Starting phenix.real_space_refine on Wed Jun 18 15:49:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wfz_37500/06_2025/8wfz_37500.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wfz_37500/06_2025/8wfz_37500.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wfz_37500/06_2025/8wfz_37500.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wfz_37500/06_2025/8wfz_37500.map" model { file = "/net/cci-nas-00/data/ceres_data/8wfz_37500/06_2025/8wfz_37500.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wfz_37500/06_2025/8wfz_37500.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.018 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 100 5.16 5 C 13811 2.51 5 N 3542 2.21 5 O 3813 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21266 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 656, 5315 Classifications: {'peptide': 656} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 636} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 5315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 656, 5315 Classifications: {'peptide': 656} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 636} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 5321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 656, 5321 Classifications: {'peptide': 656} Link IDs: {'PTRANS': 19, 'TRANS': 636} Chain: "D" Number of atoms: 5315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 656, 5315 Classifications: {'peptide': 656} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 636} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 12.58, per 1000 atoms: 0.59 Number of scatterers: 21266 At special positions: 0 Unit cell: (113.42, 104.94, 186.56, 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 100 16.00 O 3813 8.00 N 3542 7.00 C 13811 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: 4.80 Conformation dependent library (CDL) restraints added in 2.9 seconds 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4920 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 8 sheets defined 69.9% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.19 Creating SS restraints... Processing helix chain 'A' and resid 62 through 89 removed outlier: 3.574A pdb=" N VAL A 74 " --> pdb=" O MET A 70 " (cutoff:3.500A) Proline residue: A 84 - end of helix Processing helix chain 'A' and resid 94 through 115 Processing helix chain 'A' and resid 131 through 139 removed outlier: 4.215A pdb=" N ILE A 135 " --> pdb=" O LYS A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 151 Processing helix chain 'A' and resid 154 through 162 Processing helix chain 'A' and resid 164 through 169 removed outlier: 3.835A pdb=" N ARG A 168 " --> pdb=" O HIS A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 176 removed outlier: 3.672A pdb=" N LEU A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 191 removed outlier: 3.594A pdb=" N VAL A 182 " --> pdb=" O VAL A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 226 removed outlier: 4.000A pdb=" N LEU A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 233 removed outlier: 4.259A pdb=" N GLY A 232 " --> pdb=" O GLU A 229 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR A 233 " --> pdb=" O ASN A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 270 removed outlier: 4.005A pdb=" N THR A 259 " --> pdb=" O TRP A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 313 removed outlier: 3.676A pdb=" N ILE A 310 " --> pdb=" O ILE A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 333 Processing helix chain 'A' and resid 336 through 364 removed outlier: 3.839A pdb=" N ARG A 340 " --> pdb=" O GLY A 336 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER A 341 " --> pdb=" O ARG A 337 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N GLN A 342 " --> pdb=" O ASP A 338 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ILE A 343 " --> pdb=" O LEU A 339 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN A 350 " --> pdb=" O HIS A 346 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N SER A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N HIS A 354 " --> pdb=" O GLN A 350 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N THR A 356 " --> pdb=" O ASP A 352 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ASP A 357 " --> pdb=" O SER A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 384 removed outlier: 3.655A pdb=" N LEU A 378 " --> pdb=" O GLN A 374 " (cutoff:3.500A) Proline residue: A 379 - end of helix Processing helix chain 'A' and resid 391 through 401 removed outlier: 4.148A pdb=" N ILE A 395 " --> pdb=" O SER A 391 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN A 396 " --> pdb=" O THR A 392 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLN A 397 " --> pdb=" O GLU A 393 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE A 398 " --> pdb=" O PHE A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 462 Processing helix chain 'A' and resid 482 through 492 Processing helix chain 'A' and resid 492 through 510 removed outlier: 4.037A pdb=" N GLU A 508 " --> pdb=" O MET A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 516 Processing helix chain 'A' and resid 516 through 542 removed outlier: 3.566A pdb=" N GLU A 528 " --> pdb=" O ILE A 524 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA A 529 " --> pdb=" O GLY A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 553 Processing helix chain 'A' and resid 566 through 575 Processing helix chain 'A' and resid 576 through 586 removed outlier: 3.743A pdb=" N THR A 580 " --> pdb=" O TYR A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 608 Processing helix chain 'A' and resid 609 through 620 removed outlier: 3.645A pdb=" N ILE A 613 " --> pdb=" O GLN A 609 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY A 620 " --> pdb=" O LEU A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 639 Processing helix chain 'A' and resid 640 through 651 Processing helix chain 'A' and resid 663 through 672 removed outlier: 3.944A pdb=" N VAL A 667 " --> pdb=" O THR A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 682 Processing helix chain 'A' and resid 696 through 705 removed outlier: 3.796A pdb=" N GLU A 700 " --> pdb=" O SER A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 713 removed outlier: 3.795A pdb=" N ILE A 710 " --> pdb=" O ASN A 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 90 removed outlier: 3.588A pdb=" N LYS B 66 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA B 67 " --> pdb=" O ARG B 63 " (cutoff:3.500A) Proline residue: B 84 - end of helix Processing helix chain 'B' and resid 94 through 116 Processing helix chain 'B' and resid 131 through 142 removed outlier: 4.244A pdb=" N SER B 142 " --> pdb=" O ARG B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 152 removed outlier: 3.932A pdb=" N MET B 146 " --> pdb=" O SER B 142 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP B 147 " --> pdb=" O HIS B 143 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE B 152 " --> pdb=" O PHE B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 161 removed outlier: 3.786A pdb=" N ILE B 157 " --> pdb=" O PRO B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 171 removed outlier: 3.971A pdb=" N ARG B 168 " --> pdb=" O HIS B 164 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR B 169 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 177 Processing helix chain 'B' and resid 178 through 187 Processing helix chain 'B' and resid 195 through 226 removed outlier: 4.054A pdb=" N LEU B 226 " --> pdb=" O LEU B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 239 removed outlier: 3.510A pdb=" N LEU B 239 " --> pdb=" O ILE B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 270 removed outlier: 3.593A pdb=" N ARG B 257 " --> pdb=" O ASP B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 312 removed outlier: 4.118A pdb=" N PHE B 287 " --> pdb=" O ARG B 283 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL B 297 " --> pdb=" O SER B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 333 removed outlier: 3.748A pdb=" N ARG B 318 " --> pdb=" O SER B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 363 removed outlier: 3.842A pdb=" N ARG B 340 " --> pdb=" O GLY B 336 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER B 341 " --> pdb=" O ARG B 337 