Starting phenix.real_space_refine on Mon Dec 30 20:16:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9izx_61045/12_2024/9izx_61045.cif Found real_map, /net/cci-nas-00/data/ceres_data/9izx_61045/12_2024/9izx_61045.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/cci-nas-00/data/ceres_data/9izx_61045/12_2024/9izx_61045.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9izx_61045/12_2024/9izx_61045.map" model { file = "/net/cci-nas-00/data/ceres_data/9izx_61045/12_2024/9izx_61045.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9izx_61045/12_2024/9izx_61045.cif" } 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= -0.002 sd= 0.037 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 91 5.16 5 C 8986 2.51 5 N 2451 2.21 5 O 2624 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 14152 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3704 Classifications: {'peptide': 485} Link IDs: {'PTRANS': 27, 'TRANS': 457} Chain: "B" Number of atoms: 3327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3327 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 26, 'TRANS': 412} Chain breaks: 2 Chain: "C" Number of atoms: 3589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3589 Classifications: {'peptide': 470} Link IDs: {'PTRANS': 27, 'TRANS': 442} Chain breaks: 1 Chain: "D" Number of atoms: 3532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3532 Classifications: {'peptide': 463} Link IDs: {'PTRANS': 26, 'TRANS': 436} Chain breaks: 2 Time building chain proxies: 8.70, per 1000 atoms: 0.61 Number of scatterers: 14152 At special positions: 0 Unit cell: (112.888, 116.184, 117.832, 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 91 16.00 O 2624 8.00 N 2451 7.00 C 8986 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.60 Conformation dependent library (CDL) restraints added in 2.0 seconds 3678 Ramachandran restraints generated. 1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3392 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 14 sheets defined 47.6% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 43 through 64 Proline residue: A 59 - end of helix Processing helix chain 'A' and resid 65 through 83 Processing helix chain 'A' and resid 83 through 95 Processing helix chain 'A' and resid 98 through 117 Processing helix chain 'A' and resid 119 through 124 removed outlier: 3.627A pdb=" N MET A 124 " --> pdb=" O THR A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 170 Proline residue: A 165 - end of helix Processing helix chain 'A' and resid 183 through 196 Processing helix chain 'A' and resid 210 through 219 Processing helix chain 'A' and resid 230 through 243 Processing helix chain 'A' and resid 265 through 279 Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 296 through 299 Processing helix chain 'A' and resid 300 through 311 removed outlier: 3.594A pdb=" N LEU A 311 " --> pdb=" O HIS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 345 Processing helix chain 'A' and resid 379 through 384 removed outlier: 3.654A pdb=" N LYS A 383 " --> pdb=" O MET A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 409 removed outlier: 3.510A pdb=" N ASN A 409 " --> pdb=" O ILE A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 432 Processing helix chain 'A' and resid 467 through 474 Processing helix chain 'B' and resid 43 through 64 Proline residue: B 59 - end of helix Processing helix chain 'B' and resid 65 through 83 Processing helix chain 'B' and resid 83 through 96 Processing helix chain 'B' and resid 98 through 118 removed outlier: 3.590A pdb=" N SER B 118 " --> pdb=" O GLU B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 170 Proline residue: B 165 - end of helix Processing helix chain 'B' and resid 183 through 196 Processing helix chain 'B' and resid 209 through 219 removed outlier: 3.571A pdb=" N VAL B 213 " --> pdb=" O GLN B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 245 Processing helix chain 'B' and resid 265 through 279 Processing helix chain 'B' and resid 280 through 283 Processing helix chain 'B' and resid 296 through 299 Processing helix chain 'B' and resid 300 through 311 removed outlier: 3.603A pdb=" N LEU B 311 " --> pdb=" O HIS B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 346 Processing helix chain 'B' and resid 379 through 384 Processing helix chain 'B' and resid 398 through 409 removed outlier: 3.512A pdb=" N ALA B 402 " --> pdb=" O THR B 398 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN B 409 " --> pdb=" O ILE B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 432 Processing helix chain 'B' and resid 467 through 475 Processing helix chain 'C' and resid 43 through 64 Proline residue: C 59 - end of helix Processing helix chain 'C' and resid 65 through 83 removed outlier: 3.585A pdb=" N VAL C 72 " --> pdb=" O SER C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 95 Processing helix chain 'C' and resid 98 through 118 Processing helix chain 'C' and resid 157 through 170 Proline residue: C 165 - end of helix Processing helix chain 'C' and resid 183 through 196 Processing helix chain 'C' and resid 209 through 219 Processing helix chain 'C' and resid 230 through 244 removed outlier: 3.899A pdb=" N HIS C 244 " --> pdb=" O ARG C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 279 Processing helix chain 'C' and resid 280 through 283 Processing helix chain 'C' and resid 296 through 299 Processing helix chain 'C' and resid 300 through 310 Processing helix chain 'C' and resid 328 through 345 Processing helix chain 'C' and resid 379 through 384 Processing helix chain 'C' and resid 398 through 