Starting phenix.real_space_refine on Thu Feb 15 08:22:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o13_12688/02_2024/7o13_12688.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o13_12688/02_2024/7o13_12688.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o13_12688/02_2024/7o13_12688.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o13_12688/02_2024/7o13_12688.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o13_12688/02_2024/7o13_12688.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o13_12688/02_2024/7o13_12688.pdb" } resolution = 3.6 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= 0.003 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: 5 Type Number sf(0) Gaussians Mg 1 5.21 5 S 37 5.16 5 C 7466 2.51 5 N 2038 2.21 5 O 2109 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 44": "NH1" <-> "NH2" Residue "A GLU 51": "OE1" <-> "OE2" Residue "A GLU 59": "OE1" <-> "OE2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "A ARG 124": "NH1" <-> "NH2" Residue "A ARG 126": "NH1" <-> "NH2" Residue "A ARG 203": "NH1" <-> "NH2" Residue "A ASP 218": "OD1" <-> "OD2" Residue "A ARG 222": "NH1" <-> "NH2" Residue "A ARG 234": "NH1" <-> "NH2" Residue "A ARG 242": "NH1" <-> "NH2" Residue "A ASP 346": "OD1" <-> "OD2" Residue "A ARG 348": "NH1" <-> "NH2" Residue "A ARG 360": "NH1" <-> "NH2" Residue "A ASP 377": "OD1" <-> "OD2" Residue "A ARG 378": "NH1" <-> "NH2" Residue "A ARG 387": "NH1" <-> "NH2" Residue "A ARG 399": "NH1" <-> "NH2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A GLU 425": "OE1" <-> "OE2" Residue "B GLU 114": "OE1" <-> "OE2" Residue "B GLU 146": "OE1" <-> "OE2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B ARG 216": "NH1" <-> "NH2" Residue "B ASP 234": "OD1" <-> "OD2" Residue "B ASP 242": "OD1" <-> "OD2" Residue "B GLU 252": "OE1" <-> "OE2" Residue "B ARG 297": "NH1" <-> "NH2" Residue "C GLU 30": "OE1" <-> "OE2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "C ARG 124": "NH1" <-> "NH2" Residue "C ARG 148": "NH1" <-> "NH2" Residue "C ARG 173": "NH1" <-> "NH2" Residue "C ARG 216": "NH1" <-> "NH2" Residue "C ARG 226": "NH1" <-> "NH2" Residue "C ARG 233": "NH1" <-> "NH2" Residue "C ASP 234": "OD1" <-> "OD2" Residue "C ARG 239": "NH1" <-> "NH2" Residue "C GLU 252": "OE1" <-> "OE2" Residue "C ARG 269": "NH1" <-> "NH2" Residue "C GLU 278": "OE1" <-> "OE2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C GLU 288": "OE1" <-> "OE2" Residue "C ARG 297": "NH1" <-> "NH2" Residue "D ARG 145": "NH1" <-> "NH2" Residue "D GLU 170": "OE1" <-> "OE2" Residue "D ARG 222": "NH1" <-> "NH2" Residue "D ARG 273": "NH1" <-> "NH2" Residue "E ASP 14": "OD1" <-> "OD2" Residue "E ASP 219": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11651 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3140 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 16, 'TRANS': 385} Chain: "B" Number of atoms: 2303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2303 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 12, 'TRANS': 286} Chain: "C" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2295 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 12, 'TRANS': 285} Chain: "D" Number of atoms: 2015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2015 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 8, 'TRANS': 258} Chain breaks: 1 Chain: "E" Number of atoms: 1896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1896 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 8, 'TRANS': 239} Chain breaks: 2 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 6.69, per 1000 atoms: 0.57 Number of scatterers: 11651 At special positions: 0 Unit cell: (73.872, 92.016, 191.808, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 37 16.00 Mg 1 11.99 O 2109 8.00 N 2038 7.00 C 7466 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 - 3.50 Amino acid : False - 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: 4.02 Conformation dependent library (CDL) restraints added in 2.1 seconds 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2722 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 11 sheets defined 47.2% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 30 through 34 Processing helix chain 'A' and resid 344 through 348 removed outlier: 4.322A pdb=" N GLY A 347 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 383 removed outlier: 3.745A pdb=" N LEU A 380 " --> pdb=" O VAL A 376 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N TRP A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 Processing helix chain 'A' and resid 392 through 405 removed outlier: 3.642A pdb=" N TRP A 400 " --> pdb=" O GLU A 396 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG A 403 " --> pdb=" O ARG A 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 50 removed outlier: 3.804A pdb=" N ILE B 49 " --> pdb=" O SER B 45 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU B 50 " --> pdb=" O MET B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 74 Processing helix chain 'B' and resid 90 through 102 removed outlier: 3.549A pdb=" N LEU B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG B 100 " --> pdb=" O ARG B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 107 No H-bonds generated for 'chain 'B' and resid 105 through 107' Processing helix chain 'B' and resid 108 through 116 Processing helix chain 'B' and resid 130 through 143 removed outlier: 3.767A pdb=" N ALA B 142 " --> pdb=" O GLY B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 178 removed outlier: 3.694A pdb=" N GLN B 176 " --> pdb=" O ASP B 172 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG B 177 " --> pdb=" O ARG B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 192 removed outlier: 4.013A pdb=" N VAL B 191 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU B 192 " --> pdb=" O LEU B 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 187 through 192' Processing helix chain 'B' and resid 211 through 219 Processing helix chain 'B' and resid 232 through 237 Processing helix chain 'B' and resid 238 through 244 removed outlier: 3.745A pdb=" N ASP B 242 " --> pdb=" O GLN B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 275 removed outlier: 3.718A pdb=" N LEU B 268 " --> pdb=" O LYS B 264 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ARG B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLN B 270 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU B 271 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 298 