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR B 351 " --> pdb=" O VAL B 347 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP B 352 " --> pdb=" O ARG B 348 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR B 356 " --> pdb=" O ASP B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 376 Processing helix chain 'B' and resid 376 through 384 removed outlier: 4.180A pdb=" N TYR B 380 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS B 383 " --> pdb=" O PRO B 379 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL B 384 " --> pdb=" O TYR B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 401 removed outlier: 3.743A pdb=" N ARG B 401 " --> pdb=" O GLN B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 462 Processing helix chain 'B' and resid 482 through 492 Processing helix chain 'B' and resid 492 through 510 Processing helix chain 'B' and resid 516 through 541 removed outlier: 3.862A pdb=" N GLN B 541 " --> pdb=" O SER B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 554 Processing helix chain 'B' and resid 566 through 575 Processing helix chain 'B' and resid 576 through 586 removed outlier: 3.629A pdb=" N ILE B 584 " --> pdb=" O THR B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 607 removed outlier: 3.528A pdb=" N ALA B 604 " --> pdb=" O PRO B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 619 Processing helix chain 'B' and resid 627 through 639 Processing helix chain 'B' and resid 640 through 650 Processing helix chain 'B' and resid 663 through 672 Processing helix chain 'B' and resid 673 through 683 Processing helix chain 'B' and resid 684 through 688 removed outlier: 3.779A pdb=" N ILE B 688 " --> pdb=" O ALA B 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 705 removed outlier: 3.547A pdb=" N GLU B 700 " --> pdb=" O SER B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 713 Processing helix chain 'C' and resid 62 through 89 Proline residue: C 84 - end of helix Processing helix chain 'C' and resid 94 through 116 removed outlier: 3.668A pdb=" N LEU C 100 " --> pdb=" O ARG C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 142 Processing helix chain 'C' and resid 143 through 152 Processing helix chain 'C' and resid 153 through 162 Processing helix chain 'C' and resid 164 through 170 removed outlier: 3.733A pdb=" N ARG C 168 " --> pdb=" O HIS C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 177 Processing helix chain 'C' and resid 178 through 191 Processing helix chain 'C' and resid 195 through 226 removed outlier: 4.340A pdb=" N LEU C 226 " --> pdb=" O LEU C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 244 removed outlier: 4.392A pdb=" N ASP C 243 " --> pdb=" O LYS C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 270 removed outlier: 3.628A pdb=" N ARG C 257 " --> pdb=" O ASP C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 313 removed outlier: 4.101A pdb=" N ILE C 286 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N PHE C 287 " --> pdb=" O ARG C 283 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL C 288 " --> pdb=" O GLU C 284 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N MET C 289 " --> pdb=" O MET C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 334 Processing helix chain 'C' and resid 336 through 360 removed outlier: 3.982A pdb=" N ASP C 352 " --> pdb=" O ARG C 348 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N SER C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N TYR C 355 " --> pdb=" O TYR C 351 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR C 356 " --> pdb=" O ASP C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 383 removed outlier: 3.999A pdb=" N LYS C 371 " --> pdb=" O SER C 367 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE C 372 " --> pdb=" O ILE C 368 " (cutoff:3.500A) Proline residue: C 379 - end of helix Processing helix chain 'C' and resid 384 through 388 Processing helix chain 'C' and resid 391 through 401 Processing helix chain 'C' and resid 455 through 462 Processing helix chain 'C' and resid 481 through 492 Processing helix chain 'C' and resid 492 through 510 removed outlier: 3.697A pdb=" N GLU C 508 " --> pdb=" O MET C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 542 Processing helix chain 'C' and resid 543 through 553 Processing helix chain 'C' and resid 566 through 575 removed outlier: 3.833A pdb=" N LEU C 570 " --> pdb=" O SER C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 587 removed outlier: 3.505A pdb=" N GLY C 587 " --> pdb=" O LEU C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 608 Processing helix chain 'C' and resid 609 through 620 removed outlier: 3.662A pdb=" N ILE C 613 " --> pdb=" O GLN C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 639 Processing helix chain 'C' and resid 640 through 651 removed outlier: 3.703A pdb=" N LEU C 644 " --> pdb=" O ASP C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 663 through 672 removed outlier: 4.089A pdb=" N VAL C 667 " --> pdb=" O THR C 663 " (cutoff:3.500A) Processing helix chain 'C' and resid 674 through 683 Processing helix chain 'C' and resid 696 through 705 removed outlier: 3.598A pdb=" N GLU C 700 " --> pdb=" O SER C 696 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 713 Processing helix chain 'D' and resid 62 through 88 removed outlier: 3.783A pdb=" N PHE D 71 " --> pdb=" O ALA D 67 " (cutoff:3.500A) Proline residue: D 84 - end of helix Processing helix chain 'D' and resid 94 through 117 removed outlier: 3.963A pdb=" N LEU D 100 " --> pdb=" O ARG D 96 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE D 117 " --> pdb=" O VAL D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 152 removed outlier: 3.603A pdb=" N ILE D 135 " --> pdb=" O LYS D 131 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS D 141 " --> pdb=" O PHE D 137 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LEU D 145 " --> pdb=" O LYS D 141 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N MET D 146 " --> pdb=" O SER D 142 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ILE D 149 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY D 150 " --> pdb=" O MET D 146 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE D 152 " --> pdb=" O PHE D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 161 Processing helix chain 'D' and resid 164 through 171 removed outlier: 3.531A pdb=" N ARG D 168 " --> pdb=" O HIS D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 176 Processing helix chain 'D' and resid 177 through 191 removed outlier: 4.017A pdb=" N VAL D 181 " --> pdb=" O ARG D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 226 removed outlier: 3.553A pdb=" N TYR D 220 " --> pdb=" O ALA D 216 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU D 226 " --> pdb=" O LEU D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 239 removed outlier: 3.627A pdb=" N LEU D 239 " --> pdb=" O ILE D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 270 Processing helix chain 'D' and resid 281 through 312 removed outlier: 3.538A pdb=" N PHE D 287 " --> pdb=" O ARG D 283 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL D 297 " --> pdb=" O SER D 293 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE D 310 " --> pdb=" O ILE D 306 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 334 Processing helix chain 'D' and resid 336 through 362 removed outlier: 4.079A pdb=" N SER D 341 " --> pdb=" O ARG D 337 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL D 359 " --> pdb=" O TYR D 355 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET D 360 " --> pdb=" O THR D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 384 removed outlier: 3.847A pdb=" N LYS D 371 " --> pdb=" O SER D 367 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE D 372 " --> pdb=" O ILE D 368 " (cutoff:3.500A) Proline residue: D 379 - end of helix removed outlier: 3.878A pdb=" N VAL D 384 " --> pdb=" O TYR D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 400 Processing helix chain 'D' and resid 455 through 461 Processing helix chain 'D' and resid 482 through 492 Processing helix chain 'D' and resid 492 through 507 Processing helix chain 'D' and resid 510 through 541 removed outlier: 5.047A pdb=" N SER D 518 " --> pdb=" O LYS D 514 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ASP D 519 " --> pdb=" O