Starting phenix.real_space_refine on Wed Jan 22 12:20:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9blr_44674/01_2025/9blr_44674_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9blr_44674/01_2025/9blr_44674.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9blr_44674/01_2025/9blr_44674.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9blr_44674/01_2025/9blr_44674.map" model { file = "/net/cci-nas-00/data/ceres_data/9blr_44674/01_2025/9blr_44674_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9blr_44674/01_2025/9blr_44674_trim.cif" } resolution = 3.38 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 78 5.16 5 C 5962 2.51 5 N 1587 2.21 5 O 1799 1.98 5 H 8811 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 18237 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 5317 Classifications: {'peptide': 342} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 322} Chain breaks: 5 Chain: "B" Number of atoms: 6598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 6598 Classifications: {'peptide': 421} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 399} Chain breaks: 2 Chain: "C" Number of atoms: 6093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 6093 Classifications: {'peptide': 385} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 367} Chain breaks: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 9.18, per 1000 atoms: 0.50 Number of scatterers: 18237 At special positions: 0 Unit cell: (109.004, 101.791, 96.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 78 16.00 O 1799 8.00 N 1587 7.00 C 5962 6.00 H 8811 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=25, symmetry=0 Simple disulfide: pdb=" SG CYS A 134 " - pdb=" SG CYS A 286 " distance=2.03 Simple disulfide: pdb=" SG CYS A 210 " - pdb=" SG CYS A 217 " distance=2.03 Simple disulfide: pdb=" SG CYS A 263 " - pdb=" SG CYS A 270 " distance=2.04 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS A 392 " - pdb=" SG CYS A 451 " distance=2.03 Simple disulfide: pdb=" SG CYS A 396 " - pdb=" SG CYS A 447 " distance=2.03 Simple disulfide: pdb=" SG CYS A 405 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 407 " - pdb=" SG CYS A 421 " distance=2.03 Simple disulfide: pdb=" SG CYS B 98 " - pdb=" SG CYS B 272 " distance=2.03 Simple disulfide: pdb=" SG CYS B 184 " - pdb=" SG CYS B 189 " distance=2.04 Simple disulfide: pdb=" SG CYS B 196 " - pdb=" SG CYS B 203 " distance=2.03 Simple disulfide: pdb=" SG CYS B 249 " - pdb=" SG CYS B 256 " distance=2.03 Simple disulfide: pdb=" SG CYS B 361 " - pdb=" SG CYS B 448 " distance=2.03 Simple disulfide: pdb=" SG CYS B 386 " - pdb=" SG CYS B 444 " distance=2.03 Simple disulfide: pdb=" SG CYS B 390 " - pdb=" SG CYS B 440 " distance=2.04 Simple disulfide: pdb=" SG CYS B 399 " - pdb=" SG CYS B 426 " distance=2.03 Simple disulfide: pdb=" SG CYS B 401 " - pdb=" SG CYS B 415 " distance=2.03 Simple disulfide: pdb=" SG CYS C 100 " - pdb=" SG CYS C 283 " distance=2.03 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 260 " - pdb=" SG CYS C 267 " distance=2.03 Simple disulfide: pdb=" SG CYS C 372 " - pdb=" SG CYS C 457 " distance=2.03 Simple disulfide: pdb=" SG CYS C 394 " - pdb=" SG CYS C 453 " distance=2.03 Simple disulfide: pdb=" SG CYS C 398 " - pdb=" SG CYS C 449 " distance=2.03 Simple disulfide: pdb=" SG CYS C 407 " - pdb=" SG CYS C 434 " distance=2.04 Simple disulfide: pdb=" SG CYS C 409 " - pdb=" SG CYS C 423 " distance=2.03 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " NAG-ASN " NAG A 701 " - " ASN A 333 " " NAG B 701 " - " ASN B 449 " " NAG B 702 " - " ASN B 364 " " NAG B 703 " - " ASN B 378 " " NAG C 701 " - " ASN C 248 " " NAG C 702 " - " ASN C 421 " " NAG D 1 " - " ASN B 141 " Time building additional restraints: 4.73 Conformation dependent library (CDL) restraints added in 1.5 seconds 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2172 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 14 sheets defined 33.0% alpha, 31.