Starting phenix.real_space_refine on Thu Sep 26 01:30:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o10_12685/09_2024/7o10_12685.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o10_12685/09_2024/7o10_12685.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/7o10_12685/09_2024/7o10_12685.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o10_12685/09_2024/7o10_12685.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o10_12685/09_2024/7o10_12685.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o10_12685/09_2024/7o10_12685.cif" } 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= 0.002 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. Time to flip 43 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 7.16, per 1000 atoms: 0.61 Number of scatterers: 11651 At special positions: 0 Unit cell: (86.184, 168.264, 138.51, 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.71 Conformation dependent library (CDL) restraints added in 1.4 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 12 sheets defined 47.1% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 30 through 34 Processing helix chain 'A' and resid 344 through 348 removed outlier: 4.243A pdb=" N GLY A 347 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 383 removed outlier: 3.560A pdb=" N LEU A 380 " --> pdb=" O VAL A 376 " (cutoff:3.500A) removed outlier: 4.267A 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: 3.559A pdb=" N GLN A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG A 403 " --> pdb=" O ARG A 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 50 removed outlier: 3.907A pdb=" N SER B 45 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS B 47 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU B 50 " --> pdb=" O MET B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 65 Processing helix chain 'B' and resid 69 through 74 removed outlier: 3.532A pdb=" N ARG B 74 " --> pdb=" O PRO B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 102 Processing helix chain 'B' and resid 106 through 116 removed outlier: 4.589A pdb=" N ASP B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU B 114 " --> pdb=" O ASP B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 141 Processing helix chain 'B' and resid 160 through 177 removed outlier: 3.601A pdb=" N GLN B 165 " --> pdb=" O PRO B 161 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP B 166 " --> pdb=" O ILE B 162 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN B 176 " --> pdb=" O ASP B 172 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG B 177 " --> pdb=" O ARG B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 192 removed outlier: 4.293A pdb=" N VAL B 191 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 4.271A 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 264 through 270 Processing helix chain 'B' and resid 270 through 275 removed outlier: 3.843A pdb=" N GLU B 274 " --> pdb=" O GLN B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 298 removed outlier: 3.718A pdb=" N GLU B 296 " --> pdb=" O ARG B 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 51 removed outlier: 4.015A pdb=" N SER C 45 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE C 49 " --> pdb=" O SER C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 74 removed outlier: 3.723A pdb=" N ARG C 73 " --> pdb=" O ASP C 69 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG C 74 " --> pdb=" O PRO C 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 69 through 74' Processing helix chain 'C' and resid 90 through 103 removed outlier: 3.684A pdb=" N THR C 94 " --> pdb=" O SER C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 114 removed outlier: 3.894A pdb=" N GLU C 111 " --> pdb=" O THR C 107 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU C 113 " --> pdb=" O VAL C 109 " (cutoff:3.500A) 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 177 removed outlier: 3.566A pdb=" N GLN C 176 " --> pdb=" O ASP C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 194 removed outlier: 4.164A pdb=" N ALA C 193 " --> pdb=" O GLY C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 219 Processing helix chain 'C' and resid 233 through 241 removed outlier: 3.510A pdb=" N ARG C 239 " --> pdb=" O SER C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 274 removed outlier: 3.574A pdb=" N LEU C 268 " --> pdb=" O LYS C 264 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG C 269 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU C 271 " --> pdb=" O LEU C 267 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY C 273 " --> pdb=" O ARG C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 298 removed outlier: 3.542A pdb=" N LEU C 290 " --> pdb=" O SER C 286 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU C 296 " --> pdb=" O ARG C 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 15 removed outlier: 3.588A pdb=" N ILE D 7 " --> pdb=" O GLN D 3 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS D 10 " --> pdb=" O ASN D 6 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU D 11 " --> pdb=" O ILE D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 42 removed outlier: 3.516A pdb=" N ILE D 24 " --> pdb=" O TRP D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 75 removed outlier: 3.513A pdb=" N ILE D 55 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA D 56 " --> pdb=" O PRO D 52 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU D 58 " --> pdb=" O THR D 54 " (cutoff:3.500A) Proline residue: D 67 - end of helix removed outlier: 3.540A 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: 3.731A pdb=" N LEU D 89 " --> pdb=" O GLY D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 129 removed outlier: 4.113A pdb=" N LYS D 104 " --> pdb=" O ILE D 100 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE D 111 