removed outlier: 3.509A pdb=" N GLU B 296 " --> pdb=" O ARG B 292 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA B 298 " --> pdb=" O TYR B 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 50 removed outlier: 3.784A pdb=" N SER C 45 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE C 49 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU C 50 " --> pdb=" O MET C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 74 Processing helix chain 'C' and resid 90 through 102 Processing helix chain 'C' and resid 105 through 109 Processing helix chain 'C' and resid 125 through 129 Processing helix chain 'C' and resid 130 through 141 Processing helix chain 'C' and resid 160 through 178 removed outlier: 3.717A pdb=" N GLN C 176 " --> pdb=" O ASP C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 194 removed outlier: 3.662A pdb=" N ALA C 193 " --> pdb=" O GLY C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 218 Processing helix chain 'C' and resid 240 through 244 removed outlier: 3.794A pdb=" N ALA C 243 " --> pdb=" O TRP C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 274 removed outlier: 3.551A pdb=" N LEU C 267 " --> pdb=" O HIS C 263 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU C 268 " --> pdb=" O LYS C 264 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU C 274 " --> pdb=" O GLN C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 299 removed outlier: 3.857A pdb=" N GLU C 296 " --> pdb=" O ARG C 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 15 removed outlier: 3.551A pdb=" N ILE D 7 " --> pdb=" O GLN D 3 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS D 10 " --> pdb=" O ASN D 6 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU D 11 " --> pdb=" O ILE D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 42 removed outlier: 3.583A pdb=" N ILE D 24 " --> pdb=" O TRP D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 75 removed outlier: 3.632A pdb=" N ALA D 56 " --> pdb=" O PRO D 52 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU D 58 " --> pdb=" O THR D 54 " (cutoff:3.500A) Proline residue: D 67 - end of helix removed outlier: 3.599A pdb=" N TYR D 75 " --> pdb=" O LEU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 83 Processing helix chain 'D' and resid 85 through 91 removed outlier: 3.668A pdb=" N LEU D 89 " --> pdb=" O GLY D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 129 removed outlier: 4.064A pdb=" N LYS D 104 " --> pdb=" O ILE D 100 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE D 111 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU D 117 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE D 127 " --> pdb=" O ALA D 123 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU D 129 " --> pdb=" O LEU D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 167 removed outlier: 3.588A pdb=" N SER D 149 " --> pdb=" O ARG D 145 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR D 151 " --> pdb=" O MET D 147 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LEU D 152 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL D 163 " --> pdb=" O ALA D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 188 removed outlier: 3.670A pdb=" N GLY D 176 " --> pdb=" O SER D 172 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL D 186 " --> pdb=" O TRP D 182 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL D 188 " --> pdb=" O LEU D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 200 removed outlier: 3.549A pdb=" N SER D 200 " --> pdb=" O LEU D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 215 Processing helix chain 'D' and resid 216 through 226 removed outlier: 3.522A pdb=" N ASN D 225 " --> pdb=" O TYR D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 244 removed outlier: 3.581A pdb=" N SER D 240 " --> pdb=" O GLY D 237 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA D 243 " --> pdb=" O SER D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 272 removed outlier: 3.846A pdb=" N LEU D 252 " --> pdb=" O PRO D 248 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER D 263 " --> pdb=" O TRP D 259 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 7 removed outlier: 3.604A pdb=" N ILE E 7 " --> pdb=" O GLN E 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 3 through 7' Processing helix chain 'E' and resid 7 through 16 removed outlier: 3.567A pdb=" N GLU E 11 " --> pdb=" O ILE E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 41 removed outlier: 3.565A pdb=" N ILE E 24 " --> pdb=" O TRP E 20 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU E 38 " --> pdb=" O GLY E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 75 removed outlier: 3.812A pdb=" N SER E 57 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET E 66 " --> pdb=" O ALA E 62 " (cutoff:3.500A) Proline residue: E 67 - end of helix removed outlier: 3.515A pdb=" N TYR E 75 " --> pdb=" O LEU E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 85 Processing helix chain 'E' and resid 85 through 91 Processing helix chain 'E' and resid 96 through 120 removed outlier: 3.507A pdb=" N ILE E 100 " --> pdb=" O GLY E 96 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU E 101 " --> pdb=" O ARG E 97 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE E 111 " --> pdb=" O GLY E 107 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU E 112 " --> pdb=" O HIS E 108 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL E 116 " --> pdb=" O LEU E 112 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU E 117 " --> pdb=" O ALA E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 129 Processing helix chain 'E' and resid 135 through 143 removed outlier: 3.743A pdb=" N LEU E 139 " --> pdb=" O GLU E 135 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N TRP E 141 " --> pdb=" O GLY E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 168 Processing helix chain 'E' and resid 170 through 188 removed outlier: 3.553A pdb=" N ALA E 175 " --> pdb=" O LYS E 171 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL E 186 " --> pdb=" O TRP E 182 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL E 188 " --> pdb=" O LEU E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 199 Processing helix chain 'E' and resid 208 through 213 removed outlier: 3.506A pdb=" N LEU E 212 " --> pdb=" O LEU E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 224 removed outlier: 3.514A pdb=" N ILE E 224 " --> pdb=" O ILE E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 