Starting phenix.real_space_refine on Thu Sep 18 17:01:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9blr_44674/09_2025/9blr_44674_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9blr_44674/09_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_44674/09_2025/9blr_44674.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9blr_44674/09_2025/9blr_44674.map" model { file = "/net/cci-nas-00/data/ceres_data/9blr_44674/09_2025/9blr_44674_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9blr_44674/09_2025/9blr_44674_trim.cif" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.76, per 1000 atoms: 0.15 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: 1.49 Conformation dependent library (CDL) restraints added in 606.8 milliseconds Enol-peptide restraints added in 1.7 microseconds 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: 0.43 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: 3.77 Time building geometry restraints manager: 2.13 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: 7.350 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: 0.110 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.310 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.450 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.001 ARG A 139 TYR 0.019 0.002 TYR C 425 PHE 0.020 0.002 PHE B 328 TRP 0.021 0.002 TRP C 229 HIS 0.009 0.002 HIS A 431 Details of bonding type rmsd covalent geometry : bond 0.00461 ( 9661) covalent geometry : angle 0.85534 (13110) SS BOND : bond 0.00389 ( 25) SS BOND : angle 1.35907 ( 50) hydrogen bonds : bond 0.16152 ( 398) hydrogen bonds : angle 7.64582 ( 1161) link_BETA1-4 : bond 0.00906 ( 7) link_BETA1-4 : angle 3.43900 ( 21) link_NAG-ASN : bond 0.08172 ( 7) link_NAG-ASN : angle 4.92926 ( 21) *********************** 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 : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 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: 0.8088 (mmt) outliers start: 2 outliers final: 2 residues processed: 127 average time/residue: 0.2525 time to fit residues: 42.3765 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 : 0.534 ------------------------------------------------------------------------------- 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 108 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 GLN B 431 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 = 0.3424 r_free = 0.3424 target = 0.082445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.062362 restraints weight = 72874.829| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 4.22 r_work: 0.2852 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9700 Z= 0.213 Angle : 0.684 7.892 13202 Z= 0.354 Chirality : 0.046 0.218 1468 Planarity : 0.005 0.047 1665 Dihedral : 11.027 64.099 1607 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.24), residues: 1124 helix: -0.67 (0.28), residues: 311 sheet: 0.20 (0.30), residues: 296 loop : -0.46 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 490 TYR 0.014 0.001 TYR C 284 PHE 0.031 0.002 PHE A 343 TRP 0.016 0.001 TRP C 229 HIS 0.006 0.001 HIS C 332 Details of bonding type rmsd covalent geometry : bond 0.00470 ( 9661) covalent geometry : angle 0.67125 (13110) SS BOND : bond 0.00350 ( 25) SS BOND : angle 1.21173 ( 50) hydrogen bonds : bond 0.05196 ( 398) hydrogen bonds : angle 5.89041 ( 1161) link_BETA1-4 : bond 0.00449 ( 7) link_BETA1-4 : angle 2.59194 ( 21) link_NAG-ASN : bond 0.00482 ( 7) link_NAG-ASN : angle 1.56229 ( 21) *********************** 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 : 0.410 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: 0.7803 (tpt) cc_final: 0.7547 (tpt) REVERT: C 363 PHE cc_start: 0.9006 (m-80) cc_final: 0.8673 (m-80) REVERT: C 490 ARG cc_start: 0.8641 (tpm170) cc_final: 0.8404 (tpm170) outliers start: 6 outliers final: 5 residues processed: 93 average time/residue: 0.1913 time to fit residues: 25.0539 Evaluate side-chains 81 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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 71 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 105 optimal weight: 0.3980 chunk 51 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 A 443 HIS ** C 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.081332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.061270 restraints weight = 73548.126| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 4.25 r_work: 0.2848 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9700 Z= 0.180 Angle : 0.607 6.295 13202 Z= 0.313 Chirality : 0.043 0.187 1468 Planarity : 0.004 0.041 1665 Dihedral : 7.644 50.968 1607 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.78 % Allowed : 4.90 % Favored : 94.