Starting phenix.real_space_refine on Mon Jun 16 10:18:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9blr_44674/06_2025/9blr_44674_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9blr_44674/06_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_44674/06_2025/9blr_44674.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9blr_44674/06_2025/9blr_44674.map" model { file = "/net/cci-nas-00/data/ceres_data/9blr_44674/06_2025/9blr_44674_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9blr_44674/06_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 11.15, per 1000 atoms: 0.61 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: 4.84 Conformation dependent library (CDL) restraints added in 1.4 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: 1.56 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: 6.96 Time building geometry restraints manager: 5.88 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: 272.200 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: 0.780 Check model and map are aligned: 0.140 Set scattering table: 0.210 Process input model: 42.970 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.070 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 319.890 ------------------------------------------------------------------------------- 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 0.092 9700 Z= 0.264 Angle : 0.889 9.435 13202 Z= 0.464 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 Details of bonding type rmsd link_NAG-ASN : bond 0.08172 ( 7) link_NAG-ASN : angle 4.92926 ( 21) link_BETA1-4 : bond 0.00906 ( 7) link_BETA1-4 : angle 3.43900 ( 21) hydrogen bonds : bond 0.16152 ( 398) hydrogen bonds : angle 7.64582 ( 1161) SS BOND : bond 0.00389 ( 25) SS BOND : angle 1.35907 ( 50) covalent geometry : bond 0.00461 ( 9661) covalent geometry : angle 0.85534 (13110) *********************** 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 : 1.578 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: 0.6082 time to fit residues: 103.8117 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 : 1.407 ------------------------------------------------------------------------------- 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: 2.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- 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 = 0.3420 r_free = 0.3420 target = 0.082227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.062237 restraints weight = 73033.049| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 4.18 r_work: 0.2850 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9700 Z= 0.232 Angle : 0.691 7.897 13202 Z= 0.356 Chirality : 0.046 0.220 1468 Planarity : 0.005 0.044 1665 Dihedral : 10.957 63.214 1607 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.69 % Allowed : 4.02 % Favored : 95.29 % 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: -0.60 (0.24), residues: 1124 helix: -0.58 (0.28), residues: 304 sheet: 0.17 (0.30), residues: 296 loop : -0.48 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 229 HIS 0.006 0.001 HIS C 332 PHE 0.031 0.002 PHE A 343 TYR 0.015 0.001 TYR A 233 ARG 0.020 0.001 ARG C 490 Details of bonding type rmsd link_NAG-ASN : bond 0.00596 ( 7) link_NAG-ASN : angle 1.60585 ( 21) link_BETA1-4 : bond 0.00464 ( 7) link_BETA1-4 : angle 2.69181 ( 21) hydrogen bonds : bond 0.05054 ( 398) hydrogen bonds : angle 5.85670 ( 1161) SS BOND : bond 0.00356 ( 25) SS BOND : angle 1.22258 ( 50) covalent geometry : bond 0.00513 ( 9661) covalent geometry : angle 0.67756 (13110) *********************** 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 92 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 1.405 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: 0.7806 (tpt) cc_final: 0.7578 (tpt) REVERT: C 363 PHE cc_start: 0.9019 (m-80) cc_final: 0.8690 (m-80) REVERT: C 490 ARG cc_start: 0.8673 (tpm170) cc_final: 0.8405 (tpm170) outliers start: 7 outliers final: 6 residues processed: 92 average time/residue: 0.4668 time to fit residues: 60.9977 Evaluate side-chains 83 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain A residue 463 SER 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: 0.9990 chunk 28 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 HIS ** C 271 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 = 0.3389 r_free = 0.3389 target = 0.081217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.060969 