Starting phenix.real_space_refine on Fri Mar 15 11:49:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5s_33623/03_2024/7y5s_33623.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5s_33623/03_2024/7y5s_33623.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5s_33623/03_2024/7y5s_33623.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5s_33623/03_2024/7y5s_33623.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5s_33623/03_2024/7y5s_33623.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y5s_33623/03_2024/7y5s_33623.pdb" } resolution = 3.0 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= 0.003 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 7203 2.51 5 N 2052 2.21 5 O 2226 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 454": "OE1" <-> "OE2" Residue "A PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 454": "OE1" <-> "OE2" Residue "B PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 454": "OE1" <-> "OE2" Residue "C PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11535 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3845 Classifications: {'peptide': 505} Link IDs: {'PTRANS': 21, 'TRANS': 483} Chain: "B" Number of atoms: 3845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3845 Classifications: {'peptide': 505} Link IDs: {'PTRANS': 21, 'TRANS': 483} Chain: "C" Number of atoms: 3845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3845 Classifications: {'peptide': 505} Link IDs: {'PTRANS': 21, 'TRANS': 483} Time building chain proxies: 6.37, per 1000 atoms: 0.55 Number of scatterers: 11535 At special positions: 0 Unit cell: (92.2236, 93.3215, 148.217, 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 54 16.00 O 2226 8.00 N 2052 7.00 C 7203 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.26 Conformation dependent library (CDL) restraints added in 2.2 seconds 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2670 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 18 sheets defined 4.4% alpha, 32.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 54 through 68 Processing helix chain 'A' and resid 270 through 276 removed outlier: 3.763A pdb=" N ALA A 274 " --> pdb=" O GLY A 270 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE A 275 " --> pdb=" O SER A 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 68 Processing helix chain 'B' and resid 270 through 276 removed outlier: 3.762A pdb=" N ALA B 274 " --> pdb=" O GLY B 270 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE B 275 " --> pdb=" O SER B 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 68 Processing helix chain 'C' and resid 270 through 276 removed outlier: 3.762A pdb=" N ALA C 274 " --> pdb=" O GLY C 270 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE C 275 " --> pdb=" O SER C 271 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 72 through 74 removed outlier: 6.061A pdb=" N VAL A 73 " --> pdb=" O PHE A 115 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ILE A 124 " --> pdb=" O GLU A 156 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 74 removed outlier: 6.061A pdb=" N VAL A 73 " --> pdb=" O PHE A 115 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N VAL A 182 " --> pdb=" O ALA A 149 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N SER A 151 " --> pdb=" O VAL A 182 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ASP A 184 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A 153 " --> pdb=" O ASP A 184 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL A 224 " --> pdb=" O ASP A 184 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N HIS A 186 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL A 226 " --> pdb=" O HIS A 186 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLY A 188 " --> pdb=" O VAL A 226 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ASN A 228 " --> pdb=" O GLY A 188 " (cutoff:3.500A) removed outlier: 9.355A pdb=" N ARG A 220 " --> pdb=" O PHE A 249 " (cutoff:3.500A) removed outlier: 10.525A pdb=" N ASP A 251 " --> pdb=" O ARG A 220 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N THR A 222 " --> pdb=" O ASP A 251 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N MET A 253 " --> pdb=" O THR A 222 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL A 224 " --> pdb=" O MET A 253 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N GLN A 255 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL A 226 " --> pdb=" O GLN A 255 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N SER A 248 " --> pdb=" O LYS A 292 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N GLU A 294 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N THR A 250 " --> pdb=" O GLU A 294 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N ASN A 296 " --> pdb=" O THR A 250 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N CYS A 252 " --> pdb=" O ASN A 296 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N PHE A 298 " --> pdb=" O CYS A 252 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N CYS A 254 " --> pdb=" O PHE A 298 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 347 " --> pdb=" O VAL A 324 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 134 through 139 removed outlier: 6.799A pdb=" N LEU A 173 " --> pdb=" O PRO A 134 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N PHE A 136 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N GLN A 175 " --> pdb=" O PHE A 136 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ALA A 138 " --> pdb=" O GLN A 175 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE A 194 " --> pdb=" O GLY A 171 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LEU A 173 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N PHE A 196 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLN A 175 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ASN A 198 " --> pdb=" O GLN A 175 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ASP A 232 " --> pdb=" O ARG A 192 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLY A 263 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL A 237 " --> pdb=" O TRP A 267 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU A 307 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ARG A 331 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N HIS A 309 " --> pdb=" O ARG A 331 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N ILE A 333 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ASP A 311 " --> pdb=" O ILE A 333 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL A 328 " --> pdb=" O ASN A 351 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N VAL A 353 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N LEU A 330 " --> pdb=" O VAL A 353 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 216 through 217 removed outlier: 3.555A pdb=" N THR A 216 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N HIS A 245 " --> pdb=" O THR A 216 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ALA A 286 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ARG A 316 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL A 288 " --> pdb=" O ARG A 316 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N CYS A 318 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N GLN A 339 " --> pdb=" O ALA A 313 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N GLY A 315 " --> pdb=" O GLN A 339 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N TYR A 338 " --> pdb=" O MET A 368 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 391 through 394 removed outlier: 3.772A pdb=" N GLY B 416 " --> pdb=" O ILE B 410 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY A 432 " --> pdb=" O TRP B 419 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N TRP A 429 " --> pdb=" O GLN A 448 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLN A 448 " --> pdb=" O TRP A 429 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU A 431 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N SER B 491 " --> pdb=" O LEU C 482 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 491 through 492 removed outlier: 6.306A pdb=" N SER A 491 " --> pdb=" O LEU B 482 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N GLY B 465 " --> pdb=" O ILE C 456 " (cutoff:3.500A) removed outlier: 8.743A pdb=" N SER C 458 " --> pdb=" O GLY B 465 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N GLN B 467 " --> pdb=" O SER C 458 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU C 431 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N GLN C 448 " --> pdb=" O TRP C 429 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N TRP C 429 " --> pdb=" O GLN C 448 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ALA A 417 " --> pdb=" O ILE C 430 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N GLY C 432 " --> pdb=" O ALA A 417 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N TRP A 419 " --> pdb=" O GLY C 432 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N ARG C 434 " --> pdb=" O TRP A 419 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE A 421 " --> pdb=" O ARG C 434 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY A 416 " --> pdb=" O ILE A 410 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 391 through 394 removed outlier: 3.771A pdb=" N GLY C 416 " --> pdb=" O ILE C 410 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLY B 432 " --> pdb=" O TRP C 419 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N TRP B 429 " --> pdb=" O GLN B 448 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLN B 448 " --> pdb=" O TRP B 429 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU B 431 " --> pdb=" O VAL B 446 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N GLY A 465 " --> pdb=" O ILE B 456 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N SER B 458 " --> pdb=" O GLY A 465 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N GLN A 467 " --> pdb=" O SER B 458 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 502 through 503 Processing sheet with id=AA9, first strand: chain 'A' and resid 523 through 524 removed outlier: 6.963A pdb=" N ASN A 523 " --> pdb=" O ILE B 514 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 72 through 74 removed outlier: 6.062A pdb=" N VAL B 73 " --> pdb=" O PHE B 115 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ILE B 124 " --> pdb=" O GLU B 156 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 72 through 74 removed outlier: 6.062A pdb=" N VAL B 73 " --> pdb=" O PHE B 115 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL B 182 " --> pdb=" O ALA B 149 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N SER B 151 " --> pdb=" O VAL B 182 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ASP B 184 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU B 153 " --> pdb=" O ASP B 184 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL B 224 " --> pdb=" O ASP B 184 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N HIS B 186 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL B 226 " --> pdb=" O HIS B 186 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLY B 188 " --> pdb=" O VAL B 226 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ASN B 228 " --> pdb=" O GLY B 188 " (cutoff:3.500A) removed outlier: 9.356A pdb=" N ARG B 220 " --> pdb=" O PHE B 249 " (cutoff:3.500A) removed outlier: 10.526A pdb=" N ASP B 251 " --> pdb=" O ARG B 220 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N THR B 222 " --> pdb=" O ASP B 251 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N MET B 253 " --> pdb=" O THR B 222 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL B 224 " --> pdb=" O MET B 253 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N GLN B 255 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL B 226 " --> pdb=" O GLN B 255 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N SER B 248 " --> pdb=" O LYS B 292 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N GLU B 294 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N THR B 250 " --> pdb=" O GLU B 294 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N ASN B 296 " --> pdb=" O THR B 250 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N CYS B 252 " --> pdb=" O ASN B 296 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N PHE B 298 " --> pdb=" O CYS B 252 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N CYS B 254 " --> pdb=" O PHE B 298 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE B 347 " --> pdb=" O VAL B 324 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 134 through 139 removed outlier: 6.799A pdb=" N LEU B 173 " --> pdb=" O PRO B 134 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N PHE B 136 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N GLN B 175 " --> pdb=" O PHE B 136 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ALA B 138 " --> pdb=" O GLN B 175 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE B 194 " --> pdb=" O GLY B 171 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LEU B 173 