Starting phenix.real_space_refine on Thu Jul 31 15:32:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6s3l_10093/07_2025/6s3l_10093.cif Found real_map, /net/cci-nas-00/data/ceres_data/6s3l_10093/07_2025/6s3l_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_10093/07_2025/6s3l_10093.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6s3l_10093/07_2025/6s3l_10093.map" model { file = "/net/cci-nas-00/data/ceres_data/6s3l_10093/07_2025/6s3l_10093.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6s3l_10093/07_2025/6s3l_10093.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.78, per 1000 atoms: 0.63 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: 3.20 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.10 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: 3.95 Time building geometry restraints manager: 3.89 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: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 32.980 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.750 ------------------------------------------------------------------------------- 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 : 15.59 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.031 0.002 TRP K 48 HIS 0.005 0.002 HIS F 144 PHE 0.027 0.003 PHE K 101 TYR 0.020 0.002 TYR F 244 ARG 0.006 0.001 ARG G 54 Details of bonding type rmsd hydrogen bonds : bond 0.17150 ( 940) hydrogen bonds : angle 7.13230 ( 2799) covalent geometry : bond 0.01002 (14138) covalent geometry : angle 0.93373 (19178) *********************** 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 : 1.487 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: 0.7868 (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: 0.2236 time to fit residues: 135.0835 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 : 1.431 ------------------------------------------------------------------------------- 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 144 optimal weight: 0.7980 chunk 129 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 69 optimal weight: 0.4980 chunk 134 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 81 optimal weight: 8.9990 chunk 99 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 212 GLN D 142 GLN D 196 GLN E 131 GLN E 137 GLN E 196 GLN 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 I 86 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 = 0.3746 r_free = 0.3746 target = 0.153223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.125852 restraints weight = 16202.761| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.47 r_work: 0.3396 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14138 Z= 0.157 Angle : 0.734 11.075 19178 Z= 0.364 Chirality : 0.043 0.252 2359 Planarity : 0.006 0.114 2329 Dihedral : 6.777 68.536 1839 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.81 % Favored : 94.90 % Rotamer: Outliers : 2.59 % Allowed : 16.24 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.20), residues: 1746 helix: -0.30 (0.14), residues: 1424 sheet: None (None), residues: 0 loop : -2.83 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP K 48 HIS 0.003 0.001 HIS I 67 PHE 0.021 0.002 PHE A 119 TYR 0.014 0.002 TYR K 179 ARG 0.005 0.001 ARG H 54 Details of bonding type rmsd hydrogen bonds : bond 0.04290 ( 940) hydrogen bonds : angle 4.67401 ( 2799) covalent geometry : bond 0.00356 (14138) covalent geometry : angle 0.73359 (19178) *********************** 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 369 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 329 time to evaluate : 1.373 Fit side-chains revert: symmetry clash REVERT: B 164 ASN cc_start: 0.6875 (m-40) cc_final: 0.6649 (t0) REVERT: B 174 GLU cc_start: 0.6850 (mt-10) cc_final: 0.6626 (mt-10) REVERT: B 190 LYS cc_start: 0.8523 (ttmm) cc_final: 0.8206 (tttt) REVERT: B 232 GLU cc_start: 0.8143 (tp30) cc_final: 0.7504 (tt0) REVERT: B 264 MET cc_start: 0.7739 (mtm) cc_final: 0.7528 (ptm) REVERT: C 156 MET cc_start: 0.8681 (mmm) cc_final: 0.8475 (mmm) REVERT: C 160 PHE cc_start: 0.7584 (m-10) cc_final: 0.7269 (m-10) REVERT: C 200 LYS cc_start: 0.8449 (tmmt) cc_final: 0.8243 (ttpp) REVERT: C 242 MET cc_start: 0.8488 (mmt) cc_final: 0.7920 (mmt) REVERT: D 156 MET cc_start: 0.8044 (mmm) cc_final: 0.7604 (mmm) REVERT: D 242 MET cc_start: 0.8365 (mmt) cc_final: 0.7945 (mmt) REVERT: E 114 ILE cc_start: 0.7727 (OUTLIER) cc_final: 0.7413 (tp) REVERT: E 126 MET cc_start: 0.7946 (mmt) cc_final: 0.7338 (mmt) REVERT: E 165 GLU cc_start: 0.7183 (mp0) cc_final: 0.6935 (mm-30) REVERT: E 182 PHE cc_start: 0.8327 (t80) cc_final: 0.8026 (t80) REVERT: E 289 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8567 (mt) REVERT: I 14 LEU cc_start: 0.8858 (mm) cc_final: 0.8540 (mt) REVERT: I 49 LEU cc_start: 0.8040 (tt) cc_final: 0.7601 (mp) REVERT: I 80 MET cc_start: 0.7387 (mtm) cc_final: 0.6884 (ptp) REVERT: J 82 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7652 (mt-10) REVERT: K 31 LYS cc_start: 0.7736 (pttt) cc_final: 0.7151 (mttp) outliers start: 40 outliers final: 17 residues processed: 353 average time/residue: 0.2285 time to fit residues: 122.0147 Evaluate side-chains 317 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 297 time to evaluate : 1.560 ------------------------------------------------------------------------------- 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 G residue 28 SER 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 28 SER Chi-restraints excluded: chain I residue 43 SER 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 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 61 optimal weight: 0.5980 chunk 155 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 31 optimal weight: 0.4980 chunk 6 optimal weight: 3.9990 chunk 158 optimal weight: 0.2980 chunk 26 optimal weight: 4.9990 chunk 112 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN E 166 GLN F 101 GLN I 86 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.162633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.139650 restraints weight = 15901.823| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.27 r_work: 0.3341 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2379 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= 0.137 Angle : 0.677 9.734 19178 Z= 0.334 Chirality : 0.041 0.201 2359 Planarity : 0.005 0.110 2329 Dihedral : 5.766 69.742 1823 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.33 % Favored : 94.56 % Rotamer: Outliers : 3.88 % Allowed : 16.49 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.20), residues: 1746 helix: 0.43 (0.14), residues: 1427 sheet: None (None), residues: 0 loop : -2.56 (0.32), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP K 48 HIS 0.002 0.000 HIS I 67 PHE 0.019 0.001 PHE C 119 TYR 0.013 0.001 TYR E 171 ARG 0.003 0.000 ARG I 54 Details of bonding type rmsd hydrogen bonds : bond 0.03718 ( 940) hydrogen bonds : angle 4.34351 ( 2799) covalent geometry : bond 0.00309 (14138) covalent geometry : angle 0.67665 (19178) *********************** 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 373 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 313 time to evaluate : 1.694 Fit side-chains revert: symmetry clash REVERT: A 112 MET cc_start: 0.7289 (tpt) cc_final: 0.7023 (tpt) REVERT: A 288 LEU cc_start: 0.8535 (mt) cc_final: 0.8302 (mp) REVERT: B 174 GLU cc_start: 0.6666 (mt-10) cc_final: 0.6455 (mt-10) REVERT: B 232 GLU cc_start: 0.8090 (tp30) cc_final: 0.7384 (tt0) REVERT: C 126 MET cc_start: 0.8622 (mtp) cc_final: 0.8416 (mtp) REVERT: C 130 ARG cc_start: 0.8665 (ttp-170) cc_final: 0.8462 (ttp80) REVERT: C 160 PHE cc_start: 0.7544 (m-10) cc_final: 0.7180 (m-10) REVERT: D 131 GLN cc_start: 0.8454 (tt0) cc_final: 0.8168 (mt0) REVERT: E 114 ILE cc_start: 0.7700 (OUTLIER) cc_final: 0.7341 (tp) REVERT: E 115 LEU cc_start: 0.7993 (mt) cc_final: 0.7719 (mm) REVERT: E 126 MET cc_start: 0.7982 (mmt) cc_final: 0.7410 (mmm) REVERT: E 182 PHE cc_start: 0.8308 (t80) cc_final: 0.7989 (t80) REVERT: E 289 ILE cc_start: 0.8876 (OUTLIER) cc_final: 0.8606 (mt) REVERT: F 14 ASN cc_start: 0.8294 (t0) cc_final: 0.8090 (t0) REVERT: F 87 MET cc_start: 0.8451 (mmm) cc_final: 0.8235 (mmt) REVERT: F 181 PHE cc_start: 0.8491 (m-80) cc_final: 0.8163 (m-80) REVERT: H 73 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8358 (mt) REVERT: H 83 ARG cc_start: 0.8191 (tpp80) cc_final: 0.7311 (ttm-80) REVERT: I 1 MET cc_start: 0.2790 (OUTLIER) cc_final: 0.1631 (mtt) REVERT: I 14 LEU cc_start: 0.8826 (mm) cc_final: 0.8614 (mt) REVERT: I 49 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7635 (mp) REVERT: I 80 MET cc_start: 0.7493 (mtm) cc_final: 0.6923 (ptp) REVERT: K 70 GLU cc_start: 0.7319 (mp0) cc_final: 0.6944 (mp0) REVERT: K 145 GLU cc_start: 0.7530 (tt0) cc_final: 0.7226 (tp30) outliers start: 60 outliers final: 24 residues processed: 344 average time/residue: 0.2291 time to fit residues: 