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU D 117 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU D 129 " --> pdb=" O LEU D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 146 Processing helix chain 'D' and resid 146 through 167 removed outlier: 3.584A pdb=" N THR D 151 " --> pdb=" O MET D 147 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU D 152 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL D 163 " --> pdb=" O ALA D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 188 removed outlier: 3.596A pdb=" N GLY D 176 " --> pdb=" O SER D 172 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL D 186 " --> pdb=" O TRP D 182 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL D 188 " --> pdb=" O LEU D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 201 removed outlier: 3.548A pdb=" N SER D 200 " --> pdb=" O LEU D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 215 Processing helix chain 'D' and resid 216 through 226 removed outlier: 3.546A pdb=" N ASN D 225 " --> pdb=" O TYR D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 244 removed outlier: 3.764A pdb=" N LEU D 241 " --> pdb=" O VAL D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 272 removed outlier: 3.696A pdb=" N LEU D 252 " --> pdb=" O PRO D 248 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER D 263 " --> pdb=" O TRP D 259 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 7 removed outlier: 3.651A 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: 3.560A pdb=" N GLU E 11 " --> pdb=" O ILE E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 41 removed outlier: 3.515A pdb=" N ILE E 24 " --> pdb=" O TRP E 20 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU E 38 " --> pdb=" O GLY E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 75 removed outlier: 3.530A pdb=" N SER E 57 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET E 66 " --> pdb=" O ALA E 62 " (cutoff:3.500A) Proline residue: E 67 - end of helix removed outlier: 3.534A pdb=" N TYR E 75 " --> pdb=" O LEU E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 84 Processing helix chain 'E' and resid 85 through 91 Processing helix chain 'E' and resid 96 through 120 removed outlier: 3.808A pdb=" N ILE E 111 " --> pdb=" O GLY E 107 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU E 112 " --> pdb=" O HIS E 108 " (cutoff:3.500A) removed outlier: 4.197A 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: 3.827A pdb=" N LEU E 139 " --> pdb=" O GLU E 135 " (cutoff:3.500A) removed outlier: 3.961A 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: 3.792A 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 211 through 215 Processing helix chain 'E' and resid 216 through 224 removed outlier: 3.725A pdb=" N ILE E 224 " --> pdb=" O ILE E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 272 removed outlier: 4.066A pdb=" N LEU E 252 " --> pdb=" O PRO E 248 " (cutoff:3.500A) removed outlier: 3.549A 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: 8.081A pdb=" N ARG A 44 " --> pdb=" O PRO A 39 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N TRP A 45 " --> pdb=" O ARG A 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 53 removed outlier: 3.637A pdb=" N GLN A 73 " --> pdb=" O TYR A 52 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE A 147 " --> pdb=" O ARG A 178 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL A 177 " --> pdb=" O GLU A 200 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ILE A 199 " --> pdb=" O ARG A 222 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N SER A 243 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL A 266 " --> pdb=" O GLU A 304 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 56 through 58 removed outlier: 6.517A pdb=" N GLY A 131 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP A 135 " --> pdb=" O ILE A 111 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ILE A 162 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ASP A 187 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU A 164 " --> pdb=" O ASP A 187 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ILE A 184 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N MET A 209 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE A 186 " --> pdb=" O MET A 209 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N TYR A 204 " --> pdb=" O GLY A 227 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ALA A 229 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N VAL A 206 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N MET A 231 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N TYR A 208 " --> pdb=" O MET A 231 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N LEU A 252 " --> pdb=" O THR A 226 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N TYR A 228 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ASN A 254 " --> pdb=" O TYR A 228 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU A 230 " --> pdb=" O ASN A 254 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE A 251 " --> pdb=" O PHE A 289 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N TYR A 291 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N MET A 253 " --> pdb=" O TYR A 291 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLN A 332 " --> pdb=" O LEU A 308 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 89 through 91 removed outlier: 6.578A pdb=" N VAL A 90 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 6.452A 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 removed outlier: 7.577A pdb=" N SER A 322 " --> pdb=" O ASN A 296 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ILE A 298 " --> pdb=" O SER A 322 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 9 through 11 removed outlier: 5.740A pdb=" N VAL B 9 " --> pdb=" O ASP B 21 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 77 