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N PHE B 196 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLN B 175 " --> pdb=" O PHE B 196 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ASN B 198 " --> pdb=" O GLN B 175 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ASP B 232 " --> pdb=" O ARG B 192 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N GLY B 263 " --> pdb=" O ILE B 231 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL B 237 " --> pdb=" O TRP B 267 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU B 307 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ARG B 331 " --> pdb=" O LEU B 307 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N HIS B 309 " --> pdb=" O ARG B 331 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N ILE B 333 " --> pdb=" O HIS B 309 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ASP B 311 " --> pdb=" O ILE B 333 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL B 328 " --> pdb=" O ASN B 351 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N VAL B 353 " --> pdb=" O VAL B 328 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N LEU B 330 " --> pdb=" O VAL B 353 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 216 through 217 removed outlier: 3.556A pdb=" N THR B 216 " --> pdb=" O SER B 243 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N HIS B 245 " --> pdb=" O THR B 216 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ALA B 286 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ARG B 316 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL B 288 " --> pdb=" O ARG B 316 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N CYS B 318 " --> pdb=" O VAL B 288 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N GLN B 339 " --> pdb=" O ALA B 313 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N GLY B 315 " --> pdb=" O GLN B 339 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N TYR B 338 " --> pdb=" O MET B 368 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 523 through 524 removed outlier: 6.965A pdb=" N ASN B 523 " --> pdb=" O ILE C 514 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 72 through 74 removed outlier: 6.061A pdb=" N VAL C 73 " --> pdb=" O PHE C 115 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ILE C 124 " --> pdb=" O GLU C 156 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 72 through 74 removed outlier: 6.061A pdb=" N VAL C 73 " --> pdb=" O PHE C 115 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL C 182 " --> pdb=" O ALA C 149 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N SER C 151 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ASP C 184 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU C 153 " --> pdb=" O ASP C 184 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL C 224 " --> pdb=" O ASP C 184 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N HIS C 186 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL C 226 " --> pdb=" O HIS C 186 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLY C 188 " --> pdb=" O VAL C 226 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ASN C 228 " --> pdb=" O GLY C 188 " (cutoff:3.500A) removed outlier: 9.354A pdb=" N ARG C 220 " --> pdb=" O PHE C 249 " (cutoff:3.500A) removed outlier: 10.524A pdb=" N ASP C 251 " --> pdb=" O ARG C 220 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N THR C 222 " --> pdb=" O ASP C 251 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N MET C 253 " --> pdb=" O THR C 222 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL C 224 " --> pdb=" O MET C 253 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N GLN C 255 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL C 226 " --> pdb=" O GLN C 255 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N SER C 248 " --> pdb=" O LYS C 292 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N GLU C 294 " --> pdb=" O SER C 248 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N THR C 250 " --> pdb=" O GLU C 294 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ASN C 296 " --> pdb=" O THR C 250 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N CYS C 252 " --> pdb=" O ASN C 296 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N PHE C 298 " --> pdb=" O CYS C 252 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N CYS C 254 " --> pdb=" O PHE C 298 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE C 347 " --> pdb=" O VAL C 324 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 134 through 139 removed outlier: 6.798A pdb=" N LEU C 173 " --> pdb=" O PRO C 134 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N PHE C 136 " --> pdb=" O LEU C 173 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N GLN C 175 " --> pdb=" O PHE C 136 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N ALA C 138 " --> pdb=" O GLN C 175 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N GLY C 193 " --> pdb=" O THR C 170 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ASP C 232 " --> pdb=" O ARG C 192 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N GLY C 263 " --> pdb=" O ILE C 231 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL C 237 " --> pdb=" O TRP C 267 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU C 307 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ARG C 331 " --> pdb=" O LEU C 307 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N HIS C 309 " --> pdb=" O ARG C 331 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N ILE C 333 " --> pdb=" O HIS C 309 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ASP C 311 " --> pdb=" O ILE C 333 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL C 328 " --> pdb=" O ASN C 351 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N VAL C 353 " --> pdb=" O VAL C 328 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N LEU C 330 " --> pdb=" O VAL C 353 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 216 through 217 removed outlier: 3.555A pdb=" N THR C 216 " --> pdb=" O SER C 243 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N HIS C 245 " --> pdb=" O THR C 216 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ALA C 286 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ARG C 316 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL C 288 " --> pdb=" O ARG C 316 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N CYS C 318 " --> pdb=" O VAL C 288 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N GLN C 339 " --> pdb=" O ALA C 313 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N GLY C 315 " --> pdb=" O GLN C 339 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N TYR C 338 " --> pdb=" O MET C 368 " (cutoff:3.500A) 240 hydrogen bonds defined for protein. 