Starting phenix.real_space_refine on Wed Mar 4 12:24:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6s3l_10093/03_2026/6s3l_10093.cif Found real_map, /net/cci-nas-00/data/ceres_data/6s3l_10093/03_2026/6s3l_10093.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6s3l_10093/03_2026/6s3l_10093.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6s3l_10093/03_2026/6s3l_10093.map" model { file = "/net/cci-nas-00/data/ceres_data/6s3l_10093/03_2026/6s3l_10093.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6s3l_10093/03_2026/6s3l_10093.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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 146 5.16 5 C 9238 2.51 5 N 2113 2.21 5 O 2352 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13849 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1482 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 10, 'TRANS': 180} Chain: "B" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1513 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 10, 'TRANS': 184} Chain: "C" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1520 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 10, 'TRANS': 185} Chain: "D" Number of atoms: 1505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1505 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "E" Number of atoms: 1493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1493 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 10, 'TRANS': 181} Chain: "F" Number of atoms: 1948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1948 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 9, 'TRANS': 241} Chain: "G" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 724 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 4, 'TRANS': 84} Chain: "H" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 724 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 4, 'TRANS': 84} Chain: "I" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 724 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 4, 'TRANS': 84} Chain: "J" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 724 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 4, 'TRANS': 84} Chain: "K" Number of atoms: 1492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1492 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 5, 'TRANS': 187} Time building chain proxies: 3.12, per 1000 atoms: 0.23 Number of scatterers: 13849 At special positions: 0 Unit cell: (99.462, 102.75, 133.986, 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 146 16.00 O 2352 8.00 N 2113 7.00 C 9238 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: 0.88 Conformation dependent library (CDL) restraints added in 458.3 milliseconds 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3380 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 0 sheets defined 83.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 111 through 117 Processing helix chain 'A' and resid 118 through 133 removed outlier: 4.241A pdb=" N ILE A 122 " --> pdb=" O SER A 118 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL A 124 " --> pdb=" O THR A 120 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN A 131 " --> pdb=" O SER A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 156 Processing helix chain 'A' and resid 156 through 168 Processing helix chain 'A' and resid 168 through 173 Processing helix chain 'A' and resid 179 through 195 removed outlier: 3.799A pdb=" N GLU A 187 " --> pdb=" O ASP A 183 " (cutoff:3.500A) Proline residue: A 188 - end of helix removed outlier: 3.586A pdb=" N PHE A 192 " --> pdb=" O PRO A 188 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS A 195 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 210 Processing helix chain 'A' and resid 220 through 244 Proline residue: A 226 - end of helix removed outlier: 3.627A pdb=" N SER A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N MET A 242 " --> pdb=" O GLN A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 262 removed outlier: 3.694A pdb=" N ILE A 250 " --> pdb=" O PRO A 246 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP A 251 " --> pdb=" O PHE A 247 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET A 259 " --> pdb=" O ALA A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 283 Processing helix chain 'A' and resid 285 through 293 removed outlier: 4.479A pdb=" N SER A 291 " --> pdb=" O ASN A 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 116 removed outlier: 3.737A pdb=" N ILE B 114 " --> pdb=" O PRO B 110 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU B 115 " --> pdb=" O ALA B 111 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N MET B 116 " --> pdb=" O MET B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 134 removed outlier: 3.654A pdb=" N ILE B 122 " --> pdb=" O SER B 118 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN B 131 " --> pdb=" O SER B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 156 removed outlier: 3.785A pdb=" N GLY B 146 " --> pdb=" O GLN B 142 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU B 149 " --> pdb=" O ILE B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 167 Processing helix chain 'B' and resid 167 through 174 removed outlier: 3.547A pdb=" N ASN B 173 " --> pdb=" O GLN B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 195 removed outlier: 3.531A pdb=" N ASP B 183 " --> pdb=" O ARG B 179 " (cutoff:3.500A) Proline residue: B 188 - end of helix Processing helix chain 'B' and resid 198 through 210 Processing helix chain 'B' and resid 215 through 219 removed outlier: 3.757A pdb=" N VAL B 219 " --> pdb=" O PRO B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 243 Proline residue: B 226 - end of helix removed outlier: 3.560A pdb=" N THR B 230 " --> pdb=" O PRO B 226 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER B 231 " --> pdb=" O ALA B 227 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS B 234 " --> pdb=" O THR B 230 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THR B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 262 removed outlier: 3.792A pdb=" N ILE B 250 " --> pdb=" O PRO B 246 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N MET B 259 " --> pdb=" O ALA B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 272 removed outlier: 3.865A pdb=" N VAL B 271 " --> pdb=" O SER B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 283 removed outlier: 3.562A pdb=" N LYS B 276 " --> pdb=" O SER B 272 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 293 removed outlier: 3.712A pdb=" N SER B 291 " --> pdb=" O ASN B 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 117 removed outlier: 4.521A pdb=" N ILE C 114 " --> pdb=" O PRO C 110 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU C 115 " --> pdb=" O ALA C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 133 Processing helix chain 'C' and resid 140 through 156 Processing helix chain 'C' and resid 156 through 167 removed outlier: 4.126A pdb=" N GLN