LYS D 515 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE D 520 " --> pdb=" O LEU D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 553 Processing helix chain 'D' and resid 566 through 575 Processing helix chain 'D' and resid 576 through 587 Processing helix chain 'D' and resid 599 through 608 removed outlier: 3.696A pdb=" N GLU D 603 " --> pdb=" O THR D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 609 through 620 removed outlier: 3.581A pdb=" N ILE D 613 " --> pdb=" O GLN D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 639 removed outlier: 3.806A pdb=" N CYS D 633 " --> pdb=" O GLY D 629 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR D 634 " --> pdb=" O ASN D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 650 Processing helix chain 'D' and resid 663 through 672 Processing helix chain 'D' and resid 673 through 684 Processing helix chain 'D' and resid 696 through 705 Processing helix chain 'D' and resid 706 through 713 Processing sheet with id=AA1, first strand: chain 'A' and resid 403 through 406 removed outlier: 6.485A pdb=" N HIS A 476 " --> pdb=" O CYS A 427 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR A 424 " --> pdb=" O PHE A 454 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 443 through 448 removed outlier: 6.185A pdb=" N SER A 444 " --> pdb=" O VAL A 435 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL A 435 " --> pdb=" O SER A 444 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR A 446 " --> pdb=" O ALA A 433 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 403 through 407 removed outlier: 3.572A pdb=" N HIS B 403 " --> pdb=" O ARG B 479 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N HIS B 476 " --> pdb=" O CYS B 427 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N THR B 452 " --> pdb=" O VAL B 426 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 446 through 448 removed outlier: 3.710A pdb=" N THR B 446 " --> pdb=" O ALA B 433 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 403 through 406 removed outlier: 6.565A pdb=" N HIS C 476 " --> pdb=" O CYS C 427 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 412 through 414 removed outlier: 7.735A pdb=" N VAL C 412 " --> pdb=" O VAL C 471 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N VAL C 471 " --> pdb=" O VAL C 412 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR C 414 " --> pdb=" O VAL C 469 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N THR C 446 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL C 435 " --> pdb=" O SER C 444 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N SER C 444 " --> pdb=" O VAL C 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 405 through 407 removed outlier: 6.320A pdb=" N HIS D 476 " --> pdb=" O CYS D 427 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR D 452 " --> pdb=" O VAL D 426 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 412 through 414 removed outlier: 5.994A pdb=" N VAL D 412 " --> pdb=" O VAL D 471 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N VAL D 471 " --> pdb=" O VAL D 412 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR D 414 " --> pdb=" O VAL D 469 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL D 469 " --> pdb=" O THR D 414 " (cutoff:3.500A) 1271 hydrogen bonds defined for protein. 3723 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: 6.89 Time building geometry restraints manager: 5.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4175 1.33 - 1.45: 5364 1.45 - 1.57: 12064 1.57 - 1.69: 0 1.69 - 1.82: 156 Bond restraints: 21759 Sorted by residual: bond pdb=" N PRO C 697 " pdb=" CD PRO C 697 " ideal model delta sigma weight residual 1.473 1.415 0.058 1.40e-02 5.10e+03 1.73e+01 bond pdb=" C SER C 696 " pdb=" N PRO C 697 " ideal model delta sigma weight residual 1.335 1.388 -0.053 1.28e-02 6.10e+03 1.72e+01 bond pdb=" N LYS B 515 " pdb=" CA LYS B 515 " ideal model delta sigma weight residual 1.453 1.498 -0.045 1.22e-02 6.72e+03 1.34e+01 bond pdb=" N GLU B 189 " pdb=" CA GLU B 189 " ideal model delta sigma weight residual 1.454 1.499 -0.045 1.31e-02 5.83e+03 1.19e+01 bond pdb=" N LEU A 339 " pdb=" CA LEU A 339 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.17e-02 7.31e+03 1.05e+01 ... (remaining 21754 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 28485 2.33 - 4.65: 794 4.65 - 6.98: 129 6.98 - 9.30: 23 9.30 - 11.63: 2 Bond angle restraints: 29433 Sorted by residual: angle pdb=" N GLU A 393 " pdb=" CA GLU A 393 " pdb=" C GLU A 393 " ideal model delta sigma weight residual 111.07 101.10 9.97 1.07e+00 8.73e-01 8.69e+01 angle pdb=" N GLN D 186 " pdb=" CA GLN D 186 " pdb=" C GLN D 186 " ideal model delta sigma weight residual 111.28 102.69 8.59 1.09e+00 8.42e-01 6.21e+01 angle pdb=" N VAL B 359 " pdb=" CA VAL B 359 " pdb=" C VAL B 359 " ideal model delta sigma weight residual 110.62 117.89 -7.27 1.02e+00 9.61e-01 5.07e+01 angle pdb=" N GLU D 95 " pdb=" CA GLU D 95 " pdb=" C GLU D 95 " ideal model delta sigma weight residual 111.82 103.68 8.14 1.16e+00 7.43e-01 4.92e+01 angle pdb=" N LEU C 326 " pdb=" CA LEU C 326 " pdb=" C LEU C 326 " ideal model delta sigma weight residual 111.28 103.73 7.55 1.09e+00 8.42e-01 4.80e+01 ... (remaining 29428 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 11586 17.75 - 35.50: 1085 35.50 - 53.24: 171 53.24 - 70.99: 27 70.99 - 88.74: 22 Dihedral angle restraints: 12891 sinusoidal: 5227 harmonic: 7664 Sorted by residual: dihedral pdb=" C ASP B 511 " pdb=" N ASP B 511 " pdb=" CA ASP B 511 " pdb=" CB ASP B 511 " ideal model delta harmonic sigma weight residual -122.60 -136.45 13.85 0 2.50e+00 1.60e-01 3.07e+01 dihedral pdb=" N ASP B 511 " pdb=" C ASP B 511 " pdb=" CA ASP B 511 " pdb=" CB ASP B 511 " ideal model delta harmonic sigma weight residual 122.80 135.04 -12.24 0 2.50e+00 1.60e-01 2.40e+01 dihedral pdb=" C VAL B 359 " pdb=" N VAL B 359 " pdb=" CA VAL B 359 " pdb=" CB VAL B 359 " ideal model delta harmonic sigma weight residual -122.00 -134.15 12.15 0 2.50e+00 1.60e-01 2.36e+01 ... (remaining 12888 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 2988 0.088 - 0.176: 242 0.176 - 0.264: 37 0.264 - 0.352: 16 0.352 - 0.440: 5 Chirality restraints: 3288 Sorted by residual: chirality pdb=" CA ASP B 511 " pdb=" N ASP B 511 " pdb=" C ASP B 511 " pdb=" CB ASP B 511 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.84e+00 chirality pdb=" CA ASP B 691 " pdb=" N ASP B 691 " pdb=" C ASP B 691 " pdb=" CB ASP B 691 " both_signs ideal model delta sigma weight residual False 2.51 2.95 -0.44 2.00e-01 2.50e+01 4.81e+00 chirality pdb=" CA THR D 436 " pdb=" N THR D 436 " pdb=" C THR D 436 " pdb=" CB THR D 436 " both_signs ideal model delta sigma weight residual False 2.53 2.95 -0.42 2.00e-01 2.50e+01 4.48e+00 ... (remaining 3285 not shown) Planarity restraints: 3705 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 190 " -0.019 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C LYS B 190 " 0.067 2.00e-02 2.50e+03 pdb=" O LYS B 190 " -0.025 2.00e-02 2.50e+03 pdb=" N ASP B 191 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 337 " 0.016 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C ARG A 337 " -0.055 2.00e-02 2.50e+03 pdb=" O ARG A 337 " 0.021 2.00e-02 2.50e+03 pdb=" N ASP A 338 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 252 " 0.014 2.00e-02 2.50e+03 2.90e-02 8.41e+00 pdb=" C ILE D 252 " -0.050 2.00e-02 2.50e+03 pdb=" O ILE D 252 " 0.019 2.00e-02 2.50e+03 pdb=" N ASP D 253 " 0.017 2.00e-02 2.50e+03 ... (remaining 3702 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 285 2.63 - 3.20: 21796 3.20 - 3.77: 35672 3.77 - 4.33: 46983 4.33 - 4.90: 72463 Nonbonded interactions: 177199 Sorted by model distance: nonbonded pdb=" O ASN B 558 " pdb=" OD1 ASN B 558 " model vdw 2.063 3.040 nonbonded pdb=" O TYR B 221 " pdb=" OG1 THR B 224 " model vdw 2.195 3.040 nonbonded pdb=" O TYR A 196 " pdb=" OG1 THR A 199 " model vdw 2.199 3.040 nonbonded pdb=" NH1 ARG A 369 " pdb=" O ILE A 400 " model vdw 2.199 3.120 nonbonded pdb=" OE1 GLU A 528 " pdb=" NZ LYS A 559 " model vdw 2.208 3.120 ... (remaining 177194 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' selection = chain 'B' selection = (chain 'C' and (resid 58 through 352 or (resid 353 through 354 and (name N or na \ me CA or name C or name O or name CB )) or resid 355 through 713)) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 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: 0.800 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 46.980 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 21759 Z= 0.325 Angle : 0.893 11.626 29433 Z= 0.570 Chirality : 0.058 0.440 3288 Planarity : 0.005 0.069 3705 Dihedral : 13.955 88.738 7971 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 22.