272 removed outlier: 3.928A pdb=" N LEU E 252 " --> pdb=" O PRO E 248 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER E 263 " --> pdb=" O TRP E 259 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 40 removed outlier: 8.209A pdb=" N ARG A 44 " --> pdb=" O PRO A 39 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N TRP A 45 " --> pdb=" O ARG A 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 58 removed outlier: 6.470A pdb=" N GLY A 131 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP A 135 " --> pdb=" O ILE A 111 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N HIS A 163 " --> pdb=" O PHE A 130 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N VAL A 132 " --> pdb=" O HIS A 163 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N PHE A 165 " --> pdb=" O VAL A 132 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL A 134 " --> pdb=" O PHE A 165 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ILE A 162 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N ASP A 187 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU A 164 " --> pdb=" O ASP A 187 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE A 184 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N MET A 209 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE A 186 " --> pdb=" O MET A 209 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N TYR A 204 " --> pdb=" O GLY A 227 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ALA A 229 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N VAL A 206 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N MET A 231 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N TYR A 208 " --> pdb=" O MET A 231 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N LEU A 252 " --> pdb=" O THR A 226 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N TYR A 228 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ASN A 254 " --> pdb=" O TYR A 228 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU A 230 " --> pdb=" O ASN A 254 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE A 251 " --> pdb=" O PHE A 289 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N TYR A 291 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N MET A 253 " --> pdb=" O TYR A 291 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU A 288 " --> pdb=" O HIS A 311 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLN A 332 " --> pdb=" O LEU A 308 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 73 removed outlier: 6.286A pdb=" N ILE A 147 " --> pdb=" O ARG A 178 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL A 177 " --> pdb=" O GLU A 200 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE A 199 " --> pdb=" O ARG A 222 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N THR A 221 " --> pdb=" O GLU A 244 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N SER A 243 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL A 266 " --> pdb=" O GLU A 304 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 89 through 91 removed outlier: 6.604A pdb=" N VAL A 90 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL A 142 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 215 through 217 Processing sheet with id=AA6, first strand: chain 'B' and resid 17 through 26 removed outlier: 6.274A pdb=" N VAL B 18 " --> pdb=" O ARG B 12 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ARG B 12 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N HIS B 20 " --> pdb=" O SER B 10 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N SER B 10 " --> pdb=" O HIS B 20 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N LEU B 22 " --> pdb=" O GLY B 8 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY B 8 " --> pdb=" O LEU B 22 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL B 4 " --> pdb=" O LEU B 26 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN B 59 " --> pdb=" O GLN B 7 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 77 through 79 removed outlier: 7.595A pdb=" N GLY B 77 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ASP B 153 " --> pdb=" O GLY B 77 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU B 79 " --> pdb=" O ASP B 153 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU B 150 " --> pdb=" O ILE B 182 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N CYS B 184 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU B 152 " --> pdb=" O CYS B 184 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU B 32 " --> pdb=" O LEU B 183 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 246 through 248 removed outlier: 4.643A pdb=" N GLU B 256 " --> pdb=" O ARG B 248 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE B 255 " --> pdb=" O ALA B 227 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 22 through 25 removed outlier: 5.722A pdb=" N LEU C 22 " --> pdb=" O GLY C 8 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY C 8 " --> pdb=" O LEU C 22 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN C 59 " --> pdb=" O GLN C 7 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 76 through 79 removed outlier: 6.434A pdb=" N GLY C 77 " --> pdb=" O LEU C 151 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ASP C 153 " --> pdb=" O GLY C 77 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU C 79 " --> pdb=" O ASP C 153 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LEU C 32 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N VAL C 31 " --> pdb=" O ARG C 197 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N ALA C 199 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N GLY C 33 " --> pdb=" O ALA C 199 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU C 201 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ALA C 198 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N VAL C 209 " --> pdb=" O ALA C 198 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ILE C 200 " --> pdb=" O GLN C 207 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 224 through 226 removed outlier: 3.662A pdb=" N ILE C 225 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG C 248 " --> pdb=" O GLU C 256 " (cutoff:3.500A) 473 hydrogen bonds defined for protein. 1341 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: 3.34 Time building geometry restraints manager: 4.