C 162 " --> pdb=" O PRO C 158 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU C 165 " --> pdb=" O ASN C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 174 removed outlier: 3.579A pdb=" N ASN C 173 " --> pdb=" O GLN C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 194 removed outlier: 3.520A pdb=" N MET C 189 " --> pdb=" O ALA C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 210 removed outlier: 4.167A pdb=" N THR C 204 " --> pdb=" O LYS C 200 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N PHE C 205 " --> pdb=" O ASP C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 219 Processing helix chain 'C' and resid 220 through 245 Proline residue: C 226 - end of helix removed outlier: 3.627A pdb=" N THR C 235 " --> pdb=" O SER C 231 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU C 245 " --> pdb=" O PHE C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 261 removed outlier: 3.653A pdb=" N ILE C 250 " --> pdb=" O PRO C 246 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASP C 251 " --> pdb=" O PHE C 247 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET C 261 " --> pdb=" O VAL C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 283 removed outlier: 4.428A pdb=" N PHE C 275 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL C 281 " --> pdb=" O LEU C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 293 Processing helix chain 'D' and resid 108 through 117 removed outlier: 3.834A pdb=" N MET D 112 " --> pdb=" O PHE D 108 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE D 114 " --> pdb=" O PRO D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 133 Processing helix chain 'D' and resid 140 through 156 Processing helix chain 'D' and resid 156 through 167 Processing helix chain 'D' and resid 168 through 172 Processing helix chain 'D' and resid 181 through 197 removed outlier: 3.521A pdb=" N ALA D 185 " --> pdb=" O ALA D 181 " (cutoff:3.500A) Proline residue: D 188 - end of helix Processing helix chain 'D' and resid 198 through 210 removed outlier: 3.584A pdb=" N THR D 204 " --> pdb=" O LYS D 200 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU D 207 " --> pdb=" O GLU D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 262 Proline residue: D 226 - end of helix removed outlier: 3.558A pdb=" N THR D 230 " --> pdb=" O PRO D 226 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER D 231 " --> pdb=" O ALA D 227 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS D 234 " --> pdb=" O THR D 230 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU D 245 " --> pdb=" O PHE D 241 " (cutoff:3.500A) Proline residue: D 246 - end of helix Processing helix chain 'D' and resid 272 through 283 removed outlier: 3.704A pdb=" N VAL D 283 " --> pdb=" O LEU D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 295 removed outlier: 3.811A pdb=" N ALA D 294 " --> pdb=" O LEU D 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 116 Processing helix chain 'E' and resid 118 through 134 removed outlier: 3.793A pdb=" N GLY E 134 " --> pdb=" O ARG E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 156 Processing helix chain 'E' and resid 156 through 167 Processing helix chain 'E' and resid 167 through 173 Processing helix chain 'E' and resid 177 through 197 removed outlier: 3.735A pdb=" N GLN E 186 " --> pdb=" O PHE E 182 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLU E 187 " --> pdb=" O ASP E 183 " (cutoff:3.500A) Proline residue: E 188 - end of helix removed outlier: 3.837A pdb=" N LYS E 195 " --> pdb=" O ALA E 191 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN E 196 " --> pdb=" O PHE E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 208 removed outlier: 3.808A pdb=" N PHE E 205 " --> pdb=" O ASP E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 219 Processing helix chain 'E' and resid 220 through 261 Proline residue: E 226 - end of helix removed outlier: 3.867A pdb=" N SER E 231 " --> pdb=" O ALA E 227 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS E 234 " --> pdb=" O THR E 230 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR E 235 " --> pdb=" O SER E 231 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N MET E 242 " --> pdb=" O GLN E 238 " (cutoff:3.500A) Proline residue: E 246 - end of helix Processing helix chain 'E' and resid 272 through 283 Processing helix chain 'E' and resid 285 through 295 removed outlier: 3.583A pdb=" N GLY E 295 " --> pdb=" O SER E 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 29 removed outlier: 5.914A pdb=" N TRP F 17 " --> pdb=" O ALA F 13 " (cutoff:3.500A) Proline residue: F 18 - end of helix removed outlier: 3.915A pdb=" N VAL F 28 " --> pdb=" O ALA F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 53 removed outlier: 3.577A pdb=" N ALA F 48 " --> pdb=" O TYR F 44 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR F 50 " --> pdb=" O GLY F 46 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE F 51 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 107 removed outlier: 3.570A pdb=" N ILE F 74 " --> pdb=" O GLN F 70 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN F 78 " --> pdb=" O ILE F 74 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE F 81 " --> pdb=" O GLU F 77 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL F 88 " --> pdb=" O ALA F 84 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N THR F 89 " --> pdb=" O MET F 85 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N PHE F 96 " --> pdb=" O LEU F 92 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU F 99 " --> pdb=" O ILE F 95 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N MET F 105 " --> pdb=" O GLN F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 116 Processing helix chain 'F' and resid 124 through 141 removed outlier: 3.551A pdb=" N GLN F 128 " --> pdb=" O PRO F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 158 removed outlier: 3.773A pdb=" N LYS F 146 " --> pdb=" O ASP F 142 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL F 151 " --> pdb=" O MET F 147 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LYS F 156 " --> pdb=" O VAL F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 174 removed outlier: 3.601A pdb=" N ARG F 171 " --> pdb=" O THR F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 209 removed outlier: 3.583A pdb=" N ILE F 179 " --> pdb=" O LEU F 175 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU F 185 " --> pdb=" O PHE F 181 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER F 188 " --> pdb=" O SER F 184 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N SER F 190 " --> pdb=" O ALA F 186 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLY F 191 " --> pdb=" O VAL F 187 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA F 194 " --> pdb=" O SER F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 234 removed outlier: 3.635A pdb=" N LEU F 224 " --> pdb=" O SER F 220 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU F 234 " --> pdb=" O CYS