119.5481 Evaluate side-chains 323 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 294 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 271 VAL 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 114 ILE Chi-restraints excluded: chain E residue 264 MET Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 289 ILE 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 H residue 73 LEU Chi-restraints excluded: chain I residue 1 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 82 GLU Chi-restraints excluded: chain I residue 87 VAL 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 144 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 49 optimal weight: 0.0070 chunk 79 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 overall best weight: 0.7800 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.161410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.136112 restraints weight = 15810.083| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.45 r_work: 0.3376 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2669 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= 0.134 Angle : 0.659 9.369 19178 Z= 0.323 Chirality : 0.041 0.168 2359 Planarity : 0.005 0.101 2329 Dihedral : 5.472 67.117 1821 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.04 % Favored : 94.85 % Rotamer: Outliers : 3.23 % Allowed : 18.37 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.21), residues: 1746 helix: 0.82 (0.14), residues: 1428 sheet: None (None), residues: 0 loop : -2.48 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 48 HIS 0.001 0.000 HIS I 67 PHE 0.020 0.001 PHE C 119 TYR 0.011 0.001 TYR K 179 ARG 0.003 0.000 ARG I 54 Details of bonding type rmsd hydrogen bonds : bond 0.03481 ( 940) hydrogen bonds : angle 4.19108 ( 2799) covalent geometry : bond 0.00308 (14138) covalent geometry : angle 0.65950 (19178) *********************** 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: 50 poor density : 303 time to evaluate : 1.502 Fit side-chains revert: symmetry clash REVERT: A 288 LEU cc_start: 0.8587 (mt) cc_final: 0.8345 (mp) REVERT: B 232 GLU cc_start: 0.8109 (tp30) cc_final: 0.7432 (tt0) REVERT: C 156 MET cc_start: 0.8220 (mmm) cc_final: 0.7854 (mtp) REVERT: D 193 MET cc_start: 0.8100 (mtt) cc_final: 0.7898 (mtt) REVERT: D 265 MET cc_start: 0.8607 (mmm) cc_final: 0.8384 (mmm) REVERT: E 114 ILE cc_start: 0.7781 (OUTLIER) cc_final: 0.7382 (tp) REVERT: E 133 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.7875 (mpp) REVERT: E 182 PHE cc_start: 0.8306 (t80) cc_final: 0.8026 (t80) REVERT: F 14 ASN cc_start: 0.8324 (t0) cc_final: 0.8121 (t0) REVERT: F 87 MET cc_start: 0.8504 (mmm) cc_final: 0.8304 (mmt) REVERT: F 101 GLN cc_start: 0.8228 (tp40) cc_final: 0.8010 (tp40) REVERT: F 181 PHE cc_start: 0.8426 (m-80) cc_final: 0.8194 (m-80) REVERT: H 10 PHE cc_start: 0.7635 (OUTLIER) cc_final: 0.7425 (t80) REVERT: H 73 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8305 (mt) REVERT: I 14 LEU cc_start: 0.8854 (mm) cc_final: 0.8633 (mt) REVERT: I 49 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7618 (mp) REVERT: I 80 MET cc_start: 0.7469 (mtm) cc_final: 0.6928 (ptp) REVERT: K 70 GLU cc_start: 0.7258 (mp0) cc_final: 0.6847 (mp0) REVERT: K 145 GLU cc_start: 0.7562 (tt0) cc_final: 0.7345 (tp30) outliers start: 50 outliers final: 26 residues processed: 332 average time/residue: 0.2308 time to fit residues: 115.9655 Evaluate side-chains 321 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 290 time to evaluate : 1.652 ------------------------------------------------------------------------------- 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 284 ASP Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 135 LEU 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 206 VAL Chi-restraints excluded: chain E residue 264 MET 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 H residue 73 LEU 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 203 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 30 optimal weight: 0.9980 chunk 162 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 92 optimal weight: 0.2980 chunk 17 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 76 optimal weight: 0.0870 chunk 38 optimal weight: 10.0000 chunk 50 optimal weight: 0.0870 chunk 135 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN B 131 GLN D 142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.155436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.126235 restraints weight = 16315.846| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.59 r_work: 0.3384 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14138 Z= 0.118 Angle : 0.631 9.975 19178 Z= 0.309 Chirality : 0.040 0.165 2359 Planarity : 0.005 0.100 2329 Dihedral : 5.261 64.676 1821 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.98 % Favored : 94.90 % Rotamer: Outliers : 3.43 % Allowed : 18.