648 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: 4.12 Time building geometry restraints manager: 4.65 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: 3903 1.34 - 1.46: 2240 1.46 - 1.57: 5593 1.57 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 11820 Sorted by residual: bond pdb=" CB PRO B 277 " pdb=" CG PRO B 277 " ideal model delta sigma weight residual 1.492 1.569 -0.077 5.00e-02 4.00e+02 2.38e+00 bond pdb=" CB PRO A 277 " pdb=" CG PRO A 277 " ideal model delta sigma weight residual 1.492 1.568 -0.076 5.00e-02 4.00e+02 2.34e+00 bond pdb=" CB PRO C 277 " pdb=" CG PRO C 277 " ideal model delta sigma weight residual 1.492 1.568 -0.076 5.00e-02 4.00e+02 2.33e+00 bond pdb=" CB ASP C 396 " pdb=" CG ASP C 396 " ideal model delta sigma weight residual 1.516 1.544 -0.028 2.50e-02 1.60e+03 1.26e+00 bond pdb=" CB ASP B 396 " pdb=" CG ASP B 396 " ideal model delta sigma weight residual 1.516 1.544 -0.028 2.50e-02 1.60e+03 1.22e+00 ... (remaining 11815 not shown) Histogram of bond angle deviations from ideal: 100.49 - 107.20: 425 107.20 - 113.91: 6361 113.91 - 120.62: 4287 120.62 - 127.33: 4888 127.33 - 134.04: 140 Bond angle restraints: 16101 Sorted by residual: angle pdb=" N ILE B 521 " pdb=" CA ILE B 521 " pdb=" C ILE B 521 " ideal model delta sigma weight residual 113.53 109.52 4.01 9.80e-01 1.04e+00 1.67e+01 angle pdb=" N ILE C 521 " pdb=" CA ILE C 521 " pdb=" C ILE C 521 " ideal model delta sigma weight residual 113.53 109.56 3.97 9.80e-01 1.04e+00 1.64e+01 angle pdb=" N ILE A 521 " pdb=" CA ILE A 521 " pdb=" C ILE A 521 " ideal model delta sigma weight residual 113.53 109.57 3.96 9.80e-01 1.04e+00 1.63e+01 angle pdb=" C PHE B 499 " pdb=" N THR B 500 " pdb=" CA THR B 500 " ideal model delta sigma weight residual 121.54 129.17 -7.63 1.91e+00 2.74e-01 1.60e+01 angle pdb=" C PHE A 499 " pdb=" N THR A 500 " pdb=" CA THR A 500 " ideal model delta sigma weight residual 121.54 129.15 -7.61 1.91e+00 2.74e-01 1.59e+01 ... (remaining 16096 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.65: 6205 15.65 - 31.30: 429 31.30 - 46.95: 119 46.95 - 62.60: 12 62.60 - 78.25: 12 Dihedral angle restraints: 6777 sinusoidal: 2541 harmonic: 4236 Sorted by residual: dihedral pdb=" CA GLU C 156 " pdb=" C GLU C 156 " pdb=" N PRO C 157 " pdb=" CA PRO C 157 " ideal model delta harmonic sigma weight residual 180.00 -158.85 -21.15 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA GLU B 156 " pdb=" C GLU B 156 " pdb=" N PRO B 157 " pdb=" CA PRO B 157 " ideal model delta harmonic sigma weight residual -180.00 -158.89 -21.11 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA GLU A 156 " pdb=" C GLU A 156 " pdb=" N PRO A 157 " pdb=" CA PRO A 157 " ideal model delta harmonic sigma weight residual -180.00 -158.92 -21.08 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 6774 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1261 0.050 - 0.099: 343 0.099 - 0.149: 127 0.149 - 0.198: 0 0.198 - 0.248: 3 Chirality restraints: 1734 Sorted by residual: chirality pdb=" CB ILE B 70 " pdb=" CA ILE B 70 " pdb=" CG1 ILE B 70 " pdb=" CG2 ILE B 70 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CB ILE C 70 " pdb=" CA ILE C 70 " pdb=" CG1 ILE C 70 " pdb=" CG2 ILE C 70 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CB ILE A 70 " pdb=" CA ILE A 70 " pdb=" CG1 ILE A 70 " pdb=" CG2 ILE A 70 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 1731 not shown) Planarity restraints: 2136 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 276 " -0.055 5.00e-02 4.00e+02 8.30e-02 1.10e+01 pdb=" N PRO B 277 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO B 277 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 277 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 276 " 0.055 5.00e-02 4.00e+02 8.29e-02 1.10e+01 pdb=" N PRO C 277 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO C 277 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 277 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 276 " -0.055 5.00e-02 4.00e+02 8.27e-02 1.10e+01 pdb=" N PRO A 277 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO A 277 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 277 " -0.045 5.00e-02 4.00e+02 ... (remaining 2133 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 547 2.73 - 3.27: 11434 3.27 - 3.81: 20072 3.81 - 4.36: 25594 4.36 - 4.90: 43687 Nonbonded interactions: 101334 Sorted by model distance: nonbonded pdb=" OG SER A 278 " pdb=" OE1 GLU A 283 " model vdw 2.185 2.440 nonbonded pdb=" OG SER C 278 " pdb=" OE1 GLU C 283 " model vdw 2.185 2.440 nonbonded pdb=" OG SER B 278 " pdb=" OE1 GLU B 283 " model vdw 2.185 2.440 nonbonded pdb=" O GLY A 404 " pdb=" NH2 ARG C 434 " model vdw 2.243 2.520 nonbonded pdb=" NH2 ARG B 434 " pdb=" O GLY C 404 " model vdw 2.246 2.520 ... (remaining 101329 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' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.340 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 33.560 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 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 : 0.003 0.077 11820 Z= 0.173 Angle : 0.626 7.630 16101 Z= 0.356 Chirality : 0.049 0.248 1734 Planarity : 0.005 0.083 2136 Dihedral : 12.391 78.248 4107 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.19), residues: 1509 helix: 3.94 (0.65), residues: 48 sheet: -0.28 (0.28), residues: 390 loop : -2.27 (0.15), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 419 HIS 0.002 0.001 HIS C 186 PHE 0.011 0.001 PHE C 179 TYR 0.014 0.001 TYR A 374 ARG 0.003 0.000 ARG B 225 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 316 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 221 ILE cc_start: 0.6749 (mt) cc_final: 0.6536 (mt) REVERT: A 289 TYR cc_start: 0.8328 (p90) cc_final: 0.8088 (p90) REVERT: A 293 HIS cc_start: 0.7395 (m170) cc_final: 0.7056 (m170) REVERT: B 385 LEU cc_start: 0.8825 (mt) cc_final: 0.8609 (mt) REVERT: B 470 THR cc_start: 0.8136 (m) cc_final: 0.7821 (p) REVERT: C 76 PRO cc_start: 0.7142 (Cg_endo) cc_final: 0.6798 (Cg_exo) REVERT: C 368 MET cc_start: 0.7761 (mtp) cc_final: 0.7378 (mtm) REVERT: C 451 TYR cc_start: 0.7854 (t80) cc_final: 0.7623 (t80) REVERT: C 470 THR cc_start: 0.8211 (m) cc_final: 0.7873 (p) REVERT: C 519 ASP cc_start: 0.6226 (t0) cc_final: 