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.56 % Allowed : 0.95 % Favored : 98.48 % Cbeta Deviations : 0.20 % 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: 1.10 (0.16), residues: 2616 helix: 1.31 (0.12), residues: 1691 sheet: 1.09 (0.49), residues: 110 loop : -0.46 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 68 HIS 0.011 0.002 HIS C 278 PHE 0.039 0.002 PHE C 319 TYR 0.034 0.002 TYR D 139 ARG 0.013 0.001 ARG D 401 Details of bonding type rmsd hydrogen bonds : bond 0.16292 ( 1271) hydrogen bonds : angle 6.38074 ( 3723) covalent geometry : bond 0.00550 (21759) covalent geometry : angle 0.89321 (29433) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 347 time to evaluate : 2.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TRP cc_start: 0.8104 (t-100) cc_final: 0.7864 (t-100) REVERT: A 81 LEU cc_start: 0.8655 (tp) cc_final: 0.8165 (tp) REVERT: A 101 ASP cc_start: 0.9126 (t70) cc_final: 0.8924 (t0) REVERT: A 148 PHE cc_start: 0.8902 (p90) cc_final: 0.8424 (p90) REVERT: A 342 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.8246 (pm20) REVERT: B 197 LEU cc_start: 0.9016 (mt) cc_final: 0.8666 (mt) REVERT: B 208 GLU cc_start: 0.7474 (mm-30) cc_final: 0.6950 (mm-30) REVERT: B 296 MET cc_start: 0.8649 (mtp) cc_final: 0.8217 (mtt) REVERT: B 298 LEU cc_start: 0.8963 (tp) cc_final: 0.8653 (tp) REVERT: B 321 ASP cc_start: 0.9320 (m-30) cc_final: 0.9061 (m-30) REVERT: B 330 MET cc_start: 0.8501 (ttt) cc_final: 0.8290 (ttt) REVERT: B 688 ILE cc_start: 0.6904 (OUTLIER) cc_final: 0.6339 (mp) REVERT: C 307 THR cc_start: 0.9452 (m) cc_final: 0.9185 (p) REVERT: C 321 ASP cc_start: 0.9457 (t70) cc_final: 0.9150 (m-30) REVERT: C 327 ILE cc_start: 0.9436 (OUTLIER) cc_final: 0.9024 (mm) REVERT: C 330 MET cc_start: 0.9528 (tmm) cc_final: 0.8653 (ppp) REVERT: C 351 TYR cc_start: 0.8820 (t80) cc_final: 0.8468 (t80) REVERT: C 355 TYR cc_start: 0.8864 (p90) cc_final: 0.8576 (p90) REVERT: C 506 GLU cc_start: 0.9223 (tp30) cc_final: 0.8970 (tp30) REVERT: C 661 HIS cc_start: 0.7920 (t70) cc_final: 0.7498 (t-90) REVERT: D 146 MET cc_start: 0.8931 (mmt) cc_final: 0.8625 (mpp) REVERT: D 264 PHE cc_start: 0.8085 (t80) cc_final: 0.7750 (t80) outliers start: 13 outliers final: 1 residues processed: 358 average time/residue: 0.3146 time to fit residues: 174.9840 Evaluate side-chains 236 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 232 time to evaluate : 2.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 219 optimal weight: 0.9990 chunk 197 optimal weight: 5.9990 chunk 109 optimal weight: 7.9990 chunk 67 optimal weight: 8.9990 chunk 132 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 203 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 123 optimal weight: 7.9990 chunk 151 optimal weight: 6.9990 chunk 236 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN A 591 ASN B 416 GLN C 195 ASN C 523 HIS ** D 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.078365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.053845 restraints weight = 135215.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.055611 restraints weight = 74697.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.056707 restraints weight = 49116.329| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 21759 Z= 0.177 Angle : 0.636 8.937 29433 Z= 0.344 Chirality : 0.041 0.167 3288 Planarity : 0.005 0.046 3705 Dihedral : 4.573 21.890 2888 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.30 % Allowed : 5.58 % Favored : 94.11 % 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: 0.96 (0.16), residues: 2616 helix: 1.21 (0.12), residues: 1734 sheet: 1.20 (0.53), residues: 98 loop : -0.64 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 68 HIS 0.008 0.001 HIS A 661 PHE 0.030 0.002 PHE A 148 TYR 0.027 0.002 TYR B 351 ARG 0.008 0.001 ARG B 702 Details of bonding type rmsd hydrogen bonds : bond 0.05166 ( 1271) hydrogen bonds : angle 5.08462 ( 3723) covalent geometry : bond 0.00370 (21759) covalent geometry : angle 0.63618 (29433) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 302 time to evaluate : 2.791 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: A 68 TRP cc_start: 0.8717 (t-100) cc_final: 0.8049 (t-100) REVERT: A 81 LEU cc_start: 0.9080 (tp) cc_final: 0.8565 (tp) REVERT: A 85 MET cc_start: 0.9289 (ptp) cc_final: 0.9040 (ptt) REVERT: A 101 ASP cc_start: 0.9400 (t70) cc_final: 0.9151 (t0) REVERT: A 114 LEU cc_start: 0.9178 (mm) cc_final: 0.8946 (mm) REVERT: A 148 PHE cc_start: 0.9234 (p90) cc_final: 0.8857 (p90) REVERT: A 154 TRP cc_start: 0.8651 (m100) cc_final: 0.8335 (m100) REVERT: A 264 PHE cc_start: 0.9114 (t80) cc_final: 0.8557 (t80) REVERT: A 284 GLU cc_start: 0.8863 (mp0) cc_final: 0.8487 (mt-10) REVERT: A 285 MET cc_start: 0.9595 (tpp) cc_final: 0.9263 (mmm) REVERT: B 287 PHE cc_start: 0.9169 (t80) cc_final: 0.8924 (t80) REVERT: B 298 LEU cc_start: 0.9684 (tp) cc_final: 0.9419 (tp) REVERT: B 652 MET cc_start: 0.6530 (ppp) cc_final: 0.6171 (ppp) REVERT: C 81 LEU cc_start: 0.9336 (tp) cc_final: 0.9048 (tp) REVERT: C 154 TRP cc_start: 0.8807 (m100) cc_final: 0.8600 (m100) REVERT: C 294 PHE cc_start: 0.9369 (t80) cc_final: 0.9097 (t80) REVERT: C 296 MET cc_start: 0.9300 (tmm) cc_final: 0.9005 (tmm) REVERT: C 307 THR cc_start: 0.9703 (m) cc_final: 0.9440 (p) REVERT: C 321 ASP cc_start: 0.9559 (t70) cc_final: 0.9213 (m-30) REVERT: C 330 MET cc_start: 0.9496 (tmm) cc_final: 0.9002 (ppp) REVERT: C 351 TYR cc_start: 0.8973 (t80) cc_final: 0.8750 (t80) REVERT: C 407 PHE cc_start: 0.8836 (m-10) cc_final: 0.8429 (m-80) REVERT: C 477 LEU cc_start: 0.9357 (mp) cc_final: 0.9071 (mp) REVERT: C 506 GLU cc_start: 0.9291 (tp30) cc_final: 0.8998 (tp30) REVERT: C 661 HIS cc_start: 0.7786 (t70) cc_final: 0.7483 (t-90) REVERT: D 86 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8127 (pm20) REVERT: D 146 MET cc_start: 0.9066 (mmt) cc_final: 0.8545 (mpp) REVERT: D 199 THR cc_start: 0.9092 (m) cc_final: 0.8768 (p) REVERT: D 205 LEU cc_start: 0.9615 (tt) cc_final: 0.9404 (pp) REVERT: D 264 PHE cc_start: 0.9355 (t80) cc_final: 0.8842 (t80) REVERT: D 285 MET cc_start: 0.9388 (tpp) cc_final: 0.9127 (tpp) REVERT: D 291 TYR cc_start: 0.9332 (t80) cc_final: 0.8888 (t80) REVERT: D 296 MET cc_start: 0.9504 (ttp) cc_final: 0.9303 (ttp) REVERT: D 330 MET cc_start: 0.9255 (tpt) cc_final: 0.8911 (tpt) REVERT: D 360 MET cc_start: 0.9361 (ptp) cc_final: 0.8954 (ppp) outliers start: 7 outliers final: 3 residues processed: 308 average time/residue: 0.3551 time to fit residues: 173.4732 Evaluate side-chains 226 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 222 time to evaluate : 2.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 92 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 191 optimal weight: 30.0000 chunk 58 optimal weight: 9.9990 chunk 80 optimal weight: 2.9990 chunk 209 optimal weight: 0.9980 chunk 171 optimal weight: 10.0000 chunk 71 optimal weight: 0.5980 chunk 258 optimal weight: 0.0570 chunk 97 optimal weight: 20.0000 chunk 216 optimal weight: 0.9980 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN A 591 ASN ** B 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 541 GLN C 630 ASN ** D 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.095574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.079092 restraints weight = 160809.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.080720 restraints weight = 74628.