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.25), residues: 1124 helix: -0.04 (0.30), residues: 305 sheet: 0.28 (0.30), residues: 298 loop : -0.43 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 330 TYR 0.012 0.001 TYR C 284 PHE 0.027 0.001 PHE A 343 TRP 0.012 0.001 TRP C 229 HIS 0.005 0.001 HIS A 315 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 9661) covalent geometry : angle 0.59615 (13110) SS BOND : bond 0.00300 ( 25) SS BOND : angle 1.15567 ( 50) hydrogen bonds : bond 0.04223 ( 398) hydrogen bonds : angle 5.38935 ( 1161) link_BETA1-4 : bond 0.00430 ( 7) link_BETA1-4 : angle 2.16667 ( 21) link_NAG-ASN : bond 0.00242 ( 7) link_NAG-ASN : angle 1.36586 ( 21) *********************** 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 90 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.448 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: symmetry clash REVERT: B 454 LYS cc_start: 0.9383 (mmtp) cc_final: 0.9119 (mmtm) REVERT: C 477 GLU cc_start: 0.9318 (tt0) cc_final: 0.8767 (tm-30) REVERT: C 490 ARG cc_start: 0.8642 (tpm170) cc_final: 0.8301 (tpm170) outliers start: 8 outliers final: 8 residues processed: 89 average time/residue: 0.1802 time to fit residues: 23.1086 Evaluate side-chains 84 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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 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 36 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 94 optimal weight: 0.1980 chunk 110 optimal weight: 0.3980 chunk 92 optimal weight: 0.5980 chunk 84 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3414 r_free = 0.3414 target = 0.082425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.062859 restraints weight = 72219.223| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 4.15 r_work: 0.2881 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2615 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= 0.107 Angle : 0.532 5.389 13202 Z= 0.276 Chirality : 0.042 0.211 1468 Planarity : 0.003 0.039 1665 Dihedral : 6.252 52.249 1607 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.88 % Allowed : 5.98 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.25), residues: 1124 helix: 0.33 (0.30), residues: 305 sheet: 0.25 (0.29), residues: 314 loop : -0.26 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 317 TYR 0.010 0.001 TYR C 284 PHE 0.026 0.001 PHE A 343 TRP 0.010 0.001 TRP C 229 HIS 0.005 0.001 HIS C 439 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 9661) covalent geometry : angle 0.52215 (13110) SS BOND : bond 0.00270 ( 25) SS BOND : angle 1.08827 ( 50) hydrogen bonds : bond 0.03539 ( 398) hydrogen bonds : angle 5.01150 ( 1161) link_BETA1-4 : bond 0.00285 ( 7) link_BETA1-4 : angle 1.89217 ( 21) link_NAG-ASN : bond 0.00152 ( 7) link_NAG-ASN : angle 1.08814 ( 21) *********************** 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 92 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.324 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: A 158 ASN cc_start: 0.9154 (m-40) cc_final: 0.8853 (m-40) REVERT: B 454 LYS cc_start: 0.9407 (mmtp) cc_final: 0.9170 (mmtm) REVERT: C 490 ARG cc_start: 0.8601 (tpm170) cc_final: 0.8213 (tpm170) outliers start: 9 outliers final: 8 residues processed: 90 average time/residue: 0.2014 time to fit residues: 25.5021 Evaluate side-chains 88 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.490 ------------------------------------------------------------------------------- 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 19 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 GLN ** 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 = 0.3402 r_free = 0.3402 target = 0.081129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.061409 restraints weight = 73865.843| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 4.22 r_work: 0.2830 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9700 Z= 0.225 Angle : 0.582 9.011 13202 Z= 0.302 Chirality : 0.041 0.193 1468 Planarity : 0.003 0.037 1665 Dihedral : 6.003 50.735 1607 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.08 % Allowed : 6.47 % Favored : 92.