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.21), residues: 1746 helix: 1.18 (0.14), residues: 1429 sheet: None (None), residues: 0 loop : -2.29 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 68 HIS 0.001 0.000 HIS I 67 PHE 0.017 0.001 PHE C 119 TYR 0.009 0.001 TYR J 89 ARG 0.002 0.000 ARG I 54 Details of bonding type rmsd hydrogen bonds : bond 0.03219 ( 940) hydrogen bonds : angle 4.02710 ( 2799) covalent geometry : bond 0.00255 (14138) covalent geometry : angle 0.63095 (19178) *********************** 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 362 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 309 time to evaluate : 1.619 Fit side-chains revert: symmetry clash REVERT: A 264 MET cc_start: 0.6324 (ttm) cc_final: 0.6006 (ttp) REVERT: A 288 LEU cc_start: 0.8536 (mt) cc_final: 0.8299 (mp) REVERT: B 187 GLU cc_start: 0.7426 (tp30) cc_final: 0.6910 (tm-30) REVERT: B 232 GLU cc_start: 0.8141 (tp30) cc_final: 0.7416 (tt0) REVERT: B 259 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.8157 (mmm) REVERT: B 284 ASP cc_start: 0.8616 (t0) cc_final: 0.8369 (t0) REVERT: C 156 MET cc_start: 0.8436 (mmm) cc_final: 0.7875 (mtp) REVERT: D 131 GLN cc_start: 0.8445 (tt0) cc_final: 0.7962 (mt0) REVERT: D 208 MET cc_start: 0.7788 (tpp) cc_final: 0.7584 (tpp) REVERT: E 133 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.8299 (mmm) REVERT: E 182 PHE cc_start: 0.8208 (t80) cc_final: 0.7938 (t80) REVERT: E 189 MET cc_start: 0.8165 (tpt) cc_final: 0.7940 (tpt) REVERT: F 14 ASN cc_start: 0.8369 (t0) cc_final: 0.8156 (t0) REVERT: F 87 MET cc_start: 0.8481 (mmm) cc_final: 0.8258 (mmt) REVERT: F 255 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7948 (mt) REVERT: H 10 PHE cc_start: 0.7580 (OUTLIER) cc_final: 0.7372 (t80) REVERT: H 73 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8308 (mt) REVERT: I 1 MET cc_start: 0.2702 (mtt) cc_final: 0.1453 (mtt) REVERT: I 14 LEU cc_start: 0.8812 (mm) cc_final: 0.8464 (mt) REVERT: I 49 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7576 (mp) REVERT: I 80 MET cc_start: 0.7554 (mtm) cc_final: 0.6993 (ptp) outliers start: 53 outliers final: 26 residues processed: 336 average time/residue: 0.2327 time to fit residues: 118.4070 Evaluate side-chains 324 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 292 time to evaluate : 1.525 ------------------------------------------------------------------------------- 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 284 ASP 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 271 VAL Chi-restraints excluded: chain C residue 135 LEU 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 133 MET Chi-restraints excluded: chain E residue 264 MET Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain F residue 116 ASP 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 10 PHE Chi-restraints excluded: chain H residue 73 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 44 optimal weight: 0.2980 chunk 119 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 166 optimal weight: 0.0570 chunk 70 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 114 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.155235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.125640 restraints weight = 16354.295| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.60 r_work: 0.3382 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3177 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= 0.122 Angle : 0.638 10.761 19178 Z= 0.310 Chirality : 0.040 0.166 2359 Planarity : 0.005 0.097 2329 Dihedral : 5.172 63.799 1820 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.87 % Favored : 95.02 % Rotamer: Outliers : 3.30 % Allowed : 19.15 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.21), residues: 1746 helix: 1.35 (0.14), residues: 1429 sheet: None (None), residues: 0 loop : -2.21 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 68 HIS 0.001 0.000 HIS I 67 PHE 0.017 0.001 PHE C 119 TYR 0.009 0.001 TYR J 89 ARG 