F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 256 removed outlier: 3.614A pdb=" N ILE F 243 " --> pdb=" O THR F 239 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN F 246 " --> pdb=" O GLU F 242 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU F 247 " --> pdb=" O ILE F 243 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE F 252 " --> pdb=" O THR F 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 42 Proline residue: G 27 - end of helix Processing helix chain 'G' and resid 50 through 65 Processing helix chain 'G' and resid 65 through 83 Processing helix chain 'G' and resid 84 through 89 Processing helix chain 'H' and resid 2 through 42 Proline residue: H 27 - end of helix Processing helix chain 'H' and resid 50 through 65 Processing helix chain 'H' and resid 65 through 83 Processing helix chain 'H' and resid 84 through 89 Processing helix chain 'I' and resid 2 through 42 Proline residue: I 27 - end of helix Processing helix chain 'I' and resid 50 through 65 Processing helix chain 'I' and resid 65 through 83 Processing helix chain 'I' and resid 84 through 89 Processing helix chain 'J' and resid 2 through 42 Proline residue: J 27 - end of helix Processing helix chain 'J' and resid 50 through 65 Processing helix chain 'J' and resid 65 through 83 Processing helix chain 'J' and resid 84 through 89 Processing helix chain 'K' and resid 32 through 66 removed outlier: 3.909A pdb=" N VAL K 38 " --> pdb=" O ALA K 34 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU K 39 " --> pdb=" O SER K 35 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU K 46 " --> pdb=" O GLY K 42 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TRP K 48 " --> pdb=" O VAL K 44 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA K 52 " --> pdb=" O TRP K 48 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLN K 55 " --> pdb=" O GLU K 51 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER K 66 " --> pdb=" O GLN K 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 109 removed outlier: 3.579A pdb=" N ILE K 81 " --> pdb=" O LYS K 77 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU K 91 " --> pdb=" O VAL K 87 " (cutoff:3.500A) Proline residue: K 92 - end of helix Processing helix chain 'K' and resid 129 through 138 Processing helix chain 'K' and resid 139 through 167 removed outlier: 3.630A pdb=" N VAL K 153 " --> pdb=" O SER K 149 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N MET K 154 " --> pdb=" O ILE K 150 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL K 156 " --> pdb=" O LYS K 152 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE K 161 " --> pdb=" O ALA K 157 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR K 162 " --> pdb=" O GLY K 158 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE K 164 " --> pdb=" O ALA K 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 167 through 173 Processing helix chain 'K' and resid 178 through 200 removed outlier: 3.986A pdb=" N ILE K 183 " --> pdb=" O TYR K 179 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N PHE K 184 " --> pdb=" O PRO K 180 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE K 189 " --> pdb=" O HIS K 185 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU K 191 " --> pdb=" O LEU K 187 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ASN K 192 " --> pdb=" O ASP K 188 " (cutoff:3.500A) Processing helix chain 'K' and resid 201 through 219 Proline residue: K 210 - end of helix removed outlier: 3.603A pdb=" N ALA K 217 " --> pdb=" O ILE K 213 " (cutoff:3.500A) 940 hydrogen bonds defined for protein. 2799 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.02 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4130 1.34 - 1.46: 2410 1.46 - 1.57: 7314 1.57 - 1.69: 0 1.69 - 1.81: 284 Bond restraints: 14138 Sorted by residual: bond pdb=" CA ASN C 161 " pdb=" C ASN C 161 " ideal model delta sigma weight residual 1.522 1.481 0.041 1.72e-02 3.38e+03 5.63e+00 bond pdb=" CB ILE E 289 " pdb=" CG2 ILE E 289 " ideal model delta sigma weight residual 1.521 1.456 0.065 3.30e-02 9.18e+02 3.94e+00 bond pdb=" CG LEU F 234 " pdb=" CD2 LEU F 234 " ideal model delta sigma weight residual 1.521 1.459 0.062 3.30e-02 9.18e+02 3.49e+00 bond pdb=" CB VAL F 151 " pdb=" CG2 VAL F 151 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.36e+00 bond pdb=" C PHE A 244 " pdb=" N LEU A 245 " ideal model delta sigma weight residual 1.337 1.308 0.029 1.61e-02 3.86e+03 3.19e+00 ... (remaining 14133 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 18392 2.04 - 4.07: 634 4.07 - 6.11: 130 6.11 - 8.14: 18 8.14 - 10.18: 4 Bond angle restraints: 19178 Sorted by residual: angle pdb=" N MET E 269 " pdb=" CA MET E 269 " pdb=" C MET E 269 " ideal model delta sigma weight residual 114.56 108.01 6.55 1.27e+00 6.20e-01 2.66e+01 angle pdb=" C ASN C 173 " pdb=" N GLU C 174 " pdb=" CA GLU C 174 " ideal model delta sigma weight residual 121.54 130.67 -9.13 1.91e+00 2.74e-01 2.29e+01 angle pdb=" N VAL E 283 " pdb=" CA VAL E 283 " pdb=" C VAL E 283 " ideal model delta sigma weight residual 112.80 107.66 5.14 1.15e+00 7.56e-01 2.00e+01 angle pdb=" C GLN C 137 " pdb=" N THR C 138 " pdb=" CA THR C 138 " ideal model delta sigma weight residual 121.80 131.98 -10.18 2.44e+00 1.68e-01 1.74e+01 angle pdb=" C GLY E 262 " pdb=" N MET E 263 " pdb=" CA MET E 263 " ideal model delta sigma weight residual 121.54 129.27 -7.73 1.91e+00 2.74e-01 1.64e+01 ... (remaining 19173 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 7545 17.89 - 35.77: 734 35.77 - 53.66: 162 53.66 - 71.54: 38 71.54 - 89.43: 12 Dihedral angle restraints: 8491 sinusoidal: 3331 harmonic: 5160 Sorted by residual: dihedral pdb=" CA THR C 138 " pdb=" C THR C 138 " pdb=" N PRO C 139 " pdb=" CA PRO C 139 " ideal model delta harmonic sigma weight residual 180.00 107.39 72.61 0 5.00e+00 4.00e-02 2.11e+02 dihedral pdb=" CA THR A 138 " pdb=" C THR A 138 " pdb=" N PRO A 139 " pdb=" CA PRO A 139 " ideal model delta harmonic sigma weight residual -180.00 -122.96 -57.04 0 5.00e+00 4.00e-02 1.30e+02 dihedral pdb=" CA ILE F 256 " pdb=" C ILE F 256 " pdb=" N ARG F 257 " pdb=" CA ARG F 257 " ideal model delta harmonic sigma weight residual -180.00 -132.33 -47.67 0 5.00e+00 4.00e-02 9.09e+01 ... (remaining 8488 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1329 0.041 - 0.081: 791 0.081 - 0.122: 203 0.122 - 0.163: 32 0.163 - 0.204: 4 Chirality restraints: 2359 Sorted by residual: chirality pdb=" CB ILE K 75 " pdb=" CA ILE K 75 " pdb=" CG1 ILE K 75 " pdb=" CG2 ILE K 75 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA THR B 138 " pdb=" N THR B 138 " pdb=" C THR B 138 " pdb=" CB THR B 138 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.39e-01 chirality pdb=" CG LEU F 133 " pdb=" CB LEU F 133 " pdb=" CD1 LEU F 133 " pdb=" CD2 LEU F 133 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.17 2.00e-01 2.50e+01 7.63e-01 ... (remaining 2356 not shown) Planarity restraints: 2329 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 138 " -0.084 5.00e-02 4.00e+02 1.28e-01 2.63e+01 pdb=" N PRO C 139 " 0.222 5.00e-02 4.00e+02 pdb=" CA PRO C 139 " -0.070 5.00e-02 4.00e+02 pdb=" CD PRO C 139 " -0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 138 " 0.073 5.00e-02 4.00e+02 1.12e-01 2.01e+01 pdb=" N PRO A 139 " -0.194 5.00e-02 4.00e+02 pdb=" CA PRO A 139 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO A 139 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 169 " -0.034 5.00e-02 4.00e+02 5.10e-02 4.17e+00 pdb=" N PRO C 170 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO C 170 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 170 " -0.029 5.00e-02 4.00e+02 ... (remaining 2326 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 144 2.62 - 3.19: 13104 3.19 - 3.76: 21598 3.76 - 4.33: 30500 4.33 - 4.90: 50297 Nonbonded interactions: 115643 Sorted by model distance: nonbonded pdb=" O GLU C 174 " pdb=" N ILE C 176 " model vdw 2.050 3.120 nonbonded pdb=" O GLU D 174 " pdb=" N ILE D 176 " model vdw 2.066 3.120 nonbonded pdb=" O MET I 63 " pdb=" NZ LYS J 11 " model vdw 2.069 3.120 nonbonded pdb=" NH1 ARG B 121 " pdb=" OG SER B 296 " model vdw 2.124 3.120 nonbonded pdb=" O SER C 267 " pdb=" OG SER C 267 " model vdw 2.169 3.040 ... (remaining 115638 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' and resid 109 through 299) selection = (chain 'C' and resid 109 through 299) selection = (chain 'D' and resid 109 through 299) selection = (chain 'E' and resid 109 through 299) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 12.380 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 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 : 0.010 0.067 14138 Z= 0.417 Angle : 0.934 10.179 19178 Z= 0.516 Chirality : 0.051 0.204 2359 Planarity : 0.007 0.128 2329 Dihedral : 15.446 89.429 5111 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.84 % Favored : 93.64 % Rotamer: Outliers : 2.72 % Allowed : 9.96 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.51 (0.17), residues: 1746 helix: -1.85 (0.12), residues: 1410 sheet: None (None), residues: 0 loop : -3.56 (0.28), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 54 TYR 0.020 0.002 TYR F 244 PHE 0.027 0.003 PHE K 101 TRP 0.031 0.002 TRP K 48 HIS 0.005 0.002 HIS F 144 Details of bonding type rmsd covalent geometry : bond 0.01002 (14138) covalent geometry : angle 0.93373 (19178) hydrogen bonds : bond 0.17150 ( 940) hydrogen bonds : angle 7.13230 ( 2799) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 370 time to evaluate : 0.516 Fit side-chains REVERT: B 160 PHE cc_start: 0.8387 (m-80) cc_final: 0.8107 (m-10) REVERT: B 187 GLU cc_start: 0.7544 (tp30) cc_final: 0.7254 (tm-30) REVERT: B 190 LYS cc_start: 0.8758 (ttmm) cc_final: 0.8393 (tttt) REVERT: B 208 MET cc_start: 0.6992 (mmm) cc_final: 0.6588 (mmt) REVERT: C 232 GLU cc_start: 0.7627 (tt0) cc_final: 0.7393 (tt0) REVERT: C 251 ASP cc_start: 0.7622 (m-30) cc_final: 0.7408 (m-30) REVERT: D 242 MET cc_start: 0.7867 (mmt) cc_final: 0.7342 (mmm) REVERT: F 249 GLU cc_start: 0.7479 (tt0) cc_final: 0.7266 (tt0) REVERT: G 13 SER cc_start: 0.8649 (OUTLIER) cc_final: 0.8414 (m) REVERT: G 35 VAL cc_start: 0.8842 (OUTLIER) cc_final: 0.8628 (t) REVERT: H 31 ILE cc_start: 0.8658 (OUTLIER) cc_final: 0.8448 (tt) REVERT: H 49 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8139 (tp) REVERT: I 14 LEU cc_start: 0.8839 (mm) cc_final: 0.8541 (mt) REVERT: I 35 VAL cc_start: 0.8617 (OUTLIER) cc_final: 0.8407 (t) REVERT: I 49 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7610 (mp) REVERT: J 49 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7766 (tt) REVERT: J 57 ILE cc_start: 0.9010 (mm) cc_final: 0.8784 (tp) REVERT: K 31 LYS cc_start: 0.8093 (pttt) cc_final: 0.7412 (mttm) REVERT: K 187 LEU cc_start: 0.8836 (mt) cc_final: 0.8588 (mt) outliers start: 42 outliers final: 7 residues processed: 402 average time/residue: 0.1056 time to fit residues: 64.8580 Evaluate side-chains 319 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 305 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 49 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.2980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN A 186 GLN C 142 GLN C 196 GLN C 212 GLN D 142 GLN D 196 GLN E 131 GLN E 137 GLN E 196 GLN ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 101 GLN F 121 GLN F 240 HIS G 39 GLN G 86 GLN H 39 GLN H 86 GLN I 39 GLN I 47 GLN J 39 GLN K 129 ASN K 185 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.155109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.127988 restraints weight = 16276.570| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.46 r_work: 0.3428 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14138 Z= 0.151 Angle : 0.730 11.231 19178 Z= 0.363 Chirality : 0.043 0.257 2359 Planarity : 0.006 0.112 2329 Dihedral : 6.743 68.131 1839 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.58 % Favored : 95.13 % Rotamer: Outliers : 2.59 % Allowed : 16.04 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.20), residues: 1746 helix: -0.25 (0.14), residues: 1424 sheet: None (None), residues: 0 loop : -2.81 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 54 TYR 0.013 0.002 TYR K 179 PHE 0.022 0.002 PHE A 119 TRP 0.021 0.001 TRP K 48 HIS 0.003 0.001 HIS I 67 Details of bonding type rmsd covalent geometry : bond 0.00336 (14138) covalent geometry : angle 0.73014 (19178) hydrogen bonds : bond 0.04169 ( 940) hydrogen bonds : angle 4.62733 ( 2799) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 335 time to evaluate : 0.531 Fit side-chains revert: symmetry clash REVERT: B 174 GLU cc_start: 0.6865 (mt-10) cc_final: 0.6642 (mt-10) REVERT: B 190 LYS cc_start: 0.8513 (ttmm) cc_final: 0.8205 (tttt) REVERT: B 232 GLU cc_start: 0.8128 (tp30) cc_final: 0.7484 (tt0) REVERT: B 269 MET cc_start: 0.7993 (mpp) cc_final: 0.7590 (mmm) REVERT: C 130 ARG cc_start: 0.8793 (ttp-170) cc_final: 0.8532 (ttp80) REVERT: C 156 MET cc_start: 0.8679 (mmm) cc_final: 0.8475 (mmm) REVERT: C 160 PHE cc_start: 0.7585 (m-10) cc_final: 0.7268 (m-10) REVERT: C 242 MET cc_start: 0.8463 (mmt) cc_final: 0.7866 (mmt) REVERT: D 156 MET cc_start: 0.8022 (mmm) cc_final: 0.7602 (mmm) REVERT: D 242 MET cc_start: 0.8342 (mmt) cc_final: 0.7912 (mmt) REVERT: E 114 ILE cc_start: 0.7716 (OUTLIER) cc_final: 0.7381 (tp) REVERT: E 126 MET cc_start: 0.7930 (mmt) cc_final: 0.7346 (mmt) REVERT: E 165 GLU cc_start: 0.7198 (mp0) cc_final: 0.6933 (mm-30) REVERT: E 289 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8556 (mt) REVERT: F 87 MET cc_start: 0.8205 (tpp) cc_final: 0.7961 (mmt) REVERT: I 10 PHE cc_start: 0.7594 (OUTLIER) cc_final: 0.7335 (t80) REVERT: I 14 LEU cc_start: 0.8876 (mm) cc_final: 0.8534 (mt) REVERT: I 49 LEU cc_start: 0.8038 (tt) cc_final: 0.7613 (mp) REVERT: I 80 MET cc_start: 0.7352 (mtm) cc_final: 0.6878 (ptp) REVERT: J 82 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7642 (mt-10) REVERT: K 31 LYS cc_start: 0.7689 (pttt) cc_final: 0.7187 (mttp) outliers start: 40 outliers