2730 r_free = 0.2730 target = 0.053843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2434 r_free = 0.2434 target = 0.042606 restraints weight = 83862.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2473 r_free = 0.2473 target = 0.044079 restraints weight = 33346.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2499 r_free = 0.2499 target = 0.045045 restraints weight = 18253.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2516 r_free = 0.2516 target = 0.045678 restraints weight = 11834.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2527 r_free = 0.2527 target = 0.046098 restraints weight = 8634.635| |-----------------------------------------------------------------------------| r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 24556 Z= 0.148 Angle : 0.616 10.533 33376 Z= 0.325 Chirality : 0.045 0.173 3909 Planarity : 0.004 0.050 4265 Dihedral : 4.299 18.725 3335 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.66 % Favored : 96.02 % Rotamer: Outliers : 2.66 % Allowed : 22.61 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.14), residues: 3117 helix: 1.78 (0.25), residues: 527 sheet: -0.07 (0.28), residues: 312 loop : -1.44 (0.12), residues: 2278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 309 TYR 0.011 0.001 TYR C 47 PHE 0.011 0.001 PHE D 294 TRP 0.009 0.001 TRP L 103 HIS 0.005 0.001 HIS B 159 Details of bonding type rmsd covalent geometry : bond 0.00335 (24556) covalent geometry : angle 0.61566 (33376) hydrogen bonds : bond 0.03888 ( 743) hydrogen bonds : angle 4.91779 ( 2118) =============================================================================== Job complete usr+sys time: 4997.28 seconds wall clock time: 86 minutes 53.30 seconds (5213.30 seconds total)