Starting phenix.real_space_refine on Sun Apr 7 22:04:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o10_12685/04_2024/7o10_12685.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o10_12685/04_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_12685/04_2024/7o10_12685.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o10_12685/04_2024/7o10_12685.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o10_12685/04_2024/7o10_12685.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o10_12685/04_2024/7o10_12685.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= 0.002 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 Residue "A ARG 44": "NH1" <-> "NH2" Residue "A TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "A ARG 124": "NH1" <-> "NH2" Residue "A ARG 126": "NH1" <-> "NH2" Residue "A ASP 182": "OD1" <-> "OD2" Residue "A TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 246": "OD1" <-> "OD2" Residue "A ASP 268": "OD1" <-> "OD2" Residue "A ARG 348": "NH1" <-> "NH2" Residue "A ARG 360": "NH1" <-> "NH2" Residue "A ASP 374": "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 PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 425": "OE1" <-> "OE2" Residue "B GLU 114": "OE1" <-> "OE2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B ARG 216": "NH1" <-> "NH2" 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 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 239": "NH1" <-> "NH2" Residue "C ARG 269": "NH1" <-> "NH2" Residue "C ARG 297": "NH1" <-> "NH2" Residue "D ASP 82": "OD1" <-> "OD2" Residue "D ARG 145": "NH1" <-> "NH2" Residue "D ARG 222": "NH1" <-> "NH2" Residue "D ARG 273": "NH1" <-> "NH2" Residue "E ASP 219": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 6.88, per 1000 atoms: 0.59 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 - 3.50 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: 4.35 Conformation dependent library (CDL) restraints added in 2.3 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: 1.44 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: 3.43 Time building geometry restraints manager: 4.72 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: 98.54 - 105.79: 233 105.79 - 113.05: 6222 113.05 - 120.31: 4965 120.31 - 127.57: 4557 127.57 - 134.83: 139 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 2.440 ... (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 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: 3.350 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: 6.350 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 33.710 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.330 ------------------------------------------------------------------------------- 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 : 1.349 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: 0.3027 time to fit residues: 71.4350 Evaluate side-chains 107 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 100 time to evaluate : 1.348 ------------------------------------------------------------------------------- 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: 0.9980 chunk 112 optimal weight: 0.6980 chunk 62 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 59 optimal weight: 0.5980 chunk 116 optimal weight: 1.9990 chunk 44 optimal weight: 0.3980 chunk 70 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 134 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 75 GLN A 77 GLN A 122 ASN A 123 ASN A 141 GLN A 145 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 A 324 ASN A 417 HIS B 20 HIS B 176 GLN B 283 HIS C 2 ASN C 75 GLN C 135 GLN C 207 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: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11871 Z= 0.163 Angle : 0.588 8.704 16116 Z= 0.300 Chirality : 0.042 0.261 1861 Planarity : 0.005 0.045 2063 Dihedral : 5.159 23.789 1651 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.53 % Allowed : 16.09 % Favored : 81.37 % 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: -3.48 (0.19), residues: 1498 helix: -1.98 (0.16), residues: 660 sheet: -2.97 (0.30), residues: 192 loop : -2.28 (0.23), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 240 HIS 0.003 0.001 HIS B 97 PHE 0.011 0.001 PHE D 64 TYR 0.016 0.001 TYR E 268 ARG 0.008 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 158 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 127 time to evaluate : 1.