409 removed outlier: 3.513A pdb=" N ALA C 402 " --> pdb=" O THR C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 432 Processing helix chain 'C' and resid 467 through 474 Processing helix chain 'D' and resid 43 through 64 Proline residue: D 59 - end of helix Processing helix chain 'D' and resid 65 through 83 Processing helix chain 'D' and resid 83 through 95 Processing helix chain 'D' and resid 98 through 118 removed outlier: 3.534A pdb=" N SER D 118 " --> pdb=" O GLU D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 170 Proline residue: D 165 - end of helix Processing helix chain 'D' and resid 183 through 196 Processing helix chain 'D' and resid 209 through 219 removed outlier: 3.681A pdb=" N VAL D 213 " --> pdb=" O GLN D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 244 removed outlier: 3.681A pdb=" N HIS D 244 " --> pdb=" O ARG D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 278 Processing helix chain 'D' and resid 279 through 283 Processing helix chain 'D' and resid 296 through 299 Processing helix chain 'D' and resid 300 through 311 Processing helix chain 'D' and resid 328 through 345 removed outlier: 3.609A pdb=" N LYS D 332 " --> pdb=" O THR D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 384 Processing helix chain 'D' and resid 398 through 409 removed outlier: 3.515A pdb=" N ALA D 402 " --> pdb=" O THR D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 432 Processing helix chain 'D' and resid 467 through 474 Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 28 Processing sheet with id=AA2, first strand: chain 'B' and resid 348 through 351 removed outlier: 6.359A pdb=" N ILE B 371 " --> pdb=" O LEU B 350 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ASN B 256 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N VAL B 292 " --> pdb=" O ASN B 256 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLY B 258 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL B 294 " --> pdb=" O GLY B 258 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N VAL B 260 " --> pdb=" O VAL B 294 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LYS B 255 " --> pdb=" O ARG B 414 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N ALA B 416 " --> pdb=" O LYS B 255 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N HIS B 257 " --> pdb=" O ALA B 416 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N PHE B 418 " --> pdb=" O HIS B 257 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL B 259 " --> pdb=" O PHE B 418 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ASN B 413 " --> pdb=" O GLN B 436 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N GLY B 438 " --> pdb=" O ASN B 413 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N THR B 415 " --> pdb=" O GLY B 438 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N VAL B 437 " --> pdb=" O LEU A 477 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N THR A 479 " --> pdb=" O VAL B 437 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N VAL B 439 " --> pdb=" O THR A 479 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N THR A 481 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N MET A 135 " --> pdb=" O ILE A 131 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU A 137 " --> pdb=" O PRO A 129 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N SER A 139 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N THR A 127 " --> pdb=" O SER A 139 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ARG A 141 " --> pdb=" O GLY A 125 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N GLY A 125 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLU C 126 " --> pdb=" O SER C 139 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N MET C 135 " --> pdb=" O SER C 130 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N VAL D 437 " --> pdb=" O LEU C 477 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N THR C 479 " --> pdb=" O VAL D 437 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N VAL D 439 " --> pdb=" O THR C 479 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N THR C 481 " --> pdb=" O VAL D 439 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N THR D 415 " --> pdb=" O GLY D 438 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N HIS D 257 " --> pdb=" O ALA D 416 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N PHE D 418 " --> pdb=" O HIS D 257 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL D 259 " --> pdb=" O PHE D 418 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLY D 258 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL D 294 " --> pdb=" O GLY D 258 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL D 260 " --> pdb=" O VAL D 294 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR D 370 " --> pdb=" O LEU D 391 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N VAL D 393 " --> pdb=" O THR D 370 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE D 372 " --> pdb=" O VAL D 393 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N GLU D 395 " --> pdb=" O ILE D 372 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE D 371 " --> pdb=" O LEU D 350 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 203 through 205 removed outlier: 6.552A pdb=" N CYS A 147 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N LYS A 177 " --> pdb=" O CYS A 147 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLY A 149 " --> pdb=" O LYS A 177 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N VAL A 146 " --> pdb=" O LYS A 223 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE A 225 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ALA