through 79 removed outlier: 7.626A pdb=" N GLY B 77 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ASP B 153 " --> pdb=" O GLY B 77 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU B 79 " --> pdb=" O ASP B 153 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU B 150 " --> pdb=" O ILE B 182 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N CYS B 184 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU B 152 " --> pdb=" O CYS B 184 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LEU B 32 " --> pdb=" O LEU B 183 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 247 through 248 removed outlier: 3.535A pdb=" N ALA B 259 " --> pdb=" O VAL B 223 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG B 224 " --> pdb=" O HIS B 283 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 22 through 24 removed outlier: 5.592A pdb=" N LEU C 22 " --> pdb=" O GLY C 8 " (cutoff:3.500A) removed outlier: 3.732A 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: 6.931A pdb=" N LEU C 150 " --> pdb=" O ILE C 182 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N CYS C 184 " --> pdb=" O LEU C 150 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU C 152 " --> pdb=" O CYS C 184 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N LEU C 32 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL C 31 " --> pdb=" O ARG C 197 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N ALA C 199 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N GLY C 33 " --> pdb=" O ALA C 199 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU C 201 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA C 198 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL C 209 " --> pdb=" O ALA C 198 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ILE C 200 " --> pdb=" O GLN C 207 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 254 through 255 removed outlier: 3.590A pdb=" N ILE C 255 " --> pdb=" O ALA C 227 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 254 through 255 removed outlier: 3.590A pdb=" N ILE C 255 " --> pdb=" O ALA C 227 " (cutoff:3.500A) 484 hydrogen bonds defined for protein. 1359 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: 3.60 Time building geometry restraints manager: 3.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3678 1.34 - 1.46: 1830 1.46 - 1.57: 6297 1.57 - 1.69: 2 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 1.597 -0.072 2.10e-02 2.27e+03 1.16e+01 bond pdb=" CB THR E 218 " pdb=" CG2 THR E 218 " ideal model delta sigma weight residual 1.521 1.440 0.081 3.30e-02 9.18e+02 6.07e+00 bond pdb=" CA ILE E 51 " pdb=" CB ILE E 51 " ideal model delta sigma weight residual 1.540 1.600 -0.060 2.70e-02 1.37e+03 4.98e+00 bond pdb=" C LEU C 188 " pdb=" N PRO C 189 " ideal model delta sigma weight residual 1.334 1.385 -0.051 2.34e-02 1.83e+03 4.77e+00 bond pdb=" C ILE E 51 " pdb=" N PRO E 52 " ideal model delta sigma weight residual 1.336 1.362 -0.026 1.25e-02 6.40e+03 4.35e+00 ... (remaining 11866 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.65: 15854 3.65 - 7.30: 229 7.30 - 10.95: 29 10.95 - 14.61: 2 14.61 - 18.26: 2 Bond angle restraints: 16116 Sorted by residual: angle pdb=" CA LEU A 35 " pdb=" CB LEU A 35 " pdb=" CG LEU A 35 " ideal model delta sigma weight residual 116.30 134.56 -18.26 3.50e+00 8.16e-02 2.72e+01 angle pdb=" CA THR A 188 " pdb=" CB THR A 188 " pdb=" CG2 THR A 188 " ideal model delta sigma weight residual 110.50 119.05 -8.55 1.70e+00 3.46e-01 2.53e+01 angle pdb=" C GLN A 247 " pdb=" N ASN A 248 " pdb=" CA ASN A 248 " ideal model delta sigma weight residual 121.54 130.57 -9.03 1.91e+00 2.74e-01 2.24e+01 angle pdb=" CA LEU E 112 " pdb=" CB LEU E 112 " pdb=" CG LEU E 112 " ideal model delta sigma weight residual 116.30 132.30 -16.00 3.50e+00 8.16e-02 2.09e+01 angle pdb=" C ARG A 181 " pdb=" N ASP A 182 " pdb=" CA ASP A 182 " ideal model delta sigma weight residual 121.54 130.21 -8.67 1.91e+00 2.74e-01 2.06e+01 ... (remaining 16111 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.82: 6161 16.82 - 33.63: 678 33.63 - 50.45: 160 50.45 - 67.26: 15 67.26 - 84.07: 7 Dihedral angle restraints: 7021 sinusoidal: 2752 harmonic: 4269 Sorted by residual: dihedral pdb=" CA VAL C 83 " pdb=" C VAL C 83 " pdb=" N THR C 84 " pdb=" CA THR C 84 " ideal model delta harmonic sigma weight residual 180.00 153.81 26.19 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA TRP C 240 " pdb=" C TRP C 240 " pdb=" N THR C 241 " pdb=" CA THR C 241 " ideal model delta harmonic sigma weight residual 180.00 156.56 23.44 0 5.00e+00 4.00e-02 2.20e+01 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 -157.42 -22.58 0 5.00e+00 4.00e-02 2.04e+01 ... (remaining 7018 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1690 0.103 - 0.205: 149 0.205 - 0.308: 17 0.308 - 0.410: 2 0.410 - 0.513: 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 -2.12 -0.51 2.00e-01 2.50e+01 6.57e+00 chirality pdb=" CB ILE B 230 " pdb=" CA ILE B 230 " pdb=" CG1 ILE B 230 " pdb=" CG2 ILE B 230 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.46 2.00e-01 2.50e+01 5.30e+00 chirality pdb=" CB VAL C 260 " pdb=" CA VAL C 260 " pdb=" CG1 VAL C 260 " pdb=" CG2 VAL C 260 " both_signs ideal model delta sigma weight residual False -2.63 -2.21 -0.42 2.00e-01 2.50e+01 4.33e+00 ... (remaining 1858 not shown) Planarity restraints: 2063 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 376 " -0.022 2.00e-02 2.50e+03 4.31e-02 1.86e+01 pdb=" C VAL A 376 " 0.075 2.00e-02 2.50e+03 pdb=" O VAL A 376 " -0.028 2.00e-02 2.50e+03 pdb=" N ASP A 377 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 30 " -0.017 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C VAL D 30 " 0.057 2.00e-02 2.50e+03 pdb=" O VAL D 30 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU D 31 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 182 " 