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.99 Creating SS restraints... Processing helix chain 'A' and resid 141 through 143 No H-bonds generated for 'chain 'A' and resid 141 through 143' Processing helix chain 'A' and resid 144 through 163 removed outlier: 3.536A pdb=" N SER A 161 " --> pdb=" O GLU A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 242 removed outlier: 3.647A pdb=" N GLN A 230 " --> pdb=" O VAL A 226 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA A 242 " --> pdb=" O VAL A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 299 through 302 Processing helix chain 'A' and resid 388 through 406 Processing helix chain 'A' and resid 428 through 442 Processing helix chain 'A' and resid 446 through 451 Processing helix chain 'A' and resid 474 through 485 removed outlier: 4.254A pdb=" N THR A 478 " --> pdb=" O SER A 474 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 479 " --> pdb=" O ALA A 475 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN A 485 " --> pdb=" O THR A 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 109 Processing helix chain 'B' and resid 112 through 128 removed outlier: 3.805A pdb=" N ALA B 121 " --> pdb=" O GLU B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 132 Processing helix chain 'B' and resid 141 through 146 removed outlier: 3.856A pdb=" N TRP B 145 " --> pdb=" O ASN B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 228 Processing helix chain 'B' and resid 231 through 236 Processing helix chain 'B' and resid 241 through 245 Processing helix chain 'B' and resid 257 through 261 Processing helix chain 'B' and resid 290 through 293 Processing helix chain 'B' and resid 302 through 306 Processing helix chain 'B' and resid 328 through 333 Processing helix chain 'B' and resid 372 through 378 removed outlier: 4.551A pdb=" N ASP B 376 " --> pdb=" O PHE B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 400 removed outlier: 3.655A pdb=" N GLN B 392 " --> pdb=" O ARG B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 433 removed outlier: 3.734A pdb=" N LEU B 430 " --> pdb=" O CYS B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 442 removed outlier: 3.707A pdb=" N ARG B 437 " --> pdb=" O SER B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 478 removed outlier: 4.420A pdb=" N HIS B 473 " --> pdb=" O ASP B 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 129 removed outlier: 3.532A pdb=" N VAL C 110 " --> pdb=" O LYS C 106 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N HIS C 112 " --> pdb=" O SER C 108 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N LEU C 113 " --> pdb=" O THR C 109 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ASP C 116 " --> pdb=" O HIS C 112 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LEU C 117 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLU C 120 " --> pdb=" O ASP C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 158 Processing helix chain 'C' and resid 221 through 239 removed outlier: 3.565A pdb=" N ILE C 226 " --> pdb=" O GLY C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 249 removed outlier: 3.691A pdb=" N ASN C 248 " --> pdb=" O GLU C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 256 Processing helix chain 'C' and resid 268 through 270 No H-bonds generated for 'chain 'C' and resid 268 through 270' Processing helix chain 'C' and resid 301 through 304 Processing helix chain 'C' and resid 313 through 317 removed outlier: 3.874A pdb=" N TYR C 317 " --> pdb=" O GLU C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 344 Processing helix chain 'C' and resid 390 through 406 Processing helix chain 'C' and resid 430 through 443 removed outlier: 3.647A pdb=" N CYS C 434 " --> pdb=" O ASN C 430 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU C 438 " --> pdb=" O CYS C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 453 Processing helix chain 'C' and resid 476 through 488 removed outlier: 3.739A pdb=" N LEU C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A) Proline residue: C 482 - end of helix Processing helix chain 'C' and resid 497 through 499 No H-bonds generated for 'chain 'C' and resid 497 through 499' Processing sheet with id=AA1, first strand: chain 'A' and resid 276 through 280 Processing sheet with id=AA2, first strand: chain 'A' and resid 193 through 195 removed outlier: 6.041A pdb=" N ASP A 216 " --> pdb=" O ASN A 211 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 268 through 270 removed outlier: 3.676A pdb=" N CYS A 263 " --> pdb=" O CYS A 270 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL A 260 " --> pdb=" O ARG A 309 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ARG A 309 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N THR A 349 " --> pdb=" O LEU A 498 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 268 through 270 removed outlier: 3.676A pdb=" N CYS A 263 " --> pdb=" O CYS A 270 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL A 260 " --> pdb=" O ARG A 309 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ARG A 309 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N THR A 349 " --> pdb=" O LEU A 498 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 79 through 86 removed outlier: 4.290A pdb=" N THR B 340 " --> pdb=" O ILE B 492 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N VAL B 348 " --> pdb=" O GLN B 500 " (cutoff:3.500A) removed outlier: 9.454A pdb=" N PHE B 502 " --> pdb=" O VAL B 348 " (cutoff:3.500A) removed outlier: 10.662A pdb=" N LYS B 350 " --> pdb=" O PHE B 502 " (cutoff:3.500A) removed outlier: 9.898A pdb=" N TYR B 504 " --> pdb=" O LYS B 350 " (cutoff:3.500A) removed outlier: 12.666A pdb=" N GLN B 352 " --> pdb=" O TYR B 504 " (cutoff:3.500A) removed outlier: 9.952A pdb=" N THR B 506 " --> pdb=" O GLN B 352 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 254 through 256 removed outlier: 3.681A pdb=" N CYS B 256 " --> pdb=" O CYS B 249 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N CYS B 249 " --> pdb=" O CYS B 256 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ILE B 246 " --> pdb=" O ASP B 300 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASP B 300 " --> pdb=" O ILE B 246 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N THR B 340 " --> pdb=" O ILE B 492 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N VAL B 348 " --> pdb=" O GLN B 500 " (cutoff:3.500A) removed outlier: 9.454A pdb=" N PHE B 502 " --> pdb=" O VAL B 348 " (cutoff:3.500A) removed outlier: 10.662A pdb=" N LYS B 350 " --> pdb=" O PHE B 502 " (cutoff:3.500A) removed outlier: 9.898A pdb=" N TYR B 504 " --> pdb=" O LYS B 350 " (cutoff:3.500A) removed outlier: 12.666A pdb=" N GLN B 352 " --> pdb=" O TYR B 504 " (cutoff:3.500A) removed outlier: 9.952A pdb=" N THR B 506 " --> pdb=" O GLN B 352 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 90 through 91 removed outlier: 3.701A pdb=" N MET B 90 " --> pdb=" O SER B 286 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 262 through 266 removed outlier: 6.821A pdb=" N ASN B 271 " --> pdb=" O ASN B 99 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ASN B 99 " --> pdb=" O ASN B 271 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 162 through 165 Processing sheet with id=AB1, first strand: chain 'C' and resid 82 through 89 removed outlier: 4.638A pdb=" N MET C 351 " --> pdb=" O LEU C 501 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE C 507 " --> pdb=" O ILE C 355 " (cutoff:3.500A) removed outlier: 9.605A pdb=" N LEU C 359 " --> pdb=" O LYS C 509 " (cutoff:3.500A) removed outlier: 9.167A pdb=" N LEU C 511 " --> pdb=" O LEU C 359 " (cutoff:3.500A) removed outlier: 10.824A pdb=" N GLU C 361 " --> pdb=" O LEU C 511 " (cutoff:3.500A) removed outlier: 9.740A pdb=" N GLN C 513 " --> pdb=" O GLU C 361 " (cutoff:3.500A) removed outlier: 12.019A pdb=" N PHE C 363 " --> pdb=" O GLN C 513 " (cutoff:3.500A) removed outlier: 10.021A pdb=" N SER C 515 " --> pdb=" O PHE C 363 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 265 through 267 removed outlier: 4.075A pdb=" N CYS C 260 " --> pdb=" O CYS C 267 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE C 309 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N CYS C 260 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLN C 307 " --> pdb=" O CYS C 260 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N MET C 351 " --> pdb=" O LEU C 501 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE C 507 " --> pdb=" O ILE C 355 " (cutoff:3.500A) removed outlier: 9.605A pdb=" N LEU C 359 " --> pdb=" O LYS C 509 " (cutoff:3.500A) removed outlier: 9.167A pdb=" N LEU C 511 " --> pdb=" O LEU C 359 " (cutoff:3.500A) removed outlier: 10.824A pdb=" N GLU C 361 " --> pdb=" O LEU C 511 " (cutoff:3.500A) removed outlier: 9.740A pdb=" N GLN C 513 " --> pdb=" O GLU C 361 " (cutoff:3.500A) removed outlier: 12.019A pdb=" N PHE C 363 " --> pdb=" O GLN C 513 " (cutoff:3.500A) removed outlier: 10.021A pdb=" N SER C 515 " --> pdb=" O PHE C 363 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY C 356 " --> pdb=" O THR C 465 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 92 through 93 Processing sheet with id=AB4, first strand: chain 'C' and resid 272 through 277 removed outlier: 6.471A pdb=" N ASN C 282 " --> pdb=" O ASN C 101 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ASN C 101 " --> pdb=" O ASN C 282 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL C 97 " --> pdb=" O PHE C 286 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 160 through 162 removed outlier: 3.675A pdb=" N VAL C 202 " --> pdb=" O PHE C 219 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA C 215 " --> pdb=" O LEU C 206 " (cutoff:3.500A) 430 hydrogen bonds defined for protein. 