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.25), residues: 1124 helix: 0.46 (0.30), residues: 304 sheet: 0.21 (0.29), residues: 315 loop : -0.34 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 317 TYR 0.011 0.001 TYR C 284 PHE 0.028 0.001 PHE A 343 TRP 0.016 0.001 TRP A 248 HIS 0.004 0.001 HIS C 428 Details of bonding type rmsd covalent geometry : bond 0.00492 ( 9661) covalent geometry : angle 0.57316 (13110) SS BOND : bond 0.00480 ( 25) SS BOND : angle 1.22541 ( 50) hydrogen bonds : bond 0.03661 ( 398) hydrogen bonds : angle 5.03927 ( 1161) link_BETA1-4 : bond 0.00398 ( 7) link_BETA1-4 : angle 1.62623 ( 21) link_NAG-ASN : bond 0.00506 ( 7) link_NAG-ASN : angle 1.34112 ( 21) *********************** 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 91 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.488 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: 0.9160 (m-40) cc_final: 0.8867 (m-40) REVERT: A 473 LYS cc_start: 0.9385 (mmmt) cc_final: 0.9159 (mmtm) REVERT: B 454 LYS cc_start: 0.9431 (mmtp) cc_final: 0.9209 (mmtm) REVERT: C 403 MET cc_start: 0.8989 (tpt) cc_final: 0.8778 (tpp) REVERT: C 490 ARG cc_start: 0.8519 (tpm170) cc_final: 0.8096 (tpm170) outliers start: 11 outliers final: 10 residues processed: 88 average time/residue: 0.2098 time to fit residues: 25.8697 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 : 0.485 ------------------------------------------------------------------------------- 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 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 46 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 51 optimal weight: 0.3980 chunk 17 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 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 = 0.3418 r_free = 0.3418 target = 0.081837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.062160 restraints weight = 73124.820| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 4.18 r_work: 0.2852 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3103 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= 0.130 Angle : 0.523 8.162 13202 Z= 0.270 Chirality : 0.041 0.208 1468 Planarity : 0.003 0.036 1665 Dihedral : 5.653 50.296 1607 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.08 % Allowed : 7.16 % Favored : 91.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.25), residues: 1124 helix: 0.73 (0.30), residues: 304 sheet: 0.22 (0.29), residues: 314 loop : -0.14 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 317 TYR 0.009 0.001 TYR C 284 PHE 0.024 0.001 PHE A 343 TRP 0.009 0.001 TRP A 248 HIS 0.003 0.001 HIS C 276 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 9661) covalent geometry : angle 0.51461 (13110) SS BOND : bond 0.00314 ( 25) SS BOND : angle 1.21778 ( 50) hydrogen bonds : bond 0.03312 ( 398) hydrogen bonds : angle 4.80781 ( 1161) link_BETA1-4 : bond 0.00302 ( 7) link_BETA1-4 : angle 1.48859 ( 21) link_NAG-ASN : bond 0.00144 ( 7) link_NAG-ASN : angle 1.09356 ( 21) *********************** 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 94 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.492 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: A 158 ASN cc_start: 0.9094 (m-40) cc_final: 0.8803 (m-40) REVERT: A 473 LYS cc_start: 0.9370 (mmmt) cc_final: 0.9130 (mmtm) REVERT: B 454 LYS cc_start: 0.9430 (mmtp) cc_final: 0.9209 (mmtt) REVERT: C 403 MET cc_start: 0.8907 (tpt) cc_final: 0.8696 (tpp) REVERT: C 490 ARG cc_start: 0.8491 (tpm170) cc_final: 0.8024 (tpm170) outliers start: 11 outliers final: 9 residues processed: 92 average time/residue: 0.1928 time to fit residues: 25.1754 Evaluate side-chains 90 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 105 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 21 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 53 optimal weight: 0.0670 chunk 99 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 overall best weight: 0.7522 ------------------------------------------------------------------------------- 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 = 0.3401 r_free = 0.3401 target = 0.081819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.062054 restraints weight = 74255.672| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 4.09 r_work: 0.2867 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3275 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= 0.116 Angle : 0.505 7.398 13202 Z= 0.260 Chirality : 0.040 0.191 1468 Planarity : 0.003 0.036 1665 Dihedral : 5.386 50.785 1607 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.98 % Allowed : 7.84 % Favored : 91.