Starting phenix.real_space_refine on Fri Mar 22 16:04:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xjv_22215/03_2024/6xjv_22215_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xjv_22215/03_2024/6xjv_22215.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xjv_22215/03_2024/6xjv_22215.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xjv_22215/03_2024/6xjv_22215.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xjv_22215/03_2024/6xjv_22215_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xjv_22215/03_2024/6xjv_22215_neut.pdb" } resolution = 4.17 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 Anisotropic ADP refinement not supported. Converting 4093 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 130 5.16 5 C 19302 2.51 5 N 5092 2.21 5 O 5397 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 93": "NH1" <-> "NH2" Residue "A ARG 96": "NH1" <-> "NH2" Residue "A ARG 113": "NH1" <-> "NH2" Residue "A ARG 120": "NH1" <-> "NH2" Residue "A ARG 124": "NH1" <-> "NH2" Residue "A TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 201": "NH1" <-> "NH2" Residue "A ARG 345": "NH1" <-> "NH2" Residue "C ARG 93": "NH1" <-> "NH2" Residue "C ARG 124": "NH1" <-> "NH2" Residue "D ARG 52": "NH1" <-> "NH2" Residue "E ARG 93": "NH1" <-> "NH2" Residue "E ARG 124": "NH1" <-> "NH2" Residue "G ARG 93": "NH1" <-> "NH2" Residue "G ARG 96": "NH1" <-> "NH2" Residue "G ARG 134": "NH1" <-> "NH2" Residue "G ARG 201": "NH1" <-> "NH2" Residue "G ARG 295": "NH1" <-> "NH2" Residue "Q ARG 109": "NH1" <-> "NH2" Residue "Q ARG 119": "NH1" <-> "NH2" Residue "Q PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 443": "NH1" <-> "NH2" Residue "R ARG 253": "NH1" <-> "NH2" Residue "I ARG 96": "NH1" <-> "NH2" Residue "I ARG 113": "NH1" <-> "NH2" Residue "I ARG 120": "NH1" <-> "NH2" Residue "I TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 201": "NH1" <-> "NH2" Residue "K ARG 93": "NH1" <-> "NH2" Residue "K ARG 124": "NH1" <-> "NH2" Residue "M ARG 93": "NH1" <-> "NH2" Residue "M ARG 124": "NH1" <-> "NH2" Residue "O ARG 93": "NH1" <-> "NH2" Residue "O ARG 96": "NH1" <-> "NH2" Residue "O ARG 134": "NH1" <-> "NH2" Residue "O ARG 295": "NH1" <-> "NH2" Residue "S ARG 109": "NH1" <-> "NH2" Residue "S ARG 119": "NH1" <-> "NH2" Residue "S PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 443": "NH1" <-> "NH2" Residue "T ARG 253": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 29921 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 2254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2254 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 11, 'TRANS': 261} Chain: "B" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 416 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "C" Number of atoms: 2211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2211 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 10, 'TRANS': 257} Chain: "D" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 381 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "E" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2226 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 11, 'TRANS': 258} Chain: "F" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 414 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "G" Number of atoms: 2069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 2069 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 9, 'TRANS': 240} Chain breaks: 1 Chain: "H" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 373 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Chain: "Q" Number of atoms: 2189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2189 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 5, 'TRANS': 263} Chain breaks: 3 Chain: "R" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2423 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 3, 'TRANS': 287} Chain breaks: 2 Chain: "I" Number of atoms: 2254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2254 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 11, 'TRANS': 261} Chain: "J" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 416 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "K" Number of atoms: 2211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2211 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 10, 'TRANS': 257} Chain: "L" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 381 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "M" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2226 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 11, 'TRANS': 258} Chain: "N" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 414 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "O" Number of atoms: 2069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 2069 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 9, 'TRANS': 240} Chain breaks: 1 Chain: "P" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 373 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Chain: "S" Number of atoms: 2198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2198 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 5, 'TRANS': 264} Chain breaks: 3 Chain: "T" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2423 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 3, 'TRANS': 287} Chain breaks: 2 Time building chain proxies: 15.35, per 1000 atoms: 0.51 Number of scatterers: 29921 At special positions: 0 Unit cell: (120.785, 199.087, 182.427, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 130 16.00 O 5397 8.00 N 5092 7.00 C 19302 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: 11.27 Conformation dependent library (CDL) restraints added in 5.0 seconds 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6966 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 18 sheets defined 67.7% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.92 Creating SS restraints... Processing helix chain 'A' and resid 107 through 119 removed outlier: 3.830A pdb=" N ARG A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 145 Processing helix chain 'A' and resid 172 through 191 Processing helix chain 'A' and resid 192 through 215 removed outlier: 3.617A pdb=" N LEU A 197 " --> pdb=" O GLU A 193 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN A 198 " --> pdb=" O GLN A 194 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU A 208 " --> pdb=" O ILE A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 256 removed outlier: 4.111A pdb=" N VAL A 220 " --> pdb=" O PRO A 216 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG A 231 " --> pdb=" O LYS A 227 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU A 250 " --> pdb=" O GLN A 246 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU A 253 " --> pdb=" O ILE A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 262 Processing helix chain 'A' and resid 263 through 285 Processing helix chain 'A' and resid 290 through 310 removed outlier: 3.718A pdb=" N LEU A 300 " --> pdb=" O ASP A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 340 removed outlier: 4.523A pdb=" N ASP A 336 " --> pdb=" O LYS A 332 " (cutoff:3.500A) Proline residue: A 337 - end of helix Processing helix chain 'B' and resid 65 through 95 Proline residue: B 76 - end of helix removed outlier: 3.824A pdb=" N HIS B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 94 Processing helix chain 'C' and resid 107 through 119 Processing helix chain 'C' and resid 140 through 146 Processing helix chain 'C' and resid 171 through 190 removed outlier: 3.642A pdb=" N THR C 175 " --> pdb=" O GLU C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 215 removed outlier: 3.797A pdb=" N HIS C 195 " --> pdb=" O CYS C 191 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU C 214 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 255 removed outlier: 3.820A pdb=" N ARG C 221 " --> pdb=" O LEU C 217 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU C 250 " --> pdb=" O GLN C 246 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TRP C 255 " --> pdb=" O ALA C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 286 removed outlier: 4.414A pdb=" N MET C 263 " --> pdb=" O SER C 259 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU C 264 " --> pdb=" O TRP C 260 " (cutoff:3.500A) Proline residue: C 265 - end of helix Processing helix chain 'C' and resid 291 through 311 removed outlier: 4.094A pdb=" N ARG C 297 " --> pdb=" O GLU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 335 removed outlier: 3.671A pdb=" N ASP C 322 " --> pdb=" O ASN C 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 95 removed outlier: 3.634A pdb=" N ILE D 75 " --> pdb=" O PHE D 71 " (cutoff:3.500A) Proline residue: D 76 - end of helix removed outlier: 3.663A pdb=" N LYS D 86 " --> pdb=" O THR D 82 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LEU D 91 " --> pdb=" O ASN D 87 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N HIS D 95 " --> pdb=" O