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.081554 restraints weight = 43532.241| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21759 Z= 0.129 Angle : 0.598 7.619 29433 Z= 0.315 Chirality : 0.040 0.214 3288 Planarity : 0.004 0.049 3705 Dihedral : 4.498 19.214 2888 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.09 % Allowed : 3.90 % Favored : 96.02 % 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: 0.86 (0.16), residues: 2616 helix: 1.15 (0.12), residues: 1726 sheet: 1.15 (0.55), residues: 92 loop : -0.67 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 68 HIS 0.005 0.001 HIS A 476 PHE 0.026 0.001 PHE A 319 TYR 0.028 0.002 TYR C 246 ARG 0.010 0.001 ARG C 369 Details of bonding type rmsd hydrogen bonds : bond 0.04703 ( 1271) hydrogen bonds : angle 4.74509 ( 3723) covalent geometry : bond 0.00262 (21759) covalent geometry : angle 0.59760 (29433) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 308 time to evaluate : 2.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TRP cc_start: 0.8743 (t-100) cc_final: 0.8171 (t-100) REVERT: A 81 LEU cc_start: 0.9217 (tp) cc_final: 0.8787 (tp) REVERT: A 85 MET cc_start: 0.9246 (ptp) cc_final: 0.9022 (ptt) REVERT: A 101 ASP cc_start: 0.9305 (t70) cc_final: 0.9055 (t0) REVERT: A 114 LEU cc_start: 0.9129 (mm) cc_final: 0.8920 (mm) REVERT: A 148 PHE cc_start: 0.9164 (p90) cc_final: 0.8780 (p90) REVERT: A 154 TRP cc_start: 0.8603 (m100) cc_final: 0.8216 (m100) REVERT: A 266 ILE cc_start: 0.9786 (mm) cc_final: 0.9480 (mm) REVERT: A 284 GLU cc_start: 0.8766 (mp0) cc_final: 0.8494 (mt-10) REVERT: A 406 TYR cc_start: 0.9078 (m-80) cc_final: 0.8782 (m-80) REVERT: B 78 TYR cc_start: 0.9424 (t80) cc_final: 0.9190 (t80) REVERT: B 183 GLU cc_start: 0.9244 (tp30) cc_final: 0.8782 (tp30) REVERT: B 208 GLU cc_start: 0.9355 (mm-30) cc_final: 0.9075 (mm-30) REVERT: B 287 PHE cc_start: 0.9153 (t80) cc_final: 0.8825 (t80) REVERT: B 676 MET cc_start: 0.8209 (mtt) cc_final: 0.7776 (mtt) REVERT: C 154 TRP cc_start: 0.8741 (m100) cc_final: 0.8533 (m100) REVERT: C 294 PHE cc_start: 0.9245 (t80) cc_final: 0.8993 (t80) REVERT: C 296 MET cc_start: 0.9320 (tmm) cc_final: 0.9047 (tmm) REVERT: C 307 THR cc_start: 0.9637 (m) cc_final: 0.9348 (p) REVERT: C 321 ASP cc_start: 0.9502 (t70) cc_final: 0.9205 (m-30) REVERT: C 322 LYS cc_start: 0.9694 (pttp) cc_final: 0.9485 (pptt) REVERT: C 323 MET cc_start: 0.9730 (ptm) cc_final: 0.9365 (ptm) REVERT: C 326 LEU cc_start: 0.9382 (mt) cc_final: 0.9139 (mt) REVERT: C 330 MET cc_start: 0.9457 (tmm) cc_final: 0.8916 (ppp) REVERT: C 351 TYR cc_start: 0.9286 (t80) cc_final: 0.8659 (t80) REVERT: C 355 TYR cc_start: 0.9194 (p90) cc_final: 0.8958 (p90) REVERT: C 407 PHE cc_start: 0.8728 (m-10) cc_final: 0.8136 (m-80) REVERT: C 506 GLU cc_start: 0.9184 (tp30) cc_final: 0.8904 (tp30) REVERT: C 661 HIS cc_start: 0.7904 (t70) cc_final: 0.7631 (t-90) REVERT: D 146 MET cc_start: 0.8999 (mmt) cc_final: 0.8522 (mpp) REVERT: D 199 THR cc_start: 0.8937 (m) cc_final: 0.8674 (p) REVERT: D 205 LEU cc_start: 0.9593 (tt) cc_final: 0.9349 (pp) REVERT: D 264 PHE cc_start: 0.9445 (t80) cc_final: 0.8868 (t80) REVERT: D 291 TYR cc_start: 0.9116 (t80) cc_final: 0.8762 (t80) REVERT: D 303 ILE cc_start: 0.9819 (mm) cc_final: 0.9605 (tp) REVERT: D 330 MET cc_start: 0.9217 (tpt) cc_final: 0.8934 (tpt) REVERT: D 360 MET cc_start: 0.9278 (ptp) cc_final: 0.8806 (ppp) outliers start: 2 outliers final: 0 residues processed: 310 average time/residue: 0.3591 time to fit residues: 179.7970 Evaluate side-chains 235 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 2.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 40 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 chunk 78 optimal weight: 0.0570 chunk 126 optimal weight: 6.9990 chunk 180 optimal weight: 7.9990 chunk 124 optimal weight: 30.0000 chunk 137 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 90 optimal weight: 0.9990 chunk 203 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 591 ASN B 278 HIS D 105 GLN D 305 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.094886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.078403 restraints weight = 163302.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.079885 restraints weight = 75836.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.080818 restraints weight = 43734.904| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21759 Z= 0.128 Angle : 0.584 9.182 29433 Z= 0.308 Chirality : 0.039 0.189 3288 Planarity : 0.004 0.051 3705 Dihedral : 4.441 17.669 2888 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.09 % Allowed : 4.16 % Favored : 95.76 % 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: 0.82 (0.16), residues: 2616 helix: 1.13 (0.12), residues: 1735 sheet: 1.20 (0.53), residues: 98 loop : -0.76 (0.21), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 68 HIS 0.006 0.001 HIS B 278 PHE 0.038 0.001 PHE B 582 TYR 0.025 0.001 TYR D 139 ARG 0.012 0.000 ARG B 565 Details of bonding type rmsd hydrogen bonds : bond 0.04388 ( 1271) hydrogen bonds : angle 4.64992 ( 3723) covalent geometry : bond 0.00270 (21759) covalent geometry : angle 0.58412 (29433) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 301 time to evaluate : 2.291 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: A 68 TRP cc_start: 0.8746 (t-100) cc_final: 0.8109 (t-100) REVERT: A 81 LEU cc_start: 0.9179 (tp) cc_final: 0.8698 (tp) REVERT: A 85 MET cc_start: 0.9192 (ptp) cc_final: 0.8942 (ptt) REVERT: A 101 ASP cc_start: 0.9289 (t70) cc_final: 0.9038 (t0) REVERT: A 148 PHE cc_start: 0.9120 (p90) cc_final: 0.8725 (p90) REVERT: A 183 GLU cc_start: 0.9198 (mp0) cc_final: 0.8874 (mp0) REVERT: A 264 PHE cc_start: 0.9107 (t80) cc_final: 0.8884 (t80) REVERT: A 266 ILE cc_start: 0.9809 (mm) cc_final: 0.9514 (mm) REVERT: A 406 TYR cc_start: 0.9022 (m-80) cc_final: 0.8781 (m-80) REVERT: B 78 TYR cc_start: 0.9373 (t80) cc_final: 0.9155 (t80) REVERT: B 183 GLU cc_start: 0.9222 (tp30) cc_final: 0.8798 (tp30) REVERT: B 321 ASP cc_start: 0.9356 (m-30) cc_final: 0.9122 (m-30) REVERT: B 330 MET cc_start: 0.8628 (ttt) cc_final: 0.8328 (ttt) REVERT: B 647 LEU cc_start: 0.9467 (tp) cc_final: 0.9199 (tp) REVERT: B 676 MET cc_start: 0.8109 (mtt) cc_final: 0.7675 (mtt) REVERT: C 154 TRP cc_start: 0.8757 (m100) cc_final: 0.8557 (m100) REVERT: C 289 MET cc_start: 0.9519 (mmt) cc_final: 0.9177 (mmt) REVERT: C 294 PHE cc_start: 0.9253 (t80) cc_final: 0.9012 (t80) REVERT: C 296 MET cc_start: 0.9348 (tmm) cc_final: 0.9119 (tmm) REVERT: C 307 THR cc_start: 0.9627 (m) cc_final: 0.9332 (p) REVERT: C 321 ASP cc_start: 0.9450 (t70) cc_final: 0.9191 (m-30) REVERT: C 322 LYS cc_start: 0.9679 (pttp) cc_final: 0.9456 (pptt) REVERT: C 323 MET cc_start: 0.9740 (ptm) cc_final: 0.9411 (ptm) REVERT: C 326 LEU cc_start: 0.9354 (mt) cc_final: 0.9089 (mt) REVERT: C 351 TYR cc_start: 0.9258 (t80) cc_final: 0.8722 (t80) REVERT: C 407 PHE cc_start: 0.8658 (m-10) cc_final: 0.8084 (m-80) REVERT: C 506 GLU cc_start: 0.9153 (tp30) cc_final: 0.8874 (tp30) REVERT: C 585 GLN cc_start: 0.9468 (OUTLIER) cc_final: 0.9099 (pp30) REVERT: C 661 HIS cc_start: 0.7926 (t70) cc_final: 0.7614 (t-90) REVERT: D 146 MET cc_start: 0.9007 (mmt) cc_final: 0.8556 (mpp) REVERT: D 199 THR cc_start: 0.8960 (m) cc_final: 0.8719 (p) REVERT: D 264 PHE cc_start: 0.9473 (t80) cc_final: 0.8890 (t80) REVERT: D 291 TYR cc_start: 0.9123 (t80) cc_final: 0.8779 (t80) REVERT: D 296 MET cc_start: 0.9499 (ttp) cc_final: 0.9268 (ttp) REVERT: D 303 ILE cc_start: 0.9801 (mm) cc_final: 0.9589 (tp) REVERT: D 330 MET cc_start: 0.9181 (tpt) cc_final: 0.8801 (tpt) REVERT: D 360 MET cc_start: 0.9211 (ptp) cc_final: 0.8781 (ppp) outliers start: 2 outliers final: 0 residues processed: 303 average time/residue: 0.2950 time to fit residues: 142.7804 Evaluate side-chains 228 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 227 time to evaluate : 2.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 63 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 173 optimal weight: 8.9990 chunk 163 optimal weight: 4.9990 chunk 143 optimal weight: 8.9990 chunk 79 optimal weight: 0.9980 chunk 90 optimal weight: 9.9990 chunk 164 optimal weight: 6.9990 chunk 175 optimal weight: 9.9990 chunk 86 optimal weight: 6.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 ASN ** A 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 591 ASN ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 HIS ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.077118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.052852 restraints weight = 141067.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.054536 restraints weight = 76675.