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.25), residues: 1124 helix: 0.78 (0.30), residues: 310 sheet: 0.24 (0.29), residues: 317 loop : -0.19 (0.29), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 317 TYR 0.008 0.001 TYR C 284 PHE 0.026 0.001 PHE A 343 TRP 0.009 0.001 TRP C 229 HIS 0.004 0.001 HIS C 112 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 9661) covalent geometry : angle 0.49705 (13110) SS BOND : bond 0.00269 ( 25) SS BOND : angle 1.09119 ( 50) hydrogen bonds : bond 0.03163 ( 398) hydrogen bonds : angle 4.69752 ( 1161) link_BETA1-4 : bond 0.00307 ( 7) link_BETA1-4 : angle 1.43012 ( 21) link_NAG-ASN : bond 0.00188 ( 7) link_NAG-ASN : angle 1.10153 ( 21) *********************** 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 94 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.405 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: symmetry clash revert: symmetry clash REVERT: A 457 GLU cc_start: 0.7806 (tm-30) cc_final: 0.7502 (tm-30) REVERT: C 490 ARG cc_start: 0.8469 (tpm170) cc_final: 0.7995 (tpm170) outliers start: 10 outliers final: 10 residues processed: 93 average time/residue: 0.1909 time to fit residues: 25.6076 Evaluate side-chains 94 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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 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 47 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 93 optimal weight: 0.1980 chunk 25 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 41 optimal weight: 0.2980 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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 = 0.3410 r_free = 0.3410 target = 0.082246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.062579 restraints weight = 73646.852| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 4.06 r_work: 0.2877 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9700 Z= 0.102 Angle : 0.494 6.860 13202 Z= 0.252 Chirality : 0.040 0.210 1468 Planarity : 0.003 0.035 1665 Dihedral : 5.186 51.436 1607 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.18 % Allowed : 8.04 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.25), residues: 1124 helix: 0.91 (0.30), residues: 310 sheet: 0.32 (0.29), residues: 316 loop : -0.10 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 317 TYR 0.007 0.001 TYR C 284 PHE 0.019 0.001 PHE A 343 TRP 0.009 0.001 TRP C 229 HIS 0.004 0.001 HIS C 112 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 9661) covalent geometry : angle 0.48640 (13110) SS BOND : bond 0.00251 ( 25) SS BOND : angle 1.03323 ( 50) hydrogen bonds : bond 0.02979 ( 398) hydrogen bonds : angle 4.60493 ( 1161) link_BETA1-4 : bond 0.00338 ( 7) link_BETA1-4 : angle 1.41510 ( 21) link_NAG-ASN : bond 0.00141 ( 7) link_NAG-ASN : angle 1.05069 ( 21) *********************** 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 100 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.446 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: A 457 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7496 (tm-30) REVERT: B 452 GLN cc_start: 0.8553 (mt0) cc_final: 0.7572 (mp10) outliers start: 12 outliers final: 10 residues processed: 98 average time/residue: 0.2009 time to fit residues: 27.6541 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 : 0.406 ------------------------------------------------------------------------------- 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 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 111 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 81 optimal weight: 0.3980 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.3406 r_free = 0.3406 target = 0.081949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.062493 restraints weight = 73478.788| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 3.93 r_work: 0.2879 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 9700 Z= 0.113 Angle : 0.508 7.666 13202 Z= 0.260 Chirality : 0.040 0.195 1468 Planarity : 0.003 0.034 1665 Dihedral : 5.136 51.676 1607 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.27 % Allowed : 8.04 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.25), residues: 1124 helix: 0.92 (0.30), residues: 310 sheet: 0.29 (0.29), residues: 318 loop : -0.11 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 317 TYR 0.008 0.001 TYR B 273 PHE 0.018 0.001 PHE A 343 TRP 0.009 0.001 TRP C 229 HIS 0.004 0.001 HIS C 112 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 