0.016 2.00e-02 2.50e+03 3.17e-02 1.00e+01 pdb=" C ASP A 182 " -0.055 2.00e-02 2.50e+03 pdb=" O ASP A 182 " 0.021 2.00e-02 2.50e+03 pdb=" N GLY A 183 " 0.019 2.00e-02 2.50e+03 ... (remaining 2060 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 102 2.54 - 3.13: 7694 3.13 - 3.72: 18541 3.72 - 4.31: 26273 4.31 - 4.90: 42946 Nonbonded interactions: 95556 Sorted by model distance: nonbonded pdb="MG MG A 501 " pdb=" O HOH A 601 " model vdw 1.946 2.170 nonbonded pdb=" OD1 ASP A 359 " pdb="MG MG A 501 " model vdw 2.018 2.170 nonbonded pdb=" OD1 ASP A 363 " pdb="MG MG A 501 " model vdw 2.184 2.170 nonbonded pdb=" OD1 ASN A 361 " pdb="MG MG A 501 " model vdw 2.292 2.170 nonbonded pdb=" O SER B 90 " pdb=" OG1 THR B 94 " model vdw 2.340 3.040 ... (remaining 95551 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain '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: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 27.920 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 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 : 0.006 0.083 11871 Z= 0.385 Angle : 1.086 18.258 16116 Z= 0.570 Chirality : 0.065 0.513 1861 Planarity : 0.007 0.075 2063 Dihedral : 14.559 84.075 4299 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 1.06 % Allowed : 10.78 % Favored : 88.15 % Cbeta Deviations : 0.15 % 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: -5.64 (0.15), residues: 1498 helix: -4.51 (0.08), residues: 639 sheet: -3.63 (0.26), residues: 215 loop : -2.70 (0.21), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 240 HIS 0.009 0.002 HIS A 163 PHE 0.015 0.002 PHE E 64 TYR 0.017 0.002 TYR A 52 ARG 0.006 0.001 ARG A 360 *********************** 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 175 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 162 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8903 (mpp) cc_final: 0.8479 (mpp) REVERT: A 231 MET cc_start: 0.9149 (mtt) cc_final: 0.8858 (mtt) REVERT: A 256 ILE cc_start: 0.9218 (pt) cc_final: 0.8941 (pt) REVERT: A 420 MET cc_start: 0.8848 (mmm) cc_final: 0.8647 (mmm) REVERT: B 61 LYS cc_start: 0.8778 (mttp) cc_final: 0.8436 (mmmt) REVERT: C 86 TYR cc_start: 0.8963 (m-80) cc_final: 0.8665 (m-10) REVERT: C 283 HIS cc_start: 0.7392 (m90) cc_final: 0.7021 (m90) REVERT: C 287 LEU cc_start: 0.9380 (tp) cc_final: 0.8933 (tp) REVERT: D 75 TYR cc_start: 0.9156 (p90) cc_final: 0.8909 (p90) REVERT: D 139 LEU cc_start: 0.9176 (tp) cc_final: 0.8955 (tp) REVERT: D 169 ASN cc_start: 0.8875 (p0) cc_final: 0.8326 (p0) REVERT: D 219 ASP cc_start: 0.9034 (m-30) cc_final: 0.8745 (m-30) REVERT: E 3 GLN cc_start: 0.8347 (mt0) cc_final: 0.8090 (mt0) REVERT: E 82 ASP cc_start: 0.9165 (t0) cc_final: 0.8953 (t0) REVERT: E 118 ILE cc_start: 0.8456 (mm) cc_final: 0.8175 (tt) REVERT: E 171 LYS cc_start: 0.9232 (tttt) cc_final: 0.9016 (tttt) REVERT: E 211 TRP cc_start: 0.8527 (m100) cc_final: 0.8162 (m-10) REVERT: E 219 ASP cc_start: 0.8061 (m-30) cc_final: 0.7737 (m-30) REVERT: E 221 TYR cc_start: 0.9022 (t80) cc_final: 0.8516 (t80) outliers start: 13 outliers final: 7 residues processed: 174 average time/residue: 0.2979 time to fit residues: 70.1862 Evaluate side-chains 107 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 100 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain E residue 112 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 62 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 134 optimal weight: 0.8980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN A 122 ASN A 123 ASN A 141 GLN A 145 ASN A 160 ASN A 175 ASN A 176 HIS A 179 ASN A 190 ASN A 212 ASN ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 HIS B 11 GLN B 20 HIS B 176 GLN B 207 GLN B 283 HIS C 2 ASN C 75 GLN C 135 GLN C 214 GLN C 283 HIS D 6 ASN D 205 ASN D 225 ASN E 108 HIS E 225 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2210 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= 0.208 Angle : 0.619 8.544 16116 Z= 0.318 Chirality : 0.043 0.268 1861 Planarity : 0.005 0.044 2063 Dihedral : 5.280 24.684 1651 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.12 % Allowed : 15.52 % 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: -3.44 (0.19), residues: 1498 helix: -1.88 (0.16), residues: 655 sheet: -3.18 (0.29), residues: 201 loop : -2.24 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 240 HIS 0.004 0.001 HIS B 186 PHE 0.012 0.001 PHE D 64 TYR 0.016 0.001 TYR E 268 ARG 0.012 0.000 ARG A 117 *********************** 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 145 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 119 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8700 (mpp) cc_final: 0.8204 (mpp) REVERT: A 231 MET cc_start: 0.9155 (mtt) cc_final: 0.8847 (mtp) REVERT: A 233 SER cc_start: 0.9038 (m) cc_final: 0.8443 (t) REVERT: A 297 THR cc_start: 0.8872 (OUTLIER) cc_final: 0.7833 (p) REVERT: A 400 TRP cc_start: 0.8532 (t60) cc_final: 0.8076 (t60) REVERT: B 61 LYS cc_start: 0.8815 (mttp) cc_final: 0.8541 (mmmt) REVERT: C 78 TYR cc_start: 0.8680 (t80) cc_final: 0.8435 (t80) REVERT: C 287 LEU cc_start: 0.9457 (tp) cc_final: 0.9028 (tp) REVERT: D 117 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8725 (tt) REVERT: D 171 LYS cc_start: 0.9004 (ttpp) cc_final: 0.8790 (ttmm) REVERT: D 219 ASP cc_start: 0.9055 (m-30) cc_final: 0.8705 (m-30) REVERT: E 3 GLN cc_start: 0.8477 (mt0) cc_final: 0.8156 (mt0) REVERT: E 20 TRP cc_start: 0.8485 (m100) cc_final: 0.7903 (m-10) REVERT: E 82 ASP cc_start: 0.9153 (t0) cc_final: 0.8934 (t0) REVERT: E 211 TRP cc_start: 0.8668 (m100) cc_final: 0.8448 (m-90) REVERT: E 221 TYR cc_start: 0.9084 (t80) cc_final: 0.8835 (t80) outliers start: 26 outliers final: 11 residues processed: 142 average time/residue: 0.2290 time to fit residues: 47.8827 Evaluate side-chains 112 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 99 