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8617 (mpp) cc_final: 0.8153 (mpp) REVERT: A 297 THR cc_start: 0.8765 (OUTLIER) cc_final: 0.7882 (p) REVERT: A 400 TRP cc_start: 0.8501 (t60) cc_final: 0.8043 (t60) REVERT: B 34 LEU cc_start: 0.9262 (tp) cc_final: 0.9028 (tp) REVERT: B 61 LYS cc_start: 0.8775 (mttp) cc_final: 0.8521 (mmmt) REVERT: B 295 MET cc_start: 0.9033 (mmm) cc_final: 0.8833 (mmm) REVERT: C 78 TYR cc_start: 0.8596 (t80) cc_final: 0.8314 (t80) REVERT: C 287 LEU cc_start: 0.9422 (tp) cc_final: 0.8986 (tp) REVERT: D 117 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8740 (tt) REVERT: D 171 LYS cc_start: 0.9019 (ttpp) cc_final: 0.8818 (ttmm) REVERT: D 219 ASP cc_start: 0.8984 (m-30) cc_final: 0.8590 (m-30) REVERT: E 20 TRP cc_start: 0.8473 (m100) cc_final: 0.7886 (m-10) REVERT: E 66 MET cc_start: 0.8949 (mmm) cc_final: 0.8736 (tpp) REVERT: E 221 TYR cc_start: 0.9060 (t80) cc_final: 0.8774 (t80) outliers start: 31 outliers final: 12 residues processed: 152 average time/residue: 0.2366 time to fit residues: 53.0232 Evaluate side-chains 112 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 98 time to evaluate : 1.657 ------------------------------------------------------------------------------- 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 2 ASN Chi-restraints excluded: chain B residue 128 THR 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 289 ASP 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 190 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 37 optimal weight: 0.6980 chunk 134 optimal weight: 5.9990 chunk 145 optimal weight: 5.9990 chunk 119 optimal weight: 0.8980 chunk 133 optimal weight: 4.9990 chunk 45 optimal weight: 8.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 HIS C 245 HIS ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2688 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= 0.275 Angle : 0.618 9.492 16116 Z= 0.310 Chirality : 0.044 0.249 1861 Planarity : 0.004 0.043 2063 Dihedral : 4.935 26.529 1645 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 3.02 % Allowed : 17.08 % Favored : 79.90 % 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: -0.32 (0.20), residues: 654 sheet: -2.69 (0.32), residues: 197 loop : -2.02 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 400 HIS 0.003 0.001 HIS B 245 PHE 0.012 0.001 PHE E 157 TYR 0.015 0.001 TYR B 86 ARG 0.003 0.000 ARG A 171 *********************** 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 141 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 104 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8743 (mpp) cc_final: 0.8188 (mpp) REVERT: A 390 MET cc_start: 0.8511 (tpp) cc_final: 0.8245 (tpp) REVERT: A 400 TRP cc_start: 0.8359 (t60) cc_final: 0.8009 (t-100) REVERT: B 57 GLU cc_start: 0.7576 (tt0) cc_final: 0.6951 (tp30) REVERT: B 61 LYS cc_start: 0.8779 (mttp) cc_final: 0.8505 (mmmt) REVERT: C 78 TYR cc_start: 0.8712 (t80) cc_final: 0.8404 (t80) REVERT: C 287 LEU cc_start: 0.9465 (tp) cc_final: 0.9076 (tp) REVERT: D 63 THR cc_start: 0.9335 (m) cc_final: 0.9104 (m) REVERT: D 81 GLU cc_start: 0.7296 (mp0) cc_final: 0.6921 (mp0) REVERT: D 117 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8668 (tt) REVERT: D 171 LYS cc_start: 0.9028 (ttpp) cc_final: 0.8822 (ttmm) REVERT: D 219 ASP cc_start: 0.8961 (m-30) cc_final: 0.8584 (m-30) REVERT: E 20 TRP cc_start: 0.8549 (m100) cc_final: 0.8003 (m-10) REVERT: E 83 GLU cc_start: 0.9011 (mt-10) cc_final: 0.8670 (mt-10) REVERT: E 221 TYR cc_start: 0.9119 (t80) cc_final: 0.8902 (t80) outliers start: 37 outliers final: 30 residues processed: 135 average time/residue: 0.2255 time to fit residues: 46.0778 Evaluate side-chains 125 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 94 time to evaluate : 1.353 ------------------------------------------------------------------------------- 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 192 ASN Chi-restraints excluded: chain A residue 197 ASN 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 2 ASN Chi-restraints excluded: chain B residue 20 HIS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 192 GLU 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 C residue 289 ASP 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 244 ASP Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 100 ILE 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: 2.9990 chunk 101 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 14 optimal weight: 8.9990 chunk 64 optimal weight: 20.0000 chunk 90 optimal weight: 0.0970 chunk 135 optimal weight: 10.0000 chunk 143 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 