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.055610 restraints weight = 50314.420| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21759 Z= 0.200 Angle : 0.638 11.473 29433 Z= 0.340 Chirality : 0.040 0.173 3288 Planarity : 0.004 0.049 3705 Dihedral : 4.548 18.011 2888 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 19.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.04 % Allowed : 2.90 % Favored : 97.06 % 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: 0.79 (0.16), residues: 2616 helix: 1.12 (0.12), residues: 1731 sheet: 1.07 (0.51), residues: 96 loop : -0.78 (0.21), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 68 HIS 0.014 0.001 HIS D 143 PHE 0.021 0.002 PHE A 319 TYR 0.027 0.002 TYR D 355 ARG 0.010 0.001 ARG C 497 Details of bonding type rmsd hydrogen bonds : bond 0.04456 ( 1271) hydrogen bonds : angle 4.80844 ( 3723) covalent geometry : bond 0.00417 (21759) covalent geometry : angle 0.63775 (29433) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 276 time to evaluate : 2.447 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: A 68 TRP cc_start: 0.8820 (t-100) cc_final: 0.8212 (t-100) REVERT: A 81 LEU cc_start: 0.9111 (tp) cc_final: 0.8588 (tp) REVERT: A 85 MET cc_start: 0.9252 (ptp) cc_final: 0.8995 (ptt) REVERT: A 101 ASP cc_start: 0.9423 (t70) cc_final: 0.9206 (t0) REVERT: A 148 PHE cc_start: 0.9280 (p90) cc_final: 0.8852 (p90) REVERT: A 154 TRP cc_start: 0.8813 (m100) cc_final: 0.8305 (m100) REVERT: A 296 MET cc_start: 0.9446 (tpp) cc_final: 0.9054 (tpp) REVERT: A 406 TYR cc_start: 0.9211 (m-80) cc_final: 0.8933 (m-80) REVERT: B 78 TYR cc_start: 0.9427 (t80) cc_final: 0.9180 (t80) REVERT: B 111 ASP cc_start: 0.9420 (t70) cc_final: 0.9215 (t70) REVERT: B 183 GLU cc_start: 0.9262 (tp30) cc_final: 0.8867 (tp30) REVERT: B 208 GLU cc_start: 0.9271 (mm-30) cc_final: 0.8931 (mm-30) REVERT: B 652 MET cc_start: 0.6855 (mmt) cc_final: 0.5968 (ppp) REVERT: B 676 MET cc_start: 0.8363 (mtt) cc_final: 0.7918 (mtt) REVERT: C 154 TRP cc_start: 0.8793 (m100) cc_final: 0.8525 (m100) REVERT: C 294 PHE cc_start: 0.9376 (t80) cc_final: 0.9165 (t80) REVERT: C 296 MET cc_start: 0.9478 (tmm) cc_final: 0.9226 (tmm) REVERT: C 307 THR cc_start: 0.9697 (m) cc_final: 0.9439 (p) REVERT: C 321 ASP cc_start: 0.9589 (t70) cc_final: 0.9259 (m-30) REVERT: C 351 TYR cc_start: 0.9099 (t80) cc_final: 0.8733 (t80) REVERT: C 407 PHE cc_start: 0.8920 (m-10) cc_final: 0.8297 (m-80) REVERT: C 506 GLU cc_start: 0.9333 (tp30) cc_final: 0.9077 (tp30) REVERT: C 661 HIS cc_start: 0.7943 (t70) cc_final: 0.7679 (t-90) REVERT: D 146 MET cc_start: 0.8985 (mmt) cc_final: 0.8540 (mpp) REVERT: D 264 PHE cc_start: 0.9460 (t80) cc_final: 0.9085 (t80) REVERT: D 285 MET cc_start: 0.9005 (tpp) cc_final: 0.8488 (tpp) REVERT: D 291 TYR cc_start: 0.9297 (t80) cc_final: 0.8861 (t80) REVERT: D 296 MET cc_start: 0.9533 (ttp) cc_final: 0.9306 (ttp) REVERT: D 330 MET cc_start: 0.9349 (tpt) cc_final: 0.8848 (tpt) REVERT: D 360 MET cc_start: 0.9348 (ptp) cc_final: 0.9088 (ppp) outliers start: 1 outliers final: 0 residues processed: 277 average time/residue: 0.3039 time to fit residues: 136.0184 Evaluate side-chains 209 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 2.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 115 optimal weight: 6.9990 chunk 175 optimal weight: 10.0000 chunk 203 optimal weight: 20.0000 chunk 32 optimal weight: 9.9990 chunk 231 optimal weight: 6.9990 chunk 180 optimal weight: 9.9990 chunk 188 optimal weight: 7.9990 chunk 259 optimal weight: 30.0000 chunk 164 optimal weight: 10.0000 chunk 253 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 476 HIS ** A 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 591 ASN B 164 HIS B 305 ASN B 396 ASN ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.075180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.051606 restraints weight = 142569.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.053227 restraints weight = 77573.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.054212 restraints weight = 50496.128| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 21759 Z= 0.235 Angle : 0.668 8.277 29433 Z= 0.363 Chirality : 0.041 0.158 3288 Planarity : 0.005 0.053 3705 Dihedral : 4.731 23.226 2888 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 21.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.86 % Favored : 96.10 % Rotamer: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % 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: 0.65 (0.16), residues: 2616 helix: 1.02 (0.12), residues: 1717 sheet: 0.55 (0.49), residues: 99 loop : -0.73 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 68 HIS 0.009 0.001 HIS D 422 PHE 0.025 0.002 PHE A 319 TYR 0.029 0.002 TYR A 355 ARG 0.008 0.001 ARG C 369 Details of bonding type rmsd hydrogen bonds : bond 0.04608 ( 1271) hydrogen bonds : angle 4.94721 ( 3723) covalent geometry : bond 0.00482 (21759) covalent geometry : angle 0.66759 (29433) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 2.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TRP cc_start: 0.8883 (t-100) cc_final: 0.8236 (t-100) REVERT: A 81 LEU cc_start: 0.9101 (tp) cc_final: 0.8607 (tp) REVERT: A 85 MET cc_start: 0.9244 (ptp) cc_final: 0.8961 (ptt) REVERT: A 148 PHE cc_start: 0.9233 (p90) cc_final: 0.8845 (p90) REVERT: A 154 TRP cc_start: 0.8794 (m100) cc_final: 0.8300 (m100) REVERT: A 296 MET cc_start: 0.9484 (tpp) cc_final: 0.9081 (tpp) REVERT: A 340 ARG cc_start: 0.9174 (tpp-160) cc_final: 0.8556 (tpp80) REVERT: B 78 TYR cc_start: 0.9470 (t80) cc_final: 0.9219 (t80) REVERT: B 111 ASP cc_start: 0.9404 (t70) cc_final: 0.9193 (t70) REVERT: B 183 GLU cc_start: 0.9281 (tp30) cc_final: 0.8903 (tp30) REVERT: B 652 MET cc_start: 0.6979 (mmt) cc_final: 0.6220 (ppp) REVERT: B 676 MET cc_start: 0.8468 (mtt) cc_final: 0.8019 (mtt) REVERT: C 154 TRP cc_start: 0.8871 (m100) cc_final: 0.8520 (m100) REVERT: C 296 MET cc_start: 0.9621 (tmm) cc_final: 0.9310 (tmm) REVERT: C 307 THR cc_start: 0.9697 (m) cc_final: 0.9452 (p) REVERT: C 321 ASP cc_start: 0.9616 (t70) cc_final: 0.9277 (m-30) REVERT: C 351 TYR cc_start: 0.9028 (t80) cc_final: 0.8691 (t80) REVERT: C 407 PHE cc_start: 0.8957 (m-10) cc_final: 0.8388 (m-80) REVERT: C 506 GLU cc_start: 0.9317 (tp30) cc_final: 0.9049 (tp30) REVERT: C 661 HIS cc_start: 0.7928 (t70) cc_final: 0.7656 (t-90) REVERT: D 146 MET cc_start: 0.8957 (mmt) cc_final: 0.8476 (mpp) REVERT: D 199 THR cc_start: 0.9153 (m) cc_final: 0.8914 (p) REVERT: D 264 PHE cc_start: 0.9513 (t80) cc_final: 0.9231 (t80) REVERT: D 268 THR cc_start: 0.9572 (m) cc_final: 0.9184 (m) REVERT: D 285 MET cc_start: 0.8867 (tpp) cc_final: 0.8664 (tpp) REVERT: D 291 TYR cc_start: 0.9320 (t80) cc_final: 0.8857 (t80) REVERT: D 330 MET cc_start: 0.9306 (tpt) cc_final: 0.8810 (tpt) REVERT: D 360 MET cc_start: 0.9314 (ptp) cc_final: 0.8977 (ppp) outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 0.3355 time to fit residues: 142.9533 Evaluate side-chains 197 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 2.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 147 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 186 optimal weight: 30.0000 chunk 158 optimal weight: 8.9990 chunk 105 optimal weight: 4.9990 chunk 228 optimal weight: 0.8980 chunk 219 optimal weight: 0.7980 chunk 174 optimal weight: 9.9990 chunk 163 optimal weight: 2.9990 chunk 38 optimal weight: 0.1980 chunk 85 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 ASN A 476 HIS A 591 ASN B 350 GLN ** B 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.091081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.062076 restraints weight = 81641.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.062990 restraints weight = 64334.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.063468 restraints weight = 55316.230| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21759 Z= 0.125 Angle : 0.621 8.898 29433 Z= 0.325 Chirality : 0.040 0.165 3288 Planarity : 0.004 0.052 3705 Dihedral : 4.595 23.613 2888 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.02 % Favored : 96.94 % Rotamer: Outliers : 0.04 % Allowed : 1.86 % Favored : 98.10 % 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: 0.73 (0.16), residues: 2616 helix: 1.10 (0.12), residues: 1733 sheet: 0.59 (0.48), residues: 104 loop : -0.83 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 235 HIS 0.006 0.001 HIS C 494 PHE 0.022 0.001 PHE A 319 TYR 0.028 0.002 TYR D 355 ARG 0.009 0.001 ARG C 497 Details of bonding type rmsd hydrogen bonds : bond 0.04305 ( 1271) hydrogen bonds : angle 4.63321 ( 3723) covalent geometry : bond 0.00261 (21759) covalent geometry : angle 0.62067 (29433) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 285 time to evaluate : 2.