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain B residue 203 LYS Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain E residue 100 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 chunk 37 optimal weight: 0.8980 chunk 134 optimal weight: 3.9990 chunk 145 optimal weight: 5.9990 chunk 119 optimal weight: 0.9990 chunk 133 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11871 Z= 0.170 Angle : 0.571 10.189 16116 Z= 0.287 Chirality : 0.043 0.236 1861 Planarity : 0.004 0.043 2063 Dihedral : 4.843 24.720 1646 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.72 % Allowed : 16.99 % Favored : 81.29 % 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: -2.14 (0.21), residues: 1498 helix: -0.35 (0.20), residues: 659 sheet: -2.87 (0.31), residues: 204 loop : -1.98 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 400 HIS 0.004 0.001 HIS B 186 PHE 0.008 0.001 PHE E 157 TYR 0.014 0.001 TYR B 86 ARG 0.003 0.000 ARG A 225 *********************** 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 138 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 117 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8688 (mpp) cc_final: 0.8224 (mpp) REVERT: A 390 MET cc_start: 0.8526 (tpp) cc_final: 0.8223 (tpp) REVERT: A 400 TRP cc_start: 0.8279 (t60) cc_final: 0.7977 (t-100) REVERT: A 420 MET cc_start: 0.8717 (mmm) cc_final: 0.8340 (tpp) REVERT: B 61 LYS cc_start: 0.8822 (mttp) cc_final: 0.8550 (mmmt) REVERT: C 78 TYR cc_start: 0.8738 (t80) cc_final: 0.8378 (t80) REVERT: D 63 THR cc_start: 0.9405 (m) cc_final: 0.9134 (m) REVERT: D 117 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8630 (tt) REVERT: D 171 LYS cc_start: 0.8997 (ttpp) cc_final: 0.8696 (ttmt) REVERT: D 219 ASP cc_start: 0.9012 (m-30) cc_final: 0.8683 (m-30) REVERT: E 20 TRP cc_start: 0.8515 (m100) cc_final: 0.7923 (m-10) REVERT: E 82 ASP cc_start: 0.9064 (t0) cc_final: 0.8858 (t0) REVERT: E 83 GLU cc_start: 0.9024 (mt-10) cc_final: 0.8731 (mt-10) REVERT: E 211 TRP cc_start: 0.8649 (m100) cc_final: 0.8444 (m-90) REVERT: E 219 ASP cc_start: 0.8607 (m-30) cc_final: 0.8038 (m-30) REVERT: E 221 TYR cc_start: 0.9109 (t80) cc_final: 0.8841 (t80) outliers start: 21 outliers final: 16 residues processed: 135 average time/residue: 0.2395 time to fit residues: 47.5566 Evaluate side-chains 117 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 100 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 203 LYS Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 187 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 64 optimal weight: 20.0000 chunk 90 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 chunk 128 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 GLN C 245 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11871 Z= 0.239 Angle : 0.591 9.470 16116 Z= 0.295 Chirality : 0.043 0.246 1861 Planarity : 0.004 0.040 2063 Dihedral : 4.771 27.140 1646 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.53 % Allowed : 18.95 % Favored : 78.51 % 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: -1.54 (0.22), residues: 1498 helix: 0.31 (0.21), residues: 675 sheet: -2.53 (0.34), residues: 198 loop : -1.95 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 240 HIS 0.004 0.001 HIS B 245 PHE 0.011 0.001 PHE E 157 TYR 0.021 0.001 TYR D 268 ARG 0.003 0.000 ARG A 225 *********************** 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 135 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 104 time to evaluate : 1.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8747 (mpp) cc_final: 0.8230 (mpp) REVERT: A 233 SER cc_start: 0.8873 (m) cc_final: 0.8182 (t) REVERT: A 400 TRP cc_start: 0.8412 (t60) cc_final: 0.8044 (t-100) REVERT: A 420 MET cc_start: 0.8788 (mmm) cc_final: 0.8358 (tpp) REVERT: B 61 LYS cc_start: 0.8830 (mttp) cc_final: 0.8569 (mmmt) REVERT: B 86 TYR cc_start: 0.8864 (m-80) cc_final: 0.8508 (m-80) REVERT: B 183 LEU cc_start: 0.9529 (OUTLIER) cc_final: 0.9273 (mm) REVERT: C 78 TYR cc_start: 0.8795 (t80) cc_final: 0.8534 (t80) REVERT: D 63 THR cc_start: 0.9401 (m) cc_final: 0.9142 (m) REVERT: D 82 ASP cc_start: 0.9051 (t0) cc_final: 0.8720 (t0) REVERT: D 117 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8683 (tt) REVERT: D 171 LYS cc_start: 0.9011 (ttpp) cc_final: 0.8801 (ttmm) REVERT: D 219 ASP cc_start: 0.9011 (m-30) cc_final: 0.8703 (m-30) REVERT: E 10 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8772 (tttp) REVERT: E 20 TRP cc_start: 0.8579 (m100) cc_final: 0.7998 (m-10) REVERT: E 82 ASP cc_start: 0.9071 (t0) cc_final: 0.8815 (t0) REVERT: E 171 LYS cc_start: 0.9121 (tttt) cc_final: 0.8875 (tttm) REVERT: E 211 TRP cc_start: 0.8702 (m100) cc_final: 0.8459 (m-90) REVERT: E 219 ASP cc_start: 0.8598 (m-30) cc_final: 0.8001 (m-30) outliers start: 31 outliers final: 17 residues processed: 131 average time/residue: 0.2192 time to fit residues: 43.1080 Evaluate side-chains 121 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 101 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 236 MET Chi-restraints excluded: chain E residue 10 LYS Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 100 ILE 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: 3.9990 chunk 81 optimal weight: 2.9990 chunk 2 optimal weight: 8.9990 chunk 106 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 73 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 36 optimal weight: 0.5980 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 7 GLN E 6 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3076 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= 0.208 Angle : 0.581 11.110 16116 Z= 0.285 Chirality : 0.042 0.157 1861 Planarity : 0.003 0.039 2063 Dihedral : 4.657 30.975 1646 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.70 % Allowed : 19.44 % Favored : 77.86 % 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: -1.19 (0.22), residues: 