128 optimal weight: 7.9990 chunk 38 optimal weight: 0.6980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 GLN ** 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** ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2889 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= 0.194 Angle : 0.565 9.682 16116 Z= 0.280 Chirality : 0.042 0.220 1861 Planarity : 0.003 0.041 2063 Dihedral : 4.679 26.286 1645 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.86 % Allowed : 18.95 % Favored : 78.19 % 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: -1.40 (0.22), residues: 1498 helix: 0.40 (0.21), residues: 663 sheet: -2.26 (0.33), residues: 201 loop : -1.88 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 400 HIS 0.003 0.001 HIS B 245 PHE 0.010 0.001 PHE E 157 TYR 0.017 0.001 TYR E 268 ARG 0.002 0.000 ARG A 171 *********************** 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 139 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 104 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.7144 (mmt) cc_final: 0.6804 (mmt) REVERT: A 125 MET cc_start: 0.8839 (mpp) cc_final: 0.8308 (mpp) REVERT: A 304 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8272 (tt0) REVERT: A 390 MET cc_start: 0.8549 (tpp) cc_final: 0.8293 (tpp) REVERT: A 400 TRP cc_start: 0.8277 (t60) cc_final: 0.7976 (t-100) REVERT: A 420 MET cc_start: 0.8736 (mmm) cc_final: 0.8350 (tpp) REVERT: B 61 LYS cc_start: 0.8779 (mttp) cc_final: 0.8517 (mmmt) REVERT: B 295 MET cc_start: 0.8874 (mmm) cc_final: 0.8627 (mmm) REVERT: C 78 TYR cc_start: 0.8783 (t80) cc_final: 0.8487 (t80) REVERT: C 287 LEU cc_start: 0.9426 (tp) cc_final: 0.8984 (tp) REVERT: D 63 THR cc_start: 0.9353 (m) cc_final: 0.9085 (m) REVERT: D 117 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8705 (tt) REVERT: D 171 LYS cc_start: 0.9015 (ttpp) cc_final: 0.8794 (ttmt) REVERT: D 219 ASP cc_start: 0.8915 (m-30) cc_final: 0.8556 (m-30) REVERT: E 20 TRP cc_start: 0.8548 (m100) cc_final: 0.7976 (m-10) REVERT: E 83 GLU cc_start: 0.9053 (mt-10) cc_final: 0.8652 (mt-10) REVERT: E 171 LYS cc_start: 0.9038 (tttt) cc_final: 0.8751 (tttm) outliers start: 35 outliers final: 22 residues processed: 132 average time/residue: 0.2285 time to fit residues: 44.3898 Evaluate side-chains 124 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 100 time to evaluate : 1.401 ------------------------------------------------------------------------------- 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 304 GLU Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain B residue 2 ASN Chi-restraints excluded: chain B residue 128 THR 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 D residue 244 ASP Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 190 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 106 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 98 optimal weight: 0.0980 chunk 0 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 128 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 GLN ** 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** ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11871 Z= 0.155 Angle : 0.538 10.285 16116 Z= 0.266 Chirality : 0.042 0.217 1861 Planarity : 0.003 0.038 2063 Dihedral : 4.483 25.208 1645 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.19 % Allowed : 19.20 % Favored : 77.61 % 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: -0.93 (0.23), residues: 1498 helix: 0.87 (0.21), residues: 662 sheet: -2.06 (0.35), residues: 195 loop : -1.73 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 400 HIS 0.003 0.001 HIS B 245 PHE 0.009 0.001 PHE E 157 TYR 0.011 0.001 TYR E 221 ARG 0.002 0.000 ARG A 171 *********************** 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 149 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 110 time to evaluate : 1.342 Fit side-chains revert: symmetry clash REVERT: A 62 MET cc_start: 0.7137 (mmt) cc_final: 0.6807 (mmt) REVERT: A 125 MET cc_start: 0.8884 (mpp) cc_final: 0.8294 (mpp) REVERT: A 235 LYS cc_start: 0.9434 (tptp) cc_final: 0.9066 (mmmm) REVERT: A 304 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8268 (tt0) REVERT: A 390 MET cc_start: 0.8560 (tpp) cc_final: 0.8310 (tpp) REVERT: A 400 TRP cc_start: 0.8264 (t60) cc_final: 0.7940 (t-100) REVERT: A 420 MET cc_start: 0.8830 (mmm) cc_final: 0.8436 (tpp) REVERT: B 61 LYS cc_start: 0.8757 (mttp) cc_final: 0.8490 (mmmt) REVERT: C 13 TYR cc_start: 0.8229 (p90) cc_final: 0.7574 (p90) REVERT: C 287 LEU cc_start: 0.9387 (tp) cc_final: 