0.5852 (t0) outliers start: 0 outliers final: 2 residues processed: 316 average time/residue: 0.7651 time to fit residues: 273.8832 Evaluate side-chains 249 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 247 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain C residue 357 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 chunk 117 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 87 optimal weight: 0.8980 chunk 136 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN A 110 GLN A 247 ASN A 255 GLN A 291 ASN A 376 GLN C 56 GLN C 89 ASN C 110 GLN ** C 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 255 GLN C 376 GLN ** C 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11820 Z= 0.283 Angle : 0.648 11.951 16101 Z= 0.351 Chirality : 0.051 0.191 1734 Planarity : 0.005 0.053 2136 Dihedral : 6.032 69.196 1654 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.02 % Favored : 91.78 % Rotamer: Outliers : 4.62 % Allowed : 11.22 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.20), residues: 1509 helix: 3.96 (0.67), residues: 48 sheet: 0.03 (0.28), residues: 399 loop : -2.29 (0.15), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 419 HIS 0.007 0.001 HIS B 145 PHE 0.028 0.002 PHE B 474 TYR 0.014 0.002 TYR A 120 ARG 0.005 0.001 ARG C 440 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 269 time to evaluate : 1.347 Fit side-chains REVERT: A 212 LYS cc_start: 0.7655 (OUTLIER) cc_final: 0.7310 (ptmt) REVERT: A 301 ASP cc_start: 0.8297 (OUTLIER) cc_final: 0.8020 (m-30) REVERT: B 110 GLN cc_start: 0.6589 (OUTLIER) cc_final: 0.6305 (mt0) REVERT: B 158 VAL cc_start: 0.7243 (t) cc_final: 0.6934 (t) REVERT: B 160 TRP cc_start: 0.7449 (t60) cc_final: 0.7093 (t60) REVERT: B 266 MET cc_start: 0.7549 (OUTLIER) cc_final: 0.7204 (mtp) REVERT: B 293 HIS cc_start: 0.7835 (m170) cc_final: 0.7519 (m-70) REVERT: B 385 LEU cc_start: 0.8925 (mt) cc_final: 0.8616 (mp) REVERT: B 388 SER cc_start: 0.8559 (OUTLIER) cc_final: 0.8330 (m) REVERT: B 470 THR cc_start: 0.8173 (m) cc_final: 0.7963 (p) REVERT: C 102 ARG cc_start: 0.6718 (OUTLIER) cc_final: 0.6351 (mpt-90) REVERT: C 160 TRP cc_start: 0.7206 (t60) cc_final: 0.6886 (t-100) REVERT: C 470 THR cc_start: 0.8130 (m) cc_final: 0.7927 (p) outliers start: 56 outliers final: 22 residues processed: 292 average time/residue: 0.8378 time to fit residues: 273.3078 Evaluate side-chains 272 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 244 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 266 MET Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 357 ASP Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 378 ASN Chi-restraints excluded: chain C residue 418 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 92 optimal weight: 0.0980 chunk 37 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN A 110 GLN A 175 GLN A 242 ASN A 290 ASN A 345 HIS A 376 GLN A 399 ASN ** A 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN B 242 ASN B 255 GLN B 290 ASN ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 ASN C 56 GLN C 60 ASN ** C 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN C 290 ASN C 376 GLN ** C 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.4681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11820 Z= 0.348 Angle : 0.690 12.340 16101 Z= 0.374 Chirality : 0.053 0.216 1734 Planarity : 0.006 0.052 2136 Dihedral : 6.469 94.608 1654 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 5.03 % Allowed : 14.77 % Favored : 80.20 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.19), residues: 1509 helix: 3.92 (0.67), residues: 48 sheet: -0.45 (0.26), residues: 411 loop : -2.24 (0.15), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 419 HIS 0.008 0.002 HIS C 195 PHE 0.016 0.002 PHE C 474 TYR 0.024 0.002 TYR A 395 ARG 0.007 0.001 ARG B 225 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 249 time to evaluate : 1.284 Fit side-chains revert: symmetry clash REVERT: A 145 HIS cc_start: 0.7229 (p-80) cc_final: 0.6954 (p-80) REVERT: A 293 HIS cc_start: 0.7982 (m170) cc_final: 0.7694 (m170) REVERT: A 301 ASP cc_start: 0.8304 (OUTLIER) cc_final: 0.8064 (m-30) REVERT: A 346 SER cc_start: 0.7341 (t) cc_final: 0.7084 (p) REVERT: A 434 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.7071 (ptp90) REVERT: A 518 GLN cc_start: 0.7804 (mt0) cc_final: 0.7514 (mt0) REVERT: B 110 GLN cc_start: 0.6613 (OUTLIER) cc_final: 0.6378 (mt0) REVERT: B 158 VAL cc_start: 0.7695 (t) cc_final: 0.7419 (t) REVERT: B 255 GLN cc_start: 0.7394 (OUTLIER) cc_final: 0.7039 (tm-30) REVERT: B 293 HIS cc_start: 0.8032 (m170) cc_final: 0.7626 (m-70) REVERT: B 347 ILE cc_start: 0.7711 (OUTLIER) cc_final: 0.7352 (pp) REVERT: B 385 LEU cc_start: 0.8951 (mt) cc_final: 0.8690 (mp) REVERT: B 388 SER cc_start: 0.8678 (OUTLIER) cc_final: 0.8309 (m) REVERT: B 396 ASP cc_start: 0.6720 (t70) cc_final: 0.6466 (t0) REVERT: B 434 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7038 (ptp90) REVERT: B 447 TRP cc_start: 0.7816 (m100) cc_final: 0.7566 (m100) REVERT: C 102 ARG cc_start: 0.6706 (OUTLIER) cc_final: 0.6250 (mpt-90) REVERT: C 160 TRP cc_start: 0.7384 (t60) cc_final: 0.6960 (t-100) REVERT: C 212 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7974 (ptpp) REVERT: C 385 LEU cc_start: 0.8868 (mt) cc_final: 0.8536 (mp) outliers start: 61 outliers final: 24 residues processed: 275 average time/residue: 0.8658 time to fit residues: 266.0534 Evaluate side-chains 263 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 230 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 434 ARG Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 255 GLN Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 434 ARG Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain C residue 357 ASP Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 378 ASN Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 418 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 70 optimal weight: 0.0980 chunk 15 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 136 optimal weight: 2.9990 chunk 144 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 129 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 ASN A 399 ASN B 198 ASN B 255 GLN ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 ASN ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 HIS C 164 ASN C 376 GLN C 409 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.4833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11820 Z= 0.230 Angle : 0.621 13.539 16101 Z= 0.331 Chirality : 