A 148 " --> pdb=" O ILE A 225 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N PHE A 227 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE A 150 " --> pdb=" O PHE A 227 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG A 247 " --> pdb=" O LYS A 223 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 348 through 351 removed outlier: 5.148A pdb=" N ILE A 349 " --> pdb=" O SER A 373 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N SER A 373 " --> pdb=" O ILE A 349 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N THR A 370 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N VAL A 393 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE A 372 " --> pdb=" O VAL A 393 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N GLU A 395 " --> pdb=" O ILE A 372 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ASN A 374 " --> pdb=" O GLU A 395 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N HIS A 257 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N PHE A 418 " --> pdb=" O HIS A 257 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL A 259 " --> pdb=" O PHE A 418 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 12 Processing sheet with id=AA6, first strand: chain 'B' and resid 24 through 28 removed outlier: 3.571A pdb=" N GLY B 37 " --> pdb=" O ILE B 27 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 203 through 205 removed outlier: 6.480A pdb=" N CYS B 147 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N LYS B 177 " --> pdb=" O CYS B 147 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLY B 149 " --> pdb=" O LYS B 177 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL B 146 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA B 224 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL B 228 " --> pdb=" O ILE B 150 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N PHE B 227 " --> pdb=" O GLN B 249 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY B 229 " --> pdb=" O ASN B 251 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 24 through 28 Processing sheet with id=AA9, first strand: chain 'C' and resid 203 through 205 removed outlier: 7.186A pdb=" N VAL C 146 " --> pdb=" O LYS C 223 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE C 225 " --> pdb=" O VAL C 146 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ALA C 148 " --> pdb=" O ILE C 225 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N PHE C 227 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE C 150 " --> pdb=" O PHE C 227 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LYS C 223 " --> pdb=" O ARG C 247 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N GLN C 249 " --> pdb=" O LYS C 223 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE C 225 " --> pdb=" O GLN C 249 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N ASN C 251 " --> pdb=" O ILE C 225 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N PHE C 227 " --> pdb=" O ASN C 251 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 348 through 351 removed outlier: 6.362A pdb=" N ILE C 371 " --> pdb=" O LEU C 350 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N THR C 370 " --> pdb=" O LEU C 391 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N VAL C 393 " --> pdb=" O THR C 370 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE C 372 " --> pdb=" O VAL C 393 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N GLU C 395 " --> pdb=" O ILE C 372 " (cutoff:3.500A) removed outlier: 9.730A pdb=" N ALA C 287 " --> pdb=" O VAL C 390 " (cutoff:3.500A) removed outlier: 9.230A pdb=" N VAL C 392 " --> pdb=" O ALA C 287 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N SER C 289 " --> pdb=" O VAL C 392 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N LEU C 394 " --> pdb=" O SER C 289 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ALA C 291 " --> pdb=" O LEU C 394 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N THR C 396 " --> pdb=" O ALA C 291 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N LEU C 293 " --> pdb=" O THR C 396 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ASN C 256 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N VAL C 292 " --> pdb=" O ASN C 256 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLY C 258 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N VAL C 294 " --> pdb=" O GLY C 258 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL C 260 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N LYS C 255 " --> pdb=" O ARG C 414 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N ALA C 416 " --> pdb=" O LYS C 255 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N HIS C 257 " --> pdb=" O ALA C 416 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N PHE C 418 " --> pdb=" O HIS C 257 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL C 259 " --> pdb=" O PHE C 418 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 10 through 12 Processing sheet with id=AB3, first strand: chain 'D' and resid 24 through 28 Processing sheet with id=AB4, first strand: chain 'D' and resid 140 through 143 Processing sheet with id=AB5, first strand: chain 'D' and resid 203 through 205 removed outlier: 7.582A pdb=" N VAL D 146 " --> pdb=" O LYS D 223 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE D 225 " --> pdb=" O VAL D 146 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ALA D 148 " --> pdb=" O ILE D 225 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N PHE D 227 " --> pdb=" O ALA D 148 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ILE D 150 " --> pdb=" O PHE D 227 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLY D 229 " --> pdb=" O ILE D 150 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N LYS D 223 " --> pdb=" O ARG D 247 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N GLN D 249 " --> pdb=" O LYS D 223 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ILE D 225 " --> pdb=" O GLN D 249 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ASN D 251 " --> pdb=" O ILE D 225 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N PHE D 227 " --> pdb=" O ASN D 251 " (cutoff:3.500A) 695 hydrogen bonds defined for protein. 