1161 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: 7.36 Time building geometry restraints manager: 5.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 8811 1.02 - 1.22: 15 1.22 - 1.42: 4148 1.42 - 1.63: 5392 1.63 - 1.83: 106 Bond restraints: 18472 Sorted by residual: bond pdb=" N GLU B 78 " pdb=" H GLU B 78 " ideal model delta sigma weight residual 0.860 0.961 -0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" C LEU B 198 " pdb=" O LEU B 198 " ideal model delta sigma weight residual 1.233 1.181 0.052 1.54e-02 4.22e+03 1.13e+01 bond pdb=" C SER B 359 " pdb=" N PRO B 360 " ideal model delta sigma weight residual 1.337 1.359 -0.022 9.80e-03 1.04e+04 5.10e+00 bond pdb=" C LEU B 198 " pdb=" N ASN B 199 " ideal model delta sigma weight residual 1.333 1.304 0.029 1.39e-02 5.18e+03 4.27e+00 bond pdb=" C4 NAG E 1 " pdb=" O4 NAG E 1 " ideal model delta sigma weight residual 1.409 1.449 -0.040 2.00e-02 2.50e+03 4.09e+00 ... (remaining 18467 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 32442 1.89 - 3.77: 597 3.77 - 5.66: 56 5.66 - 7.55: 12 7.55 - 9.44: 5 Bond angle restraints: 33112 Sorted by residual: angle pdb=" N TRP B 470 " pdb=" CA TRP B 470 " pdb=" C TRP B 470 " ideal model delta sigma weight residual 114.04 109.68 4.36 1.24e+00 6.50e-01 1.24e+01 angle pdb=" C SER C 366 " pdb=" N GLU C 367 " pdb=" CA GLU C 367 " ideal model delta sigma weight residual 120.58 125.22 -4.64 1.32e+00 5.74e-01 1.24e+01 angle pdb=" N PRO B 360 " pdb=" CA PRO B 360 " pdb=" C PRO B 360 " ideal model delta sigma weight residual 114.20 118.41 -4.21 1.20e+00 6.94e-01 1.23e+01 angle pdb=" CA CYS B 390 " pdb=" CB CYS B 390 " pdb=" SG CYS B 390 " ideal model delta sigma weight residual 114.40 122.20 -7.80 2.30e+00 1.89e-01 1.15e+01 angle pdb=" N ASP B 469 " pdb=" CA ASP B 469 " pdb=" C ASP B 469 " ideal model delta sigma weight residual 112.87 116.65 -3.78 1.20e+00 6.94e-01 9.92e+00 ... (remaining 33107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.51: 8522 21.51 - 43.01: 398 43.01 - 64.52: 141 64.52 - 86.03: 44 86.03 - 107.53: 16 Dihedral angle restraints: 9121 sinusoidal: 5018 harmonic: 4103 Sorted by residual: dihedral pdb=" CA CYS C 407 " pdb=" C CYS C 407 " pdb=" N GLY C 408 " pdb=" CA GLY C 408 " ideal model delta harmonic sigma weight residual 180.00 151.22 28.78 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA ARG B 206 " pdb=" C ARG B 206 " pdb=" N ASN B 207 " pdb=" CA ASN B 207 " ideal model delta harmonic sigma weight residual -180.00 -153.46 -26.54 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA ARG C 490 " pdb=" C ARG C 490 " pdb=" N GLN C 491 " pdb=" CA GLN C 491 " ideal model delta harmonic sigma weight residual -180.00 -154.41 -25.59 0 5.00e+00 4.00e-02 2.62e+01 ... (remaining 9118 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1203 0.061 - 0.123: 218 0.123 - 0.184: 37 0.184 - 0.245: 8 0.245 - 0.307: 2 Chirality restraints: 1468 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 5.14e+01 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.32 -0.08 2.00e-02 2.50e+03 1.59e+01 chirality pdb=" C1 BMA I 3 " pdb=" O4 NAG I 2 " pdb=" C2 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.35 -0.05 2.00e-02 2.50e+03 6.79e+00 ... (remaining 1465 not shown) Planarity restraints: 2752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 1 " -0.054 2.00e-02 2.50e+03 4.48e-02 2.51e+01 pdb=" C7 NAG E 1 " 0.028 2.00e-02 2.50e+03 pdb=" C8 NAG E 1 " -0.045 2.00e-02 2.50e+03 pdb=" N2 NAG E 1 " 0.066 2.00e-02 2.50e+03 pdb=" O7 NAG E 1 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 2 " 0.052 2.00e-02 2.50e+03 4.32e-02 2.33e+01 pdb=" C7 NAG I 2 " -0.027 2.00e-02 2.50e+03 pdb=" C8 NAG I 2 " 0.043 2.00e-02 2.50e+03 pdb=" N2 NAG I 2 " -0.064 2.00e-02 2.50e+03 pdb=" O7 NAG I 2 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " -0.050 2.00e-02 2.50e+03 4.16e-02 2.16e+01 pdb=" C7 NAG D 1 " 0.027 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " -0.042 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " 0.061 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " 0.004 2.00e-02 2.50e+03 ... (remaining 2749 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 