1498 helix: 0.67 (0.21), residues: 675 sheet: -2.40 (0.34), residues: 204 loop : -1.84 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 400 HIS 0.004 0.001 HIS B 245 PHE 0.011 0.001 PHE E 157 TYR 0.009 0.001 TYR E 221 ARG 0.003 0.000 ARG A 225 *********************** 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 144 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 111 time to evaluate : 1.334 Fit side-chains revert: symmetry clash REVERT: A 62 MET cc_start: 0.6918 (mmt) cc_final: 0.6686 (mmt) REVERT: A 125 MET cc_start: 0.8791 (mpp) cc_final: 0.8234 (mpp) REVERT: A 233 SER cc_start: 0.8881 (m) cc_final: 0.8123 (t) REVERT: A 238 VAL cc_start: 0.9610 (OUTLIER) cc_final: 0.9395 (t) REVERT: A 400 TRP cc_start: 0.8304 (t60) cc_final: 0.7967 (t-100) REVERT: A 420 MET cc_start: 0.8825 (mmm) cc_final: 0.8406 (tpp) REVERT: B 61 LYS cc_start: 0.8828 (mttp) cc_final: 0.8566 (mmmt) REVERT: C 13 TYR cc_start: 0.8248 (p90) cc_final: 0.7550 (p90) REVERT: D 63 THR cc_start: 0.9388 (m) cc_final: 0.9121 (m) REVERT: D 117 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8728 (tt) REVERT: D 219 ASP cc_start: 0.9004 (m-30) cc_final: 0.8707 (m-30) REVERT: E 20 TRP cc_start: 0.8572 (m100) cc_final: 0.8068 (m-10) REVERT: E 82 ASP cc_start: 0.9053 (t0) cc_final: 0.8836 (t0) REVERT: E 88 MET cc_start: 0.8891 (tpp) cc_final: 0.8578 (tpt) REVERT: E 211 TRP cc_start: 0.8682 (m100) cc_final: 0.8445 (m-90) REVERT: E 219 ASP cc_start: 0.8586 (m-30) cc_final: 0.8053 (m-30) REVERT: E 221 TYR cc_start: 0.9122 (t80) cc_final: 0.8896 (t80) outliers start: 33 outliers final: 20 residues processed: 138 average time/residue: 0.2150 time to fit residues: 44.7242 Evaluate side-chains 121 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 99 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 93 CYS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 203 LYS Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 236 MET Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 114 LEU 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: 0.0370 chunk 128 optimal weight: 0.2980 chunk 28 optimal weight: 7.9990 chunk 83 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 143 optimal weight: 10.0000 chunk 118 optimal weight: 0.7980 chunk 66 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 47 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 11871 Z= 0.159 Angle : 0.567 10.558 16116 Z= 0.277 Chirality : 0.042 0.208 1861 Planarity : 0.003 0.038 2063 Dihedral : 4.523 38.206 1646 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.37 % Allowed : 21.08 % Favored : 76.55 % 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: -0.87 (0.23), residues: 1498 helix: 0.99 (0.22), residues: 668 sheet: -2.01 (0.38), residues: 181 loop : -1.84 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 400 HIS 0.004 0.001 HIS B 245 PHE 0.010 0.001 PHE E 146 TYR 0.019 0.001 TYR E 268 ARG 0.003 0.000 ARG A 225 *********************** 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 138 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 109 time to evaluate : 1.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8801 (mpp) cc_final: 0.8208 (mpp) REVERT: A 233 SER cc_start: 0.8899 (m) cc_final: 0.8179 (t) REVERT: A 235 LYS cc_start: 0.9422 (tptp) cc_final: 0.9075 (mmmm) REVERT: A 400 TRP cc_start: 0.8258 (t60) cc_final: 0.7920 (t-100) REVERT: A 420 MET cc_start: 0.8810 (mmm) cc_final: 0.8479 (tpp) REVERT: B 61 LYS cc_start: 0.8806 (mttp) cc_final: 0.8554 (mmmt) REVERT: B 271 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7701 (tp) REVERT: B 295 MET cc_start: 0.8873 (mmm) cc_final: 0.8633 (mmm) REVERT: C 224 ARG cc_start: 0.8746 (tmm-80) cc_final: 0.8546 (tmm-80) REVERT: D 63 THR cc_start: 0.9406 (m) cc_final: 0.9115 (m) REVERT: D 187 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.8870 (pp) REVERT: D 219 ASP cc_start: 0.9012 (m-30) cc_final: 0.8622 (m-30) REVERT: E 11 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8359 (mt-10) REVERT: E 20 TRP cc_start: 0.8556 (m100) cc_final: 0.7986 (m-10) REVERT: E 82 ASP cc_start: 0.9021 (t0) cc_final: 0.8786 (t0) REVERT: E 88 MET cc_start: 0.8869 (tpp) cc_final: 0.8512 (tpt) REVERT: E 211 TRP cc_start: 0.8588 (m100) cc_final: 0.8182 (m-10) REVERT: E 219 ASP cc_start: 0.8517 (m-30) cc_final: 0.8006 (m-30) REVERT: E 221 TYR cc_start: 0.9084 (t80) cc_final: 0.8848 (t80) outliers start: 29 outliers final: 19 residues processed: 134 average time/residue: 0.2295 time to fit residues: 45.2589 Evaluate side-chains 120 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 99 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 203 LYS Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 236 MET Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 187 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 120 optimal weight: 8.9990 chunk 79 optimal weight: 3.9990 chunk 142 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 65 optimal weight: 0.0030 chunk 88 optimal weight: 0.9990 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3340 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= 0.181 Angle : 0.577 10.410 16116 Z= 0.280 Chirality : 0.042 0.173 1861 Planarity : 0.003 0.036 2063 Dihedral : 4.503 37.351 1646 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 2.45 % Allowed : 21.32 % Favored : 76.23 % 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: -0.67 (0.23), residues: 1498 helix: 1.11 (0.22), residues: 672 sheet: -1.77 (0.41), residues: 168 loop : -1.75 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 400 HIS 0.004 0.001 HIS B 245 PHE 0.010 0.001 PHE E 157 TYR 0.018 0.001 TYR C 78 ARG 0.002 0.000 ARG A 225 *********************** 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 132 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 102 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8810 (mpp) cc_final: 0.8289 (mpp) REVERT: A 233 SER cc_start: 0.8908 (m) cc_final: 0.8197 (t) REVERT: A 400 TRP cc_start: 0.8257 (t60) cc_final: 0.7924 (t-100) REVERT: A 420 MET cc_start: 0.8800 (mmm) cc_final: 0.8389 (tpp) REVERT: B 61 LYS cc_start: 0.8788 (mttp) cc_final: 0.8539 (mmmt) REVERT: B 86 TYR cc_start: 0.8751 (m-80) cc_final: 0.8440 (m-80) REVERT: B 271 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7690 (tp) REVERT: B 295 MET cc_start: 0.8907 (mmm) cc_final: 0.8644 (mmm) REVERT: C 78 TYR cc_start: 0.8664 (t80) cc_final: 0.8308 (t80) REVERT: C 224 ARG cc_start: 0.8789 (tmm-80) cc_final: 0.8577 (tmm-80) REVERT: D 63 THR cc_start: 0.9404 (m) cc_final: 0.9120 (m) REVERT: D 88 MET cc_start: 0.8561 (ttp) cc_final: 0.7900 (tmm) REVERT: D 187 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.8889 (pp) REVERT: D 219 ASP cc_start: 0.9035 (m-30) cc_final: 0.8616 (m-30) REVERT: E 10 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8716 (tttp) REVERT: E 20 TRP cc_start: 0.8556 (m100) cc_final: 0.7995 (m-10) REVERT: E 211 TRP cc_start: 0.8585 (m100) cc_final: 0.8181 (m-10) REVERT: E 219 ASP cc_start: 0.8527 (m-30) cc_final: 0.8012 (m-30) REVERT: E 221 TYR cc_start: 0.9091 (t80) cc_final: 0.8783 (t80) outliers start: 30 outliers final: 19 residues processed: 128 average time/residue: 0.2380 time to fit residues: 45.0783 Evaluate side-chains 120 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 98 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 203 LYS Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 236 MET Chi-restraints excluded: chain E residue 10 LYS 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: 6.9990 chunk 85 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 112 optimal weight: 3.9990 chunk 129 optimal weight: 0.3980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11871 Z= 0.231 Angle : 0.611 10.456 16116 Z= 0.297 Chirality : 0.043 0.156 1861 Planarity : 0.003 0.036 2063 Dihedral : 4.585 39.415 1646 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.37 % Allowed : 21.16 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.23), residues: 1498 helix: 1.14 (0.21), residues: 672 sheet: -1.73 (0.39), residues: 184 loop : -1.69 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 400 HIS 0.004 0.001 HIS B 245 PHE 0.011 0.001 PHE E 157 TYR 0.020 0.001 TYR C 78 ARG 0.002 0.000 ARG A 399 *********************** 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 126 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 97 time to evaluate : 1.439 Fit side-chains revert: symmetry clash REVERT: A 62 MET cc_start: 0.6973 (mmt) cc_final: 0.6728 (mmt) REVERT: A 125 MET cc_start: 0.8818 (mpp) cc_final: 0.8273 (mpp) REVERT: A 209 MET cc_start: 0.8184 (mmt) cc_final: 0.7963 (mmt) REVERT: A 233 SER cc_start: 0.8778 (m) cc_final: 0.8130 (t) REVERT: A 400 TRP cc_start: 0.8239 (t60) cc_final: 0.7908 (t-100) REVERT: A 420 MET cc_start: 0.8837 (mmm) cc_final: 0.8476 (tpp) REVERT: B 61 LYS cc_start: 0.8791 (mttp) cc_final: 0.8552 (mmmt) REVERT: B 86 TYR cc_start: 0.8802 (m-80) cc_final: 0.8415 (m-80) REVERT: B 271 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7741 (tp) REVERT: B 295 MET cc_start: 0.8935 (mmm) cc_final: 0.8655 (mmm) REVERT: C 224 ARG cc_start: 0.8832 (tmm-80) cc_final: 0.8560 (tmm-80) REVERT: D 63 THR cc_start: 0.9405 (m) cc_final: 0.9127 (m) REVERT: D 88 MET cc_start: 0.8612 (ttp) cc_final: 0.8171 (tmm) REVERT: D 170 GLU cc_start: 0.6821 (pm20) cc_final: 0.6574 (mp0) REVERT: D 187 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.8896 (pp) REVERT: D 219 ASP cc_start: 0.9041 (m-30) cc_final: 0.8732 (m-30) REVERT: E 10 LYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8712 (tttp) REVERT: E 20 TRP cc_start: 0.8567 (m100) cc_final: 0.8086 (m-10) REVERT: E 88 MET cc_start: 0.8810 (tpp) cc_final: 0.8535 (tpt) REVERT: E 211 TRP cc_start: 0.8640 (m100) cc_final: 0.8190 (m-10) REVERT: E 219 ASP cc_start: 0.8555 (m-30) cc_final: 0.8025 (m-30) REVERT: E 221 TYR cc_start: 0.9133 (t80) cc_final: 0.8878 (t80) outliers start: 29 outliers final: 21 residues processed: 121 average time/residue: 0.2167 time to fit residues: 39.5042 Evaluate side-chains 119 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 95 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain B residue 20 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 203 LYS Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 236 MET Chi-restraints excluded: chain E residue 10 LYS Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 187 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 20.0000 chunk 124 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 80 optimal weight: 0.2980 chunk 57 optimal weight: 0.7980 chunk 104 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 120 optimal weight: 9.9990 chunk 125 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 140 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3525 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= 0.166 Angle : 0.583 10.411 16116 Z= 0.284 Chirality : 0.042 0.176 1861 Planarity : 0.003 0.036 2063 Dihedral : 4.491 39.392 1646 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.21 % Allowed : 20.92 % Favored : 76.88 % 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: -0.45 (0.23), residues: 1498 helix: 1.30 (0.22), residues: 671 sheet: -1.68 (0.42), residues: 168 loop : -1.63 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 400 HIS 0.004 0.001 HIS B 245 PHE 0.010 0.001 PHE A 133 TYR 0.026 0.001 TYR C 78 ARG 0.002 0.000 ARG A 171 *********************** 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 131 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 104 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8822 (mpp) cc_final: 0.8276 (mpp) REVERT: A 233 SER cc_start: 0.8901 (m) cc_final: 0.8181 (t) REVERT: A 235 LYS