2019 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: 4.64 Time building geometry restraints manager: 4.13 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: 4416 1.34 - 1.45: 1635 1.45 - 1.57: 8231 1.57 - 1.69: 0 1.69 - 1.81: 150 Bond restraints: 14432 Sorted by residual: bond pdb=" C MET D 158 " pdb=" N ILE D 159 " ideal model delta sigma weight residual 1.329 1.369 -0.040 1.13e-02 7.83e+03 1.27e+01 bond pdb=" CA MET D 158 " pdb=" C MET D 158 " ideal model delta sigma weight residual 1.531 1.487 0.044 1.35e-02 5.49e+03 1.06e+01 bond pdb=" CA ILE D 150 " pdb=" C ILE D 150 " ideal model delta sigma weight residual 1.522 1.488 0.033 1.27e-02 6.20e+03 6.83e+00 bond pdb=" N ILE D 150 " pdb=" CA ILE D 150 " ideal model delta sigma weight residual 1.458 1.429 0.029 1.21e-02 6.83e+03 5.84e+00 bond pdb=" CA ILE D 150 " pdb=" CB ILE D 150 " ideal model delta sigma weight residual 1.541 1.512 0.029 1.30e-02 5.92e+03 4.91e+00 ... (remaining 14427 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 19378 2.09 - 4.18: 158 4.18 - 6.27: 15 6.27 - 8.36: 2 8.36 - 10.45: 3 Bond angle restraints: 19556 Sorted by residual: angle pdb=" CA MET D 158 " pdb=" C MET D 158 " pdb=" O MET D 158 " ideal model delta sigma weight residual 120.71 111.92 8.79 1.34e+00 5.57e-01 4.31e+01 angle pdb=" N PRO D 152 " pdb=" CA PRO D 152 " pdb=" C PRO D 152 " ideal model delta sigma weight residual 111.11 121.42 -10.31 1.59e+00 3.96e-01 4.21e+01 angle pdb=" C MET D 158 " pdb=" CA MET D 158 " pdb=" CB MET D 158 " ideal model delta sigma weight residual 115.89 109.66 6.23 1.32e+00 5.74e-01 2.23e+01 angle pdb=" C PHE D 155 " pdb=" N PRO D 156 " pdb=" CA PRO D 156 " ideal model delta sigma weight residual 119.84 114.45 5.39 1.25e+00 6.40e-01 1.86e+01 angle pdb=" N MET D 158 " pdb=" CA MET D 158 " pdb=" C MET D 158 " ideal model delta sigma weight residual 109.02 102.41 6.61 1.68e+00 3.54e-01 1.55e+01 ... (remaining 19551 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 8475 17.11 - 34.22: 204 34.22 - 51.33: 43 51.33 - 68.45: 14 68.45 - 85.56: 7 Dihedral angle restraints: 8743 sinusoidal: 3465 harmonic: 5278 Sorted by residual: dihedral pdb=" C ILE D 150 " pdb=" N ILE D 150 " pdb=" CA ILE D 150 " pdb=" CB ILE D 150 " ideal model delta harmonic sigma weight residual -122.00 -114.15 -7.85 0 2.50e+00 1.60e-01 9.87e+00 dihedral pdb=" CB GLU A 103 " pdb=" CG GLU A 103 " pdb=" CD GLU A 103 " pdb=" OE1 GLU A 103 " ideal model delta sinusoidal sigma weight residual 0.00 85.56 -85.56 1 3.00e+01 1.11e-03 9.84e+00 dihedral pdb=" CB GLU A 18 " pdb=" CG GLU A 18 " pdb=" CD GLU A 18 " pdb=" OE1 GLU A 18 " ideal model delta sinusoidal sigma weight residual 0.00 -84.41 84.41 1 3.00e+01 1.11e-03 9.63e+00 ... (remaining 8740 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1901 0.060 - 0.121: 305 0.121 - 0.181: 14 0.181 - 0.242: 2 0.242 - 0.302: 1 Chirality restraints: 2223 Sorted by residual: chirality pdb=" CA PRO D 152 " pdb=" N PRO D 152 " pdb=" C PRO D 152 " pdb=" CB PRO D 152 " both_signs ideal model delta sigma weight residual False 2.72 2.42 0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CA ILE D 150 " pdb=" N ILE D 150 " pdb=" C ILE D 150 " pdb=" CB ILE D 150 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA MET D 158 " pdb=" N MET D 158 " pdb=" C MET D 158 " pdb=" CB MET D 158 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.27e-01 ... (remaining 2220 not shown) Planarity restraints: 2545 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 151 " -0.037 5.00e-02 4.00e+02 5.53e-02 4.89e+00 pdb=" N PRO D 152 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO D 152 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 152 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 155 " -0.031 5.00e-02 4.00e+02 4.74e-02 3.60e+00 pdb=" N PRO D 156 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO D 156 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 156 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET D 158 " -0.008 2.00e-02 2.50e+03 1.67e-02 2.78e+00 pdb=" C MET D 158 " 0.029 2.00e-02 2.50e+03 pdb=" O MET D 158 " -0.010 2.00e-02 2.50e+03 pdb=" N ILE D 159 " -0.010 2.00e-02 2.50e+03 ... (remaining 2542 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.05: 2 2.05 - 2.76: 2175 2.76 - 3.47: 21054 3.47 - 4.19: 34023 4.19 - 4.90: 61728 Nonbonded interactions: 118982 Sorted by model distance: nonbonded pdb=" CZ PHE D 155 " pdb=" CD1 PHE D 387 " model vdw 1.332 3.640 nonbonded pdb=" CZ PHE D 155 " pdb=" CE1 PHE D 387 " model vdw 1.944 3.640 nonbonded pdb=" ND2 ASN D 409 " pdb=" O TYR D 411 " model vdw 2.108 3.120 nonbonded pdb=" CE2 PHE D 155 " pdb=" CD1 PHE D 387 " model vdw 2.127 3.640 nonbonded pdb=" O LEU A 193 " pdb=" OG SER A 196 " model vdw 2.128 3.040 ... (remaining 118977 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 123 or resid 142 through 448 or resid 466 throug \ h 476)) selection = chain 'B' selection = (chain 'C' and (resid 3 through 123 or resid 142 through 448 or resid 466 throug \ h 476)) selection = (chain 'D' and (resid 3 through 123 or resid 142 through 448 or resid 466 throug \ h 476)) } 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: 1.580 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: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 33.510 Find NCS groups from input model: 0.650 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: 0.010 Load rotamer database and sin/cos tables:12.