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3506 1.33 - 1.45: 1790 1.45 - 1.57: 6507 1.57 - 1.69: 4 1.69 - 1.81: 64 Bond restraints: 11871 Sorted by residual: bond pdb=" CA ILE E 51 " pdb=" C ILE E 51 " ideal model delta sigma weight residual 1.525 1.594 -0.069 2.10e-02 2.27e+03 1.09e+01 bond pdb=" CB VAL D 251 " pdb=" CG2 VAL D 251 " ideal model delta sigma weight residual 1.521 1.448 0.073 3.30e-02 9.18e+02 4.91e+00 bond pdb=" CA ASN B 82 " pdb=" CB ASN B 82 " ideal model delta sigma weight residual 1.531 1.564 -0.033 1.51e-02 4.39e+03 4.79e+00 bond pdb=" CG GLU C 57 " pdb=" CD GLU C 57 " ideal model delta sigma weight residual 1.516 1.570 -0.054 2.50e-02 1.60e+03 4.58e+00 bond pdb=" CA ILE E 51 " pdb=" CB ILE E 51 " ideal model delta sigma weight residual 1.540 1.597 -0.057 2.70e-02 1.37e+03 4.46e+00 ... (remaining 11866 not shown) Histogram of bond angle deviations from ideal: 99.83 - 106.80: 356 106.80 - 113.76: 6509 113.76 - 120.72: 5289 120.72 - 127.69: 3827 127.69 - 134.65: 135 Bond angle restraints: 16116 Sorted by residual: angle pdb=" C LEU E 208 " pdb=" N LEU E 209 " pdb=" CA LEU E 209 " ideal model delta sigma weight residual 120.06 126.71 -6.65 1.19e+00 7.06e-01 3.12e+01 angle pdb=" CA GLU A 42 " pdb=" CB GLU A 42 " pdb=" CG GLU A 42 " ideal model delta sigma weight residual 114.10 125.21 -11.11 2.00e+00 2.50e-01 3.08e+01 angle pdb=" CA MET A 105 " pdb=" CB MET A 105 " pdb=" CG MET A 105 " ideal model delta sigma weight residual 114.10 124.25 -10.15 2.00e+00 2.50e-01 2.58e+01 angle pdb=" CA LEU A 35 " pdb=" CB LEU A 35 " pdb=" CG LEU A 35 " ideal model delta sigma weight residual 116.30 134.06 -17.76 3.50e+00 8.16e-02 2.58e+01 angle pdb=" C GLU B 81 " pdb=" N ASN B 82 " pdb=" CA ASN B 82 " ideal model delta sigma weight residual 122.40 129.57 -7.17 1.45e+00 4.76e-01 2.45e+01 ... (remaining 16111 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.74: 5919 13.74 - 27.47: 788 27.47 - 41.21: 248 41.21 - 54.95: 48 54.95 - 68.69: 18 Dihedral angle restraints: 7021 sinusoidal: 2752 harmonic: 4269 Sorted by residual: dihedral pdb=" CA LEU D 73 " pdb=" C LEU D 73 " pdb=" N ALA D 74 " pdb=" CA ALA D 74 " ideal model delta harmonic sigma weight residual -180.00 -156.96 -23.04 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" C ASN B 82 " pdb=" N ASN B 82 " pdb=" CA ASN B 82 " pdb=" CB ASN B 82 " ideal model delta harmonic sigma weight residual -122.60 -133.42 10.82 0 2.50e+00 1.60e-01 1.87e+01 dihedral pdb=" CA PRO B 277 " pdb=" C PRO B 277 " pdb=" N GLU B 278 " pdb=" CA GLU B 278 " ideal model delta harmonic sigma weight residual -180.00 -158.62 -21.38 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 7018 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1651 0.097 - 0.195: 184 0.195 - 0.292: 20 0.292 - 0.390: 3 0.390 - 0.487: 3 Chirality restraints: 1861 Sorted by residual: chirality pdb=" CB VAL A 413 " pdb=" CA VAL A 413 " pdb=" CG1 VAL A 413 " pdb=" CG2 VAL A 413 " both_signs ideal model delta sigma weight residual False -2.63 -2.14 -0.49 2.00e-01 2.50e+01 5.94e+00 chirality pdb=" CB VAL C 187 " pdb=" CA VAL C 187 " pdb=" CG1 VAL C 187 " pdb=" CG2 VAL C 187 " both_signs ideal model delta sigma weight residual False -2.63 -2.17 -0.46 2.00e-01 2.50e+01 5.38e+00 chirality pdb=" CB ILE C 255 " pdb=" CA ILE C 255 " pdb=" CG1 ILE C 255 " pdb=" CG2 ILE C 255 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.27e+00 ... (remaining 1858 not shown) Planarity restraints: 2063 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 81 " -0.018 2.00e-02 2.50e+03 3.61e-02 1.30e+01 pdb=" C GLU B 81 " 0.062 2.00e-02 2.50e+03 pdb=" O GLU B 81 " -0.024 2.00e-02 2.50e+03 pdb=" N ASN B 82 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET D 66 " -0.050 5.00e-02 4.00e+02 7.43e-02 8.84e+00 pdb=" N PRO D 67 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO D 67 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 67 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET E 66 " 0.049 5.00e-02 4.00e+02 7.34e-02 8.63e+00 pdb=" N PRO E 67 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO E 67 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO E 67 " 0.042 5.00e-02 4.00e+02 ... (remaining 2060 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 84 2.53 - 3.12: 7505 3.12 - 3.72: 18245 3.72 - 4.31: 25588 4.31 - 4.90: 42328 Nonbonded interactions: 93750 Sorted by model distance: nonbonded pdb="MG MG A 501 " pdb=" O HOH A 601 " model vdw 1.938 2.170 nonbonded pdb=" OD1 ASP A 359 " pdb="MG MG A 501 " model vdw 2.019 2.170 nonbonded pdb=" OD1 ASP A 363 " pdb="MG MG A 501 " model vdw 2.185 2.170 nonbonded pdb=" OD1 ASN A 361 " pdb="MG MG A 501 " model vdw 2.240 2.170 nonbonded pdb=" O SER A 293 " pdb=" OG SER A 316 " model vdw 2.318 2.440 ... (remaining 93745 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and resid 2 through 299) selection = chain 'C' } ncs_group { reference = (chain 'D' and (resid 2 through 42 or resid 51 through 227 or resid 245 through \ 274)) selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.420 Check model and map are aligned: 0.160 Set scattering table: 0.090 Process input model: 32.670 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 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 : 0.007 0.074 11871 Z= 0.442 Angle : 1.117 17.761 16116 Z= 0.596 Chirality : 0.066 0.487 1861 Planarity : 0.007 0.074 2063 Dihedral : 14.308 68.687 4299 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 0.82 % Allowed : 8.50 % Favored : 90.69 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.71 (0.15), residues: 1498 helix: -4.62 (0.07), residues: 645 sheet: -3.48 (0.31), residues: 184 loop : -2.80 (0.20), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 155 HIS 0.011 0.002 HIS C 37 PHE 0.020 0.002 PHE E 64 TYR 0.014 0.002 TYR C 13 ARG 0.009 0.001 ARG A 203 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 113 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 MET cc_start: 0.9013 (mmm) cc_final: 0.8791 (mmm) REVERT: A 231 MET cc_start: 0.9168 (mtt) cc_final: 0.8949 (mtm) REVERT: A 235 LYS cc_start: 0.9431 (mmtt) cc_final: 0.9085 (tppp) REVERT: A 305 LYS cc_start: 0.9165 (mmtt) cc_final: 0.8497 (mmmm) REVERT: B 131 LYS cc_start: 0.9518 (tptt) cc_final: 0.9274 (tptp) REVERT: B 283 HIS cc_start: 0.9072 (m90) cc_final: 0.7959 (m90) REVERT: B 295 MET cc_start: 0.9345 (mmp) cc_final: 0.9083 (mmm) REVERT: C 110 ASP cc_start: 0.8748 (OUTLIER) cc_final: 0.8398 (t0) REVERT: D 66 MET cc_start: 0.9229 (mmm) cc_final: 0.8796 (mmp) REVERT: D 153 LEU cc_start: 0.8978 (tp) cc_final: 0.8766 (tt) REVERT: D 169 ASN cc_start: 0.8830 (p0) cc_final: 0.8434 (m110) REVERT: D 201 GLU cc_start: 0.9288 (mt-10) cc_final: 0.9079 (mm-30) REVERT: D 219 ASP cc_start: 0.8957 (m-30) cc_final: 0.8541 (m-30) REVERT: E 10 LYS cc_start: 0.8955 (tmtt) cc_final: 0.8719 (tmtt) REVERT: E 83 GLU cc_start: 0.8727 (mt-10) cc_final: 0.8384 (mt-10) outliers start: 10 outliers final: 5 residues processed: 123 average time/residue: 0.2955 time to fit residues: 50.0390 Evaluate side-chains 84 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 78 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 110 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 62 optimal weight: 8.9990 chunk 38 optimal weight: 8.9990 chunk 75 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 116 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 77 GLN ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 GLN ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 HIS A 190 ASN A 207 HIS A 212 ASN ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 ASN A 324 ASN A 341 GLN B 11 GLN B 20 HIS B 176 GLN B 270 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 HIS C 238 GLN C 261 ASN D 205 ASN D 225 ASN E 108 HIS E 225 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11871 Z= 0.218 Angle : 0.610 8.185 16116 Z= 0.315 Chirality : 0.042 0.154 1861 Planarity : 0.005 0.042 2063 Dihedral : 5.175 28.499 1649 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.47 % Allowed : 13.48 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.52 (0.18), residues: 1498 helix: -1.97 (0.16), residues: 658 sheet: -2.60 (0.33), residues: 199 loop : -2.50 (0.23), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 20 HIS 0.014 0.001 HIS B 263 PHE 0.011 0.001 PHE D 157 TYR 0.016 0.001 TYR C 13 ARG 0.005 0.000 ARG B 224 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 85 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8477 (mpp) cc_final: 0.7807 (mpp) REVERT: A 209 MET cc_start: 0.9010 (mmm) cc_final: 0.8620 (mmm) REVERT: A 231 MET cc_start: 0.9174 (mtt) cc_final: 0.8860 (mtm) REVERT: A 305 LYS cc_start: 0.9166 (mmtt) cc_final: 0.8459 (mmmm) REVERT: A 334 LYS cc_start: 0.9143 (tttt) cc_final: 0.8531 (ttmp) REVERT: B 7 GLN cc_start: 0.8469 (tp40) cc_final: 0.8119 (tp40) REVERT: B 16 MET cc_start: 0.8444 (pmm) cc_final: 0.8077 (pmm) REVERT: B 184 CYS cc_start: 0.7040 (m) cc_final: 0.6755 (m) REVERT: B 226 ARG cc_start: 0.7699 (ttm170) cc_final: 0.7184 (tmm160) REVERT: B 283 HIS cc_start: 0.8966 (m90) cc_final: 0.8752 (m170) REVERT: B 295 MET cc_start: 0.9485 (mmp) cc_final: 0.9057 (mmm) REVERT: D 66 MET cc_start: 0.8992 (mmm) cc_final: 0.8740 (mmp) REVERT: D 88 MET cc_start: 0.8614 (tpp) cc_final: 0.8303 (tpp) REVERT: D 201 GLU cc_start: 0.9454 (mt-10) cc_final: 0.9040 (mm-30) REVERT: D 219 ASP cc_start: 0.8946 (m-30) cc_final: 0.8545 (m-30) REVERT: D 230 GLU cc_start: 0.7761 (mp0) cc_final: 0.7533 (mp0) REVERT: E 10 LYS cc_start: 0.8947 (tmtt) cc_final: 0.8480 (tmtt) REVERT: E 66 MET cc_start: 0.9092 (mmm) cc_final: 0.8828 (mmp) REVERT: E 83 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8404 (mt-10) REVERT: E 88 MET cc_start: 0.9040 (tpp) cc_final: 0.8710 (tpp) REVERT: E 147 MET cc_start: 0.8389 (mtt) cc_final: 0.8132 (mmt) REVERT: E 187 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8970 (pp) outliers start: 18 outliers final: 9 residues processed: 101 average time/residue: 0.2531 time to fit residues: 37.4512 Evaluate side-chains 81 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 71 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain C residue 13 TYR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 187 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 0.5980 chunk 41 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 134 optimal weight: 10.0000 chunk 145 optimal weight: 6.9990 chunk 119 optimal weight: 6.9990 chunk 133 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 108 optimal weight: 7.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 11871 Z= 0.383 Angle : 0.692 7.731 16116 Z= 0.347 Chirality : 0.044 0.169 1861 Planarity : 0.004 0.035 2063 Dihedral : 5.038 33.246 1646 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.04 % Allowed : 15.60 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.10 (0.21), residues: 1498 helix: -0.17 (0.20), residues: 664 sheet: -2.39 (0.33), residues: 215 loop : -2.34 (0.24), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 20 HIS 0.014 0.001 HIS B 263 PHE 0.015 0.001 PHE D 157 TYR 0.014 0.002 TYR C 13 ARG 0.006 0.001 ARG C 292 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 67 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8717 (mpp) cc_final: 0.7792 (mpp) REVERT: A 209 MET cc_start: 0.8891 (mmm) cc_final: 0.8568 (mmm) REVERT: A 235 LYS cc_start: 0.9477 (mmtt) cc_final: 0.9246 (tppt) REVERT: A 305 LYS cc_start: 0.9287 (mmtt) cc_final: 0.8586 (mmmm) REVERT: B 7 GLN cc_start: 0.8501 (tp40) cc_final: 0.8099 (tp40) REVERT: B 295 MET cc_start: 0.9415 (mmp) cc_final: 0.9163 (mmm) REVERT: C 160 ASP cc_start: 0.8939 (OUTLIER) cc_final: 0.8617 (p0) REVERT: D 88 MET cc_start: 0.8724 (tpp) cc_final: 0.8462 (tpp) REVERT: D 118 ILE cc_start: 0.9021 (OUTLIER) cc_final: 0.8663 (tt) REVERT: D 219 ASP cc_start: 0.8814 (m-30) cc_final: 0.8453 (m-30) REVERT: D 255 CYS cc_start: 0.9140 (m) cc_final: 0.8681 (t) REVERT: E 66 MET cc_start: 0.9107 (mmm) cc_final: 0.8811 (mmp) REVERT: E 147 MET cc_start: 0.8341 (mtt) cc_final: 0.8072 (mmt) REVERT: E 187 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8984 (pp) REVERT: E 190 ASP cc_start: 0.9141 (OUTLIER) cc_final: 0.8935 (m-30) outliers start: 25 outliers final: 12 residues processed: 88 average time/residue: 0.2428 time to fit residues: 32.2929 Evaluate side-chains 80 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 64 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain C residue 13 TYR Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 190 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 14 optimal weight: 9.9990 chunk 64 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 135 optimal weight: 10.0000 chunk 143 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 128 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN B 207 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 11871 Z= 0.301 Angle : 0.609 9.537 16116 Z= 0.306 Chirality : 0.043 0.157 1861 Planarity : 0.003 0.035 2063 Dihedral : 4.835 29.255 1646 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.21 % Allowed : 16.99 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.22), residues: 1498 helix: 