cc_start: 0.9402 (tptp) cc_final: 0.9077 (mmmm) REVERT: A 400 TRP cc_start: 0.8185 (t60) cc_final: 0.7880 (t-100) REVERT: A 420 MET cc_start: 0.8805 (mmm) cc_final: 0.8479 (tpp) REVERT: B 61 LYS cc_start: 0.8796 (mttp) cc_final: 0.8547 (mmmt) REVERT: B 86 TYR cc_start: 0.8742 (m-80) cc_final: 0.8340 (m-80) REVERT: B 271 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7730 (tp) REVERT: B 295 MET cc_start: 0.8934 (mmm) cc_final: 0.8674 (mmm) REVERT: C 224 ARG cc_start: 0.8820 (tmm-80) cc_final: 0.8586 (tmm-80) REVERT: D 63 THR cc_start: 0.9408 (m) cc_final: 0.9114 (m) REVERT: D 88 MET cc_start: 0.8568 (ttp) cc_final: 0.8075 (tmm) REVERT: D 170 GLU cc_start: 0.7181 (pm20) cc_final: 0.6870 (mp0) REVERT: D 187 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.8832 (pp) REVERT: D 219 ASP cc_start: 0.9039 (m-30) cc_final: 0.8607 (m-30) REVERT: E 10 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8637 (tttp) REVERT: E 11 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8372 (mt-10) REVERT: E 20 TRP cc_start: 0.8546 (m100) cc_final: 0.7980 (m-10) REVERT: E 88 MET cc_start: 0.8729 (tpp) cc_final: 0.8416 (tpt) REVERT: E 211 TRP cc_start: 0.8617 (m100) cc_final: 0.8194 (m-10) REVERT: E 219 ASP cc_start: 0.8508 (m-30) cc_final: 0.7996 (m-30) REVERT: E 221 TYR cc_start: 0.9080 (t80) cc_final: 0.8818 (t80) outliers start: 27 outliers final: 22 residues processed: 125 average time/residue: 0.2085 time to fit residues: 39.4825 Evaluate side-chains 124 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 99 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 129 TYR Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 203 LYS Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 236 MET Chi-restraints excluded: chain E residue 10 LYS Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 187 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 97 optimal weight: 4.9990 chunk 147 optimal weight: 5.9990 chunk 135 optimal weight: 0.7980 chunk 117 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 90 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 125 optimal weight: 5.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11871 Z= 0.234 Angle : 0.631 11.376 16116 Z= 0.304 Chirality : 0.043 0.178 1861 Planarity : 0.003 0.035 2063 Dihedral : 4.584 40.933 1646 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.21 % Allowed : 21.49 % Favored : 76.31 % 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: -0.43 (0.23), residues: 1498 helix: 1.29 (0.21), residues: 670 sheet: -1.52 (0.42), residues: 168 loop : -1.63 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 400 HIS 0.004 0.001 HIS B 186 PHE 0.012 0.001 PHE E 157 TYR 0.027 0.001 TYR C 78 ARG 0.002 0.000 ARG A 171 ********************** 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 125 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 98 time to evaluate : 1.334 Fit side-chains revert: symmetry clash REVERT: A 62 MET cc_start: 0.6977 (mmt) cc_final: 0.6772 (mmt) REVERT: A 125 MET cc_start: 0.8846 (mpp) cc_final: 0.8295 (mpp) REVERT: A 233 SER cc_start: 0.8894 (m) cc_final: 0.8127 (t) REVERT: A 400 TRP cc_start: 0.8245 (t60) cc_final: 0.7943 (t-100) REVERT: A 420 MET cc_start: 0.8834 (mmm) cc_final: 0.8499 (tpp) REVERT: B 61 LYS cc_start: 0.8796 (mttp) cc_final: 0.8559 (mmmt) REVERT: B 271 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7688 (tp) REVERT: B 295 MET cc_start: 0.8976 (mmm) cc_final: 0.8688 (mmm) REVERT: C 224 ARG cc_start: 0.8859 (tmm-80) cc_final: 0.8531 (tmm-80) REVERT: D 63 THR cc_start: 0.9435 (m) cc_final: 0.9157 (m) REVERT: D 88 MET cc_start: 0.8623 (ttp) cc_final: 0.8279 (tmm) REVERT: D 170 GLU cc_start: 0.7117 (pm20) cc_final: 0.6824 (mp0) REVERT: D 187 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.8856 (pp) REVERT: D 219 ASP cc_start: 0.9039 (m-30) cc_final: 0.8739 (m-30) REVERT: E 20 TRP cc_start: 0.8576 (m100) cc_final: 0.8082 (m-10) REVERT: E 88 MET cc_start: 0.8800 (tpp) cc_final: 0.8502 (tpt) REVERT: E 211 TRP cc_start: 0.8619 (m100) cc_final: 0.8174 (m-10) REVERT: E 219 ASP cc_start: 0.8544 (m-30) cc_final: 0.8025 (m-30) REVERT: E 221 TYR cc_start: 0.9149 (t80) cc_final: 0.8880 (t80) outliers start: 27 outliers final: 23 residues processed: 122 average time/residue: 0.2101 time to fit residues: 38.6964 Evaluate side-chains 118 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 93 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain B residue 20 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 203 LYS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 187 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 117 optimal weight: 0.0980 chunk 49 optimal weight: 0.7980 chunk 120 optimal weight: 0.0020 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 6 optimal weight: 9.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.063303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.050656 restraints weight = 46503.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.052438 restraints weight = 21417.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.053628 restraints weight = 13121.242| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11871 Z= 0.156 Angle : 0.592 10.657 16116 Z= 0.285 Chirality : 0.042 0.154 1861 Planarity : 0.003 0.035 2063 Dihedral : 4.465 40.422 1646 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.96 % Allowed : 21.98 % Favored : 76.06 % 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: -0.31 (0.23), residues: 1498 helix: 1.40 (0.22), residues: 671 sheet: -1.39 (0.44), residues: 157 loop : -1.61 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 400 HIS 0.004 0.001 HIS B 245 PHE 0.012 0.001 PHE A 110 TYR 0.014 0.001 TYR D 93 ARG 0.002 0.000 ARG A 171 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2100.74 seconds wall clock time: 40 minutes 12.14 seconds (2412.14 seconds total)