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TRP cc_start: 0.8782 (t-100) cc_final: 0.8323 (t-100) REVERT: A 81 LEU cc_start: 0.9130 (tp) cc_final: 0.8711 (tp) REVERT: A 101 ASP cc_start: 0.9607 (t0) cc_final: 0.9357 (t0) REVERT: A 114 LEU cc_start: 0.9264 (tt) cc_final: 0.9014 (tt) REVERT: A 148 PHE cc_start: 0.9231 (p90) cc_final: 0.8827 (p90) REVERT: A 154 TRP cc_start: 0.8660 (m100) cc_final: 0.8106 (m100) REVERT: A 183 GLU cc_start: 0.9328 (mp0) cc_final: 0.9002 (mp0) REVERT: A 266 ILE cc_start: 0.9839 (mm) cc_final: 0.9636 (tp) REVERT: A 296 MET cc_start: 0.9447 (tpp) cc_final: 0.9002 (tpp) REVERT: A 340 ARG cc_start: 0.9143 (tpp-160) cc_final: 0.8457 (tpp80) REVERT: A 407 PHE cc_start: 0.8416 (m-80) cc_final: 0.8117 (m-80) REVERT: B 78 TYR cc_start: 0.9457 (t80) cc_final: 0.9126 (t80) REVERT: B 146 MET cc_start: 0.9321 (mpp) cc_final: 0.9110 (mpp) REVERT: B 183 GLU cc_start: 0.9254 (tp30) cc_final: 0.8839 (tp30) REVERT: B 208 GLU cc_start: 0.9344 (mm-30) cc_final: 0.8872 (mm-30) REVERT: B 298 LEU cc_start: 0.9686 (tp) cc_final: 0.9277 (tp) REVERT: B 652 MET cc_start: 0.6366 (mmt) cc_final: 0.6125 (ppp) REVERT: B 676 MET cc_start: 0.7871 (mtt) cc_final: 0.7459 (mtt) REVERT: C 289 MET cc_start: 0.9219 (mmt) cc_final: 0.8990 (mmt) REVERT: C 296 MET cc_start: 0.9603 (tmm) cc_final: 0.9354 (tmm) REVERT: C 307 THR cc_start: 0.9709 (m) cc_final: 0.9473 (p) REVERT: C 321 ASP cc_start: 0.9646 (t70) cc_final: 0.9327 (m-30) REVERT: C 351 TYR cc_start: 0.8995 (t80) cc_final: 0.8686 (t80) REVERT: C 407 PHE cc_start: 0.8663 (m-10) cc_final: 0.8255 (m-80) REVERT: C 506 GLU cc_start: 0.9309 (tp30) cc_final: 0.9059 (tp30) REVERT: C 661 HIS cc_start: 0.8093 (t70) cc_final: 0.7781 (t-90) REVERT: D 146 MET cc_start: 0.8883 (mmt) cc_final: 0.8469 (mpp) REVERT: D 264 PHE cc_start: 0.9531 (t80) cc_final: 0.8979 (t80) REVERT: D 268 THR cc_start: 0.9500 (m) cc_final: 0.9190 (m) REVERT: D 285 MET cc_start: 0.8858 (tpp) cc_final: 0.8606 (tpp) REVERT: D 296 MET cc_start: 0.9570 (ttm) cc_final: 0.9276 (ttm) REVERT: D 301 TYR cc_start: 0.8686 (t80) cc_final: 0.8284 (t80) REVERT: D 305 ASN cc_start: 0.9658 (m-40) cc_final: 0.8857 (m110) REVERT: D 330 MET cc_start: 0.9557 (tpt) cc_final: 0.9070 (tpt) REVERT: D 360 MET cc_start: 0.9277 (ptp) cc_final: 0.8918 (ppp) outliers start: 1 outliers final: 0 residues processed: 285 average time/residue: 0.3732 time to fit residues: 169.7406 Evaluate side-chains 219 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 4.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 48 optimal weight: 10.0000 chunk 105 optimal weight: 9.9990 chunk 133 optimal weight: 0.9980 chunk 119 optimal weight: 20.0000 chunk 6 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 191 optimal weight: 6.9990 chunk 92 optimal weight: 8.9990 chunk 222 optimal weight: 8.9990 chunk 96 optimal weight: 4.9990 chunk 139 optimal weight: 6.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 ASN ** A 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.076091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.052166 restraints weight = 140104.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.053869 restraints weight = 76027.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.054920 restraints weight = 49646.085| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 21759 Z= 0.185 Angle : 0.640 8.289 29433 Z= 0.342 Chirality : 0.040 0.195 3288 Planarity : 0.004 0.073 3705 Dihedral : 4.642 23.302 2888 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 19.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.82 % Favored : 96.14 % Rotamer: Outliers : 0.04 % Allowed : 1.47 % Favored : 98.48 % 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: 0.75 (0.16), residues: 2616 helix: 1.13 (0.12), residues: 1715 sheet: 0.27 (0.47), residues: 113 loop : -0.77 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 68 HIS 0.005 0.001 HIS D 422 PHE 0.024 0.002 PHE C 540 TYR 0.029 0.002 TYR A 233 ARG 0.016 0.001 ARG D 552 Details of bonding type rmsd hydrogen bonds : bond 0.04366 ( 1271) hydrogen bonds : angle 4.80130 ( 3723) covalent geometry : bond 0.00391 (21759) covalent geometry : angle 0.64026 (29433) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 271 time to evaluate : 2.301 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: A 68 TRP cc_start: 0.8803 (t-100) cc_final: 0.8228 (t-100) REVERT: A 81 LEU cc_start: 0.9166 (tp) cc_final: 0.8718 (tp) REVERT: A 85 MET cc_start: 0.9212 (ptp) cc_final: 0.8870 (ptt) REVERT: A 101 ASP cc_start: 0.9593 (t0) cc_final: 0.9357 (t0) REVERT: A 148 PHE cc_start: 0.9232 (p90) cc_final: 0.8881 (p90) REVERT: A 183 GLU cc_start: 0.9359 (mp0) cc_final: 0.8956 (mp0) REVERT: A 340 ARG cc_start: 0.9186 (tpp-160) cc_final: 0.8452 (tpp80) REVERT: A 407 PHE cc_start: 0.8321 (m-80) cc_final: 0.8059 (m-80) REVERT: A 652 MET cc_start: 0.7773 (mtt) cc_final: 0.6969 (mpp) REVERT: B 78 TYR cc_start: 0.9456 (t80) cc_final: 0.9152 (t80) REVERT: B 146 MET cc_start: 0.9418 (mpp) cc_final: 0.9058 (mpp) REVERT: B 183 GLU cc_start: 0.9289 (tp30) cc_final: 0.8897 (tp30) REVERT: B 296 MET cc_start: 0.9227 (ttm) cc_final: 0.8930 (ttm) REVERT: B 652 MET cc_start: 0.7002 (mmt) cc_final: 0.6251 (ppp) REVERT: B 676 MET cc_start: 0.8442 (mtt) cc_final: 0.7977 (mtt) REVERT: C 154 TRP cc_start: 0.8824 (m100) cc_final: 0.8501 (m100) REVERT: C 296 MET cc_start: 0.9659 (tmm) cc_final: 0.9355 (tmm) REVERT: C 307 THR cc_start: 0.9715 (m) cc_final: 0.9484 (p) REVERT: C 321 ASP cc_start: 0.9610 (t70) cc_final: 0.9289 (m-30) REVERT: C 351 TYR cc_start: 0.9094 (t80) cc_final: 0.8722 (t80) REVERT: C 407 PHE cc_start: 0.8933 (m-10) cc_final: 0.8386 (m-80) REVERT: C 506 GLU cc_start: 0.9303 (tp30) cc_final: 0.9044 (tp30) REVERT: C 661 HIS cc_start: 0.7998 (t70) cc_final: 0.7709 (t-90) REVERT: D 146 MET cc_start: 0.8905 (mmt) cc_final: 0.8449 (mpp) REVERT: D 199 THR cc_start: 0.9050 (m) cc_final: 0.8809 (p) REVERT: D 264 PHE cc_start: 0.9497 (t80) cc_final: 0.9148 (t80) REVERT: D 268 THR cc_start: 0.9545 (m) cc_final: 0.9195 (m) REVERT: D 301 TYR cc_start: 0.8843 (t80) cc_final: 0.8429 (t80) REVERT: D 305 ASN cc_start: 0.9732 (m-40) cc_final: 0.9121 (m110) REVERT: D 330 MET cc_start: 0.9312 (tpt) cc_final: 0.8890 (tpt) REVERT: D 360 MET cc_start: 0.9274 (ptp) cc_final: 0.9023 (ppp) outliers start: 1 outliers final: 0 residues processed: 271 average time/residue: 0.3079 time to fit residues: 133.6678 Evaluate side-chains 203 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 2.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 191 optimal weight: 20.0000 chunk 67 optimal weight: 1.9990 chunk 18 optimal weight: 0.0970 chunk 106 optimal weight: 10.0000 chunk 110 optimal weight: 3.9990 chunk 219 optimal weight: 0.8980 chunk 138 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 253 optimal weight: 6.9990 chunk 230 optimal weight: 6.9990 overall best weight: 2.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 ASN A 305 ASN ** A 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.091839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.061358 restraints weight = 79776.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.062098 restraints weight = 65536.