0.050 0.192 1734 Planarity : 0.005 0.046 2136 Dihedral : 6.445 117.915 1652 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 4.54 % Allowed : 17.33 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.20), residues: 1509 helix: 3.71 (0.66), residues: 48 sheet: -0.45 (0.27), residues: 402 loop : -2.18 (0.16), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 419 HIS 0.004 0.001 HIS C 195 PHE 0.017 0.002 PHE B 115 TYR 0.012 0.001 TYR A 235 ARG 0.005 0.001 ARG B 530 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 232 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 HIS cc_start: 0.7207 (p-80) cc_final: 0.6958 (p-80) REVERT: A 293 HIS cc_start: 0.7952 (m170) cc_final: 0.7718 (m170) REVERT: A 346 SER cc_start: 0.7270 (t) cc_final: 0.7014 (p) REVERT: A 434 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.6945 (ptp90) REVERT: A 438 ASP cc_start: 0.6963 (OUTLIER) cc_final: 0.6747 (p0) REVERT: A 518 GLN cc_start: 0.7722 (mt0) cc_final: 0.7498 (mt0) REVERT: B 41 VAL cc_start: 0.8168 (m) cc_final: 0.7960 (p) REVERT: B 228 ASN cc_start: 0.7640 (m-40) cc_final: 0.7433 (m110) REVERT: B 255 GLN cc_start: 0.7388 (OUTLIER) cc_final: 0.7014 (tm-30) REVERT: B 293 HIS cc_start: 0.7881 (m170) cc_final: 0.7448 (m-70) REVERT: B 347 ILE cc_start: 0.7587 (OUTLIER) cc_final: 0.7311 (pp) REVERT: B 352 THR cc_start: 0.8075 (OUTLIER) cc_final: 0.7753 (p) REVERT: B 385 LEU cc_start: 0.8911 (mt) cc_final: 0.8673 (mp) REVERT: B 388 SER cc_start: 0.8653 (OUTLIER) cc_final: 0.8296 (m) REVERT: B 444 ARG cc_start: 0.7821 (mmt180) cc_final: 0.7598 (mmt90) REVERT: C 102 ARG cc_start: 0.6675 (OUTLIER) cc_final: 0.6276 (mpt-90) REVERT: C 385 LEU cc_start: 0.8803 (mt) cc_final: 0.8541 (mp) outliers start: 55 outliers final: 25 residues processed: 263 average time/residue: 0.8451 time to fit residues: 248.0578 Evaluate side-chains 253 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 221 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 414 ASN Chi-restraints excluded: chain A residue 434 ARG Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain B residue 255 GLN Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 378 ASN Chi-restraints excluded: chain C residue 414 ASN Chi-restraints excluded: chain C residue 439 SER Chi-restraints excluded: chain C residue 455 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 3.9990 chunk 82 optimal weight: 0.1980 chunk 2 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 123 optimal weight: 0.6980 chunk 100 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 74 optimal weight: 0.0570 chunk 130 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 overall best weight: 0.5700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 HIS A 399 ASN B 255 GLN ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 ASN C 164 ASN ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 376 GLN C 399 ASN ** C 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.4933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11820 Z= 0.178 Angle : 0.595 12.248 16101 Z= 0.315 Chirality : 0.049 0.183 1734 Planarity : 0.004 0.046 2136 Dihedral : 5.564 24.388 1650 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 3.88 % Allowed : 18.56 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.20), residues: 1509 helix: 3.69 (0.65), residues: 48 sheet: -0.44 (0.27), residues: 402 loop : -2.15 (0.16), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 142 HIS 0.003 0.001 HIS B 145 PHE 0.012 0.001 PHE C 115 TYR 0.015 0.001 TYR B 395 ARG 0.006 0.000 ARG C 316 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 242 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 HIS cc_start: 0.7171 (p-80) cc_final: 0.6933 (p-80) REVERT: A 301 ASP cc_start: 0.8278 (OUTLIER) cc_final: 0.8049 (m-30) REVERT: A 346 SER cc_start: 0.7256 (t) cc_final: 0.7014 (p) REVERT: A 396 ASP cc_start: 0.6968 (OUTLIER) cc_final: 0.6715 (t0) REVERT: A 434 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.6931 (ptp90) REVERT: A 438 ASP cc_start: 0.6843 (OUTLIER) cc_final: 0.6610 (p0) REVERT: A 518 GLN cc_start: 0.7755 (mt0) cc_final: 0.7537 (mt0) REVERT: B 110 GLN cc_start: 0.6545 (OUTLIER) cc_final: 0.6314 (mt0) REVERT: B 139 ARG cc_start: 0.7298 (OUTLIER) cc_final: 0.5807 (mtt-85) REVERT: B 235 TYR cc_start: 0.7471 (m-80) cc_final: 0.7264 (m-80) REVERT: B 352 THR cc_start: 0.8026 (OUTLIER) cc_final: 0.7745 (p) REVERT: B 388 SER cc_start: 0.8629 (OUTLIER) cc_final: 0.8270 (m) REVERT: B 396 ASP cc_start: 0.6449 (t70) cc_final: 0.6223 (OUTLIER) REVERT: C 102 ARG cc_start: 0.6631 (OUTLIER) cc_final: 0.6242 (mpt-90) REVERT: C 145 HIS cc_start: 0.7131 (p-80) cc_final: 0.6452 (p-80) REVERT: C 385 LEU cc_start: 0.8769 (mt) cc_final: 0.8544 (mp) REVERT: C 396 ASP cc_start: 0.6794 (t0) cc_final: 0.6590 (t0) REVERT: C 480 THR cc_start: 0.7529 (m) cc_final: 0.7319 (t) REVERT: C 483 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.6842 (ptt-90) outliers start: 47 outliers final: 23 residues processed: 267 average time/residue: 0.8434 time to fit residues: 251.3303 Evaluate side-chains 264 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 232 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 434 ARG Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 409 ASN Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 438 ASP Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 378 ASN Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 483 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 35 optimal weight: 0.4980 chunk 145 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 139 optimal weight: 0.7980 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 291 ASN A 399 ASN A 463 ASN ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 HIS B 414 ASN ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 ASN C 164 ASN C 242 ASN C 376 GLN C 399 ASN C 409 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.5607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 11820 Z= 0.484 Angle : 0.769 11.419 16101 Z= 0.410 Chirality : 0.056 0.250 1734 Planarity : 0.006 0.049 2136 Dihedral : 6.274 24.359 1650 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 6.02 % Allowed : 17.82 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.20), residues: 1509 helix: 3.30 (0.67), residues: 48 sheet: -0.77 (0.25), residues: 417 loop : -2.34 (0.16), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP B 419 HIS 0.009 0.003 HIS B 195 PHE 0.037 0.003 PHE B 474 TYR 0.019 0.002 TYR A 485 ARG 0.007 0.001 ARG A 225 