0.63 (0.21), residues: 678 sheet: -2.11 (0.33), residues: 218 loop : -2.22 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 20 HIS 0.019 0.001 HIS B 263 PHE 0.015 0.001 PHE D 157 TYR 0.013 0.001 TYR B 86 ARG 0.003 0.000 ARG B 173 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 70 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TRP cc_start: 0.8809 (m100) cc_final: 0.8572 (m100) REVERT: A 62 MET cc_start: 0.8713 (mmm) cc_final: 0.8307 (tpp) REVERT: A 125 MET cc_start: 0.8924 (mpp) cc_final: 0.8121 (mpp) REVERT: A 209 MET cc_start: 0.9068 (mmm) cc_final: 0.8475 (mmm) REVERT: A 231 MET cc_start: 0.9004 (mtm) cc_final: 0.8472 (mtm) REVERT: A 235 LYS cc_start: 0.9460 (mmtt) cc_final: 0.9219 (tppt) REVERT: B 183 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8783 (mt) REVERT: B 295 MET cc_start: 0.9335 (mmp) cc_final: 0.9126 (mmm) REVERT: C 160 ASP cc_start: 0.8891 (OUTLIER) cc_final: 0.8605 (p0) REVERT: C 181 ILE cc_start: 0.9041 (mt) cc_final: 0.8796 (mm) REVERT: D 81 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8459 (mt-10) REVERT: D 88 MET cc_start: 0.8765 (tpp) cc_final: 0.8484 (tpp) REVERT: D 219 ASP cc_start: 0.8792 (m-30) cc_final: 0.8208 (m-30) REVERT: D 255 CYS cc_start: 0.9200 (m) cc_final: 0.8789 (t) REVERT: E 11 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8821 (mm-30) REVERT: E 66 MET cc_start: 0.9109 (mmm) cc_final: 0.8891 (mmp) REVERT: E 88 MET cc_start: 0.9017 (tpp) cc_final: 0.8810 (tpp) REVERT: E 147 MET cc_start: 0.8258 (mtt) cc_final: 0.8007 (mmt) REVERT: E 187 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8961 (pp) REVERT: E 219 ASP cc_start: 0.9114 (t0) cc_final: 0.8684 (t0) outliers start: 27 outliers final: 18 residues processed: 94 average time/residue: 0.2203 time to fit residues: 31.7258 Evaluate side-chains 86 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 65 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain C residue 13 TYR Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 187 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 chunk 2 optimal weight: 8.9990 chunk 106 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 chunk 128 optimal weight: 0.9980 chunk 36 optimal weight: 7.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11871 Z= 0.183 Angle : 0.530 8.782 16116 Z= 0.265 Chirality : 0.041 0.156 1861 Planarity : 0.003 0.032 2063 Dihedral : 4.512 24.325 1646 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.21 % Allowed : 18.22 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.90 (0.23), residues: 1498 helix: 1.14 (0.21), residues: 683 sheet: -2.02 (0.34), residues: 228 loop : -2.11 (0.24), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 37 HIS 0.007 0.001 HIS B 245 PHE 0.013 0.001 PHE D 157 TYR 0.014 0.001 TYR C 13 ARG 0.002 0.000 ARG D 222 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 72 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8697 (mmm) cc_final: 0.8441 (tpp) REVERT: A 125 MET cc_start: 0.8922 (mpp) cc_final: 0.8143 (mpp) REVERT: A 197 ASN cc_start: 0.9315 (OUTLIER) cc_final: 0.8581 (m-40) REVERT: A 209 MET cc_start: 0.9042 (mmm) cc_final: 0.8640 (mmm) REVERT: A 231 MET cc_start: 0.9015 (mtm) cc_final: 0.8610 (mtt) REVERT: A 235 LYS cc_start: 0.9482 (mmtt) cc_final: 0.9201 (tppp) REVERT: A 305 LYS cc_start: 0.9363 (mmmt) cc_final: 0.9028 (mmmm) REVERT: A 334 LYS cc_start: 0.9089 (tttt) cc_final: 0.8468 (ttmp) REVERT: B 16 MET cc_start: 0.8492 (pmm) cc_final: 0.8173 (pmm) REVERT: B 183 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8676 (mt) REVERT: C 160 ASP cc_start: 0.8877 (OUTLIER) cc_final: 0.8639 (p0) REVERT: D 81 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8426 (mt-10) REVERT: D 88 MET cc_start: 0.8748 (tpp) cc_final: 0.8452 (tpp) REVERT: D 219 ASP cc_start: 0.8820 (m-30) cc_final: 0.8226 (m-30) REVERT: D 255 CYS cc_start: 0.9139 (m) cc_final: 0.8784 (t) REVERT: E 66 MET cc_start: 0.9008 (mmm) cc_final: 0.8802 (mmp) REVERT: E 88 MET cc_start: 0.8985 (tpp) cc_final: 0.8756 (tpp) REVERT: E 147 MET cc_start: 0.8274 (mtt) cc_final: 0.8041 (mmt) REVERT: E 187 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8968 (pp) REVERT: E 219 ASP cc_start: 0.9249 (t0) cc_final: 0.8708 (t0) outliers start: 27 outliers final: 17 residues processed: 95 average time/residue: 0.2267 time to fit residues: 32.9083 Evaluate side-chains 88 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 67 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 362 ASN Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain C residue 13 TYR Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 187 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 143 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11871 Z= 0.207 Angle : 0.546 9.080 16116 Z= 0.270 Chirality : 0.042 0.149 1861 Planarity : 0.003 0.030 2063 Dihedral : 4.454 26.106 1646 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.61 % Allowed : 18.14 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.23), residues: 1498 helix: 1.42 (0.21), residues: 681 sheet: -1.90 (0.34), residues: 228 loop : -1.98 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 45 HIS 0.006 0.001 HIS B 245 PHE 0.013 0.001 PHE D 157 TYR 0.013 0.001 TYR C 13 ARG 0.002 0.000 ARG D 222 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 65 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.8839 (mmm) cc_final: 0.8545 (mmm) REVERT: A 125 MET cc_start: 0.8925 (mpp) cc_final: 0.8147 (mpp) REVERT: A 197 ASN cc_start: 0.9294 (OUTLIER) cc_final: 0.8590 (m-40) REVERT: A 209 MET cc_start: 0.9062 (mmm) cc_final: 0.8622 (mmm) REVERT: A 231 MET cc_start: 0.8994 (mtm) cc_final: 0.8586 (mtt) REVERT: A 235 LYS cc_start: 0.9489 (mmtt) cc_final: 0.9215 (tppt) REVERT: A 334 LYS cc_start: 0.9075 (tttt) cc_final: 0.8379 (ttmp) REVERT: B 16 MET cc_start: 0.8419 (pmm) cc_final: 0.8094 (pmm) REVERT: B 95 LEU cc_start: 0.9295 (mt) cc_final: 0.8781 (tp) REVERT: B 183 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8774 (mt) REVERT: C 160 ASP cc_start: 0.8902 (OUTLIER) cc_final: 0.8608 (p0) REVERT: C 295 MET cc_start: 0.8809 (mmm) cc_final: 0.8555 (mmm) REVERT: D 81 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8422 (mt-10) REVERT: D 88 MET cc_start: 0.8769 (tpp) cc_final: 0.8473 (tpp) REVERT: D 219 ASP cc_start: 0.8756 (m-30) cc_final: 0.8149 (m-30) REVERT: D 255 CYS cc_start: 0.9089 (m) cc_final: 0.8734 (t) REVERT: E 147 MET cc_start: 0.8279 (mtt) cc_final: 0.8039 (mmt) REVERT: E 219 ASP cc_start: 0.9226 (t0) cc_final: 