LEU D 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 119 removed outlier: 3.543A pdb=" N PHE E 111 " --> pdb=" O SER E 107 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP E 119 " --> pdb=" O LEU E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 145 Processing helix chain 'E' and resid 169 through 190 Processing helix chain 'E' and resid 191 through 256 removed outlier: 3.739A pdb=" N HIS E 195 " --> pdb=" O CYS E 191 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU E 200 " --> pdb=" O GLN E 196 " (cutoff:3.500A) Proline residue: E 216 - end of helix removed outlier: 3.793A pdb=" N LYS E 219 " --> pdb=" O ALA E 215 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N PHE E 247 " --> pdb=" O MET E 243 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N TRP E 255 " --> pdb=" O ALA E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 285 removed outlier: 3.752A pdb=" N MET E 263 " --> pdb=" O SER E 259 " (cutoff:3.500A) Proline residue: E 265 - end of helix removed outlier: 3.650A pdb=" N TYR E 279 " --> pdb=" O ALA E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 311 Processing helix chain 'E' and resid 313 through 335 removed outlier: 3.743A pdb=" N LEU E 320 " --> pdb=" O LYS E 316 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA E 325 " --> pdb=" O LYS E 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 95 removed outlier: 3.589A pdb=" N PHE F 71 " --> pdb=" O LEU F 67 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE F 73 " --> pdb=" O ARG F 69 " (cutoff:3.500A) Proline residue: F 76 - end of helix removed outlier: 3.512A pdb=" N SER F 85 " --> pdb=" O GLY F 81 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA F 90 " --> pdb=" O LYS F 86 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N HIS F 95 " --> pdb=" O LEU F 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 119 removed outlier: 3.862A pdb=" N ASP G 119 " --> pdb=" O LEU G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 145 Processing helix chain 'G' and resid 178 through 191 removed outlier: 3.575A pdb=" N LEU G 182 " --> pdb=" O ASP G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 192 through 257 removed outlier: 3.709A pdb=" N ARG G 201 " --> pdb=" O LEU G 197 " (cutoff:3.500A) Proline residue: G 216 - end of helix removed outlier: 3.782A pdb=" N VAL G 220 " --> pdb=" O PRO G 216 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU G 223 " --> pdb=" O LYS G 219 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU G 253 " --> pdb=" O ILE G 249 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N THR G 254 " --> pdb=" O LEU G 250 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TRP G 255 " --> pdb=" O ALA G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 263 through 286 removed outlier: 4.190A pdb=" N THR G 271 " --> pdb=" O THR G 267 " (cutoff:3.500A) Processing helix chain 'G' and resid 290 through 310 Processing helix chain 'G' and resid 313 through 334 Processing helix chain 'H' and resid 65 through 93 removed outlier: 3.527A pdb=" N ILE H 73 " --> pdb=" O ARG H 69 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE H 75 " --> pdb=" O PHE H 71 " (cutoff:3.500A) Proline residue: H 76 - end of helix removed outlier: 3.682A pdb=" N LEU H 91 " --> pdb=" O ASN H 87 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLU H 93 " --> pdb=" O ALA H 89 " (cutoff:3.500A) Processing helix chain 'Q' and resid 109 through 122 removed outlier: 3.717A pdb=" N TYR Q 121 " --> pdb=" O ARG Q 117 " (cutoff:3.500A) Processing helix chain 'Q' and resid 123 through 131 Processing helix chain 'Q' and resid 148 through 157 Processing helix chain 'Q' and resid 194 through 199 Processing helix chain 'Q' and resid 206 through 217 removed outlier: 3.676A pdb=" N ILE Q 210 " --> pdb=" O PHE Q 206 " (cutoff:3.500A) Processing helix chain 'Q' and resid 219 through 231 Processing helix chain 'Q' and resid 239 through 252 removed outlier: 3.835A pdb=" N ILE Q 249 " --> pdb=" O GLN Q 245 " (cutoff:3.500A) Processing helix chain 'Q' and resid 277 through 283 removed outlier: 3.551A pdb=" N PHE Q 283 " --> pdb=" O THR Q 279 " (cutoff:3.500A) Processing helix chain 'Q' and resid 292 through 315 removed outlier: 3.800A pdb=" N PHE Q 296 " --> pdb=" O THR Q 292 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N HIS Q 315 " --> pdb=" O GLU Q 311 " (cutoff:3.500A) Processing helix chain 'Q' and resid 323 through 336 Processing helix chain 'Q' and resid 340 through 353 removed outlier: 4.426A pdb=" N LYS Q 350 " --> pdb=" O GLN Q 346 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N LYS Q 351 " --> pdb=" O ARG Q 347 " (cutoff:3.500A) Processing helix chain 'Q' and resid 361 through 373 removed outlier: 3.927A pdb=" N ASN Q 373 " --> pdb=" O THR Q 369 " (cutoff:3.500A) Processing helix chain 'Q' and resid 373 through 386 removed outlier: 4.140A pdb=" N THR Q 379 " --> pdb=" O ASN Q 375 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ALA Q 380 " --> pdb=" O ASP Q 376 " (cutoff:3.500A) Processing helix chain 'Q' and resid 392 through 404 removed outlier: 3.742A pdb=" N MET Q 396 " --> pdb=" O ASP Q 392 " (cutoff:3.500A) Processing helix chain 'Q' and resid 409 through 421 Processing helix chain 'Q' and resid 433 through 443 Processing helix chain 'R' and resid 86 through 93 removed outlier: 3.609A pdb=" N PHE R 90 " --> pdb=" O ARG R 86 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 115 Processing helix chain 'R' and resid 128 through 137 Processing helix chain 'R' and resid 138 through 142 Processing helix chain 'R' and resid 147 through 153 Processing helix chain 'R' and resid 159 through 172 Processing helix chain 'R' and resid 176 through 184 Processing helix chain 'R' and resid 193 through 208 removed outlier: 3.756A pdb=" N PHE R 197 " --> pdb=" O GLU R 193 " (cutoff:3.500A) Processing helix chain 'R' and resid 232 through 240 Processing helix chain 'R' and resid 248 through 272 removed outlier: 3.568A pdb=" N PHE R 252 " --> pdb=" O HIS R 248 " (cutoff:3.500A) Processing helix chain 'R' and resid 279 through 288 Processing helix chain 'R' and resid 292 through 307 removed outlier: 3.527A pdb=" N LEU R 307 " --> pdb=" O VAL R 303 " (cutoff:3.500A) Processing helix chain 'R' and resid 314 through 325 removed outlier: 3.734A pdb=" N PHE R 318 " --> pdb=" O SER R 314 " (cutoff:3.500A) Processing helix chain 'R' and resid 327 through 341 removed outlier: 3.993A pdb=" N ILE R 333 " --> pdb=" O GLU R 329 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ALA R 334 " --> pdb=" O ASP R 330 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N MET R 335 " --> pdb=" O PHE R 331 " (cutoff:3.500A) Processing helix chain 'R' and resid 346 through 359 Processing helix chain 'R' and resid 363 through 375 Processing helix chain 'R' and resid 383 through 395 Processing helix chain 'I' and resid 107 through 119 removed outlier: 3.817A pdb=" N ARG I 113 " --> pdb=" O GLY I 109 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP I 119 " --> pdb=" O LEU I 115 " (cutoff:3.500A) Processing helix chain 'I' and resid 140 through 145 Processing helix chain 'I' and resid 172 through 191 removed outlier: 4.286A pdb=" N LEU I 176 " --> pdb=" O ASN I 172 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ASP I 178 " --> pdb=" O ALA I 174 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN I 184 " --> pdb=" O LYS I 180 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR I 189 " --> pdb=" O GLN I 185 " (cutoff:3.500A) Processing helix chain 'I' and resid 191 through 256 removed outlier: 3.779A pdb=" N LEU I 197 " --> pdb=" O GLU I 193 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN I 198 " --> pdb=" O GLN I 194 " (cutoff:3.500A) Proline residue: I 216 - end of helix removed outlier: 4.708A pdb=" N LYS I 219 " --> pdb=" O ALA I 215 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VAL I 220 " --> pdb=" O PRO I 216 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG I 221 " --> pdb=" O LEU I 217 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG I 231 " --> pdb=" O LYS I 227 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N MET I 243 " --> pdb=" O GLY I 239 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU I 250 " --> pdb=" O GLN I 246 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG I 252 " --> pdb=" O GLY I 248 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU I 253 " --> pdb=" O ILE I 249 " (cutoff:3.500A) Processing helix chain 'I' and resid 259 through 262 Processing helix chain 'I' and resid 263 through 285 removed outlier: 3.833A pdb=" N PHE I 269 " --> pdb=" O PRO I 265 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR I 271 " --> pdb=" O THR I 267 " (cutoff:3.500A) Processing helix chain 'I' and resid 290 through 310 removed outlier: 4.122A pdb=" N LEU I 300 " --> pdb=" O ASP I 296 " (cutoff:3.500A) Processing helix chain 'I' and resid 314 through 340 removed outlier: 3.586A pdb=" N GLN I 319 " --> pdb=" O GLU I 315 