0.8943 (tp) REVERT: D 63 THR cc_start: 0.9369 (m) cc_final: 0.9080 (m) REVERT: D 117 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8685 (tt) REVERT: D 219 ASP cc_start: 0.8954 (m-30) cc_final: 0.8566 (m-30) REVERT: E 10 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8804 (tttp) REVERT: E 11 GLU cc_start: 0.8896 (mm-30) cc_final: 0.8502 (mt-10) REVERT: E 20 TRP cc_start: 0.8565 (m100) cc_final: 0.7988 (m-10) REVERT: E 76 ASP cc_start: 0.8771 (p0) cc_final: 0.8547 (p0) REVERT: E 83 GLU cc_start: 0.9060 (mt-10) cc_final: 0.8806 (mt-10) REVERT: E 171 LYS cc_start: 0.9086 (tttt) cc_final: 0.8870 (tttm) outliers start: 39 outliers final: 26 residues processed: 141 average time/residue: 0.2198 time to fit residues: 46.2956 Evaluate side-chains 126 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 97 time to evaluate : 1.322 ------------------------------------------------------------------------------- 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 197 ASN Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain B residue 2 ASN Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 289 ASP 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 C residue 289 ASP 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 D residue 244 ASP Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain E residue 10 LYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 0.3980 chunk 128 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 143 optimal weight: 10.0000 chunk 118 optimal weight: 2.9990 chunk 66 optimal weight: 0.4980 chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 GLN ** 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** ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 7 GLN C 97 HIS ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11871 Z= 0.257 Angle : 0.590 11.112 16116 Z= 0.291 Chirality : 0.043 0.188 1861 Planarity : 0.003 0.038 2063 Dihedral : 4.581 27.068 1645 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 3.43 % Allowed : 19.61 % Favored : 76.96 % 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: -0.77 (0.23), residues: 1498 helix: 1.05 (0.21), residues: 660 sheet: -1.87 (0.36), residues: 201 loop : -1.73 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 400 HIS 0.003 0.001 HIS B 194 PHE 0.012 0.001 PHE E 157 TYR 0.018 0.001 TYR E 268 ARG 0.001 0.000 ARG A 360 *********************** 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 140 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 98 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.7128 (mmt) cc_final: 0.6801 (mmt) REVERT: A 125 MET cc_start: 0.8933 (mpp) cc_final: 0.8558 (mpp) REVERT: A 304 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8326 (tt0) REVERT: A 400 TRP cc_start: 0.8330 (t60) cc_final: 0.8001 (t-100) REVERT: A 420 MET cc_start: 0.8873 (mmm) cc_final: 0.8524 (tpp) REVERT: B 61 LYS cc_start: 0.8749 (mttp) cc_final: 0.8504 (mmmt) REVERT: B 271 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7784 (tp) REVERT: D 63 THR cc_start: 0.9384 (m) cc_final: 0.9128 (m) REVERT: D 117 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8738 (tt) REVERT: D 187 LEU cc_start: 0.9404 (OUTLIER) cc_final: 0.8954 (pp) REVERT: D 219 ASP cc_start: 0.8963 (m-30) cc_final: 0.8595 (m-30) REVERT: E 20 TRP cc_start: 0.8583 (m100) cc_final: 0.8099 (m-10) REVERT: E 83 GLU cc_start: 0.9109 (mt-10) cc_final: 0.8850 (mt-10) REVERT: E 88 MET cc_start: 0.8845 (tpp) cc_final: 0.8616 (tpt) REVERT: E 147 MET cc_start: 0.8143 (mmt) cc_final: 0.7923 (mmt) outliers start: 42 outliers final: 27 residues processed: 132 average time/residue: 0.2112 time to fit residues: 41.8662 Evaluate side-chains 124 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 93 time to evaluate : 1.326 ------------------------------------------------------------------------------- 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 197 ASN Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain B residue 2 ASN Chi-restraints excluded: chain B residue 20 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 289 ASP 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 C residue 289 ASP Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 265 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 Chi-restraints excluded: chain E residue 190 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 104 optimal weight: 0.8980 chunk 120 optimal weight: 0.4980 chunk 79 optimal weight: 6.9990 chunk 142 optimal weight: 0.6980 chunk 89 optimal weight: 0.5980 chunk 86 optimal weight: 6.9990 chunk 65 optimal weight: 8.9990 chunk 88 optimal weight: 5.