1023 2.22 - 2.82: 36694 2.82 - 3.41: 46596 3.41 - 4.01: 62538 4.01 - 4.60: 96081 Nonbonded interactions: 242932 Sorted by model distance: nonbonded pdb=" O TYR C 412 " pdb=" HG SER C 413 " model vdw 1.627 2.450 nonbonded pdb=" HG1 THR B 362 " pdb=" OE2 GLU B 367 " model vdw 1.637 2.450 nonbonded pdb=" OD2 ASP A 135 " pdb=" HG SER A 285 " model vdw 1.651 2.450 nonbonded pdb=" O LEU C 92 " pdb=" HG SER C 296 " model vdw 1.661 2.450 nonbonded pdb=" HG1 THR C 373 " pdb=" OD1 ASP C 378 " model vdw 1.679 2.450 ... (remaining 242927 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 'D' selection = chain 'E' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.030 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: 0.310 Extract box with map and model: 0.620 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 39.800 Find NCS groups from input model: 0.280 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 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 : 0.005 0.052 9661 Z= 0.301 Angle : 0.855 9.435 13110 Z= 0.457 Chirality : 0.052 0.307 1468 Planarity : 0.007 0.062 1665 Dihedral : 15.966 107.534 3777 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 1.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.20 % Allowed : 1.57 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -1.18 (0.23), residues: 1124 helix: -1.61 (0.25), residues: 301 sheet: 0.11 (0.29), residues: 276 loop : -0.63 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 229 HIS 0.009 0.002 HIS A 431 PHE 0.020 0.002 PHE B 328 TYR 0.019 0.002 TYR C 425 ARG 0.004 0.001 ARG A 139 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 125 time to evaluate : 1.304 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: B 162 MET cc_start: 0.7844 (tpt) cc_final: 0.7548 (tpt) REVERT: B 337 MET cc_start: 0.8255 (ttp) cc_final: 0.7972 (ttp) REVERT: C 351 MET cc_start: 0.8491 (mmt) cc_final: 0.8089 (mmt) outliers start: 2 outliers final: 2 residues processed: 127 average time/residue: 0.6054 time to fit residues: 104.0672 Evaluate side-chains 82 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 80 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain C residue 267 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 GLN A 443 HIS B 431 GLN ** C 271 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 = 0.3431 r_free = 0.3431 target = 0.082857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.062710 restraints weight = 72611.069| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 4.27 r_work: 0.2860 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9661 Z= 0.273 Angle : 0.660 7.922 13110 Z= 0.344 Chirality : 0.045 0.232 1468 Planarity : 0.005 0.045 1665 Dihedral : 10.965 64.223 1607 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.59 % Allowed : 4.02 % Favored : 95.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.24), residues: 1124 helix: -0.62 (0.28), residues: 311 sheet: 0.21 (0.29), residues: 290 loop : -0.43 (0.27), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 229 HIS 0.006 0.001 HIS A 315 PHE 0.029 0.002 PHE A 343 TYR 0.014 0.001 TYR C 284 ARG 0.007 0.000 ARG C 490 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 162 MET cc_start: 0.7804 (tpt) cc_final: 0.7579 (tpt) REVERT: B 207 ASN cc_start: 0.8879 (t0) cc_final: 0.8648 (t0) REVERT: C 357 MET cc_start: 0.9293 (mtm) cc_final: 0.9045 (mtm) REVERT: C 363 PHE cc_start: 0.9003 (m-80) cc_final: 0.8670 (m-80) REVERT: C 490 ARG cc_start: 0.8671 (tpm170) cc_final: 0.8415 (tpm170) outliers start: 6 outliers final: 5 residues processed: 93 average time/residue: 0.5170 time to fit residues: 68.7895 Evaluate side-chains 82 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 77 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain C residue 364 LYS Chi-restraints excluded: chain C residue 487 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 35 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 75 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 GLN A 315 HIS A 334 HIS ** C 271 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 = 0.3377 r_free = 0.3377 target = 0.080624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.060570 restraints weight = 74044.656| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 4.20 r_work: 0.2829 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9661 Z= 0.332 Angle : 0.617 6.429 13110 Z= 0.326 Chirality : 0.044 0.204 1468 Planarity : 0.004 0.041 1665 Dihedral : 7.719 50.028 1607 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.78 % Allowed : 4.51 % Favored : 94.