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ASP I 336 " --> pdb=" O LYS I 332 " (cutoff:3.500A) Proline residue: I 337 - end of helix Processing helix chain 'J' and resid 65 through 95 removed outlier: 3.927A pdb=" N PHE J 71 " --> pdb=" O LEU J 67 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE J 73 " --> pdb=" O ARG J 69 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE J 75 " --> pdb=" O PHE J 71 " (cutoff:3.500A) Proline residue: J 76 - end of helix removed outlier: 3.554A pdb=" N LYS J 86 " --> pdb=" O THR J 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 94 Processing helix chain 'K' and resid 107 through 119 Processing helix chain 'K' and resid 140 through 146 Processing helix chain 'K' and resid 171 through 190 removed outlier: 3.908A pdb=" N THR K 175 " --> pdb=" O GLU K 171 " (cutoff:3.500A) Processing helix chain 'K' and resid 191 through 215 removed outlier: 3.820A pdb=" N HIS K 195 " --> pdb=" O CYS K 191 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU K 214 " --> pdb=" O LEU K 210 " (cutoff:3.500A) Processing helix chain 'K' and resid 217 through 255 removed outlier: 3.680A pdb=" N ARG K 221 " --> pdb=" O LEU K 217 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE K 224 " --> pdb=" O VAL K 220 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N MET K 243 " --> pdb=" O GLY K 239 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY K 248 " --> pdb=" O ALA K 244 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU K 250 " --> pdb=" O GLN K 246 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG K 252 " --> pdb=" O GLY K 248 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TRP K 255 " --> pdb=" O ALA K 251 " (cutoff:3.500A) Processing helix chain 'K' and resid 259 through 286 removed outlier: 3.785A pdb=" N MET K 263 " --> pdb=" O SER K 259 " (cutoff:3.500A) Proline residue: K 265 - end of helix removed outlier: 3.540A pdb=" N TYR K 279 " --> pdb=" O ALA K 275 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE K 282 " --> pdb=" O MET K 278 " (cutoff:3.500A) Processing helix chain 'K' and resid 290 through 311 Processing helix chain 'K' and resid 313 through 335 removed outlier: 3.559A pdb=" N GLN K 319 " --> pdb=" O GLU K 315 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS K 332 " --> pdb=" O GLU K 328 " (cutoff:3.500A) Processing helix chain 'L' and resid 65 through 95 removed outlier: 3.668A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) Proline residue: L 76 - end of helix removed outlier: 3.593A pdb=" N LYS L 86 " --> pdb=" O THR L 82 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE L 88 " --> pdb=" O ILE L 84 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N LEU L 91 " --> pdb=" O ASN L 87 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU L 93 " --> pdb=" O ALA L 89 " (cutoff:3.500A) Processing helix chain 'M' and resid 107 through 119 removed outlier: 3.523A pdb=" N PHE M 111 " --> pdb=" O SER M 107 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASP M 119 " --> pdb=" O LEU M 115 " (cutoff:3.500A) Processing helix chain 'M' and resid 140 through 145 Processing helix chain 'M' and resid 169 through 190 Processing helix chain 'M' and resid 191 through 213 removed outlier: 3.600A pdb=" N HIS M 195 " --> pdb=" O CYS M 191 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU M 197 " --> pdb=" O GLU M 193 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU M 200 " --> pdb=" O GLN M 196 " (cutoff:3.500A) Processing helix chain 'M' and resid 213 through 256 removed outlier: 4.625A pdb=" N LEU M 217 " --> pdb=" O GLN M 213 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS M 219 " --> pdb=" O ALA M 215 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU M 223 " --> pdb=" O LYS M 219 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N PHE M 247 " --> pdb=" O MET M 243 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ARG M 252 " --> pdb=" O GLY M 248 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU M 253 " --> pdb=" O ILE M 249 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N THR M 254 " --> pdb=" O LEU M 250 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TRP M 255 " --> pdb=" O ALA M 251 " (cutoff:3.500A) Processing helix chain 'M' and resid 259 through 285 removed outlier: 3.912A pdb=" N MET M 263 " --> pdb=" O SER M 259 " (cutoff:3.500A) Proline residue: M 265 - end of helix removed outlier: 3.971A pdb=" N THR M 271 " --> pdb=" O THR M 267 " (cutoff:3.500A) Processing helix chain 'M' and resid 290 through 311 removed outlier: 3.567A pdb=" N LEU M 300 " --> pdb=" O ASP M 296 " (cutoff:3.500A) Processing helix chain 'M' and resid 313 through 335 removed outlier: 3.794A pdb=" N LEU M 320 " --> pdb=" O LYS M 316 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA M 325 " --> pdb=" O LYS M 321 " (cutoff:3.500A) Processing helix chain 'N' and resid 65 through 95 removed outlier: 3.915A pdb=" N ILE N 73 " --> pdb=" O ARG N 69 " (cutoff:3.500A) Proline residue: N 76 - end of helix removed outlier: 3.665A pdb=" N TYR N 79 " --> pdb=" O ILE N 75 " (cutoff:3.500A) Processing helix chain 'O' and resid 107 through 119 removed outlier: 3.944A pdb=" N ASP O 119 " --> pdb=" O LEU O 115 " (cutoff:3.500A) Processing helix chain 'O' and resid 140 through 145 Processing helix chain 'O' and resid 178 through 191 removed outlier: 3.667A pdb=" N THR O 189 " --> pdb=" O GLN O 185 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU O 190 " --> pdb=" O LEU O 186 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N CYS O 191 " --> pdb=" O TYR O 187 " (cutoff:3.500A) Processing helix chain 'O' and resid 192 through 257 removed outlier: 3.683A pdb=" N ARG O 201 " --> pdb=" O LEU O 197 " (cutoff:3.500A) Proline residue: O 216 - end of helix removed outlier: 3.980A pdb=" N LYS O 219 " --> pdb=" O ALA O 215 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL O 220 " --> pdb=" O PRO O 216 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU O 234 " --> pdb=" O LYS O 230 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU O 240 " --> pdb=" O LEU O 236 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG O 252 " --> pdb=" O GLY O 248 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU O 253 " --> pdb=" O ILE O 249 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N THR O 254 " --> pdb=" O LEU O 250 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TRP O 255 " --> pdb=" O ALA O 251 " (cutoff:3.500A) Processing helix chain 'O' and resid 263 through 286 removed outlier: 3.673A pdb=" N ILE O 270 " --> pdb=" O VAL O 266 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N THR O 271 " --> pdb=" O THR O 267 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE O 282 " --> pdb=" O MET O 278 " (cutoff:3.500A) Processing helix chain 'O' and resid 290 through 310 Processing helix chain 'O' and resid 313 through 334 removed outlier: 3.761A pdb=" N GLN O 319 " --> pdb=" O GLU O 315 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG O 333 " --> pdb=" O MET O 329 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU O 334 " --> pdb=" O ASP O 330 " (cutoff:3.500A) Processing helix chain 'P' and resid 65 through 93 removed outlier: 3.685A pdb=" N ILE P 73 " --> pdb=" O ARG P 69 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE P 75 " --> pdb=" O PHE P 71 " (cutoff:3.500A) Proline residue: P 76 - end of helix removed outlier: 3.618A pdb=" N GLY P 81 " --> pdb=" O PHE P 77 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS P 86 " --> pdb=" O THR P 82 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU P 91 " --> pdb=" O ASN P 87 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLU P 93 " --> pdb=" O ALA P 89 " (cutoff:3.500A) Processing helix chain 'S' and resid 109 through 122 removed outlier: 3.755A pdb=" N TYR S 114 " --> pdb=" O LYS S 110 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASN S 116 " --> pdb=" O MET S 112 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ARG S 117 " --> pdb=" O GLU S 113 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE S 118 " --> pdb=" O TYR S 114 " (cutoff:3.500A) Processing helix chain 'S' and resid 123 through 132 removed outlier: 3.582A pdb=" N PHE S 131 " --> pdb=" O ILE S 127 " (cutoff:3.500A) Processing helix chain 'S' and resid 150 through 157 removed outlier: 3.643A pdb=" N ARG S 154 " --> pdb=" O GLU S 150 " (cutoff:3.500A) Processing helix chain 'S' and resid 194 through 199 removed outlier: 3.834A pdb=" N GLY S 199 " --> pdb=" O PHE S 195 " (cutoff:3.500A) Processing helix chain 'S' and resid 206 through 217 removed outlier: 3.608A pdb=" N ILE S 210 " --> pdb=" O PHE S 206 " (cutoff:3.500A) Processing helix chain 'S' and resid 219 through 231 removed outlier: 3.892A pdb=" N ILE S 225 " --> pdb=" O ARG S 221 " (cutoff:3.500A) Processing helix chain 'S' and resid 239 through 252 removed outlier: 3.504A pdb=" N PHE S 243 " --> pdb=" O ASP S 239 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE S 249 " --> pdb=" O