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 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 : 0.002 0.047 14432 Z= 0.147 Angle : 0.506 10.453 19556 Z= 0.290 Chirality : 0.042 0.302 2223 Planarity : 0.003 0.055 2545 Dihedral : 8.946 85.557 5351 Min Nonbonded Distance : 1.332 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.34 % Favored : 97.55 % Rotamer: Outliers : 0.46 % Allowed : 3.48 % Favored : 96.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.19), residues: 1839 helix: 1.17 (0.18), residues: 807 sheet: -0.75 (0.27), residues: 315 loop : -1.39 (0.23), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 162 HIS 0.002 0.000 HIS B 219 PHE 0.014 0.001 PHE D 155 TYR 0.007 0.001 TYR A 76 ARG 0.003 0.000 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3678 Ramachandran restraints generated. 1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3678 Ramachandran restraints generated. 1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 298 time to evaluate : 1.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6772 (pm20) REVERT: B 76 TYR cc_start: 0.6551 (t80) cc_final: 0.6258 (t80) REVERT: B 123 MET cc_start: 0.1737 (tmm) cc_final: 0.0419 (tpt) outliers start: 7 outliers final: 1 residues processed: 303 average time/residue: 1.3369 time to fit residues: 442.2982 Evaluate side-chains 165 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 163 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain C residue 433 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.7980 chunk 139 optimal weight: 0.4980 chunk 77 optimal weight: 0.7980 chunk 47 optimal weight: 10.0000 chunk 94 optimal weight: 9.9990 chunk 74 optimal weight: 0.4980 chunk 144 optimal weight: 9.9990 chunk 55 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 167 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN A 204 ASN A 210 HIS A 214 ASN A 272 GLN A 307 HIS ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 HIS A 476 GLN B 41 GLN B 209 GLN C 28 HIS C 251 ASN C 272 GLN ** C 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 365 ASN D 77 GLN D 115 HIS D 251 ASN ** D 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14432 Z= 0.202 Angle : 0.695 11.459 19556 Z= 0.334 Chirality : 0.046 0.179 2223 Planarity : 0.005 0.060 2545 Dihedral : 4.836 95.744 1956 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.50 % Favored : 97.39 % Rotamer: Outliers : 2.49 % Allowed : 10.83 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.20), residues: 1839 helix: 1.79 (0.18), residues: 817 sheet: -0.22 (0.27), residues: 327 loop : -0.72 (0.25), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 24 HIS 0.009 0.001 HIS A 115 PHE 0.032 0.002 PHE D 387 TYR 0.018 0.002 TYR D 76 ARG 0.009 0.001 ARG D 243 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3678 Ramachandran restraints generated. 1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3678 Ramachandran restraints generated. 1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 187 time to evaluate : 1.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 MET cc_start: 0.1949 (tmm) cc_final: 0.0549 (tpt) REVERT: D 413 ASN cc_start: 0.7273 (OUTLIER) cc_final: 0.6423 (p0) outliers start: 38 outliers final: 9 residues processed: 206 average time/residue: 1.3166 time to fit residues: 299.8865 Evaluate side-chains 157 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 147 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 381 CYS Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 164 PHE Chi-restraints excluded: chain D residue 413 ASN Chi-restraints excluded: chain D residue 445 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 139 optimal weight: 0.5980 chunk 113 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 167 optimal weight: 0.8980 chunk 180 optimal weight: 9.9990 chunk 149 optimal weight: 0.2980 chunk 165 optimal weight: 6.9990 chunk 57 optimal weight: 8.9990 chunk 134 optimal weight: 9.9990 overall best weight: 2.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 GLN B 219 HIS C 154 ASN C 268 ASN C 307 HIS ** C 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 472 GLN D 172 ASN D 256 ASN ** D 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14432 Z= 0.247 Angle : 0.639 11.621 19556 Z= 0.312 Chirality : 0.045 0.169 2223 Planarity : 0.004 0.053 2545 Dihedral : 3.901 17.409 1951 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.99 % Favored : 96.95 % Rotamer: Outliers : 2.36 % Allowed : 13.52 % Favored : 84.12 % 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: 1.05 (0.20), residues: 1839 helix: 2.00 (0.18), residues: 825 sheet: 0.08 (0.27), residues: 320 loop : -0.56 (0.25), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 162 HIS 0.011 0.001 HIS A 115 PHE 0.019 0.001 PHE D 164 TYR 0.022 0.002 TYR D 76 ARG 0.009 0.001 ARG D 414 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3678 Ramachandran restraints generated. 1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3678 Ramachandran restraints generated. 1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 161 time to evaluate : 1.