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 256 time to evaluate : 1.210 Fit side-chains revert: symmetry clash REVERT: A 83 MET cc_start: 0.5697 (tpt) cc_final: 0.5451 (tmm) REVERT: A 212 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7640 (ptmt) REVERT: A 262 ILE cc_start: 0.8002 (OUTLIER) cc_final: 0.7736 (mp) REVERT: A 293 HIS cc_start: 0.8110 (m170) cc_final: 0.7788 (m-70) REVERT: A 301 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.8070 (m-30) REVERT: A 346 SER cc_start: 0.7401 (t) cc_final: 0.7143 (p) REVERT: A 396 ASP cc_start: 0.6735 (OUTLIER) cc_final: 0.6524 (t0) REVERT: A 434 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.7288 (ptp90) REVERT: A 538 THR cc_start: 0.8159 (p) cc_final: 0.7921 (m) REVERT: B 139 ARG cc_start: 0.7449 (OUTLIER) cc_final: 0.5884 (mtt-85) REVERT: B 388 SER cc_start: 0.8696 (OUTLIER) cc_final: 0.8318 (m) REVERT: B 434 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7026 (ptp90) REVERT: B 444 ARG cc_start: 0.7952 (mmt180) cc_final: 0.7653 (mmt90) REVERT: B 447 TRP cc_start: 0.7841 (m100) cc_final: 0.7602 (m100) REVERT: C 102 ARG cc_start: 0.6774 (OUTLIER) cc_final: 0.6380 (mpt-90) REVERT: C 145 HIS cc_start: 0.7198 (p-80) cc_final: 0.6395 (p-80) REVERT: C 385 LEU cc_start: 0.8853 (mt) cc_final: 0.8590 (mp) REVERT: C 396 ASP cc_start: 0.7104 (t0) cc_final: 0.6880 (t0) REVERT: C 483 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.6824 (ptt-90) outliers start: 73 outliers final: 37 residues processed: 298 average time/residue: 0.8587 time to fit residues: 284.7581 Evaluate side-chains 288 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 241 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 414 ASN Chi-restraints excluded: chain A residue 434 ARG Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 357 ASP Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 434 ARG Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 357 ASP Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 378 ASN Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 414 ASN Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain C residue 439 SER Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 483 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 81 optimal weight: 7.9990 chunk 144 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 66 optimal weight: 0.0020 chunk 89 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 159 ASN ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 376 GLN A 399 ASN ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 ASN ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 GLN C 164 ASN C 376 GLN C 409 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.5608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11820 Z= 0.232 Angle : 0.659 11.140 16101 Z= 0.346 Chirality : 0.050 0.194 1734 Planarity : 0.005 0.048 2136 Dihedral : 5.954 22.649 1650 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 4.21 % Allowed : 20.87 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.19), residues: 1509 helix: 3.51 (0.67), residues: 48 sheet: -0.70 (0.26), residues: 387 loop : -2.30 (0.16), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 419 HIS 0.005 0.001 HIS B 145 PHE 0.030 0.002 PHE B 474 TYR 0.014 0.001 TYR A 395 ARG 0.006 0.001 ARG B 530 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 247 time to evaluate : 1.216 Fit side-chains REVERT: A 301 ASP cc_start: 0.8280 (OUTLIER) cc_final: 0.8053 (m-30) REVERT: A 346 SER cc_start: 0.7291 (t) cc_final: 0.7059 (p) REVERT: A 434 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7078 (ptp90) REVERT: B 139 ARG cc_start: 0.7357 (OUTLIER) cc_final: 0.5846 (mtt-85) REVERT: B 235 TYR cc_start: 0.7539 (m-80) cc_final: 0.7314 (m-80) REVERT: B 388 SER cc_start: 0.8650 (OUTLIER) cc_final: 0.8307 (m) REVERT: B 396 ASP cc_start: 0.6657 (t70) cc_final: 0.6358 (t0) REVERT: C 102 ARG cc_start: 0.6576 (OUTLIER) cc_final: 0.6253 (mpt-90) REVERT: C 145 HIS cc_start: 0.7205 (p-80) cc_final: 0.6488 (p-80) REVERT: C 385 LEU cc_start: 0.8822 (mt) cc_final: 0.8607 (mp) outliers start: 51 outliers final: 29 residues processed: 275 average time/residue: 0.8356 time to fit residues: 256.5116 Evaluate side-chains 266 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 232 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 434 ARG Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 438 ASP Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 378 ASN Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain C residue 455 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 0.3980 chunk 43 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 138 optimal weight: 0.9990 chunk 126 optimal weight: 0.0470 overall best weight: 1.0884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 219 ASN ** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 ASN ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 ASN ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 GLN C 60 ASN C 376 GLN C 409 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.5709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11820 Z= 0.258 Angle : 0.665 12.381 16101 Z= 0.349 Chirality : 0.051 0.191 1734 Planarity : 0.005 0.051 2136 Dihedral : 5.887 23.296 1650 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 4.13 % Allowed : 21.29 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.19), residues: 1509 helix: 3.64 (0.67), residues: 48 sheet: -0.72 (0.26), residues: 387 loop : -2.29 (0.16), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 419 HIS 0.006 0.001 HIS A 145 PHE 0.028 0.002 PHE B 474 TYR 0.012 0.001 TYR A 235 ARG 0.007 0.001 ARG B 331 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 239 time to evaluate : 1.088 Fit side-chains REVERT: A 139 ARG cc_start: 0.7280 (OUTLIER) cc_final: 0.5613 (mtt-85) REVERT: A 301 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.8057 (m-30) REVERT: A 346 SER cc_start: 0.7342 (t) cc_final: 0.7108 (p) REVERT: A 434 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7136 (ptp90) REVERT: B 139 ARG cc_start: 0.7351 (OUTLIER) cc_final: 0.5830 (mtt-85) REVERT: B 235 TYR cc_start: 0.7560 (m-80) cc_final: 0.7339 (m-80) REVERT: B 388 SER cc_start: 0.8628 (OUTLIER) cc_final: 0.8284 (m) REVERT: B 396 ASP cc_start: 0.6744 (t70) cc_final: 0.6522 (OUTLIER) REVERT: C 102 ARG cc_start: 0.6567 (OUTLIER) cc_final: 0.6243 (mpt-90) REVERT: C 145 HIS cc_start: 0.7212 (p-80) cc_final: 0.6496 (p-80) REVERT: C 385 LEU cc_start: 0.8838 (mt) cc_final: 