GLN S 245 " (cutoff:3.500A) Processing helix chain 'S' and resid 278 through 283 Processing helix chain 'S' and resid 292 through 315 removed outlier: 3.729A pdb=" N PHE S 296 " --> pdb=" O THR S 292 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN S 300 " --> pdb=" O PHE S 296 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N HIS S 315 " --> pdb=" O GLU S 311 " (cutoff:3.500A) Processing helix chain 'S' and resid 323 through 336 Processing helix chain 'S' and resid 339 through 353 removed outlier: 3.512A pdb=" N ARG S 347 " --> pdb=" O THR S 343 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LYS S 350 " --> pdb=" O GLN S 346 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LYS S 351 " --> pdb=" O ARG S 347 " (cutoff:3.500A) Processing helix chain 'S' and resid 361 through 373 removed outlier: 3.653A pdb=" N THR S 369 " --> pdb=" O GLU S 365 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASN S 373 " --> pdb=" O THR S 369 " (cutoff:3.500A) Processing helix chain 'S' and resid 373 through 386 removed outlier: 4.107A pdb=" N THR S 379 " --> pdb=" O ASN S 375 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ALA S 380 " --> pdb=" O ASP S 376 " (cutoff:3.500A) Processing helix chain 'S' and resid 392 through 403 removed outlier: 3.506A pdb=" N MET S 396 " --> pdb=" O ASP S 392 " (cutoff:3.500A) Processing helix chain 'S' and resid 409 through 421 Processing helix chain 'S' and resid 433 through 443 Processing helix chain 'T' and resid 86 through 93 removed outlier: 3.611A pdb=" N PHE T 90 " --> pdb=" O ARG T 86 " (cutoff:3.500A) Processing helix chain 'T' and resid 105 through 115 Processing helix chain 'T' and resid 128 through 137 Processing helix chain 'T' and resid 138 through 142 Processing helix chain 'T' and resid 147 through 153 Processing helix chain 'T' and resid 159 through 172 Processing helix chain 'T' and resid 176 through 184 Processing helix chain 'T' and resid 193 through 208 removed outlier: 3.756A pdb=" N PHE T 197 " --> pdb=" O GLU T 193 " (cutoff:3.500A) Processing helix chain 'T' and resid 232 through 240 Processing helix chain 'T' and resid 248 through 272 removed outlier: 3.569A pdb=" N PHE T 252 " --> pdb=" O HIS T 248 " (cutoff:3.500A) Processing helix chain 'T' and resid 279 through 288 Processing helix chain 'T' and resid 292 through 307 removed outlier: 3.527A pdb=" N LEU T 307 " --> pdb=" O VAL T 303 " (cutoff:3.500A) Processing helix chain 'T' and resid 314 through 325 removed outlier: 3.733A pdb=" N PHE T 318 " --> pdb=" O SER T 314 " (cutoff:3.500A) Processing helix chain 'T' and resid 327 through 341 removed outlier: 3.993A pdb=" N ILE T 333 " --> pdb=" O GLU T 329 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ALA T 334 " --> pdb=" O ASP T 330 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N MET T 335 " --> pdb=" O PHE T 331 " (cutoff:3.500A) Processing helix chain 'T' and resid 346 through 359 Processing helix chain 'T' and resid 363 through 375 Processing helix chain 'T' and resid 383 through 395 Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 80 removed outlier: 3.501A pdb=" N THR A 76 " --> pdb=" O SER A 87 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ARG A 96 " --> pdb=" O ARG C 134 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ILE C 127 " --> pdb=" O VAL C 135 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 126 through 128 Processing sheet with id=AA3, first strand: chain 'C' and resid 76 through 80 Processing sheet with id=AA4, first strand: chain 'E' and resid 76 through 80 removed outlier: 3.650A pdb=" N ARG G 134 " --> pdb=" O ARG E 96 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 126 through 128 Processing sheet with id=AA6, first strand: chain 'G' and resid 76 through 78 removed outlier: 4.122A pdb=" N THR G 76 " --> pdb=" O SER G 87 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL G 78 " --> pdb=" O VAL G 85 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 126 through 128 removed outlier: 3.576A pdb=" N TYR G 158 " --> pdb=" O LEU G 151 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Q' and resid 321 through 322 Processing sheet with id=AA9, first strand: chain 'R' and resid 101 through 103 removed outlier: 3.979A pdb=" N LEU R 96 " --> pdb=" O TYR R 103 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 76 through 80 removed outlier: 6.489A pdb=" N ARG I 96 " --> pdb=" O ARG K 134 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ILE K 127 " --> pdb=" O VAL K 135 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE K 149 " --> pdb=" O VAL K 160 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 126 through 128 Processing sheet with id=AB3, first strand: chain 'K' and resid 76 through 80 Processing sheet with id=AB4, first strand: chain 'M' and resid 76 through 80 removed outlier: 3.621A pdb=" N ARG O 134 " --> pdb=" O ARG M 96 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 126 through 128 removed outlier: 3.518A pdb=" N LEU M 156 " --> pdb=" O ILE M 153 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'O' and resid 76 through 78 removed outlier: 4.165A pdb=" N THR O 76 " --> pdb=" O SER O 87 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL O 78 " --> pdb=" O VAL O 85 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'O' and resid 126 through 128 removed outlier: 3.532A pdb=" N TYR O 158 " --> pdb=" O LEU O 151 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'S' and resid 321 through 322 Processing sheet with id=AB9, first strand: chain 'T' and resid 101 through 103 removed outlier: 3.979A pdb=" N LEU T 96 " --> pdb=" O TYR T 103 " (cutoff:3.500A) 1824 hydrogen bonds defined for protein. 5337 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: 9.65 Time building geometry restraints manager: 12.18 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: 9308 1.34 - 1.46: 6538 1.46 - 1.58: 14451 1.58 - 1.70: 0 1.70 - 1.82: 232 Bond restraints: 30529 Sorted by residual: bond pdb=" C PRO C 162 " pdb=" N PRO C 163 " ideal model delta sigma weight residual 1.337 1.412 -0.075 9.80e-03 1.04e+04 5.87e+01 bond pdb=" C VAL J 99 " pdb=" N PRO J 100 " ideal model delta sigma weight residual 1.332 1.434 -0.102 1.34e-02 5.57e+03 5.79e+01 bond pdb=" C ILE L 75 " pdb=" N PRO L 76 " ideal model delta sigma weight residual 1.336 1.389 -0.053 1.23e-02 6.61e+03 1.85e+01 bond pdb=" C TYR I 291 " pdb=" N PRO I 292 " ideal model delta sigma weight residual 1.336 1.378 -0.042 1.20e-02 6.94e+03 1.25e+01 bond pdb=" CA THR E 157 " pdb=" CB THR E 157 " ideal model delta sigma weight residual 1.524 1.488 0.036 1.33e-02 5.65e+03 7.35e+00 ... (remaining 30524 not shown) Histogram of bond angle deviations from ideal: 97.17 - 105.01: 488 105.01 - 112.84: 15980 112.84 - 120.68: 15109 120.68 - 128.52: 9401 128.52 - 136.36: 203 Bond angle restraints: 41181 Sorted by residual: angle pdb=" N ILE F 73 " pdb=" CA ILE F 73 " pdb=" C ILE F 73 " ideal model delta sigma weight residual 112.96 107.58 5.38 1.00e+00 1.00e+00 2.90e+01 angle pdb=" N PRO C 162 " pdb=" CA PRO C 162 " pdb=" C PRO C 162 " ideal model delta sigma weight residual 110.70 117.02 -6.32 1.22e+00 6.72e-01 2.68e+01 angle pdb=" CA PRO C 162 " pdb=" C PRO C 162 " pdb=" N PRO C 163 " ideal model delta sigma weight residual 117.93 124.15 -6.22 1.20e+00 6.94e-01 2.68e+01 angle pdb=" N ILE K 153 " pdb=" CA ILE K 153 " pdb=" C ILE K 153 " ideal model delta sigma weight residual 109.46 102.32 7.14 1.38e+00 5.25e-01 2.68e+01 angle pdb=" C ASN E 154 " pdb=" N ASP E 155 " pdb=" CA ASP E 155 " ideal model delta sigma weight residual 121.54 131.33 -9.79 1.91e+00 2.74e-01 2.63e+01 ... (remaining 41176 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.89: 17409 15.89 - 31.78: 792 31.78 - 47.66: 252 47.66 - 63.55: 6 63.55 - 79.44: 24 Dihedral angle restraints: 18483 sinusoidal: 7752 harmonic: 10731 Sorted by residual: dihedral pdb=" CA PRO A 91 " pdb=" C PRO A 91 " pdb=" N SER A 92 " pdb=" CA SER A 92 " ideal model delta harmonic sigma weight residual -180.00 -135.94 -44.06 0 5.00e+00 4.00e-02 7.77e+01 dihedral pdb=" CA PRO I 91 " pdb=" C PRO I 91 " pdb=" N SER I 92 " pdb=" CA SER I 92 " ideal model delta harmonic sigma weight residual 180.00 -136.69 -43.31 0 5.00e+00 4.00e-02 7.50e+01 dihedral pdb=" CA ARG K 161 " pdb=" C ARG K 161 " pdb=" N PRO K 162 " pdb=" CA PRO K 162 " ideal model delta harmonic sigma weight residual 180.00 146.46 33.54 0 5.00e+00 4.00e-02 4.50e+01 ... (remaining 18480 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 3664 0.067 - 0.134: 832 0.134 - 0.202: 93 0.202 - 0.269: 21 0.269 - 0.336: 3 Chirality restraints: 4613 Sorted by residual: chirality pdb=" CB VAL B 99 " pdb=" CA VAL B 99 " pdb=" CG1 VAL B 99 " pdb=" CG2 VAL B 99 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" CB ILE J 97 " pdb=" CA ILE J 97 " pdb=" CG1 ILE J 97 " pdb=" CG2 ILE J 97 " both_signs ideal model delta sigma weight residual False 2.64 2.95 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CB ILE O 153 " pdb=" CA ILE O 153 " pdb=" CG1 ILE O 153 " pdb=" CG2 ILE O 153 " both_signs ideal model delta sigma weight residual False 2.64 2.93 -0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 4610 not shown) Planarity restraints: 5211 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG K 161 " 0.074 5.00e-02 4.00e+02 1.12e-01 1.99e+01 pdb=" N PRO K 162 " -0.193 5.00e-02 4.00e+02 pdb=" CA PRO K 162 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO K 162 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 99 " 0.061 5.00e-02 4.00e+02 9.14e-02 1.34e+01 pdb=" N PRO B 100 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO B 100 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 100 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 161 " 0.061 5.00e-02 4.00e+02 9.07e-02 1.32e+01 pdb=" N PRO C 162 " -0.157 5.00e-02 4.00e+02 pdb=" CA PRO C 162 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO C 162 " 0.050 5.00e-02 4.00e+02 ... (remaining 5208 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 5669 2.77 - 3.30: 28497 3.30 - 3.84: 49754 3.84 - 4.37: 55133 4.37 - 4.90: 92909 Nonbonded interactions: 231962 Sorted by model distance: nonbonded pdb=" O PHE R 90 " pdb=" OG SER R 94 " model vdw 2.238 2.440 nonbonded pdb=" O PHE T 90 " pdb=" OG SER T 94 " model vdw 2.238 2.440 nonbonded pdb=" OG SER R 363 " pdb=" OD1 ASN R 365 " model vdw 2.267 2.440 nonbonded pdb=" OG SER T 363 " pdb=" OD1 ASN T 365 " model vdw 2.268 2.440 nonbonded pdb=" OG1 THR T 186 " pdb=" OE2 GLU T 196 " model vdw 2.283 2.440 ... (remaining 231957 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 'A' and (resid 75 through 164 or resid 177 through 336)) selection = (chain 'C' and (resid 75 through 164 or resid 177 through 336)) selection = (chain 'E' and (resid 75 through 164 or resid 177 through 336)) selection = chain 'G' selection = (chain 'I' and (resid 75 through 164 or resid 177 through 336)) selection = (chain 'K' and (resid 75 through 164 or resid 177 through 336)) selection = (chain 'M' and (resid 75 through 164 or resid 177 through 336)) selection = chain 'O' } ncs_group { reference = (chain 'B' and resid 49 through 95) selection = (chain 'D' and resid 49 through 95) selection = (chain 'F' and resid 49 through 95) selection = (chain 'H' and resid 49 through 95) selection = (chain 'J' and resid 49 through 95) selection = (chain 'L' and resid 49 through 95) selection = (chain 'N' and resid 49 through 95) selection = (chain 'P' and resid 49 through 95) } ncs_group { reference = chain 'Q' selection = (chain 'S' and (resid 108 through 134 or resid 145 through 443)) } ncs_group { reference = chain 'R' selection = chain 'T' } 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: 2.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.160 Construct map_model_manager: 0.020 Extract box with map and model: 11.170 Check model and map are aligned: 0.440 Set scattering table: 0.260 Process input model: 73.820 Find NCS groups from input model: 2.210 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 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 0.102 30529 Z= 0.379 Angle : 1.012 12.747 41181 Z= 0.539 Chirality : 0.056 0.336 4613 Planarity : 0.007 0.112 5211 Dihedral : 10.807 79.438 11517 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.97 % Favored : 94.87 % Rotamer: Outliers : 0.27 % Allowed : 4.40 % Favored : 95.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.09 % 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: -3.26 (0.12), residues: 3585 helix: -1.94 (0.08), residues: 2323 sheet: -1.68 (0.37), residues: 172 loop : -2.30 (0.18), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP E 255 HIS 0.016 0.002 HIS S 385 PHE 0.059 0.003 PHE Q 296 TYR 0.030 0.002 TYR G 79 ARG 0.012 0.001 ARG C 134 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 823 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 814 time to evaluate : 3.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7792 (tm-30) REVERT: A 246 GLN cc_start: 0.8564 (tm130) cc_final: 0.8347 (tp40) REVERT: A 296 ASP cc_start: 0.8645 (m-30) cc_final: 0.8311 (m-30) REVERT: B 79 TYR cc_start: 0.7573 (t80) cc_final: 0.7337 (t80) REVERT: B 97 ILE cc_start: 0.7493 (mt) cc_final: 0.7232 (mt) REVERT: C 290 VAL cc_start: 0.8886 (t) cc_final: 0.8619 (m) REVERT: D 67 LEU cc_start: 0.8163 (tm) cc_final: 0.6606 (pt) REVERT: D 79 TYR cc_start: 0.8068 (t80) cc_final: 0.7326 (m-10) REVERT: E 250 LEU cc_start: 0.8751 (mm) cc_final: 0.8307 (tp) REVERT: E 278 MET cc_start: 0.8440 (mtm) cc_final: 0.8200 (mpp) REVERT: E 298 GLN cc_start: 0.8368 (tp-100) cc_final: 0.7823 (tp-100) REVERT: F 71 PHE cc_start: 0.8470 (m-80) cc_final: 0.8245 (m-10) REVERT: F 75 ILE cc_start: 0.8966 (mm) cc_final: 0.8729 (pt) REVERT: G 127 ILE cc_start: 0.8708 (mt) cc_final: 0.8507 (mm) REVERT: H 88 PHE cc_start: 0.8159 (t80) cc_final: 0.7166 (t80) REVERT: Q 319 ASP cc_start: 0.8422 (m-30) cc_final: 0.8053 (p0) REVERT: Q 436 ILE cc_start: 0.8911 (mt) cc_final: 0.8683 (tp) REVERT: R 164 LEU cc_start: 0.9309 (mt) cc_final: 0.9041 (mt) REVERT: R 373 ILE cc_start: 0.9118 (mt) cc_final: 0.8731 (mt) REVERT: I 246 GLN cc_start: 0.8637 (tm130) cc_final: 0.8167 (tm-30) REVERT: I 256 TRP cc_start: 0.7598 (m-90) cc_final: 0.7173 (m-90) REVERT: I 296 ASP cc_start: 0.8578 (m-30) cc_final: 0.8229 (m-30) REVERT: J 79 TYR cc_start: 0.7184 (t80) cc_final: 0.6961 (t80) REVERT: K 284 MET cc_start: 0.8686 (mtp) cc_final: 0.8317 (ttm) REVERT: L 67 LEU cc_start: 0.8039 (tm) cc_final: 0.7418 (pp) REVERT: L 84 ILE cc_start: 0.9529 (tt) cc_final: 0.9200 (tp) REVERT: M 298 GLN cc_start: 0.8336 (tp-100) cc_final: 0.7813 (tp-100) REVERT: N 73 ILE cc_start: 0.8676 (mt) cc_final: 0.8446 (mt) REVERT: N 97 ILE cc_start: 0.8746 (mt) cc_final: 0.8528 (mm) REVERT: O 127 ILE cc_start: 0.8716 (mt) cc_final: 0.8474 (mm) REVERT: O 186 LEU cc_start: 0.8322 (tp) cc_final: 0.8079 (tt) REVERT: P 88 PHE cc_start: 0.8029 (t80) cc_final: 0.7137 (t80) REVERT: S 311 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7833 (tp30) REVERT: S 319 ASP cc_start: 0.8685 (m-30) cc_final: 0.8255 (p0) REVERT: S 322 ILE cc_start: 0.8385 (pt) cc_final: 0.7266 (pt) REVERT: T 256 MET cc_start: 0.7873 (mtm) cc_final: 0.7565 (mtm) REVERT: T 373 ILE cc_start: 0.9121 (mt) cc_final: 0.8749 (mt) outliers start: 9 outliers final: 2 residues processed: 821 average time/residue: 0.4583 time to fit residues: 562.4035 Evaluate side-chains 361 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 359 time to evaluate : 3.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 301 optimal weight: 20.0000 chunk 270 optimal weight: 8.9990 chunk 150 optimal weight: 20.0000 chunk 92 optimal weight: 5.9990 chunk 182 optimal weight: 9.9990 chunk 144 optimal weight: 5.9990 chunk 279 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 170 optimal weight: 0.0770 chunk 208 optimal weight: 4.9990 chunk 324 optimal weight: 20.0000 overall best weight: 4.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 GLN ** C 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 172 ASN E 196 GLN E 287 GLN E 339 GLN ** G 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 247 GLN Q 300 GLN Q 373 ASN R 178 HIS R 295 ASN ** R 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 323 HIS R 393 ASN I 195 HIS K 114 GLN ** K 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 95 HIS M 172 ASN ** M 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 196 GLN ** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 339 GLN ** O 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 247 GLN S 373 ASN ** S 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 295 ASN ** T 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 323 HIS T 393 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 30529 Z= 0.277 Angle : 0.692 8.106 41181 Z= 0.361 Chirality : 0.043 0.180 4613 Planarity : 0.005 0.085 5211 Dihedral : 5.580 37.454 4021 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.63 % Favored : 95.31 % Rotamer: Outliers : 0.09 % Allowed : 3.12 % Favored : 96.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.13), residues: 3585 helix: -0.32 (0.10), residues: 2361 sheet: -1.45 (0.35), residues: 172 loop : -1.90 (0.19), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 286 HIS 0.017 0.002 HIS R 248 PHE 0.027 0.002 PHE Q 296 TYR 0.033 0.002 TYR O 268 ARG 0.007 0.001 ARG G 295 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 477 time to evaluate : 3.