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 GLN ** 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** ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 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 0.040 11871 Z= 0.212 Angle : 0.589 11.079 16116 Z= 0.287 Chirality : 0.042 0.179 1861 Planarity : 0.003 0.036 2063 Dihedral : 4.511 26.781 1645 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.51 % Allowed : 20.34 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.60 (0.23), residues: 1498 helix: 1.21 (0.22), residues: 667 sheet: -1.73 (0.37), residues: 200 loop : -1.72 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 400 HIS 0.003 0.001 HIS B 245 PHE 0.011 0.001 PHE E 157 TYR 0.018 0.001 TYR C 78 ARG 0.002 0.000 ARG A 171 *********************** 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 141 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 98 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.7078 (mmt) cc_final: 0.6731 (mmt) REVERT: A 125 MET cc_start: 0.8950 (mpp) cc_final: 0.8552 (mpp) REVERT: A 231 MET cc_start: 0.8933 (ptp) cc_final: 0.8545 (ptp) REVERT: A 261 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8619 (mm) REVERT: A 304 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8341 (tt0) REVERT: A 400 TRP cc_start: 0.8269 (t60) cc_final: 0.7924 (t-100) REVERT: A 420 MET cc_start: 0.8852 (mmm) cc_final: 0.8516 (tpp) REVERT: B 61 LYS cc_start: 0.8802 (mttp) cc_final: 0.8534 (mmmt) REVERT: B 271 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7844 (tp) REVERT: C 223 VAL cc_start: 0.8895 (OUTLIER) cc_final: 0.8684 (p) REVERT: D 63 THR cc_start: 0.9375 (m) cc_final: 0.9103 (m) REVERT: D 187 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.8939 (pp) REVERT: D 219 ASP cc_start: 0.8930 (m-30) cc_final: 0.8565 (m-30) REVERT: E 20 TRP cc_start: 0.8564 (m100) cc_final: 0.8078 (m-10) REVERT: E 76 ASP cc_start: 0.8845 (p0) cc_final: 0.8637 (p0) REVERT: E 83 GLU cc_start: 0.9119 (mt-10) cc_final: 0.8848 (mt-10) REVERT: E 187 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8764 (pp) outliers start: 43 outliers final: 25 residues processed: 135 average time/residue: 0.2128 time to fit residues: 43.6535 Evaluate side-chains 128 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 97 time to evaluate : 1.338 ------------------------------------------------------------------------------- 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 197 ASN Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain B residue 2 ASN Chi-restraints excluded: chain B residue 20 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 201 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 B residue 289 ASP 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 C residue 289 ASP 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 187 LEU Chi-restraints excluded: chain D residue 244 ASP Chi-restraints excluded: chain D residue 265 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 0.0570 chunk 85 optimal weight: 0.6980 chunk 42 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 112 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 overall best weight: 1.5504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 GLN ** 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** ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3434 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= 0.235 Angle : 0.598 10.544 16116 Z= 0.291 Chirality : 0.042 0.163 1861 Planarity : 0.003 0.029 2063 Dihedral : 4.515 27.170 1644 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 3.59 % Allowed : 20.10 % 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: -0.55 (0.23), residues: 1498 helix: 1.26 (0.22), residues: 668 sheet: -1.72 (0.37), residues: 201 loop : -1.69 (0.25), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 400 HIS 0.003 0.001 HIS B 194 PHE 0.013 0.001 PHE E 157 TYR 0.018 0.001 TYR E 268 ARG 0.002 0.000 ARG A 171 *********************** 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 143 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 99 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.7073 (mmt) cc_final: 0.6686 (mmt) REVERT: A 125 MET cc_start: 0.8958 (mpp) cc_final: 0.8547 (mpp) REVERT: A 231 MET cc_start: 0.8929 (ptp) cc_final: 0.8539 (ptp) REVERT: A 261 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8670 (mm) REVERT: A 304 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8358 (tt0) REVERT: A 400 TRP cc_start: 0.8202 (t60) cc_final: 0.7858 (t-100) REVERT: A 420 MET cc_start: 0.8842 (mmm) cc_final: 0.8511 (tpp) REVERT: B 57 GLU cc_start: 0.7735 (tt0) cc_final: 0.7210 (tp30) REVERT: B 61 LYS cc_start: 0.8821 (mttp) cc_final: 0.8551 (mmmt) REVERT: B 271 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7829 (tp) REVERT: D 63 THR cc_start: 0.9410 (m) cc_final: 0.9131 (m) REVERT: D 187 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.8910 (pp) REVERT: D 219 ASP cc_start: 0.8958 (m-30) cc_final: 0.8600 (m-30) REVERT: E 20 TRP cc_start: 0.8592 (m100) cc_final: 0.8167 (m-10) REVERT: E 83 GLU cc_start: 0.9112 (mt-10) cc_final: 0.8820 (mt-10) REVERT: E 187 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8796 (pp) outliers start: 44 outliers final: 31 residues processed: 134 average time/residue: 0.1953 time to fit residues: 40.1361 Evaluate side-chains 132 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 96 time to evaluate : 1.186 ------------------------------------------------------------------------------- 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 192 ASN Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain B residue 2 ASN Chi-restraints excluded: chain B residue 20 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 201 LEU 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 B residue 289 ASP 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 C residue 289 ASP 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 244 ASP Chi-restraints excluded: chain D residue 265 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 Chi-restraints excluded: chain E residue 190 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 10.0000 chunk 124 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 104 optimal weight: 0.5980 chunk 40 optimal weight: 5.9990 chunk 120 optimal weight: 9.9990 chunk 125 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 140 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 GLN ** 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** ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3487 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= 0.187 Angle : 0.586 10.580 16116 Z= 0.284 Chirality : 0.042 0.157 1861 Planarity : 0.003 0.030 2063 Dihedral : 4.401 26.308 1644 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.86 % Allowed : 20.51 % Favored : 76.63 % 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: -0.40 (0.23), residues: 1498 helix: 1.41 (0.22), residues: 667 sheet: -1.55 (0.38), residues: 196 loop : -1.70 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 400 HIS 0.003 0.001 HIS B 245 PHE 0.011 0.001 PHE E 157 TYR 0.017 0.001 TYR C 78 ARG 0.002 0.000 ARG E 9 *********************** 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 136 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 101 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.7090 (mmt) cc_final: 0.6733 (mmt) REVERT: A 125 MET cc_start: 0.8952 (mpp) cc_final: 0.8533 (mpp) REVERT: A 231 MET cc_start: 0.8927 (ptp) cc_final: 0.8527 (ptp) REVERT: A 261 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8594 (mm) REVERT: A 400 TRP cc_start: 0.8188 (t60) cc_final: 0.7887 (t-100) REVERT: A 420 MET cc_start: 0.8841 (mmm) cc_final: 0.8518 (tpp) REVERT: B 61 LYS cc_start: 0.8849 (mttp) cc_final: 0.8634 (mmmt) REVERT: B 271 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7825 (tp) REVERT: D 63 THR cc_start: 0.9388 (m) cc_final: 0.9122 (m) REVERT: D 187 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.8921 (pp) REVERT: D 219 ASP cc_start: 0.8942 (m-30) cc_final: 0.8599 (m-30) REVERT: E 11 GLU cc_start: 0.8894 (mm-30) cc_final: 0.8287 (mt-10) REVERT: E 83 GLU cc_start: 0.9068 (mt-10) cc_final: 0.8761 (mt-10) REVERT: E 88 MET cc_start: 0.8771 (tpp) cc_final: 0.8514 (tpt) REVERT: E 187 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8774 (pp) REVERT: E 221 TYR cc_start: 0.8937 (t80) cc_final: 0.8713 (t80) outliers start: 35 outliers final: 29 residues processed: 129 average time/residue: 0.2214 time to fit residues: 43.1535 Evaluate side-chains 127 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 94 time to evaluate : 1.482 ------------------------------------------------------------------------------- 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 261 ILE Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain B residue 2 ASN Chi-restraints excluded: chain B residue 20 HIS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 183 LEU 