0.8611 (mp) outliers start: 50 outliers final: 34 residues processed: 267 average time/residue: 0.8171 time to fit residues: 244.3466 Evaluate side-chains 271 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 232 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 434 ARG Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 438 ASP Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 378 ASN Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain C residue 455 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 105 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 121 optimal weight: 0.6980 chunk 127 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 219 ASN ** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 ASN ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 ASN ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 ASN C 376 GLN C 409 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.5801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11820 Z= 0.288 Angle : 0.673 12.331 16101 Z= 0.355 Chirality : 0.051 0.193 1734 Planarity : 0.005 0.051 2136 Dihedral : 5.935 20.866 1650 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 4.46 % Allowed : 21.70 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.19), residues: 1509 helix: 3.49 (0.67), residues: 48 sheet: -0.73 (0.26), residues: 387 loop : -2.33 (0.16), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 419 HIS 0.006 0.001 HIS C 186 PHE 0.026 0.002 PHE B 474 TYR 0.013 0.001 TYR A 235 ARG 0.006 0.001 ARG A 444 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 242 time to evaluate : 1.172 Fit side-chains REVERT: A 139 ARG cc_start: 0.7315 (OUTLIER) cc_final: 0.5669 (mtt-85) REVERT: A 301 ASP cc_start: 0.8287 (OUTLIER) cc_final: 0.8050 (m-30) REVERT: A 346 SER cc_start: 0.7374 (t) cc_final: 0.7129 (p) REVERT: A 434 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7105 (ptp90) REVERT: A 538 THR cc_start: 0.8266 (p) cc_final: 0.8040 (m) REVERT: B 139 ARG cc_start: 0.7366 (OUTLIER) cc_final: 0.5809 (mtt-85) REVERT: B 235 TYR cc_start: 0.7574 (m-80) cc_final: 0.7292 (m-80) REVERT: B 388 SER cc_start: 0.8619 (OUTLIER) cc_final: 0.8336 (m) REVERT: B 396 ASP cc_start: 0.6653 (t70) cc_final: 0.6420 (OUTLIER) REVERT: C 83 MET cc_start: 0.5856 (OUTLIER) cc_final: 0.5545 (tpt) REVERT: C 102 ARG cc_start: 0.6599 (OUTLIER) cc_final: 0.6283 (mpt-90) REVERT: C 396 ASP cc_start: 0.6850 (t0) cc_final: 0.6648 (t0) outliers start: 54 outliers final: 33 residues processed: 274 average time/residue: 0.8514 time to fit residues: 261.4651 Evaluate side-chains 268 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 229 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 434 ARG Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 378 ASN Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 506 ASP Chi-restraints excluded: chain C residue 529 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 0.1980 chunk 99 optimal weight: 6.9990 chunk 149 optimal weight: 6.9990 chunk 137 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 94 optimal weight: 0.0980 chunk 126 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 ASN ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 ASN ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 GLN C 376 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.5822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11820 Z= 0.219 Angle : 0.644 12.036 16101 Z= 0.338 Chirality : 0.050 0.182 1734 Planarity : 0.005 0.050 2136 Dihedral : 5.788 20.843 1650 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 3.38 % Allowed : 22.85 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.19), residues: 1509 helix: 3.55 (0.66), residues: 48 sheet: -0.50 (0.28), residues: 363 loop : -2.35 (0.16), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 419 HIS 0.005 0.001 HIS C 186 PHE 0.025 0.001 PHE B 474 TYR 0.013 0.001 TYR A 235 ARG 0.006 0.001 ARG A 444 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 239 time to evaluate : 1.159 Fit side-chains revert: symmetry clash REVERT: A 301 ASP cc_start: 0.8266 (OUTLIER) cc_final: 0.8053 (m-30) REVERT: A 346 SER cc_start: 0.7295 (t) cc_final: 0.7055 (p) REVERT: A 434 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.7258 (ptp90) REVERT: A 538 THR cc_start: 0.8258 (p) cc_final: 0.8023 (m) REVERT: B 139 ARG cc_start: 0.7264 (OUTLIER) cc_final: 0.5763 (mtt-85) REVERT: B 235 TYR cc_start: 0.7558 (m-80) cc_final: 0.7240 (m-80) REVERT: B 388 SER cc_start: 0.8610 (OUTLIER) cc_final: 0.8315 (m) REVERT: C 83 MET cc_start: 0.5784 (OUTLIER) cc_final: 0.5529 (tpt) REVERT: C 102 ARG cc_start: 0.6550 (OUTLIER) cc_final: 0.6253 (mpt-90) REVERT: C 387 THR cc_start: 0.8575 (OUTLIER) cc_final: 0.7905 (t) outliers start: 41 outliers final: 26 residues processed: 262 average time/residue: 0.8211 time to fit residues: 241.5012 Evaluate side-chains 267 residues out of total 1212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 234 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 434 ARG Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 506 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 chunk 49 optimal weight: 0.0970 chunk 122 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 86 optimal weight: 0.9980 overall best weight: 0.7978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 ASN A 512 ASN B 164 ASN ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 ASN ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 GLN C 60 ASN C 376 GLN C 409 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.141246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.128538 restraints weight = 16001.900| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.03 r_work: 0.3640 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.5834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11820 Z= 0.218 Angle : 0.639 11.938 16101 Z= 0.336 Chirality : 0.050 0.185 1734 Planarity : 0.005 0.050 2136 Dihedral : 5.751 20.587 1650 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 3.22 % Allowed : 23.51 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.20), residues: 1509 helix: 3.66 (0.67), residues: 48 sheet: -0.45 (0.28), residues: 378 loop : -2.30 (0.16), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 419 HIS 0.005 0.001 HIS B 145 PHE 0.025 0.001 PHE B 474 TYR 0.013 0.001 TYR A 235 ARG 0.007 0.001 ARG A 444 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4546.80 seconds wall clock time: 81 minutes 0.54 seconds (4860.54 seconds total)