restraints weight = 73573.859| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 4.24 r_work: 0.2841 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9700 Z= 0.197 Angle : 0.609 5.922 13202 Z= 0.316 Chirality : 0.043 0.196 1468 Planarity : 0.004 0.041 1665 Dihedral : 7.340 50.615 1607 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.69 % Allowed : 4.71 % Favored : 94.61 % 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: 0.03 (0.29), residues: 305 sheet: 0.23 (0.29), residues: 314 loop : -0.43 (0.27), residues: 505 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 0.030 0.001 PHE A 343 TYR 0.012 0.001 TYR C 284 ARG 0.005 0.000 ARG B 330 Details of bonding type rmsd link_NAG-ASN : bond 0.00266 ( 7) link_NAG-ASN : angle 1.33222 ( 21) link_BETA1-4 : bond 0.00582 ( 7) link_BETA1-4 : angle 2.06170 ( 21) hydrogen bonds : bond 0.04143 ( 398) hydrogen bonds : angle 5.32446 ( 1161) SS BOND : bond 0.00448 ( 25) SS BOND : angle 1.15267 ( 50) covalent geometry : bond 0.00429 ( 9661) covalent geometry : angle 0.59884 (13110) *********************** 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 87 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 1.436 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: C 477 GLU cc_start: 0.9319 (tt0) cc_final: 0.8782 (tm-30) REVERT: C 490 ARG cc_start: 0.8593 (tpm170) cc_final: 0.8238 (tpm170) outliers start: 7 outliers final: 7 residues processed: 87 average time/residue: 0.4655 time to fit residues: 57.9072 Evaluate side-chains 81 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 1.572 ------------------------------------------------------------------------------- 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: 0.8980 chunk 86 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 94 optimal weight: 0.0970 chunk 39 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 79 optimal weight: 0.2980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3403 r_free = 0.3403 target = 0.081751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.061530 restraints weight = 72877.687| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 4.27 r_work: 0.2855 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9700 Z= 0.128 Angle : 0.544 6.005 13202 Z= 0.281 Chirality : 0.042 0.212 1468 Planarity : 0.003 0.039 1665 Dihedral : 6.310 50.953 1607 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.98 % Allowed : 6.27 % Favored : 92.75 % 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: 0.01 (0.25), residues: 1124 helix: 0.45 (0.30), residues: 305 sheet: 0.19 (0.29), residues: 314 loop : -0.25 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 229 HIS 0.004 0.001 HIS C 276 PHE 0.026 0.001 PHE A 343 TYR 0.010 0.001 TYR C 284 ARG 0.002 0.000 ARG B 317 Details of bonding type rmsd link_NAG-ASN : bond 0.00147 ( 7) link_NAG-ASN : angle 1.13902 ( 21) link_BETA1-4 : bond 0.00225 ( 7) link_BETA1-4 : angle 1.78976 ( 21) hydrogen bonds : bond 0.03586 ( 398) hydrogen bonds : angle 5.01897 ( 1161) SS BOND : bond 0.00257 ( 25) SS BOND : angle 1.08447 ( 50) covalent geometry : bond 0.00285 ( 9661) covalent geometry : angle 0.53509 (13110) *********************** 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 91 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 1.448 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: C 403 MET cc_start: 0.8874 (tpt) cc_final: 0.8602 (tpp) REVERT: C 490 ARG cc_start: 0.8578 (tpm170) cc_final: 0.8171 (tpm170) outliers start: 10 outliers final: 8 residues processed: 89 average time/residue: 0.4587 time to fit residues: 57.9696 Evaluate side-chains 85 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 45 optimal weight: 0.9980 chunk 20 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 chunk 15 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN A 279 HIS ** 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 = 0.3397 r_free = 0.3397 target = 0.080937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.061059 restraints weight = 74169.993| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 4.21 r_work: 0.2828 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9700 Z= 0.200 Angle : 0.572 9.320 13202 Z= 0.296 Chirality : 0.041 0.189 1468 Planarity : 0.003 0.037 1665 Dihedral : 6.018 49.976 1607 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.08 % Allowed : 6.67 % Favored : 92.25 % 