0.002 0.000 ARG G 83 Details of bonding type rmsd hydrogen bonds : bond 0.03193 ( 940) hydrogen bonds : angle 3.96741 ( 2799) covalent geometry : bond 0.00274 (14138) covalent geometry : angle 0.63842 (19178) *********************** 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 352 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 301 time to evaluate : 1.510 Fit side-chains revert: symmetry clash REVERT: A 156 MET cc_start: 0.8093 (mtp) cc_final: 0.7876 (mtp) REVERT: A 288 LEU cc_start: 0.8547 (mt) cc_final: 0.8315 (mp) REVERT: B 133 MET cc_start: 0.8256 (OUTLIER) cc_final: 0.7495 (mpp) REVERT: B 187 GLU cc_start: 0.7419 (tp30) cc_final: 0.6896 (tm-30) REVERT: B 232 GLU cc_start: 0.8208 (tp30) cc_final: 0.7432 (tt0) REVERT: B 259 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.8097 (mmm) REVERT: C 156 MET cc_start: 0.8441 (mmm) cc_final: 0.7938 (mtp) REVERT: D 149 LEU cc_start: 0.8491 (tp) cc_final: 0.8252 (mp) REVERT: E 182 PHE cc_start: 0.8236 (t80) cc_final: 0.7969 (t80) REVERT: F 87 MET cc_start: 0.8521 (mmm) cc_final: 0.8310 (mmt) REVERT: H 10 PHE cc_start: 0.7583 (OUTLIER) cc_final: 0.7364 (t80) REVERT: H 73 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8184 (mt) REVERT: I 14 LEU cc_start: 0.8830 (mm) cc_final: 0.8604 (mt) REVERT: I 49 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7578 (mp) REVERT: I 80 MET cc_start: 0.7522 (mtm) cc_final: 0.6970 (ptp) REVERT: K 137 MET cc_start: 0.7178 (OUTLIER) cc_final: 0.6821 (ttp) outliers start: 51 outliers final: 27 residues processed: 329 average time/residue: 0.2301 time to fit residues: 115.4552 Evaluate side-chains 324 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 291 time to evaluate : 1.429 ------------------------------------------------------------------------------- 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 B residue 114 ILE 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 135 LEU 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 264 MET 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 73 LEU 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 87 VAL Chi-restraints excluded: chain K residue 137 MET 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 66 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 161 optimal weight: 9.9990 chunk 124 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 105 optimal weight: 0.6980 chunk 26 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 131 GLN D 142 GLN E 166 GLN F 94 GLN K 215 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.146732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.116610 restraints weight = 16432.373| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.66 r_work: 0.3170 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14138 Z= 0.210 Angle : 0.733 8.982 19178 Z= 0.356 Chirality : 0.044 0.177 2359 Planarity : 0.005 0.101 2329 Dihedral : 5.475 67.020 1820 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.38 % Favored : 94.44 % Rotamer: Outliers : 3.82 % Allowed : 18.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.21), residues: 1746 helix: 1.12 (0.14), residues: 1416 sheet: None (None), residues: 0 loop : -2.27 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 68 HIS 0.003 0.001 HIS F 144 PHE 0.021 0.002 PHE D 119 TYR 0.017 0.002 TYR F 244 ARG 0.005 0.001 ARG E 121 Details of bonding type rmsd hydrogen bonds : bond 0.03960 ( 940) hydrogen bonds : angle 4.21431 ( 2799) covalent geometry : bond 0.00521 (14138) covalent geometry : angle 0.73267 (19178) *********************** 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 352 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 293 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 288 LEU cc_start: 0.8600 (mt) cc_final: 0.8357 (mp) REVERT: B 133 MET cc_start: 0.8318 (OUTLIER) cc_final: 0.7394 (mpp) REVERT: B 187 GLU cc_start: 0.7331 (tp30) cc_final: 0.6907 (tm-30) REVERT: B 232 GLU cc_start: 0.8229 (tp30) cc_final: 0.7448 (tt0) REVERT: B 259 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.8212 (mmm) REVERT: D 149 LEU cc_start: 0.8534 (tp) cc_final: 0.8309 (mp) REVERT: D 156 MET cc_start: 0.8140 (mmm) cc_final: 0.7719 (mmm) REVERT: E 182 PHE cc_start: 0.8254 (t80) cc_final: 0.8034 (t80) REVERT: E 244 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.8104 (m-80) REVERT: F 87 MET cc_start: 0.8714 (mmm) cc_final: 0.8465 (mmt) REVERT: F 101 GLN cc_start: 0.8439 (tp-100) cc_final: 0.8173 (tp40) REVERT: H 10 PHE cc_start: 0.7842 (OUTLIER) cc_final: 0.7613 (t80) REVERT: I 1 MET cc_start: 0.3380 (mtt) cc_final: 0.2066 (mmm) REVERT: I 14 LEU cc_start: 0.8818 (mm) cc_final: 0.8590 (mt) REVERT: J 73 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8434 (tt) REVERT: K 141 GLN cc_start: 0.6720 (OUTLIER) cc_final: 0.6274 (tm-30) REVERT: K 161 PHE cc_start: 0.8133 (m-80) cc_final: 0.7893 (m-80) outliers start: 59 outliers final: 38 residues processed: 327 average time/residue: 0.2298 time to fit residues: 113.8047 Evaluate side-chains 331 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 287 time to evaluate : 1.397 ------------------------------------------------------------------------------- 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 129 LEU Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 259 MET Chi-restraints excluded: chain B residue 271 VAL 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 261 MET Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 116 MET 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 244 PHE Chi-restraints excluded: chain E residue 264 MET Chi-restraints excluded: chain F residue 94 GLN Chi-restraints excluded: chain F residue 99 LEU 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 10 PHE 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 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 141 GLN Chi-restraints excluded: chain K residue 147 LEU 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 98 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 chunk 124 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 151 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 147 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 47 optimal weight: 0.1980 chunk 50 optimal weight: 0.0050 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 131 GLN D 142 GLN F 101 GLN G 39 GLN H 67 HIS K 215 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.152309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.121509 restraints weight = 16388.354| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.71 r_work: 0.3295 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14138 Z= 0.126 Angle : 0.661 8.898 19178 Z= 0.322 Chirality : 0.041 0.187 2359 Planarity : 0.005 0.095 2329 Dihedral : 5.308 65.267 1820 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.70 % Favored : 95.19 % Rotamer: Outliers : 3.30 % Allowed : 19.79 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.21), residues: 1746 helix: 1.41 (0.14), residues: 1420 sheet: None (None), residues: 0 loop : -2.11 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 68 HIS 0.008 0.001 HIS H 67 PHE 0.018 0.001 PHE C 119 TYR 0.011 0.001 TYR K 179 ARG 0.003 0.000 ARG F 257 Details of bonding type rmsd hydrogen bonds : bond 0.03365 ( 940) hydrogen bonds : angle 4.02689 ( 2799) covalent geometry : bond 0.00283 (14138) covalent geometry : angle 0.66079 (19178) *********************** 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 352 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 301 time to evaluate : 1.554 Fit side-chains revert: symmetry clash REVERT: A 288 LEU cc_start: 0.8558 (mt) cc_final: 0.8314 (mp) REVERT: B 133 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.7351 (mpp) REVERT: B 187 GLU cc_start: 0.7350 (tp30) cc_final: 0.6893 (tm-30) REVERT: B 232 GLU cc_start: 0.8202 (tp30) cc_final: 0.7438 (tt0) REVERT: B 259 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.8196 (mmm) REVERT: D 131 GLN cc_start: 0.8474 (tt0) cc_final: 0.7981 (mt0) REVERT: D 149 LEU cc_start: 0.8539 (tp) cc_final: 0.8331 (mp) REVERT: D 156 MET cc_start: 0.8137 (mmm) cc_final: 0.7639 (mmm) REVERT: D 259 MET cc_start: 0.8663 (tpt) cc_final: 0.8292 (tpt) REVERT: E 114 ILE cc_start: 0.7733 (OUTLIER) cc_final: 0.7343 (tp) REVERT: E 165 GLU cc_start: 0.7057 (mp0) cc_final: 0.6591 (mp0) REVERT: E 182 PHE cc_start: 0.8187 (t80) cc_final: 0.7971 (t80) REVERT: F 14 ASN cc_start: 0.8407 (t0) cc_final: 0.8179 (t0) REVERT: F 87 MET cc_start: 0.8567 (mmm) cc_final: 0.8354 (mmt) REVERT: F 94 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.8389 (mm-40) REVERT: I 1 MET cc_start: 0.3029 (mtt) cc_final: 0.1943 (mtt) REVERT: I 49 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7399 (mp) REVERT: K 161 PHE cc_start: 0.8086 (m-80) cc_final: 0.7843 (m-80) REVERT: K 187 LEU cc_start: 0.8561 (mm) cc_final: 0.8303 (mt) outliers start: 51 outliers final: 26 