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.34 (0.25), residues: 1124 helix: -0.05 (0.29), residues: 298 sheet: 0.20 (0.29), residues: 318 loop : -0.47 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 229 HIS 0.006 0.001 HIS C 332 PHE 0.029 0.002 PHE A 343 TYR 0.013 0.001 TYR C 284 ARG 0.003 0.000 ARG B 259 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 1.395 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: C 477 GLU cc_start: 0.9316 (tt0) cc_final: 0.8783 (tm-30) REVERT: C 490 ARG cc_start: 0.8591 (tpm170) cc_final: 0.8244 (tpm170) outliers start: 8 outliers final: 7 residues processed: 82 average time/residue: 0.4825 time to fit residues: 56.1833 Evaluate side-chains 79 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 463 SER Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 256 CYS Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain C residue 364 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 32 optimal weight: 0.0570 chunk 8 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.082299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.062198 restraints weight = 72837.558| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 4.26 r_work: 0.2867 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9661 Z= 0.162 Angle : 0.528 6.187 13110 Z= 0.276 Chirality : 0.042 0.212 1468 Planarity : 0.003 0.040 1665 Dihedral : 6.299 50.923 1607 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.98 % Allowed : 5.88 % Favored : 93.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.02 (0.25), residues: 1124 helix: 0.41 (0.30), residues: 304 sheet: 0.22 (0.29), residues: 314 loop : -0.29 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 229 HIS 0.006 0.001 HIS C 439 PHE 0.026 0.001 PHE A 343 TYR 0.010 0.001 TYR C 284 ARG 0.003 0.000 ARG B 317 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 1.450 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: A 158 ASN cc_start: 0.9008 (m-40) cc_final: 0.8218 (m110) REVERT: B 454 LYS cc_start: 0.9428 (mmtp) cc_final: 0.9205 (mmtm) REVERT: C 403 MET cc_start: 0.8893 (tpt) cc_final: 0.8595 (tpp) REVERT: C 490 ARG cc_start: 0.8583 (tpm170) cc_final: 0.8175 (tpm170) outliers start: 10 outliers final: 9 residues processed: 90 average time/residue: 0.5030 time to fit residues: 64.1052 Evaluate side-chains 87 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain A residue 341 HIS Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 256 CYS Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain C residue 364 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 24 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 HIS A 296 GLN ** C 271 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 = 0.3396 r_free = 0.3396 target = 0.080813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.060916 restraints weight = 74633.284| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 4.23 r_work: 0.2821 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9661 Z= 0.325 Angle : 0.582 8.710 13110 Z= 0.303 Chirality : 0.042 0.195 1468 Planarity : 0.003 0.038 1665 Dihedral : 6.122 49.719 1607 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.18 % Allowed : 6.67 % Favored : 92.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.08 (0.25), residues: 1124 helix: 0.49 (0.30), residues: 304 sheet: 0.11 (0.29), residues: 319 loop : -0.38 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 248 HIS 0.004 0.001 HIS C 428 PHE 0.027 0.001 PHE A 343 TYR 0.011 0.001 TYR C 284 ARG 0.004 0.000 ARG B 317 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 1.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 ASN cc_start: 0.9035 (m-40) cc_final: 0.8259 (m110) REVERT: A 473 LYS cc_start: 0.9392 (mmmt) cc_final: 0.9164 (mmtm) REVERT: B 454 LYS cc_start: 0.9434 (mmtp) cc_final: 0.9217 (mmtm) REVERT: C 403 MET cc_start: 0.9004 (tpt) cc_final: 0.8775 (tpp) REVERT: C 490 ARG cc_start: 0.8512 (tpm170) cc_final: 0.8065 (tpm170) outliers start: 12 outliers final: 10 residues processed: 86 average time/residue: 0.5105 time to fit residues: 62.9356 Evaluate side-chains 88 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain A residue 341 HIS Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 256 CYS Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 399 CYS Chi-restraints excluded: chain C residue 267 CYS Chi-restraints