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 282 ILE Chi-restraints excluded: chain B residue 289 ASP 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 C residue 289 ASP 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 244 ASP Chi-restraints excluded: chain D residue 265 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 Chi-restraints excluded: chain E residue 190 ASP 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: 8.9990 chunk 97 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 135 optimal weight: 5.9990 chunk 117 optimal weight: 0.3980 chunk 12 optimal weight: 8.9990 chunk 90 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 125 optimal weight: 0.9980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 GLN ** 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** ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 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 : 0.003 0.038 11871 Z= 0.173 Angle : 0.592 11.769 16116 Z= 0.284 Chirality : 0.042 0.172 1861 Planarity : 0.003 0.028 2063 Dihedral : 4.360 25.658 1644 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 2.61 % Allowed : 21.08 % 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: -0.36 (0.23), residues: 1498 helix: 1.46 (0.22), residues: 668 sheet: -1.55 (0.39), residues: 195 loop : -1.69 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 400 HIS 0.003 0.001 HIS B 245 PHE 0.010 0.001 PHE E 157 TYR 0.018 0.001 TYR E 268 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 129 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 97 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 MET cc_start: 0.8929 (ptp) cc_final: 0.8563 (ptp) REVERT: A 261 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8579 (mm) REVERT: A 400 TRP cc_start: 0.8170 (t60) cc_final: 0.7873 (t-100) REVERT: A 420 MET cc_start: 0.8873 (mmm) cc_final: 0.8562 (tpp) REVERT: B 61 LYS cc_start: 0.8847 (mttp) cc_final: 0.8629 (mmmt) REVERT: B 271 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7790 (tp) REVERT: C 223 VAL cc_start: 0.8706 (OUTLIER) cc_final: 0.8495 (p) REVERT: D 63 THR cc_start: 0.9408 (m) cc_final: 0.9119 (m) REVERT: D 187 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.8885 (pp) REVERT: D 219 ASP cc_start: 0.8956 (m-30) cc_final: 0.8594 (m-30) REVERT: E 83 GLU cc_start: 0.9072 (mt-10) cc_final: 0.8760 (mt-10) REVERT: E 88 MET cc_start: 0.8754 (tpp) cc_final: 0.8495 (tpt) REVERT: E 187 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8786 (pp) outliers start: 32 outliers final: 26 residues processed: 123 average time/residue: 0.2150 time to fit residues: 40.3053 Evaluate side-chains 124 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 93 time to evaluate : 1.270 ------------------------------------------------------------------------------- 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 261 ILE Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain B residue 2 ASN Chi-restraints excluded: chain B residue 20 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 183 LEU 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 B residue 289 ASP 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 C residue 289 ASP 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 244 ASP Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 190 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 120 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 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** ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.061965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.049206 restraints weight = 46721.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.050922 restraints weight = 22130.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.052079 restraints weight = 13720.930| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11871 Z= 0.287 Angle : 0.648 10.278 16116 Z= 0.313 Chirality : 0.044 0.225 1861 Planarity : 0.003 0.030 2063 Dihedral : 4.566 27.713 1644 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 3.02 % Allowed : 20.83 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.44 (0.23), residues: 1498 helix: 1.41 (0.21), residues: 665 sheet: -1.57 (0.37), residues: 211 loop : -1.72 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 400 HIS 0.005 0.001 HIS C 283 PHE 0.013 0.001 PHE E 157 TYR 0.027 0.001 TYR C 78 ARG 0.002 0.000 ARG E 9 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2092.01 seconds wall clock time: 41 minutes 55.71 seconds (2515.71 seconds total)