residues processed: 326 average time/residue: 0.2247 time to fit residues: 111.8320 Evaluate side-chains 324 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 293 time to evaluate : 1.520 ------------------------------------------------------------------------------- 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 A residue 284 ASP Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 259 MET Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 264 MET Chi-restraints excluded: chain F residue 94 GLN Chi-restraints excluded: chain G residue 2 THR 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 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 203 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 42 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 75 optimal weight: 0.6980 chunk 63 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 154 optimal weight: 3.9990 chunk 141 optimal weight: 0.5980 chunk 140 optimal weight: 0.0980 chunk 69 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 120 optimal weight: 0.3980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 142 GLN E 166 GLN ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.155235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.126039 restraints weight = 16245.475| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.57 r_work: 0.3360 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14138 Z= 0.126 Angle : 0.658 8.691 19178 Z= 0.322 Chirality : 0.041 0.181 2359 Planarity : 0.005 0.098 2329 Dihedral : 5.265 63.776 1820 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.10 % Favored : 94.85 % Rotamer: Outliers : 2.20 % Allowed : 21.86 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.21), residues: 1746 helix: 1.52 (0.14), residues: 1423 sheet: None (None), residues: 0 loop : -1.94 (0.35), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 68 HIS 0.001 0.000 HIS F 144 PHE 0.018 0.001 PHE C 119 TYR 0.009 0.001 TYR E 171 ARG 0.002 0.000 ARG E 121 Details of bonding type rmsd hydrogen bonds : bond 0.03281 ( 940) hydrogen bonds : angle 3.96772 ( 2799) covalent geometry : bond 0.00283 (14138) covalent geometry : angle 0.65836 (19178) *********************** 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 326 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 292 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.8080 (mtt) cc_final: 0.7595 (mtt) REVERT: A 288 LEU cc_start: 0.8505 (mt) cc_final: 0.8300 (mp) REVERT: B 187 GLU cc_start: 0.7352 (tp30) cc_final: 0.6915 (tm-30) REVERT: B 232 GLU cc_start: 0.8186 (tp30) cc_final: 0.7426 (tt0) REVERT: B 259 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.8167 (mmm) REVERT: C 112 MET cc_start: 0.7225 (mtm) cc_final: 0.6891 (mtt) REVERT: D 149 LEU cc_start: 0.8552 (tp) cc_final: 0.8325 (mp) REVERT: D 200 LYS cc_start: 0.8060 (tmmt) cc_final: 0.7830 (tmmt) REVERT: D 259 MET cc_start: 0.8589 (tpt) cc_final: 0.8327 (tpp) REVERT: E 114 ILE cc_start: 0.7789 (OUTLIER) cc_final: 0.7360 (tp) REVERT: F 14 ASN cc_start: 0.8397 (t0) cc_final: 0.8186 (t0) REVERT: F 87 MET cc_start: 0.8527 (mmm) cc_final: 0.8298 (mmt) REVERT: I 1 MET cc_start: 0.2855 (mtt) cc_final: 0.1750 (mtt) REVERT: K 161 PHE cc_start: 0.8043 (m-80) cc_final: 0.7807 (m-80) REVERT: K 187 LEU cc_start: 0.8494 (mm) cc_final: 0.8242 (mt) outliers start: 34 outliers final: 28 residues processed: 310 average time/residue: 0.2293 time to fit residues: 108.2275 Evaluate side-chains 314 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 284 time to evaluate : 1.393 ------------------------------------------------------------------------------- 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 A residue 284 ASP Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 259 MET 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 189 MET 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 264 MET 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 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 203 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 1 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 chunk 131 optimal weight: 0.6980 chunk 72 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 135 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 287 ASN E 166 GLN ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 86 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.152985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.122509 