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 MET cc_start: 0.2103 (tmm) cc_final: 0.0641 (tpt) REVERT: D 168 MET cc_start: 0.8079 (OUTLIER) cc_final: 0.7710 (mtp) outliers start: 36 outliers final: 16 residues processed: 185 average time/residue: 1.1796 time to fit residues: 242.4487 Evaluate side-chains 159 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 219 HIS Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 381 CYS Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 164 PHE Chi-restraints excluded: chain D residue 168 MET Chi-restraints excluded: chain D residue 252 MET Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 413 ASN Chi-restraints excluded: chain D residue 445 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 4.9990 chunk 125 optimal weight: 20.0000 chunk 86 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 112 optimal weight: 1.9990 chunk 167 optimal weight: 0.9990 chunk 177 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 159 optimal weight: 8.9990 chunk 47 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 GLN B 219 HIS C 436 GLN D 172 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14432 Z= 0.237 Angle : 0.646 14.225 19556 Z= 0.313 Chirality : 0.045 0.200 2223 Planarity : 0.004 0.085 2545 Dihedral : 3.981 18.175 1951 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.10 % Favored : 96.85 % Rotamer: Outliers : 2.69 % Allowed : 15.03 % Favored : 82.28 % 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: 1.21 (0.20), residues: 1839 helix: 2.04 (0.18), residues: 831 sheet: 0.31 (0.28), residues: 317 loop : -0.47 (0.25), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 24 HIS 0.012 0.001 HIS A 115 PHE 0.024 0.001 PHE B 164 TYR 0.028 0.002 TYR D 76 ARG 0.004 0.000 ARG D 414 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3678 Ramachandran restraints generated. 1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3678 Ramachandran restraints generated. 1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 154 time to evaluate : 1.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 107 PHE cc_start: 0.6525 (t80) cc_final: 0.5890 (t80) REVERT: B 123 MET cc_start: 0.2255 (tmm) cc_final: 0.0714 (tpt) outliers start: 41 outliers final: 18 residues processed: 179 average time/residue: 1.1564 time to fit residues: 230.4190 Evaluate side-chains 153 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 CYS Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 381 CYS Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 164 PHE Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 434 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 7.9990 chunk 100 optimal weight: 0.9990 chunk 2 optimal weight: 30.0000 chunk 132 optimal weight: 8.9990 chunk 73 optimal weight: 6.9990 chunk 151 optimal weight: 9.9990 chunk 122 optimal weight: 0.9990 chunk 0 optimal weight: 40.0000 chunk 90 optimal weight: 0.0570 chunk 159 optimal weight: 8.9990 chunk 44 optimal weight: 50.0000 overall best weight: 3.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 28 HIS ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 231 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14432 Z= 0.279 Angle : 0.660 12.545 19556 Z= 0.320 Chirality : 0.045 0.192 2223 Planarity : 0.004 0.095 2545 Dihedral : 4.088 16.074 1951 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.15 % Favored : 96.79 % Rotamer: Outliers : 2.49 % Allowed : 15.75 % Favored : 81.76 % 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: 1.24 (0.20), residues: 1839 helix: 2.01 (0.18), residues: 836 sheet: 0.43 (0.28), residues: 319 loop : -0.44 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 162 HIS 0.012 0.001 HIS A 115 PHE 0.023 0.002 PHE B 107 TYR 0.032 0.002 TYR D 76 ARG 0.003 0.000 ARG D 243 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3678 Ramachandran restraints generated. 1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3678 Ramachandran restraints generated. 1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 147 time to evaluate : 1.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 VAL cc_start: 0.7197 (OUTLIER) cc_final: 0.6982 (t) REVERT: B 123 MET cc_start: 0.2305 (tmm) cc_final: 0.0538 (tpt) REVERT: B 176 MET cc_start: 0.7444 (tpp) cc_final: 0.7049 (tpp) REVERT: C 164 PHE cc_start: 0.8033 (OUTLIER) cc_final: 0.7617 (t80) outliers start: 38 outliers final: 18 residues processed: 172 average time/residue: 1.0799 time to fit residues: 208.0151 Evaluate side-chains 152 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 2.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 413 ASN Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 164 PHE Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 381 CYS Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 164 PHE Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 445 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 2.9990 chunk 160 optimal weight: 10.0000 chunk 35 optimal weight: 0.2980 chunk 104 optimal weight: 5.9990 chunk 43 optimal weight: 0.4980 chunk 178 optimal weight: 6.9990 chunk 147 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 14 optimal weight: 20.0000 chunk 58 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN A 77 GLN ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 28 HIS ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14432 Z= 0.197 Angle : 0.672 13.736 19556 Z= 0.319 Chirality : 0.045 0.206 2223 Planarity : 0.005 0.094 2545 Dihedral : 4.133 20.463 1951 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.15 % Favored : 96.79 % Rotamer: Outliers : 2.69 % Allowed : 15.75 % Favored : 81.56 % 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: 1.27 (0.20), residues: 1839 helix: 1.99 (0.18), residues: 835 sheet: 0.55 (0.29), residues: 318 loop : -0.41 (0.25), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 162 HIS 0.013 0.001 HIS A 115 PHE 0.026 0.001 PHE B 164 TYR 0.033 0.002 TYR D 76 ARG 0.006 0.000 ARG A 312 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3678 Ramachandran restraints generated. 