excluded: chain C residue 364 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.081497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.061738 restraints weight = 73992.610| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 4.24 r_work: 0.2838 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9661 Z= 0.204 Angle : 0.522 8.076 13110 Z= 0.272 Chirality : 0.041 0.213 1468 Planarity : 0.003 0.037 1665 Dihedral : 5.773 49.061 1607 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.18 % Allowed : 7.55 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.16 (0.25), residues: 1124 helix: 0.77 (0.31), residues: 298 sheet: 0.13 (0.29), residues: 318 loop : -0.17 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 248 HIS 0.003 0.001 HIS C 112 PHE 0.026 0.001 PHE A 343 TYR 0.009 0.001 TYR C 284 ARG 0.004 0.000 ARG B 317 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 ASN cc_start: 0.9029 (m-40) cc_final: 0.8252 (m110) REVERT: C 403 MET cc_start: 0.8918 (tpt) cc_final: 0.8686 (tpp) REVERT: C 490 ARG cc_start: 0.8494 (tpm170) cc_final: 0.8012 (tpm170) outliers start: 12 outliers final: 10 residues processed: 89 average time/residue: 0.4902 time to fit residues: 61.7153 Evaluate side-chains 86 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain A residue 341 HIS Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 463 SER Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 256 CYS Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 399 CYS Chi-restraints excluded: chain C residue 267 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 47 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 110 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.081610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.062219 restraints weight = 74295.558| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 4.00 r_work: 0.2849 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9661 Z= 0.220 Angle : 0.518 7.264 13110 Z= 0.269 Chirality : 0.041 0.188 1468 Planarity : 0.003 0.036 1665 Dihedral : 5.579 48.735 1607 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.08 % Allowed : 7.84 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.14 (0.25), residues: 1124 helix: 0.78 (0.30), residues: 304 sheet: 0.12 (0.29), residues: 319 loop : -0.21 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 229 HIS 0.003 0.001 HIS C 428 PHE 0.022 0.001 PHE A 343 TYR 0.009 0.001 TYR C 284 ARG 0.004 0.000 ARG B 317 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 ASN cc_start: 0.9044 (m-40) cc_final: 0.8300 (m110) REVERT: C 490 ARG cc_start: 0.8428 (tpm170) cc_final: 0.7925 (tpm170) outliers start: 11 outliers final: 11 residues processed: 86 average time/residue: 0.4496 time to fit residues: 55.2958 Evaluate side-chains 89 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain A residue 341 HIS Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 463 SER Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 256 CYS Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 399 CYS Chi-restraints excluded: chain C residue 267 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 58 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.080579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.061332 restraints weight = 74594.448| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 3.96 r_work: 0.2834 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9661 Z= 0.275 Angle : 0.540 7.089 13110 Z= 0.280 Chirality : 0.041 0.211 1468 Planarity : 0.003 0.036 1665 Dihedral : 5.596 47.309 1607 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.18 % Allowed : 8.14 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.11 (0.25), residues: 1124 helix: 0.76 (0.30), residues: 304 sheet: 0.09 (0.29), residues: 315 loop : -0.23 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 229 HIS 0.004 0.001 HIS C 428 PHE 0.020 0.001 PHE A 343 TYR 0.009 0.001 TYR C 284 ARG 0.005 0.000 ARG B 317 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 1.486 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: A 158 ASN cc_start: 0.9059 (m-40) cc_final: 0.8358 (m110) REVERT: B 452 GLN cc_start: 0.8499 (mt0) cc_final: 0.7511 (mp10) outliers start: 12 outliers final: 10 residues processed: 86 average time/residue: 0.4714 time to fit residues: 58.1208 Evaluate side-chains 87 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 463 SER Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 256 