restraints weight = 16368.321| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.70 r_work: 0.3300 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14138 Z= 0.136 Angle : 0.672 9.725 19178 Z= 0.326 Chirality : 0.041 0.199 2359 Planarity : 0.005 0.096 2329 Dihedral : 5.263 63.500 1820 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.10 % Favored : 94.85 % Rotamer: Outliers : 2.13 % Allowed : 21.93 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.21), residues: 1746 helix: 1.55 (0.14), residues: 1423 sheet: None (None), residues: 0 loop : -1.93 (0.35), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 68 HIS 0.001 0.000 HIS F 144 PHE 0.019 0.001 PHE E 182 TYR 0.009 0.001 TYR J 89 ARG 0.003 0.000 ARG G 83 Details of bonding type rmsd hydrogen bonds : bond 0.03292 ( 940) hydrogen bonds : angle 3.97277 ( 2799) covalent geometry : bond 0.00317 (14138) covalent geometry : angle 0.67174 (19178) ********************** 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 314 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 281 time to evaluate : 1.532 Fit side-chains revert: symmetry clash REVERT: A 288 LEU cc_start: 0.8522 (mt) cc_final: 0.8301 (mp) REVERT: B 187 GLU cc_start: 0.7307 (tp30) cc_final: 0.6855 (tm-30) REVERT: B 232 GLU cc_start: 0.8213 (tp30) cc_final: 0.7454 (tt0) REVERT: B 259 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.8228 (mmm) REVERT: D 149 LEU cc_start: 0.8565 (tp) cc_final: 0.8343 (mp) REVERT: D 156 MET cc_start: 0.8068 (mmm) cc_final: 0.7858 (mmm) REVERT: D 200 LYS cc_start: 0.8078 (tmmt) cc_final: 0.7833 (tmmt) REVERT: D 259 MET cc_start: 0.8627 (tpt) cc_final: 0.8377 (tpp) REVERT: E 114 ILE cc_start: 0.7732 (OUTLIER) cc_final: 0.7305 (tp) REVERT: E 165 GLU cc_start: 0.7056 (mp0) cc_final: 0.6607 (mp0) REVERT: E 166 GLN cc_start: 0.7360 (OUTLIER) cc_final: 0.5668 (mp-120) REVERT: F 14 ASN cc_start: 0.8416 (t0) cc_final: 0.8214 (t0) REVERT: F 87 MET cc_start: 0.8583 (mmm) cc_final: 0.8353 (mmt) REVERT: I 1 MET cc_start: 0.2947 (mtt) cc_final: 0.1829 (mtt) REVERT: K 161 PHE cc_start: 0.8069 (m-80) cc_final: 0.7854 (m-80) REVERT: K 168 GLN cc_start: 0.7998 (tt0) cc_final: 0.7715 (mt0) REVERT: K 187 LEU cc_start: 0.8481 (mm) cc_final: 0.8227 (mt) outliers start: 33 outliers final: 28 residues processed: 300 average time/residue: 0.2131 time to fit residues: 98.3164 Evaluate side-chains 311 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 280 time to evaluate : 1.409 ------------------------------------------------------------------------------- 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 A residue 284 ASP 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 287 ASN Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain D residue 112 MET 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 264 MET 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 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 203 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 63 optimal weight: 5.9990 chunk 13 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 99 optimal weight: 0.8980 chunk 7 optimal weight: 7.9990 chunk 4 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 ASN ** 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 = 0.3807 r_free = 0.3807 target = 0.158874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.132516 restraints weight = 16123.959| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.43 r_work: 0.3306 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3588 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= 0.135 Angle : 0.669 9.435 19178 Z= 0.324 Chirality : 0.041 0.194 2359 Planarity : 0.005 0.097 2329 Dihedral : 5.243 63.077 1820 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.21 % Favored : 94.73 % Rotamer: Outliers : 2.26 % Allowed : 21.86 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.21), residues: 1746 helix: 1.61 (0.14), residues: 1418 sheet: None (None), residues: 0 loop : -1.89 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 68 HIS 0.001 0.000 HIS I 67 PHE 0.019 0.001 PHE H 76 TYR 0.009 0.001 TYR E 171 ARG 0.003 0.000 ARG G 83 Details of bonding type rmsd hydrogen bonds : bond 0.03287 ( 940) hydrogen bonds : angle 3.96115 ( 2799) covalent geometry : bond 0.00315 (14138) covalent geometry : angle 0.66870 (19178) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7730.91 seconds wall clock time: 132 minutes 35.18 seconds (7955.18 seconds total)