1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3678 Ramachandran restraints generated. 1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 151 time to evaluate : 1.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 MET cc_start: 0.2273 (tmm) cc_final: 0.0499 (tpt) REVERT: B 176 MET cc_start: 0.7427 (tpp) cc_final: 0.7197 (tpp) REVERT: B 411 TYR cc_start: 0.6264 (OUTLIER) cc_final: 0.6036 (p90) outliers start: 41 outliers final: 21 residues processed: 175 average time/residue: 1.0780 time to fit residues: 212.1994 Evaluate side-chains 156 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 285 CYS Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 411 TYR Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 381 CYS Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 164 PHE Chi-restraints excluded: chain D residue 252 MET Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 445 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 9.9990 chunk 20 optimal weight: 30.0000 chunk 101 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 100 optimal weight: 7.9990 chunk 149 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 177 optimal weight: 6.9990 chunk 110 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 28 HIS B 207 HIS ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.4276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14432 Z= 0.261 Angle : 0.710 14.508 19556 Z= 0.338 Chirality : 0.046 0.240 2223 Planarity : 0.005 0.100 2545 Dihedral : 4.250 25.471 1951 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.37 % Favored : 96.57 % Rotamer: Outliers : 2.69 % Allowed : 16.93 % Favored : 80.38 % 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: 1.26 (0.20), residues: 1839 helix: 2.03 (0.18), residues: 830 sheet: 0.58 (0.29), residues: 318 loop : -0.50 (0.25), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 162 HIS 0.003 0.001 HIS D 219 PHE 0.038 0.002 PHE B 164 TYR 0.039 0.002 TYR D 76 ARG 0.009 0.000 ARG A 312 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3678 Ramachandran restraints generated. 1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3678 Ramachandran restraints generated. 1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 145 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 MET cc_start: 0.2465 (tmm) cc_final: 0.2009 (tpt) REVERT: C 164 PHE cc_start: 0.8042 (OUTLIER) cc_final: 0.7620 (t80) outliers start: 41 outliers final: 21 residues processed: 173 average time/residue: 1.0508 time to fit residues: 204.2631 Evaluate side-chains 151 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 285 CYS Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 164 PHE Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 381 CYS Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 164 PHE Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 445 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 0.9980 chunk 70 optimal weight: 10.0000 chunk 105 optimal weight: 0.0370 chunk 53 optimal weight: 10.0000 chunk 34 optimal weight: 30.0000 chunk 112 optimal weight: 7.9990 chunk 120 optimal weight: 9.9990 chunk 87 optimal weight: 8.9990 chunk 16 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 161 optimal weight: 8.9990 overall best weight: 2.6064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN A 71 GLN ** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 28 HIS ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.4407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14432 Z= 0.251 Angle : 0.759 14.992 19556 Z= 0.356 Chirality : 0.046 0.216 2223 Planarity : 0.005 0.102 2545 Dihedral : 4.315 32.613 1951 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.94 % Favored : 96.95 % Rotamer: Outliers : 2.49 % Allowed : 17.45 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % 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: 1.17 (0.20), residues: 1839 helix: 1.97 (0.18), residues: 830 sheet: 0.52 (0.29), residues: 318 loop : -0.55 (0.25), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 162 HIS 0.008 0.001 HIS A 115 PHE 0.022 0.001 PHE D 164 TYR 0.041 0.002 TYR D 76 ARG 0.008 0.000 ARG A 312 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3678 Ramachandran restraints generated. 1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3678 Ramachandran restraints generated. 1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 139 time to evaluate : 1.