final: 15 residues processed: 359 average time/residue: 0.1026 time to fit residues: 56.4175 Evaluate side-chains 316 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 297 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain I residue 10 PHE Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 43 SER Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain J residue 50 SER Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain K residue 203 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 47 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 130 optimal weight: 0.5980 chunk 68 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 156 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 chunk 131 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN E 166 GLN F 101 GLN K 215 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.154655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.127131 restraints weight = 16235.313| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.46 r_work: 0.3398 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14138 Z= 0.166 Angle : 0.705 9.728 19178 Z= 0.346 Chirality : 0.043 0.197 2359 Planarity : 0.005 0.110 2329 Dihedral : 5.883 69.954 1823 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.44 % Favored : 94.44 % Rotamer: Outliers : 3.82 % Allowed : 17.01 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.20), residues: 1746 helix: 0.33 (0.14), residues: 1429 sheet: None (None), residues: 0 loop : -2.66 (0.32), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 121 TYR 0.014 0.002 TYR K 179 PHE 0.020 0.001 PHE A 119 TRP 0.018 0.001 TRP K 48 HIS 0.002 0.000 HIS I 67 Details of bonding type rmsd covalent geometry : bond 0.00400 (14138) covalent geometry : angle 0.70520 (19178) hydrogen bonds : bond 0.03936 ( 940) hydrogen bonds : angle 4.42108 ( 2799) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 307 time to evaluate : 0.453 Fit side-chains revert: symmetry clash REVERT: B 174 GLU cc_start: 0.6700 (mt-10) cc_final: 0.6494 (mt-10) REVERT: B 190 LYS cc_start: 0.8555 (ttmm) cc_final: 0.8330 (tttt) REVERT: B 232 GLU cc_start: 0.8199 (tp30) cc_final: 0.7468 (tt0) REVERT: C 160 PHE cc_start: 0.7589 (m-10) cc_final: 0.7228 (m-10) REVERT: D 116 MET cc_start: 0.8244 (mtp) cc_final: 0.8037 (tpp) REVERT: D 131 GLN cc_start: 0.8530 (tt0) cc_final: 0.8235 (mt0) REVERT: E 114 ILE cc_start: 0.7723 (OUTLIER) cc_final: 0.7332 (tp) REVERT: E 126 MET cc_start: 0.8091 (mmt) cc_final: 0.7437 (mmm) REVERT: E 165 GLU cc_start: 0.7223 (mp0) cc_final: 0.6655 (mp0) REVERT: E 182 PHE cc_start: 0.8302 (t80) cc_final: 0.7985 (t80) REVERT: F 87 MET cc_start: 0.8269 (tpp) cc_final: 0.7914 (mmt) REVERT: F 181 PHE cc_start: 0.8558 (m-80) cc_final: 0.8267 (m-80) REVERT: H 83 ARG cc_start: 0.8375 (tpp80) cc_final: 0.7468 (ttm-80) REVERT: I 10 PHE cc_start: 0.7677 (OUTLIER) cc_final: 0.7297 (t80) REVERT: I 14 LEU cc_start: 0.8860 (mm) cc_final: 0.8642 (mt) REVERT: I 49 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7628 (mp) REVERT: I 80 MET cc_start: 0.7455 (mtm) cc_final: 0.6897 (ptp) REVERT: K 70 GLU cc_start: 0.7338 (mp0) cc_final: 0.6969 (mp0) outliers start: 59 outliers final: 29 residues processed: 338 average time/residue: 0.0983 time to fit residues: 51.0967 Evaluate side-chains 328 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 296 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 263 MET Chi-restraints excluded: chain E residue 264 MET Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain I residue 10 PHE Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain I residue 43 SER Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain J residue 50 SER Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain K residue 203 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 36 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 11 optimal weight: 0.0010 chunk 62 optimal weight: 5.9990 chunk 86 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN A 287 ASN E 166 GLN K 215 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.151803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.122828 restraints weight = 16310.302| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.58 r_work: 0.3319 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14138 Z= 0.140 Angle : 0.668 9.271 19178 Z= 0.327 Chirality : 0.041 0.173 2359 Planarity : 0.005 0.102 2329 Dihedral : 5.543 68.302 1821 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.04 % Favored : 94.85 % Rotamer: Outliers : 3.62 % Allowed : 18.31 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.21), residues: 1746 helix: 0.76 (0.14), residues: 1424 sheet: None (None), residues: 0 loop : -2.50 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 54 TYR 0.012 0.001 TYR K 179 PHE 0.019 0.001 PHE C 119 TRP 0.017 0.001 TRP K 48 HIS 0.001 0.000 HIS I 67 Details of bonding type rmsd covalent geometry : bond 0.00326 (14138) covalent geometry : angle 0.66778 (19178) hydrogen bonds : bond 0.03567 ( 940) hydrogen bonds : angle 4.22048 ( 2799) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 297 time to evaluate : 0.438 Fit side-chains revert: symmetry clash REVERT: B 190 LYS cc_start: 0.8466 (ttmm) cc_final: 0.8210 (tttt) REVERT: B 232 GLU cc_start: 0.8209 (tp30) cc_final: 0.7437 (tt0) REVERT: C 156 MET cc_start: 0.8332 (mmm) cc_final: 0.7923 (mtp) REVERT: D 156 MET cc_start: 0.8022 (mmm) cc_final: 0.7628 (mmm) REVERT: E 114 ILE cc_start: 0.7681 (OUTLIER) cc_final: 0.7259 (tp) REVERT: E 133 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.8004 (mpp) REVERT: E 182 PHE cc_start: 0.8267 (t80) cc_final: 0.8005 (t80) REVERT: F 14 ASN cc_start: 0.8453 (t0) cc_final: 0.8233 (t0) REVERT: F 181 PHE cc_start: 0.8499 (m-80) cc_final: 0.8180 (m-80) REVERT: H 10 PHE cc_start: 0.7641 (OUTLIER) cc_final: 0.7439 (t80) REVERT: I 14 LEU cc_start: 0.8837 (mm) cc_final: 0.8623 (mt) REVERT: I 49 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7582 (mp) REVERT: I 80 MET cc_start: 0.7576 (mtm) cc_final: 0.7017 (ptp) REVERT: K 70 GLU cc_start: 0.7299 (mp0) cc_final: 0.7079 (mp0) REVERT: K 145 GLU cc_start: 0.7433 (tt0) cc_final: 0.7203 (tp30) outliers start: 56 outliers final: 27 residues processed: 330 average time/residue: 0.1017 time to fit residues: 51.7702 Evaluate side-chains 317 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 286 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain E residue 264 MET Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 257 ARG Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain H residue 10 PHE Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 43 SER Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain J residue 50 SER Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain K residue 203 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 119 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 97 optimal weight: 0.1980 chunk 20 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 144 