CYS Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 399 CYS Chi-restraints excluded: chain C residue 267 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 67 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 443 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.081454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.062100 restraints weight = 74321.768| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 4.00 r_work: 0.2854 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9661 Z= 0.172 Angle : 0.502 6.889 13110 Z= 0.259 Chirality : 0.040 0.202 1468 Planarity : 0.003 0.036 1665 Dihedral : 5.429 48.374 1607 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.98 % Allowed : 8.14 % Favored : 90.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.26 (0.25), residues: 1124 helix: 0.96 (0.30), residues: 304 sheet: 0.10 (0.29), residues: 315 loop : -0.14 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 248 HIS 0.004 0.001 HIS C 112 PHE 0.019 0.001 PHE A 343 TYR 0.008 0.001 TYR B 273 ARG 0.007 0.000 ARG B 330 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 1.430 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: A 158 ASN cc_start: 0.9028 (m-40) cc_final: 0.8308 (m110) REVERT: B 452 GLN cc_start: 0.8520 (mt0) cc_final: 0.7576 (mp10) outliers start: 10 outliers final: 10 residues processed: 87 average time/residue: 0.5112 time to fit residues: 64.0905 Evaluate side-chains 85 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 463 SER Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 256 CYS Chi-restraints excluded: chain B residue 399 CYS Chi-restraints excluded: chain C residue 267 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 69 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.080517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.061000 restraints weight = 74198.480| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 3.98 r_work: 0.2846 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 9661 Z= 0.236 Angle : 0.529 8.554 13110 Z= 0.274 Chirality : 0.040 0.204 1468 Planarity : 0.004 0.090 1665 Dihedral : 5.450 48.362 1607 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.08 % Allowed : 8.14 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.24 (0.25), residues: 1124 helix: 0.93 (0.30), residues: 304 sheet: 0.11 (0.29), residues: 315 loop : -0.15 (0.29), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 248 HIS 0.003 0.001 HIS C 428 PHE 0.017 0.001 PHE A 343 TYR 0.008 0.001 TYR C 284 ARG 0.014 0.000 ARG B 330 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 1.482 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: A 158 ASN cc_start: 0.9070 (m-40) cc_final: 0.8355 (m110) REVERT: A 473 LYS cc_start: 0.9422 (mmmt) cc_final: 0.9124 (mmtm) REVERT: B 438 GLU cc_start: 0.8940 (mm-30) cc_final: 0.8651 (tm-30) REVERT: B 452 GLN cc_start: 0.8494 (mt0) cc_final: 0.7558 (mp10) outliers start: 11 outliers final: 10 residues processed: 87 average time/residue: 0.4659 time to fit residues: 57.9682 Evaluate side-chains 88 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 463 SER Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 256 CYS Chi-restraints excluded: chain B residue 399 CYS Chi-restraints excluded: chain C residue 267 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 93 optimal weight: 1.9990 chunk 59 optimal weight: 0.3980 chunk 21 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 96 optimal weight: 0.0870 chunk 10 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 112 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.081323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.061730 restraints weight = 73686.511| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 4.00 r_work: 0.2865 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 9661 Z= 0.162 Angle : 0.509 9.327 13110 Z= 0.263 Chirality : 0.040 0.197 1468 Planarity : 0.003 0.041 1665 Dihedral : 5.326 49.465 1607 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.88 % Allowed : 8.04 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.35 (0.25), residues: 1124 helix: 0.98 (0.30), residues: 309 sheet: 0.19 (0.29), residues: 310 loop : -0.07 (0.29), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 248 HIS 0.004 0.001 HIS C 112 PHE 0.017 0.001 PHE A 343 TYR 0.021 0.001 TYR A 265 ARG 0.014 0.000 ARG B 330 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7367.48 seconds wall clock time: 135 minutes 14.35 seconds (8114.35 seconds total)