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8545 (pp30) cc_final: 0.8182 (pp30) REVERT: A 250 LEU cc_start: 0.9298 (mm) cc_final: 0.9026 (mm) REVERT: A 330 ASP cc_start: 0.7710 (m-30) cc_final: 0.7093 (m-30) REVERT: B 79 TYR cc_start: 0.7605 (t80) cc_final: 0.7279 (t80) REVERT: C 263 MET cc_start: 0.7822 (mmm) cc_final: 0.7567 (mmt) REVERT: C 288 GLU cc_start: 0.8025 (tp30) cc_final: 0.7772 (tp30) REVERT: C 298 GLN cc_start: 0.8769 (tp-100) cc_final: 0.8537 (mm-40) REVERT: D 67 LEU cc_start: 0.8272 (tt) cc_final: 0.7409 (pt) REVERT: E 250 LEU cc_start: 0.8763 (mm) cc_final: 0.8518 (tp) REVERT: E 298 GLN cc_start: 0.8401 (tp-100) cc_final: 0.7943 (tp-100) REVERT: F 67 LEU cc_start: 0.8438 (tp) cc_final: 0.8214 (pt) REVERT: H 88 PHE cc_start: 0.8117 (t80) cc_final: 0.7132 (t80) REVERT: Q 229 MET cc_start: 0.8857 (tmm) cc_final: 0.8161 (tmm) REVERT: Q 334 TYR cc_start: 0.6964 (t80) cc_final: 0.6682 (t80) REVERT: R 256 MET cc_start: 0.7979 (mtm) cc_final: 0.7640 (mtm) REVERT: R 335 MET cc_start: 0.7855 (mtp) cc_final: 0.7650 (mtp) REVERT: J 79 TYR cc_start: 0.7332 (t80) cc_final: 0.6932 (t80) REVERT: K 150 LYS cc_start: 0.8259 (mttt) cc_final: 0.7971 (mttp) REVERT: K 284 MET cc_start: 0.8561 (mtp) cc_final: 0.8207 (ttm) REVERT: K 288 GLU cc_start: 0.8150 (tp30) cc_final: 0.7865 (tp30) REVERT: K 290 VAL cc_start: 0.8787 (t) cc_final: 0.8316 (m) REVERT: M 298 GLN cc_start: 0.8387 (tp-100) cc_final: 0.7916 (tp-100) REVERT: O 127 ILE cc_start: 0.8727 (mt) cc_final: 0.8505 (mm) REVERT: O 186 LEU cc_start: 0.8309 (tp) cc_final: 0.8079 (tt) REVERT: O 284 MET cc_start: 0.7933 (ptm) cc_final: 0.7103 (tmm) REVERT: P 88 PHE cc_start: 0.7993 (t80) cc_final: 0.7059 (t80) REVERT: S 229 MET cc_start: 0.8886 (tmm) cc_final: 0.8231 (tmm) REVERT: S 311 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7920 (tp30) REVERT: S 334 TYR cc_start: 0.7101 (t80) cc_final: 0.6887 (t80) REVERT: S 345 MET cc_start: 0.8383 (mtm) cc_final: 0.7990 (ptp) REVERT: S 368 PHE cc_start: 0.7947 (m-80) cc_final: 0.7734 (m-80) REVERT: S 437 MET cc_start: 0.7294 (tpt) cc_final: 0.6757 (tpt) REVERT: T 256 MET cc_start: 0.7840 (mtm) cc_final: 0.7468 (mtm) REVERT: T 335 MET cc_start: 0.7856 (mtp) cc_final: 0.7655 (mtp) outliers start: 3 outliers final: 1 residues processed: 480 average time/residue: 0.4241 time to fit residues: 328.8295 Evaluate side-chains 311 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 310 time to evaluate : 3.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 180 optimal weight: 2.9990 chunk 100 optimal weight: 8.9990 chunk 269 optimal weight: 20.0000 chunk 220 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 chunk 324 optimal weight: 8.9990 chunk 350 optimal weight: 9.9990 chunk 289 optimal weight: 9.9990 chunk 322 optimal weight: 20.0000 chunk 110 optimal weight: 10.0000 chunk 260 optimal weight: 9.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN A 196 GLN ** C 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 ASN ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 116 ASN Q 295 ASN ** Q 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 352 HIS ** R 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 364 ASN I 159 HIS ** K 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 304 HIS ** O 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 295 ASN ** S 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 315 HIS ** T 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 30529 Z= 0.401 Angle : 0.788 13.146 41181 Z= 0.412 Chirality : 0.046 0.205 4613 Planarity : 0.006 0.089 5211 Dihedral : 5.614 34.540 4021 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.86 % Favored : 94.09 % Rotamer: Outliers : 0.31 % Allowed : 5.41 % Favored : 94.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.14), residues: 3585 helix: 0.13 (0.10), residues: 2368 sheet: -1.52 (0.34), residues: 186 loop : -2.03 (0.20), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP T 286 HIS 0.013 0.002 HIS Q 385 PHE 0.029 0.003 PHE S 223 TYR 0.027 0.003 TYR O 268 ARG 0.006 0.001 ARG M 89 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 384 time to evaluate : 3.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 MET cc_start: 0.9339 (mtp) cc_final: 0.8845 (mtt) REVERT: A 296 ASP cc_start: 0.8630 (m-30) cc_final: 0.8405 (m-30) REVERT: B 79 TYR cc_start: 0.7569 (t80) cc_final: 0.7308 (t80) REVERT: C 263 MET cc_start: 0.8139 (mmm) cc_final: 0.7709 (mmt) REVERT: D 67 LEU cc_start: 0.8158 (tt) cc_final: 0.7592 (pt) REVERT: H 88 PHE cc_start: 0.8082 (t80) cc_final: 0.7208 (t80) REVERT: Q 229 MET cc_start: 0.8890 (tmm) cc_final: 0.8453 (tmm) REVERT: Q 345 MET cc_start: 0.8533 (mtm) cc_final: 0.8232 (ptp) REVERT: R 187 ASP cc_start: 0.7176 (OUTLIER) cc_final: 0.6789 (p0) REVERT: R 236 MET cc_start: 0.8237 (mtm) cc_final: 0.8009 (ttm) REVERT: R 335 MET cc_start: 0.7936 (mtp) cc_final: 0.7700 (mtp) REVERT: I 296 ASP cc_start: 0.8598 (m-30) cc_final: 0.8371 (m-30) REVERT: J 79 TYR cc_start: 0.7360 (t80) cc_final: 0.6920 (t80) REVERT: K 284 MET cc_start: 0.8519 (mtp) cc_final: 0.8154 (ttm) REVERT: K 288 GLU cc_start: 0.8220 (tp30) cc_final: 0.7931 (tp30) REVERT: K 290 VAL cc_start: 0.8979 (t) cc_final: 0.8750 (m) REVERT: M 278 MET cc_start: 0.8610 (mtt) cc_final: 0.8326 (mpp) REVERT: N 73 ILE cc_start: 0.8822 (mm) cc_final: 0.8537 (mm) REVERT: O 276 MET cc_start: 0.7931 (mtp) cc_final: 0.7610 (mtp) REVERT: O 284 MET cc_start: 0.7942 (ptm) cc_final: 0.7127 (tmm) REVERT: P 88 PHE cc_start: 0.7863 (t80) cc_final: 0.6773 (t80) REVERT: S 345 MET cc_start: 0.8580 (mtm) cc_final: 0.8183 (ptp) REVERT: S 393 LYS cc_start: 0.8524 (pptt) cc_final: 0.8240 (tmmt) REVERT: T 164 LEU cc_start: 0.9402 (mt) cc_final: 0.9129 (pp) REVERT: T 335 MET cc_start: 0.7974 (mtp) cc_final: 0.7748 (mtp) outliers start: 10 outliers final: 3 residues processed: 393 average time/residue: 0.3974 time to fit residues: 258.5295 Evaluate side-chains 277 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 273 time to evaluate : 3.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 320 optimal weight: 5.9990 chunk 244 optimal weight: 0.0040 chunk 168 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 154 optimal weight: 3.9990 chunk 218 optimal weight: 0.1980 chunk 325 optimal weight: 3.9990 chunk 345 optimal weight: 8.9990 chunk 170 optimal weight: 9.9990 chunk 308 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 overall best weight: 1.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 HIS E 287 GLN E 304 HIS G 154 ASN ** Q 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 323 HIS R 393 ASN ** I 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 323 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30529 Z= 0.171 Angle : 0.619 11.858 41181 Z= 0.314 Chirality : 0.042 0.178 4613 Planarity : 0.004 0.077 5211 Dihedral : 5.091 34.851 4021 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.93 % Favored : 96.01 % Rotamer: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.14), residues: 3585 helix: 0.79 (0.11), residues: 2367 sheet: -1.30 (0.35), residues: 186 loop : -1.76 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 260 HIS 0.010 0.001 HIS C 159 PHE 0.027 0.001 PHE Q 368 TYR 0.024 0.001 TYR R 299 ARG 0.004 0.000 ARG C 165 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 413 time to evaluate : 3.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8526 (pp30) cc_final: 0.8275 (pp30) REVERT: A 145 LEU cc_start: 0.8162 (tp) cc_final: 0.7691 (tp) REVERT: A 263 MET cc_start: 0.9302 (mtp) cc_final: 0.8945 (mtt) REVERT: C 263 MET cc_start: 0.7427 (mmm) cc_final: 0.6834 (mmm) REVERT: E 250 LEU cc_start: 0.8825 (mm) cc_final: 0.8428 (tp) REVERT: H 88 PHE cc_start: 0.8073 (t80) cc_final: 0.7050 (t80) REVERT: Q 229 MET cc_start: 0.8927 (tmm) cc_final: 0.8471 (tmm) REVERT: R 179 VAL cc_start: 0.8963 (m) cc_final: 0.8738 (p) REVERT: I 330 ASP cc_start: 0.7905 (m-30) cc_final: 0.7636 (m-30) REVERT: J 69 ARG cc_start: 0.8061 (ttp-170) cc_final: 0.7838 (tpt-90) REVERT: J 79 TYR cc_start: 0.7314 (t80) cc_final: 0.6913 (t80) REVERT: K 284 MET cc_start: 0.8509 (mtp) cc_final: 0.8169 (ttm) REVERT: M 278 MET cc_start: 0.8449 (mtt) cc_final: 0.8218 (mpp) REVERT: N 73 ILE cc_start: 0.8824 (mm) cc_final: 0.8613 (mm) REVERT: O 284 MET cc_start: 0.7815 (ptm) cc_final: 0.7181 (tmm) REVERT: P 88 PHE cc_start: 0.7831 (t80) cc_final: 0.6785 (t80) REVERT: S 368 PHE cc_start: 0.7841 (m-80) cc_final: 0.7562 (m-10) REVERT: S 393 LYS cc_start: 0.8333 (pptt) cc_final: 0.7836 (ptpt) REVERT: T 191 MET cc_start: 0.7650 (tpp) cc_final: 0.7246 (tpp) outliers start: 0 outliers final: 0 residues processed: 413 average time/residue: 0.3762 time to fit residues: 254.5415 Evaluate side-chains 286 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 286 time to evaluate : 3.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 287 optimal weight: 5.9990 chunk 195 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 256 optimal weight: 9.9990 chunk 142 optimal weight: 8.9990 chunk 294 optimal weight: 9.9990 chunk 238 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 176 optimal weight: 10.0000 chunk 309 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 overall best weight: 8.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 HIS ** C 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 ASN ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 397 GLN R 364 ASN ** K 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 366 ASN T 364 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.4740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 30529 Z= 0.446 Angle : 0.791 10.549 41181 Z= 0.411 Chirality : 0.046 0.157 4613 Planarity : 0.006 0.078 5211 Dihedral : 5.456 34.428 4021 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 18.