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 13)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.062410 restraints weight = 57904.694| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21759 Z= 0.141 Angle : 0.634 8.612 29433 Z= 0.331 Chirality : 0.040 0.156 3288 Planarity : 0.004 0.051 3705 Dihedral : 4.605 22.869 2888 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.52 % Favored : 96.44 % Rotamer: Outliers : 0.04 % Allowed : 0.91 % Favored : 99.05 % 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 (0.16), residues: 2616 helix: 1.10 (0.12), residues: 1727 sheet: 0.33 (0.47), residues: 113 loop : -0.79 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 154 HIS 0.006 0.001 HIS C 569 PHE 0.019 0.001 PHE A 319 TYR 0.039 0.002 TYR A 355 ARG 0.012 0.001 ARG D 552 Details of bonding type rmsd hydrogen bonds : bond 0.04284 ( 1271) hydrogen bonds : angle 4.69349 ( 3723) covalent geometry : bond 0.00302 (21759) covalent geometry : angle 0.63368 (29433) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 278 time to evaluate : 2.385 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: A 68 TRP cc_start: 0.8851 (t-100) cc_final: 0.8337 (t-100) REVERT: A 81 LEU cc_start: 0.9131 (tp) cc_final: 0.8741 (tp) REVERT: A 85 MET cc_start: 0.9323 (ptp) cc_final: 0.9025 (ptt) REVERT: A 101 ASP cc_start: 0.9595 (t0) cc_final: 0.9354 (t0) REVERT: A 114 LEU cc_start: 0.9255 (tt) cc_final: 0.9037 (tt) REVERT: A 148 PHE cc_start: 0.9245 (p90) cc_final: 0.8863 (p90) REVERT: A 152 PHE cc_start: 0.9058 (t80) cc_final: 0.8853 (t80) REVERT: A 154 TRP cc_start: 0.8569 (m100) cc_final: 0.8002 (m100) REVERT: A 183 GLU cc_start: 0.9274 (mp0) cc_final: 0.8865 (mp0) REVERT: A 407 PHE cc_start: 0.8531 (m-80) cc_final: 0.8175 (m-80) REVERT: B 78 TYR cc_start: 0.9483 (t80) cc_final: 0.9132 (t80) REVERT: B 146 MET cc_start: 0.9329 (mpp) cc_final: 0.9033 (mpp) REVERT: B 183 GLU cc_start: 0.9246 (tp30) cc_final: 0.8840 (tp30) REVERT: B 676 MET cc_start: 0.7952 (mtt) cc_final: 0.7554 (mtt) REVERT: C 154 TRP cc_start: 0.8901 (m100) cc_final: 0.8577 (m100) REVERT: C 285 MET cc_start: 0.8506 (tpp) cc_final: 0.8297 (tpp) REVERT: C 289 MET cc_start: 0.9249 (mmt) cc_final: 0.9025 (mmt) REVERT: C 296 MET cc_start: 0.9649 (tmm) cc_final: 0.9399 (tmm) REVERT: C 307 THR cc_start: 0.9701 (m) cc_final: 0.9473 (p) REVERT: C 321 ASP cc_start: 0.9669 (t70) cc_final: 0.9416 (m-30) REVERT: C 323 MET cc_start: 0.9640 (mtt) cc_final: 0.9350 (mpp) REVERT: C 407 PHE cc_start: 0.8674 (m-10) cc_final: 0.8298 (m-80) REVERT: C 506 GLU cc_start: 0.9324 (tp30) cc_final: 0.9067 (tp30) REVERT: C 661 HIS cc_start: 0.8119 (t70) cc_final: 0.7810 (t-90) REVERT: D 146 MET cc_start: 0.8888 (mmt) cc_final: 0.8483 (mpp) REVERT: D 199 THR cc_start: 0.8981 (m) cc_final: 0.8755 (p) REVERT: D 264 PHE cc_start: 0.9547 (t80) cc_final: 0.9177 (t80) REVERT: D 268 THR cc_start: 0.9513 (m) cc_final: 0.9139 (m) REVERT: D 285 MET cc_start: 0.9082 (tpp) cc_final: 0.8403 (tpp) REVERT: D 301 TYR cc_start: 0.8722 (t80) cc_final: 0.8299 (t80) REVERT: D 305 ASN cc_start: 0.9680 (m-40) cc_final: 0.8882 (m110) REVERT: D 330 MET cc_start: 0.9570 (tpt) cc_final: 0.9052 (tpt) REVERT: D 360 MET cc_start: 0.9257 (ptp) cc_final: 0.8951 (ppp) outliers start: 1 outliers final: 1 residues processed: 278 average time/residue: 0.3050 time to fit residues: 134.2637 Evaluate side-chains 216 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 215 time to evaluate : 2.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 185 optimal weight: 20.0000 chunk 64 optimal weight: 5.9990 chunk 116 optimal weight: 10.0000 chunk 82 optimal weight: 0.9980 chunk 71 optimal weight: 9.9990 chunk 231 optimal weight: 10.0000 chunk 107 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 202 optimal weight: 20.0000 chunk 207 optimal weight: 0.5980 chunk 214 optimal weight: 9.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 315 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.075674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.051117 restraints weight = 141088.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.052924 restraints weight = 74183.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.054023 restraints weight = 47405.264| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21759 Z= 0.133 Angle : 0.637 9.561 29433 Z= 0.331 Chirality : 0.040 0.169 3288 Planarity : 0.004 0.051 3705 Dihedral : 4.561 22.474 2888 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.71 % Favored : 96.25 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % 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: 0.75 (0.16), residues: 2616 helix: 1.12 (0.12), residues: 1726 sheet: 0.37 (0.47), residues: 113 loop : -0.77 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 154 HIS 0.005 0.001 HIS C 569 PHE 0.031 0.001 PHE A 294 TYR 0.020 0.001 TYR D 139 ARG 0.011 0.001 ARG D 552 Details of bonding type rmsd hydrogen bonds : bond 0.04214 ( 1271) hydrogen bonds : angle 4.64006 ( 3723) covalent geometry : bond 0.00284 (21759) covalent geometry : angle 0.63651 (29433) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 2.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TRP cc_start: 0.8867 (t-100) cc_final: 0.8387 (t-100) REVERT: A 81 LEU cc_start: 0.9166 (tp) cc_final: 0.8737 (tp) REVERT: A 85 MET cc_start: 0.9214 (ptp) cc_final: 0.8857 (ptt) REVERT: A 101 ASP cc_start: 0.9603 (t0) cc_final: 0.9358 (t0) REVERT: A 148 PHE cc_start: 0.9244 (p90) cc_final: 0.8863 (p90) REVERT: A 152 PHE cc_start: 0.9079 (t80) cc_final: 0.8866 (t80) REVERT: A 154 TRP cc_start: 0.8585 (m100) cc_final: 0.8058 (m100) REVERT: A 183 GLU cc_start: 0.9257 (mp0) cc_final: 0.8856 (mp0) REVERT: A 407 PHE cc_start: 0.8341 (m-80) cc_final: 0.8020 (m-80) REVERT: A 652 MET cc_start: 0.7818 (mtt) cc_final: 0.7012 (mpp) REVERT: B 78 TYR cc_start: 0.9491 (t80) cc_final: 0.9117 (t80) REVERT: B 146 MET cc_start: 0.9292 (mpp) cc_final: 0.9016 (mpp) REVERT: B 183 GLU cc_start: 0.9311 (tp30) cc_final: 0.8914 (tp30) REVERT: B 676 MET cc_start: 0.8494 (mtt) cc_final: 0.8050 (mtt) REVERT: C 170 LEU cc_start: 0.9106 (mm) cc_final: 0.8897 (mm) REVERT: C 289 MET cc_start: 0.9368 (mmt) cc_final: 0.9150 (mmt) REVERT: C 294 PHE cc_start: 0.9294 (t80) cc_final: 0.9029 (t80) REVERT: C 296 MET cc_start: 0.9671 (tmm) cc_final: 0.9394 (tmm) REVERT: C 307 THR cc_start: 0.9687 (m) cc_final: 0.9446 (p) REVERT: C 321 ASP cc_start: 0.9614 (t70) cc_final: 0.9324 (m-30) REVERT: C 351 TYR cc_start: 0.9161 (t80) cc_final: 0.8564 (t80) REVERT: C 407 PHE cc_start: 0.9002 (m-10) cc_final: 0.8353 (m-80) REVERT: C 506 GLU cc_start: 0.9335 (tp30) cc_final: 0.9083 (tp30) REVERT: C 661 HIS cc_start: 0.8080 (t70) cc_final: 0.7811 (t-90) REVERT: D 146 MET cc_start: 0.8865 (mmt) cc_final: 0.8395 (mpp) REVERT: D 199 THR cc_start: 0.9174 (m) cc_final: 0.8933 (p) REVERT: D 264 PHE cc_start: 0.9473 (t80) cc_final: 0.9103 (t80) REVERT: D 285 MET cc_start: 0.8995 (tpp) cc_final: 0.8697 (tpp) REVERT: D 301 TYR cc_start: 0.8863 (t80) cc_final: 0.8475 (t80) REVERT: D 305 ASN cc_start: 0.9753 (m-40) cc_final: 0.9139 (m110) REVERT: D 330 MET cc_start: 0.9417 (tpt) cc_final: 0.8931 (tpt) REVERT: D 360 MET cc_start: 0.9298 (ptp) cc_final: 0.8901 (ppp) outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 0.2977 time to fit residues: 129.6507 Evaluate side-chains 212 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 2.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 83 optimal weight: 0.0270 chunk 57 optimal weight: 40.0000 chunk 164 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 126 optimal weight: 20.0000 chunk 39 optimal weight: 7.9990 chunk 172 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 153 optimal weight: 3.9990 chunk 130 optimal weight: 20.0000 chunk 151 optimal weight: 0.4980 overall best weight: 2.9044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 315 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.090421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.074037 restraints weight = 165455.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.075423 restraints weight = 76478.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.076326 restraints weight = 44068.811| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21759 Z= 0.143 Angle : 0.634 9.600 29433 Z= 0.330 Chirality : 0.040 0.170 3288 Planarity : 0.004 0.051 3705 Dihedral : 4.542 22.415 2888 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 17.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.78 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.16), residues: 2616 helix: 1.14 (0.12), residues: 1731 sheet: 0.39 (0.47), residues: 113 loop : -0.78 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 68 HIS 0.005 0.001 HIS D 346 PHE 0.019 0.001 PHE A 319 TYR 0.023 0.002 TYR D 355 ARG 0.018 0.001 ARG C 497 Details of bonding type rmsd hydrogen bonds : bond 0.04148 ( 1271) hydrogen bonds : angle 4.64817 ( 3723) covalent geometry : bond 0.00306 (21759) covalent geometry : angle 0.63412 (29433) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7450.52 seconds wall clock time: 132 minutes 59.55 seconds (7979.55 seconds total)