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 MET cc_start: 0.2562 (tmm) cc_final: 0.2111 (tpt) REVERT: B 176 MET cc_start: 0.7468 (tpp) cc_final: 0.6966 (tpp) outliers start: 38 outliers final: 23 residues processed: 164 average time/residue: 1.0327 time to fit residues: 191.5332 Evaluate side-chains 153 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 285 CYS Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 381 CYS Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 164 PHE Chi-restraints excluded: chain D residue 381 CYS Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 445 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 4.9990 chunk 155 optimal weight: 0.9980 chunk 165 optimal weight: 3.9990 chunk 99 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 129 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 149 optimal weight: 8.9990 chunk 156 optimal weight: 0.8980 chunk 164 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN ** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 28 HIS ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.4544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 14432 Z= 0.232 Angle : 0.803 15.598 19556 Z= 0.371 Chirality : 0.046 0.221 2223 Planarity : 0.005 0.100 2545 Dihedral : 4.368 31.628 1951 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.43 % Favored : 96.52 % Rotamer: Outliers : 2.17 % Allowed : 18.24 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % 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: 1.09 (0.20), residues: 1839 helix: 1.93 (0.18), residues: 822 sheet: 0.54 (0.29), residues: 317 loop : -0.63 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 162 HIS 0.006 0.001 HIS A 115 PHE 0.040 0.002 PHE B 164 TYR 0.038 0.002 TYR D 76 ARG 0.007 0.000 ARG A 312 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3678 Ramachandran restraints generated. 1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3678 Ramachandran restraints generated. 1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 145 time to evaluate : 1.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 MET cc_start: 0.2663 (tmm) cc_final: 0.2241 (tpt) REVERT: B 176 MET cc_start: 0.7446 (tpp) cc_final: 0.7016 (tpp) outliers start: 33 outliers final: 23 residues processed: 169 average time/residue: 1.0485 time to fit residues: 200.4959 Evaluate side-chains 153 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 285 CYS Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 381 CYS Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 164 PHE Chi-restraints excluded: chain D residue 381 CYS Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 445 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 10.0000 chunk 106 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 121 optimal weight: 1.9990 chunk 183 optimal weight: 7.9990 chunk 168 optimal weight: 5.9990 chunk 145 optimal weight: 0.8980 chunk 15 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 115 optimal weight: 6.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN A 77 GLN ** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 ASN A 483 GLN B 28 HIS ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 476 GLN D 77 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 14432 Z= 0.340 Angle : 0.862 16.049 19556 Z= 0.401 Chirality : 0.048 0.256 2223 Planarity : 0.005 0.109 2545 Dihedral : 4.502 32.749 1951 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.70 % Favored : 96.19 % Rotamer: Outliers : 2.43 % Allowed : 18.31 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.20), residues: 1839 helix: 1.72 (0.18), residues: 829 sheet: 0.42 (0.29), residues: 311 loop : -0.66 (0.24), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 162 HIS 0.006 0.001 HIS A 115 PHE 0.036 0.002 PHE B 164 TYR 0.043 0.002 TYR D 76 ARG 0.008 0.001 ARG A 108 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3678 Ramachandran restraints generated. 1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3678 Ramachandran restraints generated. 1839 Oldfield, 0 Emsley, 1839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 140 time to evaluate : 1.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 MET cc_start: 0.2623 (tmm) cc_final: 0.2032 (tpt) REVERT: B 176 MET cc_start: 0.7524 (tpp) cc_final: 0.7012 (tpp) outliers start: 37 outliers final: 25 residues processed: 166 average time/residue: 1.0691 time to fit residues: 199.1985 Evaluate side-chains 154 residues out of total 1524 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 430 HIS Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 285 CYS Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 381 CYS Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 164 PHE Chi-restraints excluded: chain D residue 381 CYS Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 445 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 2.9990 chunk 44 optimal weight: 40.0000 chunk 134 optimal weight: 0.9980 chunk 21 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 146 optimal weight: 0.9990 chunk 61 optimal weight: 0.0980 chunk 150 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 128 optimal weight: 5.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN ** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 28 HIS ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 HIS ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 476 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.080608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.051889 restraints weight = 52226.842| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 4.59 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.4743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 14432 Z= 0.248 Angle : 0.855 16.347 19556 Z= 0.394 Chirality : 0.047 0.247 2223 Planarity : 0.005 0.102 2545 Dihedral : 4.432 23.955 1951 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.64 % Favored : 96.30 % Rotamer: Outliers : 1.97 % Allowed : 18.90 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.20), residues: 1839 helix: 1.71 (0.18), residues: 821 sheet: 0.41 (0.29), residues: 311 loop : -0.70 (0.24), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 162 HIS 0.006 0.001 HIS A 115 PHE 0.024 0.002 PHE C 164 TYR 0.039 0.002 TYR A 76 ARG 0.006 0.000 ARG A 312 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4518.95 seconds wall clock time: 82 minutes 54.21 seconds (4974.21 seconds total)