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: -0.03 (0.25), residues: 1124 helix: 0.55 (0.30), residues: 304 sheet: 0.07 (0.29), residues: 319 loop : -0.30 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 248 HIS 0.004 0.001 HIS A 236 PHE 0.026 0.001 PHE A 343 TYR 0.010 0.001 TYR C 284 ARG 0.003 0.000 ARG B 317 Details of bonding type rmsd link_NAG-ASN : bond 0.00384 ( 7) link_NAG-ASN : angle 1.26515 ( 21) link_BETA1-4 : bond 0.00350 ( 7) link_BETA1-4 : angle 1.67648 ( 21) hydrogen bonds : bond 0.03634 ( 398) hydrogen bonds : angle 4.98192 ( 1161) SS BOND : bond 0.00349 ( 25) SS BOND : angle 1.26143 ( 50) covalent geometry : bond 0.00438 ( 9661) covalent geometry : angle 0.56247 (13110) *********************** 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 88 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 ASN cc_start: 0.9018 (m110) cc_final: 0.8794 (m110) REVERT: A 473 LYS cc_start: 0.9387 (mmmt) cc_final: 0.9160 (mmtm) REVERT: C 403 MET cc_start: 0.8969 (tpt) cc_final: 0.8731 (tpp) REVERT: C 490 ARG cc_start: 0.8526 (tpm170) cc_final: 0.8084 (tpm170) outliers start: 11 outliers final: 9 residues processed: 85 average time/residue: 0.4788 time to fit residues: 57.6280 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 : 1.420 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.3980 chunk 69 optimal weight: 3.9990 chunk 81 optimal weight: 0.3980 chunk 13 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 = 0.3402 r_free = 0.3402 target = 0.081602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.061496 restraints weight = 73421.458| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 4.23 r_work: 0.2858 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9700 Z= 0.108 Angle : 0.517 7.909 13202 Z= 0.267 Chirality : 0.041 0.211 1468 Planarity : 0.003 0.036 1665 Dihedral : 5.638 50.177 1607 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.08 % Allowed : 7.45 % Favored : 91.47 % 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: 0.78 (0.30), residues: 304 sheet: 0.18 (0.29), residues: 314 loop : -0.09 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 248 HIS 0.004 0.001 HIS C 112 PHE 0.026 0.001 PHE A 343 TYR 0.009 0.001 TYR C 304 ARG 0.003 0.000 ARG B 317 Details of bonding type rmsd link_NAG-ASN : bond 0.00124 ( 7) link_NAG-ASN : angle 1.05322 ( 21) link_BETA1-4 : bond 0.00294 ( 7) link_BETA1-4 : angle 1.51249 ( 21) hydrogen bonds : bond 0.03267 ( 398) hydrogen bonds : angle 4.75374 ( 1161) SS BOND : bond 0.00305 ( 25) SS BOND : angle 1.18014 ( 50) covalent geometry : bond 0.00242 ( 9661) covalent geometry : angle 0.50798 (13110) *********************** 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 93 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 1.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 ASN cc_start: 0.8906 (m110) cc_final: 0.8604 (m110) REVERT: A 473 LYS cc_start: 0.9364 (mmmt) cc_final: 0.9127 (mmtm) REVERT: C 403 MET cc_start: 0.8882 (tpt) cc_final: 0.8649 (tpp) REVERT: C 490 ARG cc_start: 0.8489 (tpm170) cc_final: 0.8020 (tpm170) outliers start: 11 outliers final: 8 residues processed: 91 average time/residue: 0.4691 time to fit residues: 61.4198 Evaluate side-chains 85 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.7980 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: 3.9990 chunk 110 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3417 r_free = 0.3417 target = 0.082450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.063913 restraints weight = 73541.475| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 3.91 r_work: 0.2860 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 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 0.038 9700 Z= 0.149 Angle : 0.524 7.002 13202 Z= 0.269 Chirality : 0.040 0.186 1468 Planarity : 0.003 0.035 1665 Dihedral : 5.498 49.724 1607 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.98 % Allowed : 7.65 % Favored : 91.37 % 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: 0.19 (0.25), residues: 1124 helix: 0.79 (0.30), residues: 310 sheet: 0.17 (0.29), residues: 315 loop : -0.18 (0.28), residues: 499 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 0.024 0.001 PHE A 343 TYR 0.009 0.001 TYR C 284 ARG 0.004 0.000 ARG B 317 Details of bonding type rmsd link_NAG-ASN : bond 0.00283 ( 7) link_NAG-ASN : angle 1.17183 ( 21) link_BETA1-4 : bond 0.00301 ( 7) link_BETA1-4 : angle 1.50533 ( 21) hydrogen bonds : bond 0.03233 ( 398) hydrogen bonds : angle 4.75768 ( 1161) SS BOND : bond 0.00302 ( 25) SS BOND : angle 1.14288 ( 50) covalent geometry : bond 0.00329 ( 9661) covalent geometry : angle 0.51505 (13110) *********************** 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 88 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 1.