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.05 % Favored : 93.89 % Rotamer: Outliers : 0.09 % Allowed : 3.61 % Favored : 96.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.56 (0.14), residues: 3585 helix: 0.48 (0.10), residues: 2375 sheet: -1.43 (0.34), residues: 186 loop : -2.08 (0.20), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP T 286 HIS 0.014 0.002 HIS Q 385 PHE 0.023 0.002 PHE R 290 TYR 0.023 0.002 TYR F 79 ARG 0.005 0.001 ARG C 295 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 353 time to evaluate : 3.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 LEU cc_start: 0.8301 (tp) cc_final: 0.7826 (tp) REVERT: A 263 MET cc_start: 0.9430 (mtp) cc_final: 0.9071 (mtt) REVERT: H 88 PHE cc_start: 0.8086 (t80) cc_final: 0.7264 (t80) REVERT: Q 229 MET cc_start: 0.8910 (tmm) cc_final: 0.8361 (tmm) REVERT: R 179 VAL cc_start: 0.9027 (m) cc_final: 0.8794 (p) REVERT: I 145 LEU cc_start: 0.8227 (tp) cc_final: 0.7671 (tp) REVERT: J 79 TYR cc_start: 0.7403 (t80) cc_final: 0.6944 (t80) REVERT: K 284 MET cc_start: 0.8495 (mtp) cc_final: 0.8069 (ttm) REVERT: K 290 VAL cc_start: 0.9023 (t) cc_final: 0.8800 (m) REVERT: M 243 MET cc_start: 0.8083 (ptp) cc_final: 0.7742 (ptp) REVERT: M 278 MET cc_start: 0.8637 (mtt) cc_final: 0.8344 (mpp) REVERT: P 88 PHE cc_start: 0.7915 (t80) cc_final: 0.6848 (t80) REVERT: T 256 MET cc_start: 0.8034 (ptt) cc_final: 0.7814 (ptt) outliers start: 3 outliers final: 0 residues processed: 354 average time/residue: 0.3515 time to fit residues: 209.7259 Evaluate side-chains 265 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 265 time to evaluate : 3.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 116 optimal weight: 4.9990 chunk 310 optimal weight: 5.9990 chunk 68 optimal weight: 8.9990 chunk 202 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 345 optimal weight: 5.9990 chunk 286 optimal weight: 5.9990 chunk 159 optimal weight: 20.0000 chunk 28 optimal weight: 10.0000 chunk 114 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 287 GLN ** G 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 397 GLN I 196 GLN K 177 ASN ** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.4743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30529 Z= 0.192 Angle : 0.628 10.118 41181 Z= 0.319 Chirality : 0.042 0.191 4613 Planarity : 0.004 0.075 5211 Dihedral : 5.107 34.792 4021 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.41 % Favored : 95.54 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.04 (0.14), residues: 3585 helix: 0.88 (0.11), residues: 2378 sheet: -1.35 (0.34), residues: 186 loop : -1.87 (0.20), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP T 286 HIS 0.010 0.001 HIS Q 385 PHE 0.018 0.001 PHE N 71 TYR 0.022 0.001 TYR G 268 ARG 0.005 0.000 ARG C 252 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 386 time to evaluate : 3.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 LEU cc_start: 0.8270 (tp) cc_final: 0.7822 (tp) REVERT: A 171 GLU cc_start: 0.7213 (pm20) cc_final: 0.6890 (pm20) REVERT: A 263 MET cc_start: 0.9296 (mtp) cc_final: 0.8821 (mtt) REVERT: E 250 LEU cc_start: 0.8850 (mm) cc_final: 0.8378 (tp) REVERT: H 88 PHE cc_start: 0.8031 (t80) cc_final: 0.6942 (t80) REVERT: Q 229 MET cc_start: 0.8909 (tmm) cc_final: 0.8379 (tmm) REVERT: Q 368 PHE cc_start: 0.8014 (m-80) cc_final: 0.7784 (m-80) REVERT: R 179 VAL cc_start: 0.9010 (m) cc_final: 0.8767 (p) REVERT: R 299 TYR cc_start: 0.8308 (m-10) cc_final: 0.7706 (m-80) REVERT: I 145 LEU cc_start: 0.8246 (tp) cc_final: 0.7699 (tp) REVERT: I 296 ASP cc_start: 0.8523 (m-30) cc_final: 0.8307 (m-30) REVERT: J 79 TYR cc_start: 0.7361 (t80) cc_final: 0.6886 (t80) REVERT: K 284 MET cc_start: 0.8469 (mtp) cc_final: 0.8037 (ttm) REVERT: K 290 VAL cc_start: 0.8904 (t) cc_final: 0.8614 (m) REVERT: N 73 ILE cc_start: 0.8829 (mm) cc_final: 0.8618 (mm) REVERT: O 284 MET cc_start: 0.7766 (ptt) cc_final: 0.7250 (tmm) REVERT: P 88 PHE cc_start: 0.7834 (t80) cc_final: 0.6765 (t80) REVERT: S 393 LYS cc_start: 0.8350 (pptt) cc_final: 0.8066 (tmmt) REVERT: T 164 LEU cc_start: 0.9327 (mt) cc_final: 0.9111 (pp) REVERT: T 179 VAL cc_start: 0.8979 (m) cc_final: 0.8730 (p) REVERT: T 299 TYR cc_start: 0.8329 (m-10) cc_final: 0.7717 (m-80) outliers start: 0 outliers final: 0 residues processed: 386 average time/residue: 0.3644 time to fit residues: 233.4263 Evaluate side-chains 294 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 294 time to evaluate : 3.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 333 optimal weight: 30.0000 chunk 38 optimal weight: 9.9990 chunk 196 optimal weight: 1.9990 chunk 252 optimal weight: 3.9990 chunk 195 optimal weight: 5.9990 chunk 290 optimal weight: 5.9990 chunk 192 optimal weight: 7.9990 chunk 344 optimal weight: 7.9990 chunk 215 optimal weight: 6.9990 chunk 209 optimal weight: 5.9990 chunk 158 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 HIS D 95 HIS E 287 GLN ** G 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 397 GLN ** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.4954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 30529 Z= 0.271 Angle : 0.654 9.620 41181 Z= 0.335 Chirality : 0.043 0.171 4613 Planarity : 0.005 0.075 5211 Dihedral : 5.059 33.478 4021 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.69 % Favored : 94.25 % Rotamer: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.03 (0.14), residues: 3585 helix: 0.90 (0.11), residues: 2380 sheet: -1.20 (0.35), residues: 186 loop : -1.94 (0.20), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP T 286 HIS 0.009 0.001 HIS Q 385 PHE 0.017 0.002 PHE S 368 TYR 0.024 0.002 TYR E 268 ARG 0.007 0.000 ARG A 226 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 371 time to evaluate : 3.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 LEU cc_start: 0.8319 (tp) cc_final: 0.7818 (tp) REVERT: A 171 GLU cc_start: 0.7330 (pm20) cc_final: 0.6854 (pm20) REVERT: A 263 MET cc_start: 0.9351 (mtp) cc_final: 0.8972 (mtt) REVERT: A 296 ASP cc_start: 0.8405 (m-30) cc_final: 0.8134 (p0) REVERT: E 250 LEU cc_start: 0.8793 (mm) cc_final: 0.8311 (tp) REVERT: H 88 PHE cc_start: 0.7992 (t80) cc_final: 0.7085 (t80) REVERT: R 179 VAL cc_start: 0.9049 (m) cc_final: 0.8802 (p) REVERT: R 299 TYR cc_start: 0.8374 (m-10) cc_final: 0.7790 (m-80) REVERT: I 114 GLN cc_start: 0.8676 (pp30) cc_final: 0.8411 (pp30) REVERT: I 145 LEU cc_start: 0.8257 (tp) cc_final: 0.7691 (tp) REVERT: J 79 TYR cc_start: 0.7378 (t80) cc_final: 0.6895 (t80) REVERT: K 284 MET cc_start: 0.8420 (mtp) cc_final: 0.8058 (ttm) REVERT: N 73 ILE cc_start: 0.8882 (mm) cc_final: 0.8644 (mm) REVERT: O 284 MET cc_start: 0.7748 (ptt) cc_final: 0.7115 (tmm) REVERT: P 88 PHE cc_start: 0.7847 (t80) cc_final: 0.6766 (t80) REVERT: S 345 MET cc_start: 0.8519 (mtm) cc_final: 0.8292 (ptp) REVERT: S 393 LYS cc_start: 0.8403 (pptt) cc_final: 0.8032 (tmmt) REVERT: T 118 MET cc_start: 0.6046 (mpp) cc_final: 0.5252 (tmm) REVERT: T 179 VAL cc_start: 0.9022 (m) cc_final: 0.8773 (p) REVERT: T 299 TYR cc_start: 0.8352 (m-10) cc_final: 0.7770 (m-80) outliers start: 0 outliers final: 0 residues processed: 371 average time/residue: 0.3518 time to fit residues: 219.0513 Evaluate side-chains 286 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 286 time to evaluate : 3.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 212 optimal weight: 4.9990 chunk 137 optimal weight: 0.9990 chunk 205 optimal weight: 7.9990 chunk 103 optimal weight: 9.9990 chunk 67 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 218 optimal weight: 4.9990 chunk 234 optimal weight: 0.9980 chunk 170 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 270 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 287 GLN ** G 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 397 GLN ** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.5033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30529 Z= 0.169 Angle : 0.606 8.684 41181 Z= 0.306 Chirality : 0.041 0.171 4613 Planarity : 0.004 0.074 5211 Dihedral : 4.865 33.889 4021 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.16 % Favored : 95.79 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.29 (0.14), residues: 3585 helix: 1.15 (0.11), residues: 2377 sheet: -1.18 (0.34), residues: 186 loop : -1.80 (0.20), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP T 286 HIS 0.006 0.001 HIS Q 385 PHE 0.026 0.001 PHE S 368 TYR 0.019 0.001 TYR E 268 ARG 0.005 0.000 ARG A 226 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 394 time to evaluate : 3.