0.8723 (t0) outliers start: 32 outliers final: 21 residues processed: 92 average time/residue: 0.2351 time to fit residues: 32.3239 Evaluate side-chains 87 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 63 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 362 ASN Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain C residue 13 TYR Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 92 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 81 optimal weight: 9.9990 chunk 104 optimal weight: 0.8980 chunk 120 optimal weight: 10.0000 chunk 79 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 65 optimal weight: 30.0000 chunk 88 optimal weight: 0.5980 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 11871 Z= 0.295 Angle : 0.602 9.691 16116 Z= 0.296 Chirality : 0.043 0.156 1861 Planarity : 0.003 0.029 2063 Dihedral : 4.560 26.915 1646 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 2.86 % Allowed : 18.46 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.23), residues: 1498 helix: 1.57 (0.22), residues: 673 sheet: -1.81 (0.34), residues: 230 loop : -1.92 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 20 HIS 0.008 0.001 HIS B 245 PHE 0.013 0.001 PHE D 157 TYR 0.013 0.001 TYR C 13 ARG 0.003 0.000 ARG B 175 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 64 time to evaluate : 1.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.8439 (tt0) REVERT: A 62 MET cc_start: 0.9156 (mmm) cc_final: 0.8316 (tpp) REVERT: A 105 MET cc_start: 0.8905 (mmm) cc_final: 0.8616 (mmm) REVERT: A 125 MET cc_start: 0.8890 (mpp) cc_final: 0.8158 (mpp) REVERT: A 197 ASN cc_start: 0.9256 (OUTLIER) cc_final: 0.8552 (m-40) REVERT: A 209 MET cc_start: 0.9075 (mmm) cc_final: 0.8599 (mmm) REVERT: A 305 LYS cc_start: 0.9409 (mmmt) cc_final: 0.8768 (mmmm) REVERT: B 16 MET cc_start: 0.8306 (pmm) cc_final: 0.7978 (pmm) REVERT: B 95 LEU cc_start: 0.9248 (mt) cc_final: 0.8787 (tp) REVERT: B 183 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8815 (mt) REVERT: C 160 ASP cc_start: 0.8962 (OUTLIER) cc_final: 0.8626 (p0) REVERT: C 295 MET cc_start: 0.8773 (mmm) cc_final: 0.8568 (mmm) REVERT: D 81 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8436 (mt-10) REVERT: D 88 MET cc_start: 0.8800 (tpp) cc_final: 0.8514 (tpp) REVERT: D 169 ASN cc_start: 0.9189 (OUTLIER) cc_final: 0.8960 (p0) REVERT: D 219 ASP cc_start: 0.8762 (m-30) cc_final: 0.8012 (m-30) REVERT: D 255 CYS cc_start: 0.9160 (m) cc_final: 0.8801 (t) REVERT: E 88 MET cc_start: 0.9168 (tpp) cc_final: 0.8944 (tpp) REVERT: E 147 MET cc_start: 0.8247 (mtt) cc_final: 0.7994 (mmt) REVERT: E 187 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8961 (pp) REVERT: E 219 ASP cc_start: 0.9252 (t0) cc_final: 0.8747 (t0) outliers start: 35 outliers final: 22 residues processed: 94 average time/residue: 0.2204 time to fit residues: 31.6050 Evaluate side-chains 90 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 62 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 362 ASN Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain C residue 13 TYR Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 169 ASN Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 187 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 90 optimal weight: 8.9990 chunk 97 optimal weight: 0.4980 chunk 70 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 112 optimal weight: 0.8980 chunk 129 optimal weight: 0.9980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11871 Z= 0.187 Angle : 0.538 9.867 16116 Z= 0.265 Chirality : 0.041 0.151 1861 Planarity : 0.003 0.031 2063 Dihedral : 4.383 23.512 1646 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.37 % Allowed : 18.95 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.23), residues: 1498 helix: 1.79 (0.22), residues: 672 sheet: -1.90 (0.33), residues: 238 loop : -1.85 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 37 HIS 0.006 0.001 HIS B 245 PHE 0.013 0.001 PHE D 157 TYR 0.013 0.001 TYR C 13 ARG 0.004 0.000 ARG B 175 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 67 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.9133 (mmm) cc_final: 0.8248 (tpp) REVERT: A 105 MET cc_start: 0.9000 (mmm) cc_final: 0.8731 (mmm) REVERT: A 125 MET cc_start: 0.8893 (mpp) cc_final: 0.8102 (mpp) REVERT: A 172 VAL cc_start: 0.9304 (OUTLIER) cc_final: 0.8912 (p) REVERT: A 197 ASN cc_start: 0.9267 (OUTLIER) cc_final: 0.8590 (m-40) REVERT: A 209 MET cc_start: 0.8945 (mmm) cc_final: 0.8493 (mmm) REVERT: A 231 MET cc_start: 0.9042 (mtt) cc_final: 0.8585 (mtm) REVERT: A 305 LYS cc_start: 0.9407 (mmmt) cc_final: 0.8750 (mmmm) REVERT: A 334 LYS cc_start: 0.9059 (tttt) cc_final: 0.8401 (ttmp) REVERT: B 16 MET cc_start: 0.8256 (pmm) cc_final: 0.8006 (pmm) REVERT: B 46 MET cc_start: 0.9643 (mmt) cc_final: 0.9391 (mmm) REVERT: B 95 LEU cc_start: 0.9290 (mt) cc_final: 0.8785 (tp) REVERT: B 183 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8862 (mt) REVERT: C 160 ASP cc_start: 0.8895 (OUTLIER) cc_final: 0.8611 (p0) REVERT: D 81 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8395 (mt-10) REVERT: D 88 MET cc_start: 0.8778 (tpp) cc_final: 0.8488 (tpp) REVERT: D 219 ASP cc_start: 0.8813 (m-30) cc_final: 0.8208 (m-30) REVERT: D 255 CYS cc_start: 0.9113 (m) cc_final: 0.8784 (t) REVERT: E 88 MET cc_start: 0.9114 (tpp) cc_final: 0.8867 (tpp) REVERT: E 147 MET cc_start: 0.8222 (mtt) cc_final: 0.7984 (mmt) REVERT: E 219 ASP cc_start: 0.9229 (t0) cc_final: 0.8797 (t0) outliers start: 29 outliers final: 21 residues processed: 91 average time/residue: 0.2024 time to fit residues: 28.3631 Evaluate side-chains 89 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 64 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 362 ASN Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain C residue 13 TYR Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain E residue 92 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 5.9990 chunk 124 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 chunk 104 optimal weight: 0.8980 chunk 40 optimal weight: 0.0470 chunk 120 optimal weight: 9.9990 chunk 125 optimal weight: 7.9990 chunk 87 optimal weight: 0.9980 chunk 140 optimal weight: 6.9990 overall best weight: 1.3680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 HIS ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11871 Z= 0.167 Angle : 0.543 10.175 16116 Z= 0.263 Chirality : 0.041 0.151 1861 Planarity : 0.003 0.031 2063 Dihedral : 4.258 23.555 1646 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.37 % Allowed : 19.36 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.23), residues: 1498 helix: 1.92 (0.22), residues: 677 sheet: -1.78 (0.33), residues: 238 loop : -1.89 (0.25), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 240 HIS 0.005 0.001 HIS B 245 PHE 0.012 0.001 PHE D 157 TYR 0.013 0.001 TYR C 13 ARG 0.003 0.000 ARG B 175 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 68 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.9104 (mmm) cc_final: 0.8252 (tpp) REVERT: A 105 MET cc_start: 0.8978 (mmm) cc_final: 0.8720 (mmm) REVERT: A 125 MET cc_start: 0.8912 (mpp) cc_final: 0.8131 (mpp) REVERT: A 172 VAL cc_start: 0.9279 (OUTLIER) cc_final: 0.8906 (p) REVERT: A 197 ASN cc_start: 0.9202 (OUTLIER) cc_final: 0.8480 (m-40) REVERT: A 209 MET cc_start: 0.8974 (mmm) cc_final: 0.8449 (mmm) REVERT: A 231 MET cc_start: 0.9035 (mtt) cc_final: 0.8648 (mtm) REVERT: A 235 LYS cc_start: 0.9489 (mmtt) cc_final: 0.9218 (tppt) REVERT: A 305 LYS cc_start: 0.9409 (mmmt) cc_final: 0.8737 (mmmm) REVERT: A 334 LYS cc_start: 0.9050 (tttt) cc_final: 0.8842 (tttp) REVERT: B 16 MET cc_start: 0.8244 (pmm) cc_final: 0.7993 (pmm) REVERT: B 95 LEU cc_start: 0.9282 (mt) cc_final: 0.8772 (tp) REVERT: B 183 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8858 (mt) REVERT: C 133 MET cc_start: 0.9390 (mtm) cc_final: 0.8995 (mtm) REVERT: C 160 ASP cc_start: 0.8920 (OUTLIER) cc_final: 0.8651 (p0) REVERT: D 81 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8405 (mt-10) REVERT: D 88 MET cc_start: 0.8783 (tpp) cc_final: 0.8483 (tpp) REVERT: D 169 ASN cc_start: 0.9192 (OUTLIER) cc_final: 0.8974 (p0) REVERT: D 219 ASP cc_start: 0.8832 (m-30) cc_final: 0.8229 (m-30) REVERT: D 255 CYS cc_start: 0.9053 (m) cc_final: 0.8746 (t) REVERT: E 88 MET cc_start: 0.9016 (tpp) cc_final: 0.8785 (tpp) REVERT: E 219 ASP cc_start: 0.9221 (t0) cc_final: 0.8792 (t0) outliers start: 29 outliers final: 23 residues processed: 92 average time/residue: 0.2205 time to fit residues: 31.1392 Evaluate side-chains 94 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 66 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 362 ASN Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain C residue 13 TYR Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 169 ASN Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 92 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 chunk 147 optimal weight: 7.9990 chunk 135 optimal weight: 0.0070 chunk 117 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 125 optimal weight: 10.0000 overall best weight: 2.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 HIS ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11871 Z= 0.210 Angle : 0.552 10.189 16116 Z= 0.270 Chirality : 0.042 0.153 1861 Planarity : 0.003 0.030 2063 Dihedral : 4.308 25.657 1646 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.61 % Allowed : 19.12 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.23), residues: 1498 helix: 1.95 (0.22), residues: 678 sheet: -1.62 (0.34), residues: 232 loop : -1.88 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 240 HIS 0.006 0.001 HIS B 245 PHE 0.013 0.001 PHE D 157 TYR 0.013 0.001 TYR C 13 ARG 0.004 0.000 ARG B 175 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 65 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.9104 (mmm) cc_final: 0.8349 (tpt) REVERT: A 105 MET cc_start: 0.9003 (mmm) cc_final: 0.8738 (mmm) REVERT: A 125 MET cc_start: 0.8899 (mpp) cc_final: 0.8117 (mpp) REVERT: A 172 VAL cc_start: 0.9304 (OUTLIER) cc_final: 0.8926 (p) REVERT: A 197 ASN cc_start: 0.9161 (OUTLIER) cc_final: 0.8406 (m-40) REVERT: A 209 MET cc_start: 0.8976 (mmm) cc_final: 0.8587 (mmm) REVERT: A 235 LYS cc_start: 0.9514 (mmtt) cc_final: 0.9235 (tppt) REVERT: A 305 LYS cc_start: 0.9413 (mmmt) cc_final: 0.8745 (mmmm) REVERT: A 334 LYS cc_start: 0.9064 (tttt) cc_final: 0.8398 (ttmp) REVERT: B 16 MET cc_start: 0.8252 (pmm) cc_final: 0.7961 (pmm) REVERT: B 95 LEU cc_start: 0.9238 (mt) cc_final: 0.8784 (tp) REVERT: B 183 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8879 (mt) REVERT: C 133 MET cc_start: 0.9394 (mtm) cc_final: 0.9023 (mtm) REVERT: C 160 ASP cc_start: 0.8928 (OUTLIER) cc_final: 0.8518 (p0) REVERT: D 81 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8394 (mt-10) REVERT: D 88 MET cc_start: 0.8806 (tpp) cc_final: 0.8510 (tpp) REVERT: D 169 ASN cc_start: 0.9208 (OUTLIER) cc_final: 0.8993 (p0) REVERT: D 219 ASP cc_start: 0.8767 (m-30) cc_final: 0.8006 (m-30) REVERT: D 255 CYS cc_start: 0.9056 (m) cc_final: 0.8757 (t) REVERT: E 88 MET cc_start: 0.9041 (tpp) cc_final: 0.8803 (tpp) REVERT: E 219 ASP cc_start: 0.9241 (t0) cc_final: 0.8802 (t0) outliers start: 32 outliers final: 24 residues processed: 92 average time/residue: 0.2196 time to fit residues: 31.0576 Evaluate side-chains 91 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 62 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 362 ASN Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 261 ASN Chi-restraints excluded: chain C residue 13 TYR Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 169 ASN Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 92 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 0.0980 chunk 108 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 120 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 HIS ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.058935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.043473 restraints weight = 53902.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.044962 restraints weight = 27220.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.045982 restraints weight = 17655.456| |-----------------------------------------------------------------------------| r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11871 Z= 0.238 Angle : 0.577 10.765 16116 Z= 0.280 Chirality : 0.042 0.150 1861 Planarity : 0.003 0.030 2063 Dihedral : 4.345 25.974 1646 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.61 % Allowed : 19.44 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.23), residues: 1498 helix: 1.94 (0.22), residues: 678 sheet: -1.60 (0.34), residues: 232 loop : -1.92 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 240 HIS 0.008 0.001 HIS B 186 PHE 0.013 0.001 PHE D 157 TYR 0.013 0.001 TYR C 13 ARG 0.004 0.000 ARG B 175 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1891.00 seconds wall clock time: 35 minutes 45.69 seconds (2145.69 seconds total)