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 ASN cc_start: 0.8933 (m110) cc_final: 0.8596 (m110) outliers start: 10 outliers final: 10 residues processed: 86 average time/residue: 0.4588 time to fit residues: 56.5357 Evaluate side-chains 89 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 1.376 ------------------------------------------------------------------------------- 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 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 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: 3.9990 chunk 94 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 overall best weight: 1.5188 ------------------------------------------------------------------------------- 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 = 0.3398 r_free = 0.3398 target = 0.081215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.061866 restraints weight = 74354.206| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 4.00 r_work: 0.2837 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9700 Z= 0.190 Angle : 0.542 6.832 13202 Z= 0.279 Chirality : 0.041 0.219 1468 Planarity : 0.003 0.036 1665 Dihedral : 5.538 47.728 1607 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.27 % Allowed : 7.65 % 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: 0.81 (0.30), residues: 304 sheet: 0.09 (0.29), residues: 313 loop : -0.22 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 248 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 0.006 0.000 ARG B 317 Details of bonding type rmsd link_NAG-ASN : bond 0.00364 ( 7) link_NAG-ASN : angle 1.21166 ( 21) link_BETA1-4 : bond 0.00311 ( 7) link_BETA1-4 : angle 1.46856 ( 21) hydrogen bonds : bond 0.03254 ( 398) hydrogen bonds : angle 4.80947 ( 1161) SS BOND : bond 0.00321 ( 25) SS BOND : angle 1.12858 ( 50) covalent geometry : bond 0.00420 ( 9661) covalent geometry : angle 0.53394 (13110) *********************** 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 92 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 1.552 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: 0.8889 (m110) cc_final: 0.8537 (m110) REVERT: B 452 GLN cc_start: 0.8514 (mt0) cc_final: 0.7561 (mp10) outliers start: 13 outliers final: 10 residues processed: 88 average time/residue: 0.4620 time to fit residues: 58.5660 Evaluate side-chains 89 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 1.536 ------------------------------------------------------------------------------- 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 341 GLU 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: 0.8980 chunk 55 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 65 optimal weight: 0.4980 chunk 60 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3415 r_free = 0.3415 target = 0.082033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.062743 restraints weight = 73273.460| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 3.98 r_work: 0.2860 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9700 Z= 0.114 Angle : 0.505 6.621 13202 Z= 0.258 Chirality : 0.040 0.199 1468 Planarity : 0.003 0.035 1665 Dihedral : 5.354 48.166 1607 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.78 % Allowed : 8.14 % 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: 0.33 (0.25), residues: 1124 helix: 1.01 (0.30), residues: 310 sheet: 0.17 (0.29), residues: 308 loop : -0.12 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 248 HIS 0.004 0.001 HIS C 112 PHE 0.019 0.001 PHE A 343 TYR 0.009 0.001 TYR B 273 ARG 0.003 0.000 ARG B 317 Details of bonding type rmsd link_NAG-ASN : bond 0.00140 ( 7) link_NAG-ASN : angle 1.07696 ( 21) link_BETA1-4 : bond 0.00255 ( 7) link_BETA1-4 : angle 1.47432 ( 21) hydrogen bonds : bond 0.03054 ( 398) hydrogen bonds : angle 4.63075 ( 1161) SS BOND : bond 0.00264 ( 25) SS BOND : angle 1.05317 ( 50) covalent geometry : bond 0.00257 ( 9661) covalent geometry : angle 0.49692 (13110) *********************** 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 89 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 1.