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8628 (pp30) cc_final: 0.8327 (pp30) REVERT: A 145 LEU cc_start: 0.8302 (tp) cc_final: 0.7798 (tp) REVERT: A 171 GLU cc_start: 0.7161 (pm20) cc_final: 0.6723 (pm20) REVERT: E 243 MET cc_start: 0.8013 (ptp) cc_final: 0.7678 (ptm) REVERT: E 250 LEU cc_start: 0.8769 (mm) cc_final: 0.8341 (tp) REVERT: H 88 PHE cc_start: 0.7944 (t80) cc_final: 0.6887 (t80) REVERT: Q 229 MET cc_start: 0.8936 (tmm) cc_final: 0.8394 (tmm) REVERT: Q 330 MET cc_start: 0.7499 (mmm) cc_final: 0.7282 (mmm) REVERT: R 179 VAL cc_start: 0.9002 (m) cc_final: 0.8748 (p) REVERT: R 299 TYR cc_start: 0.8279 (m-10) cc_final: 0.7713 (m-80) REVERT: I 114 GLN cc_start: 0.8541 (pp30) cc_final: 0.8311 (pp30) REVERT: I 145 LEU cc_start: 0.8300 (tp) cc_final: 0.7689 (tp) REVERT: J 79 TYR cc_start: 0.7390 (t80) cc_final: 0.6911 (t80) REVERT: K 284 MET cc_start: 0.8368 (mtp) cc_final: 0.8016 (ttm) REVERT: K 290 VAL cc_start: 0.8826 (t) cc_final: 0.8565 (m) REVERT: M 243 MET cc_start: 0.8448 (ptm) cc_final: 0.7925 (ptp) REVERT: O 284 MET cc_start: 0.7687 (ptt) cc_final: 0.7233 (tmm) REVERT: P 88 PHE cc_start: 0.7823 (t80) cc_final: 0.6788 (t80) REVERT: S 130 TYR cc_start: 0.6996 (t80) cc_final: 0.6759 (t80) REVERT: S 345 MET cc_start: 0.8525 (mtm) cc_final: 0.8177 (ptp) REVERT: S 393 LYS cc_start: 0.8324 (pptt) cc_final: 0.7983 (tmmt) REVERT: T 118 MET cc_start: 0.6131 (mpp) cc_final: 0.5329 (tmm) REVERT: T 179 VAL cc_start: 0.8974 (m) cc_final: 0.8718 (p) REVERT: T 299 TYR cc_start: 0.8331 (m-10) cc_final: 0.7705 (m-80) outliers start: 0 outliers final: 0 residues processed: 394 average time/residue: 0.3807 time to fit residues: 249.2680 Evaluate side-chains 292 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 292 time to evaluate : 3.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 313 optimal weight: 4.9990 chunk 329 optimal weight: 30.0000 chunk 300 optimal weight: 1.9990 chunk 320 optimal weight: 5.9990 chunk 192 optimal weight: 9.9990 chunk 139 optimal weight: 10.0000 chunk 251 optimal weight: 7.9990 chunk 98 optimal weight: 10.0000 chunk 289 optimal weight: 5.9990 chunk 303 optimal weight: 4.9990 chunk 319 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 HIS E 287 GLN ** G 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 397 GLN ** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.5193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 30529 Z= 0.270 Angle : 0.666 9.645 41181 Z= 0.340 Chirality : 0.043 0.178 4613 Planarity : 0.005 0.073 5211 Dihedral : 4.942 33.131 4021 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.41 % Favored : 94.53 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.19 (0.14), residues: 3585 helix: 1.09 (0.11), residues: 2373 sheet: -1.15 (0.35), residues: 186 loop : -1.88 (0.20), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP T 286 HIS 0.005 0.001 HIS Q 385 PHE 0.032 0.002 PHE G 269 TYR 0.024 0.002 TYR E 268 ARG 0.005 0.000 ARG A 226 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 358 time to evaluate : 3.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 LEU cc_start: 0.8346 (tp) cc_final: 0.7731 (tp) REVERT: A 263 MET cc_start: 0.8777 (mtm) cc_final: 0.8574 (mtm) REVERT: A 296 ASP cc_start: 0.8046 (p0) cc_final: 0.7837 (p0) REVERT: C 142 ASP cc_start: 0.6716 (p0) cc_final: 0.6205 (p0) REVERT: E 243 MET cc_start: 0.8389 (ptp) cc_final: 0.8051 (ptm) REVERT: E 250 LEU cc_start: 0.8830 (mm) cc_final: 0.8372 (tp) REVERT: H 88 PHE cc_start: 0.7972 (t80) cc_final: 0.7036 (t80) REVERT: Q 330 MET cc_start: 0.7577 (mmm) cc_final: 0.7317 (mmm) REVERT: R 179 VAL cc_start: 0.9041 (m) cc_final: 0.8791 (p) REVERT: R 256 MET cc_start: 0.7976 (ptt) cc_final: 0.7701 (ptt) REVERT: R 299 TYR cc_start: 0.8352 (m-10) cc_final: 0.7746 (m-80) REVERT: J 79 TYR cc_start: 0.7435 (t80) cc_final: 0.6927 (t80) REVERT: K 284 MET cc_start: 0.8424 (mtp) cc_final: 0.8015 (ttm) REVERT: K 290 VAL cc_start: 0.8961 (t) cc_final: 0.8694 (m) REVERT: N 73 ILE cc_start: 0.8939 (mm) cc_final: 0.8685 (mm) REVERT: O 284 MET cc_start: 0.7764 (ptt) cc_final: 0.7186 (tmm) REVERT: P 88 PHE cc_start: 0.7916 (t80) cc_final: 0.6853 (t80) REVERT: S 345 MET cc_start: 0.8528 (mtm) cc_final: 0.8226 (ptp) REVERT: S 393 LYS cc_start: 0.8397 (pptt) cc_final: 0.8032 (tmmt) REVERT: T 118 MET cc_start: 0.6128 (mpp) cc_final: 0.5264 (tmm) REVERT: T 179 VAL cc_start: 0.9036 (m) cc_final: 0.8782 (p) outliers start: 0 outliers final: 0 residues processed: 358 average time/residue: 0.3790 time to fit residues: 232.0150 Evaluate side-chains 273 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 273 time to evaluate : 3.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 210 optimal weight: 10.0000 chunk 339 optimal weight: 10.0000 chunk 206 optimal weight: 4.9990 chunk 160 optimal weight: 0.6980 chunk 235 optimal weight: 8.9990 chunk 355 optimal weight: 20.0000 chunk 327 optimal weight: 5.9990 chunk 283 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 218 optimal weight: 10.0000 chunk 173 optimal weight: 10.0000 overall best weight: 4.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 HIS E 287 GLN ** G 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 397 GLN ** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.5309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 30529 Z= 0.248 Angle : 0.652 9.486 41181 Z= 0.332 Chirality : 0.043 0.189 4613 Planarity : 0.004 0.074 5211 Dihedral : 4.976 33.274 4021 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.08 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.20 (0.14), residues: 3585 helix: 1.10 (0.11), residues: 2375 sheet: -1.16 (0.35), residues: 186 loop : -1.88 (0.20), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 255 HIS 0.005 0.001 HIS R 342 PHE 0.026 0.001 PHE S 368 TYR 0.030 0.002 TYR K 258 ARG 0.005 0.000 ARG A 226 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 357 time to evaluate : 3.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8661 (pp30) cc_final: 0.8370 (pp30) REVERT: A 145 LEU cc_start: 0.8376 (tp) cc_final: 0.7743 (tp) REVERT: A 296 ASP cc_start: 0.8052 (p0) cc_final: 0.7838 (p0) REVERT: C 142 ASP cc_start: 0.6696 (p0) cc_final: 0.6185 (p0) REVERT: E 250 LEU cc_start: 0.8835 (mm) cc_final: 0.8354 (tp) REVERT: H 88 PHE cc_start: 0.8002 (t80) cc_final: 0.7080 (t80) REVERT: Q 330 MET cc_start: 0.7575 (mmm) cc_final: 0.7329 (mmm) REVERT: R 118 MET cc_start: 0.6313 (mpp) cc_final: 0.5246 (tmm) REVERT: R 179 VAL cc_start: 0.9028 (m) cc_final: 0.8777 (p) REVERT: R 256 MET cc_start: 0.8000 (ptt) cc_final: 0.7749 (ptt) REVERT: R 299 TYR cc_start: 0.8325 (m-10) cc_final: 0.7706 (m-80) REVERT: J 79 TYR cc_start: 0.7375 (t80) cc_final: 0.6861 (t80) REVERT: K 284 MET cc_start: 0.8428 (mtp) cc_final: 0.7998 (ttm) REVERT: K 290 VAL cc_start: 0.8849 (t) cc_final: 0.8609 (m) REVERT: N 73 ILE cc_start: 0.8926 (mm) cc_final: 0.8708 (mm) REVERT: O 284 MET cc_start: 0.7715 (ptt) cc_final: 0.7169 (tmm) REVERT: P 88 PHE cc_start: 0.7901 (t80) cc_final: 0.6810 (t80) REVERT: S 130 TYR cc_start: 0.7342 (t80) cc_final: 0.7034 (t80) REVERT: S 345 MET cc_start: 0.8495 (mtm) cc_final: 0.8204 (ptp) REVERT: S 393 LYS cc_start: 0.8376 (pptt) cc_final: 0.8024 (tmmt) REVERT: T 118 MET cc_start: 0.6062 (mpp) cc_final: 0.5310 (tmm) REVERT: T 179 VAL cc_start: 0.9024 (m) cc_final: 0.8763 (p) outliers start: 0 outliers final: 0 residues processed: 357 average time/residue: 0.3369 time to fit residues: 205.8889 Evaluate side-chains 279 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 279 time to evaluate : 3.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 224 optimal weight: 4.9990 chunk 301 optimal weight: 30.0000 chunk 86 optimal weight: 8.9990 chunk 261 optimal weight: 0.9990 chunk 41 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 283 optimal weight: 9.9990 chunk 118 optimal weight: 0.9990 chunk 291 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 HIS E 287 GLN ** G 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 397 GLN ** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 327 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.058857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.049672 restraints weight = 196852.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.050250 restraints weight = 132691.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.050828 restraints weight = 92169.000| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.5357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 30529 Z= 0.228 Angle : 0.644 9.306 41181 Z= 0.327 Chirality : 0.042 0.203 4613 Planarity : 0.004 0.074 5211 Dihedral : 4.909 32.746 4021 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.08 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.25 (0.14), residues: 3585 helix: 1.13 (0.11), residues: 2379 sheet: -1.15 (0.35), residues: 186 loop : -1.86 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 255 HIS 0.005 0.001 HIS R 342 PHE 0.032 0.001 PHE S 230 TYR 0.027 0.001 TYR A 242 ARG 0.005 0.000 ARG A 226 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5915.35 seconds wall clock time: 107 minutes 58.18 seconds (6478.18 seconds total)