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 GLN D 142 GLN E 166 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.162036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.136500 restraints weight = 15831.739| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.45 r_work: 0.3350 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14138 Z= 0.133 Angle : 0.650 9.949 19178 Z= 0.319 Chirality : 0.041 0.173 2359 Planarity : 0.005 0.102 2329 Dihedral : 5.398 66.710 1821 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.38 % Favored : 94.50 % Rotamer: Outliers : 4.01 % Allowed : 18.50 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.21), residues: 1746 helix: 1.06 (0.14), residues: 1424 sheet: None (None), residues: 0 loop : -2.46 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 54 TYR 0.011 0.001 TYR K 179 PHE 0.018 0.001 PHE C 119 TRP 0.015 0.001 TRP C 286 HIS 0.001 0.000 HIS I 67 Details of bonding type rmsd covalent geometry : bond 0.00308 (14138) covalent geometry : angle 0.65017 (19178) hydrogen bonds : bond 0.03427 ( 940) hydrogen bonds : angle 4.11287 ( 2799) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 295 time to evaluate : 0.607 Fit side-chains revert: symmetry clash REVERT: B 190 LYS cc_start: 0.8570 (ttmm) cc_final: 0.8302 (tttt) REVERT: B 232 GLU cc_start: 0.8088 (tp30) cc_final: 0.7393 (tt0) REVERT: B 259 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.7918 (mmm) REVERT: C 156 MET cc_start: 0.8414 (mmm) cc_final: 0.7831 (mtp) REVERT: D 131 GLN cc_start: 0.8439 (tt0) cc_final: 0.8022 (mt0) REVERT: D 208 MET cc_start: 0.7805 (tpp) cc_final: 0.7602 (tpp) REVERT: D 259 MET cc_start: 0.8678 (tpt) cc_final: 0.8238 (tpt) REVERT: E 114 ILE cc_start: 0.7743 (OUTLIER) cc_final: 0.7327 (tp) REVERT: E 133 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.8212 (mtp) REVERT: E 182 PHE cc_start: 0.8289 (t80) cc_final: 0.8060 (t80) REVERT: F 181 PHE cc_start: 0.8474 (m-80) cc_final: 0.8187 (m-80) REVERT: F 255 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7948 (mt) REVERT: I 14 LEU cc_start: 0.8872 (mm) cc_final: 0.8650 (mt) REVERT: I 49 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7640 (mp) REVERT: I 80 MET cc_start: 0.7525 (mtm) cc_final: 0.6986 (ptp) outliers start: 62 outliers final: 30 residues processed: 328 average time/residue: 0.1029 time to fit residues: 51.5762 Evaluate side-chains 319 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 284 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 259 MET Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 171 TYR Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 264 MET Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 257 ARG Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 43 SER Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain J residue 50 SER Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain K residue 137 MET Chi-restraints excluded: chain K residue 203 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 139 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 141 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 121 optimal weight: 0.7980 chunk 49 optimal weight: 0.1980 chunk 123 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 215 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.157052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.128368 restraints weight = 16232.203| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.52 r_work: 0.3371 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14138 Z= 0.127 Angle : 0.640 9.446 19178 Z= 0.314 Chirality : 0.041 0.176 2359 Planarity : 0.005 0.098 2329 Dihedral : 5.255 65.208 1820 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.21 % Favored : 94.67 % Rotamer: Outliers : 3.62 % Allowed : 19.08 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.21), residues: 1746 helix: 1.30 (0.14), residues: 1422 sheet: None (None), residues: 0 loop : -2.25 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 54 TYR 0.014 0.001 TYR F 241 PHE 0.017 0.001 PHE C 119 TRP 0.014 0.001 TRP H 68 HIS 0.001 0.000 HIS I 67 Details of bonding type rmsd covalent geometry : bond 0.00290 (14138) covalent geometry : angle 0.63962 (19178) hydrogen bonds : bond 0.03299 ( 940) hydrogen bonds : angle 4.01923 ( 2799) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 299 time to evaluate : 0.528 Fit side-chains revert: symmetry clash REVERT: B 133 MET cc_start: 0.8250 (OUTLIER) cc_final: 0.7527 (mpp) REVERT: B 190 LYS cc_start: 0.8516 (ttmm) cc_final: 0.8307 (tttt) REVERT: B 232 GLU cc_start: 0.8143 (tp30) cc_final: 0.7410 (tt0) REVERT: B 284 ASP cc_start: 0.8583 (t0) cc_final: 0.8324 (t0) REVERT: D 149 LEU cc_start: 0.8505 (tp) cc_final: 0.8293 (mp) REVERT: D 259 MET cc_start: 0.8655 (tpt) cc_final: 0.8226 (tpt) REVERT: E 114 ILE cc_start: 0.7771 (OUTLIER) cc_final: 0.7361 (tp) REVERT: E 182 PHE cc_start: 0.8272 (t80) cc_final: 0.8059 (t80) REVERT: F 87 MET cc_start: 0.8528 (mmm) cc_final: 0.8317 (mmt) REVERT: F 181 PHE cc_start: 0.8497 (m-80) cc_final: 0.8244 (m-80) REVERT: H 9 LEU cc_start: 0.8159 (tp) cc_final: 0.7896 (tp) REVERT: I 14 LEU cc_start: 0.8861 (mm) cc_final: 0.8642 (mt) REVERT: I 49 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7633 (mp) REVERT: I 80 MET cc_start: 0.7567 (mtm) cc_final: 0.7002 (ptp) REVERT: K 141 GLN cc_start: 0.6637 (OUTLIER) cc_final: 0.6394 (tm-30) outliers start: 56 outliers final: 40 residues processed: 329 average time/residue: 0.1050 time to fit residues: 52.7754 Evaluate side-chains 330 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 286 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 162 GLN Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 171 TYR Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 264 MET Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 257 ARG Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain I residue 43 SER Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain J residue 7 VAL Chi-restraints excluded: chain J residue 50 SER Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain K residue 137 MET Chi-restraints excluded: chain K residue 141 GLN Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain K residue 203 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 77 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 112 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 160 optimal weight: 20.0000 chunk 91 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 HIS K 215 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.154224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.124658 restraints weight = 16358.653| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.60 r_work: 0.3339 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14138 Z= 0.133 Angle : 0.649 11.375 19178 Z= 0.315 Chirality : 0.041 0.174 2359 Planarity : 0.005 0.098 2329 Dihedral : 5.225 64.353 1820 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.27 % Favored : 94.62 % Rotamer: Outliers : 3.43 % Allowed : 19.92 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.21), residues: 1746 helix: 1.41 (0.14), residues: 1425 sheet: None (None), residues: 0 loop : -2.21 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 63 TYR 0.012 0.001 TYR F 241 PHE 0.016 0.001 PHE C 119 TRP 0.015 0.001 TRP H 68 HIS 0.007 0.001 HIS H 67 Details of bonding type rmsd covalent geometry : bond 0.00310 (14138) covalent geometry : angle 0.64884 (19178) hydrogen bonds : bond 0.03302 ( 940) hydrogen bonds : angle 3.98634 ( 2799) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 294 time to evaluate : 0.519 Fit side-chains revert: symmetry clash REVERT: B 133 MET cc_start: 0.8206 (OUTLIER) cc_final: 0.7493 (mpp) REVERT: B 190 LYS cc_start: 0.8476 (ttmm) cc_final: 0.8210 (tttt) REVERT: B 232 GLU cc_start: 0.8188 (tp30) cc_final: 0.7426 (tt0) REVERT: D 149 LEU cc_start: 0.8499 (tp) cc_final: 0.8290 (mp) REVERT: D 156 MET cc_start: 0.8091 (mmm) cc_final: 0.7586 (mmm) REVERT: D 259 MET cc_start: 0.8650 (tpt) cc_final: 0.8192 (tpt) REVERT: E 114 ILE cc_start: 0.7777 (OUTLIER) cc_final: 0.7359 (tp) REVERT: E 166 GLN cc_start: 0.7314 (OUTLIER) cc_final: 0.7078 (mp10) REVERT: E 182 PHE cc_start: 0.8245 (t80) cc_final: 0.8021 (t80) REVERT: F 87 MET cc_start: 0.8542 (mmm) cc_final: 0.8318 (mmt) REVERT: F 255 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7911 (mt) REVERT: I 14 LEU cc_start: 0.8840 (mm) cc_final: 0.8485 (mt) REVERT: I 49 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7547 (mp) REVERT: I 80 MET cc_start: 0.7657 (mtm) cc_final: 0.7055 (ptp) REVERT: K 137 MET cc_start: 0.7105 (OUTLIER) cc_final: 0.6770 (ttp) outliers start: 53 outliers final: 34 residues processed: 321 average time/residue: 0.0958 time to fit residues: 47.6409 Evaluate side-chains 328 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 288 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 162 GLN Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 171 TYR Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 166 GLN Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 264 MET Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain I residue 43 SER Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain J residue 7 VAL Chi-restraints excluded: chain J residue 50 SER Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain K residue 137 MET Chi-restraints excluded: chain K residue 203 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 78 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 chunk 165 optimal weight: 0.8980 chunk 10 optimal weight: 0.0370 chunk 76 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 22 optimal weight: 0.4980 chunk 138 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 153 optimal weight: 3.9990 overall best weight: 0.8862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.159385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.133173 restraints weight = 15923.705| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.45 r_work: 0.3297 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14138 Z= 0.135 Angle : 0.651 9.881 19178 Z= 0.316 Chirality : 0.041 0.177 2359 Planarity : 0.005 0.097 2329 Dihedral : 5.209 64.225 1820 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.15 % Favored : 94.73 % Rotamer: Outliers : 3.04 % Allowed : 20.89 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.21), residues: 1746 helix: 1.47 (0.14), residues: 1425 sheet: None (None), residues: 0 loop : -2.14 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 257 TYR 0.011 0.001 TYR F 241 PHE 0.018 0.001 PHE C 119 TRP 0.015 0.001 TRP H 68 HIS 0.002 0.000 HIS F 144 Details of bonding type rmsd covalent geometry : bond 0.00316 (14138) covalent geometry : angle 0.65080 (19178) hydrogen bonds : bond 0.03305 ( 940) hydrogen bonds : angle 3.95931 ( 2799) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 298 time to evaluate : 0.535 Fit side-chains revert: symmetry clash REVERT: B 133 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7302 (mpp) REVERT: B 232 GLU cc_start: 0.8133 (tp30) cc_final: 0.7368 (tt0) REVERT: B 259 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.7924 (mmm) REVERT: D 131 GLN cc_start: 0.8347 (tt0) cc_final: 0.7861 (mt0) REVERT: D 149 LEU cc_start: 0.8483 (tp) cc_final: 0.8264 (mp) REVERT: D 259 MET cc_start: 0.8680 (tpt) cc_final: 0.8229 (tpt) REVERT: E 114 ILE cc_start: 0.7754 (OUTLIER) cc_final: 0.7326 (tp) REVERT: E 165 GLU cc_start: 0.6922 (mp0) cc_final: 0.6627 (mp0) REVERT: E 166 GLN cc_start: 0.7261 (OUTLIER) cc_final: 0.5688 (mp-120) REVERT: F 87 MET cc_start: 0.8446 (mmm) cc_final: 0.8212 (mmt) REVERT: F 255 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7836 (mt) REVERT: H 9 LEU cc_start: 0.7983 (tp) cc_final: 0.7776 (tp) REVERT: I 14 LEU cc_start: 0.8799 (mm) cc_final: 0.8455 (mt) REVERT: I 49 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7506 (mp) REVERT: K 137 MET cc_start: 0.7082 (OUTLIER) cc_final: 0.6750 (ttp) outliers start: 47 outliers final: 32 residues processed: 323 average time/residue: 0.1046 time to fit residues: 52.3473 Evaluate side-chains 331 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 292 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 162 GLN Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 259 MET Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 171 TYR Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 166 GLN Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 264 MET Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain I residue 43 SER Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain J residue 50 SER Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 80 MET Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain K residue 137 MET Chi-restraints excluded: chain K residue 203 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 149 optimal weight: 0.9990 chunk 130 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 140 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 114 optimal weight: 6.9990 chunk 43 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.150945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.120248 restraints weight = 16463.054| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.71 r_work: 0.3252 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14138 Z= 0.142 Angle : 0.666 9.487 19178 Z= 0.322 Chirality : 0.042 0.179 2359 Planarity : 0.005 0.097 2329 Dihedral : 5.231 63.870 1820 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.38 % Favored : 94.56 % Rotamer: Outliers : 2.98 % Allowed : 21.60 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.21), residues: 1746 helix: 1.50 (0.14), residues: 1425 sheet: None (None), residues: 0 loop : -2.10 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 257 TYR 0.012 0.001 TYR F 241 PHE 0.019 0.001 PHE E 182 TRP 0.013 0.001 TRP K 48 HIS 0.001 0.000 HIS F 144 Details of bonding type rmsd covalent geometry : bond 0.00340 (14138) covalent geometry : angle 0.66606 (19178) hydrogen bonds : bond 0.03364 ( 940) hydrogen bonds : angle 3.98391 ( 2799) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 293 time to evaluate : 0.540 Fit side-chains revert: symmetry clash REVERT: A 193 MET cc_start: 0.8098 (mtt) cc_final: 0.7639 (mtt) REVERT: B 133 MET cc_start: 0.8230 (OUTLIER) cc_final: 0.7363 (mpp) REVERT: B 232 GLU cc_start: 0.8212 (tp30) cc_final: 0.7439 (tt0) REVERT: B 259 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.8143 (mmm) REVERT: D 131 GLN cc_start: 0.8433 (tt0) cc_final: 0.7970 (mt0) REVERT: D 149 LEU cc_start: 0.8590 (tp) cc_final: 0.8381 (mp) REVERT: D 259 MET cc_start: 0.8726 (tpt) cc_final: 0.8281 (tpt) REVERT: E 114 ILE cc_start: 0.7747 (OUTLIER) cc_final: 0.7351 (tp) REVERT: E 165 GLU cc_start: 0.7072 (mp0) cc_final: 0.6697 (mp0) REVERT: E 166 GLN cc_start: 0.7229 (OUTLIER) cc_final: 0.5620 (mp-120) REVERT: F 87 MET cc_start: 0.8594 (mmm) cc_final: 0.8368 (mmt) REVERT: F 255 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7792 (mt) REVERT: H 9 LEU cc_start: 0.8005 (tp) cc_final: 0.7787 (tp) REVERT: K 137 MET cc_start: 0.7104 (OUTLIER) cc_final: 0.6783 (ttp) outliers start: 46 outliers final: 35 residues processed: 317 average time/residue: 0.1114 time to fit residues: 55.0389 Evaluate side-chains 329 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 288 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 162 GLN Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 259 MET Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 166 GLN Chi-restraints excluded: chain E residue 187 GLU Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 264 MET Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain I residue 43 SER Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain J residue 31 ILE Chi-restraints excluded: chain J residue 50 SER Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 80 MET Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain K residue 137 MET Chi-restraints excluded: chain K residue 203 VAL Chi-restraints excluded: chain K residue 215 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 6 optimal weight: 0.5980 chunk 125 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 109 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 35 optimal weight: 0.3980 chunk 145 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.152681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.122192 restraints weight = 16423.339| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.69 r_work: 0.3250 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14138 Z= 0.128 Angle : 0.653 9.168 19178 Z= 0.316 Chirality : 0.041 0.180 2359 Planarity : 0.005 0.095 2329 Dihedral : 5.172 62.968 1820 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.04 % Favored : 94.90 % Rotamer: Outliers : 2.72 % Allowed : 21.54 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.21), residues: 1746 helix: 1.60 (0.14), residues: 1425 sheet: None (None), residues: 0 loop : -2.04 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 121 TYR 0.011 0.001 TYR F 241 PHE 0.019 0.001 PHE E 182 TRP 0.012 0.001 TRP H 68 HIS 0.001 0.000 HIS I 67 Details of bonding type rmsd covalent geometry : bond 0.00295 (14138) covalent geometry : angle 0.65338 (19178) hydrogen bonds : bond 0.03243 ( 940) hydrogen bonds : angle 3.93356 ( 2799) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3492 Ramachandran restraints generated. 1746 Oldfield, 0 Emsley, 1746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 285 time to evaluate : 0.571 Fit side-chains revert: symmetry clash REVERT: A 193 MET cc_start: 0.8099 (mtt) cc_final: 0.7665 (mtt) REVERT: B 133 MET cc_start: 0.8197 (OUTLIER) cc_final: 0.7421 (mpp) REVERT: B 232 GLU cc_start: 0.8176 (tp30) cc_final: 0.7395 (tt0) REVERT: B 259 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.8085 (mmm) REVERT: D 131 GLN cc_start: 0.8360 (tt0) cc_final: 0.7877 (mt0) REVERT: D 149 LEU cc_start: 0.8526 (tp) cc_final: 0.8323 (mp) REVERT: D 200 LYS cc_start: 0.8014 (tmmt) cc_final: 0.7761 (tmmt) REVERT: D 259 MET cc_start: 0.8709 (tpt) cc_final: 0.8313 (tpt) REVERT: E 114 ILE cc_start: 0.7705 (OUTLIER) cc_final: 0.7262 (tp) REVERT: E 166 GLN cc_start: 0.7163 (OUTLIER) cc_final: 0.6896 (mp10) REVERT: F 87 MET cc_start: 0.8505 (mmm) cc_final: 0.8276 (mmt) REVERT: F 255 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7726 (mt) REVERT: I 1 MET cc_start: 0.2998 (mtt) cc_final: 0.1599 (mtt) REVERT: I 14 LEU cc_start: 0.8792 (mm) cc_final: 0.8463 (mt) REVERT: K 137 MET cc_start: 0.7001 (OUTLIER) cc_final: 0.6715 (ttp) REVERT: K 168 GLN cc_start: 0.7954 (tt0) cc_final: 0.7675 (mt0) outliers start: 42 outliers final: 33 residues processed: 308 average time/residue: 0.1012 time to fit residues: 49.1659 Evaluate side-chains 322 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 283 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 162 GLN Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 259 MET Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 166 GLN Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 264 MET Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain I residue 43 SER Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain J residue 7 VAL Chi-restraints excluded: chain J residue 50 SER Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 80 MET Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain K residue 137 MET Chi-restraints excluded: chain K residue 203 VAL Chi-restraints excluded: chain K residue 215 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 169 optimal weight: 4.9990 chunk 115 optimal weight: 0.1980 chunk 88 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 112 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 160 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 65 optimal weight: 0.0570 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.153953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.123481 restraints weight = 16356.942| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.69 r_work: 0.3290 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14138 Z= 0.125 Angle : 0.656 10.100 19178 Z= 0.317 Chirality : 0.041 0.179 2359 Planarity : 0.005 0.095 2329 Dihedral : 5.146 61.962 1820 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.15 % Favored : 94.79 % Rotamer: Outliers : 2.72 % Allowed : 21.73 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.21), residues: 1746 helix: 1.65 (0.14), residues: 1425 sheet: None (None), residues: 0 loop : -1.96 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 83 TYR 0.011 0.001 TYR F 241 PHE 0.019 0.001 PHE E 182 TRP 0.014 0.001 TRP H 68 HIS 0.001 0.000 HIS F 144 Details of bonding type rmsd covalent geometry : bond 0.00285 (14138) covalent geometry : angle 0.65608 (19178) hydrogen bonds : bond 0.03198 ( 940) hydrogen bonds : angle 3.91818 ( 2799) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3798.97 seconds wall clock time: 65 minutes 37.55 seconds (3937.55 seconds total)