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 ASN cc_start: 0.8843 (m110) cc_final: 0.8454 (m110) REVERT: A 473 LYS cc_start: 0.9419 (mmmt) cc_final: 0.9117 (mmtm) REVERT: B 452 GLN cc_start: 0.8509 (mt0) cc_final: 0.7558 (mp10) outliers start: 8 outliers final: 7 residues processed: 88 average time/residue: 0.4853 time to fit residues: 59.9548 Evaluate side-chains 85 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 270 CYS 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 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: 2.9990 chunk 17 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 45 optimal weight: 0.3980 chunk 60 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 75 optimal weight: 0.0870 chunk 64 optimal weight: 1.9990 chunk 57 optimal weight: 0.1980 overall best weight: 0.7160 ------------------------------------------------------------------------------- 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 = 0.3421 r_free = 0.3421 target = 0.082258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.062734 restraints weight = 73750.768| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 4.06 r_work: 0.2860 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9700 Z= 0.117 Angle : 0.517 7.233 13202 Z= 0.266 Chirality : 0.040 0.203 1468 Planarity : 0.003 0.034 1665 Dihedral : 5.278 48.825 1607 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.78 % Allowed : 8.33 % 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: 0.31 (0.25), residues: 1124 helix: 0.98 (0.30), residues: 309 sheet: 0.17 (0.29), residues: 311 loop : -0.12 (0.29), residues: 504 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 0.017 0.001 PHE A 343 TYR 0.008 0.001 TYR B 273 ARG 0.004 0.000 ARG B 317 Details of bonding type rmsd link_NAG-ASN : bond 0.00183 ( 7) link_NAG-ASN : angle 1.10687 ( 21) link_BETA1-4 : bond 0.00237 ( 7) link_BETA1-4 : angle 1.45885 ( 21) hydrogen bonds : bond 0.03186 ( 398) hydrogen bonds : angle 4.63460 ( 1161) SS BOND : bond 0.00270 ( 25) SS BOND : angle 1.43340 ( 50) covalent geometry : bond 0.00267 ( 9661) covalent geometry : angle 0.50603 (13110) ********************** 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 89 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 1.457 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: A 158 ASN cc_start: 0.8834 (m110) cc_final: 0.8468 (m110) REVERT: A 473 LYS cc_start: 0.9424 (mmmt) cc_final: 0.9116 (mmtm) REVERT: B 452 GLN cc_start: 0.8547 (mt0) cc_final: 0.7630 (mp10) outliers start: 8 outliers final: 7 residues processed: 88 average time/residue: 0.4564 time to fit residues: 57.6295 Evaluate side-chains 86 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 270 CYS 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 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: 0.9990 chunk 59 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 96 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 112 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3414 r_free = 0.3414 target = 0.081856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.062763 restraints weight = 72494.635| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 3.93 r_work: 0.2868 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 9700 Z= 0.123 Angle : 0.522 8.961 13202 Z= 0.268 Chirality : 0.040 0.189 1468 Planarity : 0.003 0.034 1665 Dihedral : 5.242 49.011 1607 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.78 % Allowed : 8.24 % Favored : 90.98 % 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: 0.36 (0.25), residues: 1124 helix: 1.03 (0.30), residues: 309 sheet: 0.19 (0.29), residues: 310 loop : -0.09 (0.29), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 229 HIS 0.003 0.001 HIS C 112 PHE 0.017 0.001 PHE A 343 TYR 0.013 0.001 TYR A 265 ARG 0.004 0.000 ARG B 317 Details of bonding type rmsd link_NAG-ASN : bond 0.00181 ( 7) link_NAG-ASN : angle 1.11991 ( 21) link_BETA1-4 : bond 0.00271 ( 7) link_BETA1-4 : angle 1.45681 ( 21) hydrogen bonds : bond 0.03171 ( 398) hydrogen bonds : angle 4.63484 ( 1161) SS BOND : bond 0.00257 ( 25) SS BOND : angle 1.58540 ( 50) covalent geometry : bond 0.00283 ( 9661) covalent geometry : angle 0.50917 (13110) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9278.18 seconds wall clock time: 161 minutes 25.95 seconds (9685.95 seconds total)