9661) covalent geometry : angle 0.49689 (13110) SS BOND : bond 0.00250 ( 25) SS BOND : angle 1.41038 ( 50) hydrogen bonds : bond 0.03143 ( 398) hydrogen bonds : angle 4.58529 ( 1161) link_BETA1-4 : bond 0.00284 ( 7) link_BETA1-4 : angle 1.39317 ( 21) link_NAG-ASN : bond 0.00172 ( 7) link_NAG-ASN : angle 1.08099 ( 21) *********************** 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 95 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.481 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: A 457 GLU cc_start: 0.7814 (tm-30) cc_final: 0.7515 (tm-30) REVERT: B 452 GLN cc_start: 0.8530 (mt0) cc_final: 0.7576 (mp10) outliers start: 13 outliers final: 10 residues processed: 93 average time/residue: 0.1866 time to fit residues: 24.9346 Evaluate side-chains 94 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.493 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 70 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 91 optimal weight: 0.3980 chunk 93 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3408 r_free = 0.3408 target = 0.082009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.062454 restraints weight = 73699.149| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 3.96 r_work: 0.2877 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 9700 Z= 0.113 Angle : 0.513 8.703 13202 Z= 0.262 Chirality : 0.040 0.198 1468 Planarity : 0.003 0.035 1665 Dihedral : 5.063 51.904 1607 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.98 % Allowed : 8.04 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.25), residues: 1124 helix: 1.03 (0.30), residues: 309 sheet: 0.34 (0.29), residues: 317 loop : -0.08 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 317 TYR 0.007 0.001 TYR B 273 PHE 0.016 0.001 PHE A 343 TRP 0.018 0.001 TRP A 248 HIS 0.004 0.001 HIS C 112 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 9661) covalent geometry : angle 0.50054 (13110) SS BOND : bond 0.00254 ( 25) SS BOND : angle 1.53736 ( 50) hydrogen bonds : bond 0.03110 ( 398) hydrogen bonds : angle 4.58198 ( 1161) link_BETA1-4 : bond 0.00302 ( 7) link_BETA1-4 : angle 1.39014 ( 21) link_NAG-ASN : bond 0.00157 ( 7) link_NAG-ASN : angle 1.07814 ( 21) ********************** 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 96 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.484 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 457 GLU cc_start: 0.7793 (tm-30) cc_final: 0.7496 (tm-30) REVERT: B 452 GLN cc_start: 0.8530 (mt0) cc_final: 0.7578 (mp10) outliers start: 10 outliers final: 10 residues processed: 95 average time/residue: 0.2051 time to fit residues: 27.8952 Evaluate side-chains 92 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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 386 SER Chi-restraints excluded: chain A residue 463 SER Chi-restraints excluded: chain B residue 256 CYS Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 347 LEU 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 34 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 99 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 1 optimal weight: 0.0970 chunk 27 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 = 0.3411 r_free = 0.3411 target = 0.082258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.062618 restraints weight = 74075.003| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 3.98 r_work: 0.2877 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9700 Z= 0.111 Angle : 0.513 8.691 13202 Z= 0.263 Chirality : 0.040 0.190 1468 Planarity : 0.003 0.034 1665 Dihedral : 5.020 52.008 1607 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.98 % Allowed : 8.24 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.25), residues: 1124 helix: 1.10 (0.30), residues: 309 sheet: 0.34 (0.29), residues: 317 loop : -0.07 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 317 TYR 0.026 0.001 TYR C 304 PHE 0.016 0.001 PHE A 343 TRP 0.017 0.001 TRP A 248 HIS 0.003 0.001 HIS C 112 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 9661) covalent geometry : angle 0.50309 (13110) SS BOND : bond 0.00245 ( 25) SS BOND : angle 1.37643 ( 50) hydrogen bonds : bond 0.03066 ( 398) hydrogen bonds : angle 4.56787 ( 1161) link_BETA1-4 : bond 0.00295 ( 7) link_BETA1-4 : angle 1.38829 ( 21) link_NAG-ASN : bond 0.00159 ( 7) link_NAG-ASN : angle 1.07990 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3635.87 seconds wall clock time: 62 minutes 26.28 seconds (3746.28 seconds total)