Starting phenix.real_space_refine on Sat Sep 12 08:20:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6yup_10933/09_2026/6yup_10933.cif Found real_map, /net/cci-nas-00/data/ceres_data/6yup_10933/09_2026/6yup_10933.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6yup_10933/09_2026/6yup_10933.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6yup_10933/09_2026/6yup_10933.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6yup_10933/09_2026/6yup_10933.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6yup_10933/09_2026/6yup_10933.cif" model { file = "/net/cci-nas-00/data/ceres_data/6yup_10933/09_2026/6yup_10933.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6yup_10933/09_2026/6yup_10933.cif" } resolution = 2.9 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= 0.002 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 Ca 2 9.91 5 S 76 5.16 5 C 9620 2.51 5 N 2366 2.21 5 O 2710 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 115 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14774 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4834 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 22, 'TRANS': 571} Chain: "C" Number of atoms: 4834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4834 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 22, 'TRANS': 571} Chain: "D" Number of atoms: 2496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2496 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 18, 'TRANS': 309} Chain breaks: 7 Chain: "E" Number of atoms: 2496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2496 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 18, 'TRANS': 309} Chain breaks: 7 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' CA': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' CA': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 3.53, per 1000 atoms: 0.24 Number of scatterers: 14774 At special positions: 0 Unit cell: (133.92, 92.907, 127.224, 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) Ca 2 19.99 S 76 16.00 O 2710 8.00 N 2366 7.00 C 9620 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 242 " - pdb=" SG CYS A 273 " distance=2.03 Simple disulfide: pdb=" SG CYS A 571 " - pdb=" SG CYS A 666 " distance=2.16 Simple disulfide: pdb=" SG CYS A 673 " - pdb=" SG CYS A 685 " distance=2.04 Simple disulfide: pdb=" SG CYS C 242 " - pdb=" SG CYS C 273 " distance=2.03 Simple disulfide: pdb=" SG CYS C 571 " - pdb=" SG CYS C 666 " distance=2.10 Simple disulfide: pdb=" SG CYS C 673 " - pdb=" SG CYS C 685 " distance=2.04 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 Atom "HETATM14700 O5 NAG A 703 .*. O " rejected from bonding due to valence issues. Atom "HETATM14771 O5 NAG C 704 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 701 " - " ASN A 332 " " NAG A 702 " - " ASN A 513 " " NAG A 703 " - " ASN A 575 " " NAG A 704 " - " ASN A 261 " " NAG C 701 " - " ASN C 332 " " NAG C 702 " - " ASN C 513 " " NAG C 703 " - " ASN C 575 " " NAG C 704 " - " ASN C 261 " Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 681.7 milliseconds 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3464 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 18 sheets defined 47.2% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 92 through 111 removed outlier: 4.259A pdb=" N LEU A 98 " --> pdb=" O VAL A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 148 removed outlier: 3.649A pdb=" N ILE A 145 " --> pdb=" O ASP A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 155 removed outlier: 3.578A pdb=" N ILE A 152 " --> pdb=" O LYS A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 203 removed outlier: 3.567A pdb=" N LYS A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 227 Processing helix chain 'A' and resid 230 through 236 removed outlier: 3.597A pdb=" N TYR A 233 " --> pdb=" O THR A 230 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR A 234 " --> pdb=" O GLY A 231 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP A 235 " --> pdb=" O LYS A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 307 removed outlier: 3.762A pdb=" N LYS A 297 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS A 306 " --> pdb=" O PHE A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 369 Processing helix chain 'A' and resid 370 through 372 No H-bonds generated for 'chain 'A' and resid 370 through 372' Processing helix chain 'A' and resid 389 through 394 Processing helix chain 'A' and resid 420 through 435 removed outlier: 3.672A pdb=" N ASN A 434 " --> pdb=" O SER A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 457 Processing helix chain 'A' and resid 458 through 460 No H-bonds generated for 'chain 'A' and resid 458 through 460' Processing helix chain 'A' and resid 461 through 471 Processing helix chain 'A' and resid 503 through 507 removed outlier: 3.982A pdb=" N SER A 507 " --> pdb=" O ARG A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 519 Processing helix chain 'A' and resid 537 through 544 Processing helix chain 'A' and resid 549 through 562 Processing helix chain 'A' and resid 562 through 567 removed outlier: 3.775A pdb=" N ASN A 566 " --> pdb=" O GLU A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 659 Processing helix chain 'C' and resid 93 through 111 removed outlier: 4.258A pdb=" N LEU C 98 " --> pdb=" O VAL C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 148 removed outlier: 3.648A pdb=" N ILE C 145 " --> pdb=" O ASP C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 155 removed outlier: 3.578A pdb=" N ILE C 152 " --> pdb=" O LYS C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 203 removed outlier: 3.566A pdb=" N LYS C 203 " --> pdb=" O ALA C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 227 Processing helix chain 'C' and resid 230 through 236 removed outlier: 3.596A pdb=" N TYR C 233 " --> pdb=" O THR C 230 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR C 234 " --> pdb=" O GLY C 231 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP C 235 " --> pdb=" O LYS C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 307 removed outlier: 3.759A pdb=" N LYS C 297 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS C 306 " --> pdb=" O PHE C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 369 Processing helix chain 'C' and resid 370 through 372 No H-bonds generated for 'chain 'C' and resid 370 through 372' Processing helix chain 'C' and resid 389 through 394 Processing helix chain 'C' and resid 420 through 435 removed outlier: 3.671A pdb=" N ASN C 434 " --> pdb=" O SER C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 457 Processing helix chain 'C' and resid 458 through 460 No H-bonds generated for 'chain 'C' and resid 458 through 460' Processing helix chain 'C' and resid 461 through 471 Processing helix chain 'C' and resid 503 through 507 removed outlier: 3.980A pdb=" N SER C 507 " --> pdb=" O ARG C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 519 Processing helix chain 'C' and resid 537 through 544 Processing helix chain 'C' and resid 549 through 562 Processing helix chain 'C' and resid 562 through 567 removed outlier: 3.774A pdb=" N ASN C 566 " --> pdb=" O GLU C 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 659 Processing helix chain 'D' and resid 32 through 42 Processing helix chain 'D' and resid 50 through 60 removed outlier: 4.267A pdb=" N SER D 54 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER D 57 " --> pdb=" O LYS D 53 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASN D 58 " --> pdb=" O SER D 54 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR D 59 " --> pdb=" O VAL D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 87 removed outlier: 3.567A pdb=" N GLU D 85 " --> pdb=" O LEU D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 116 Processing helix chain 'D' and resid 120 through 137 removed outlier: 3.564A pdb=" N CYS D 129 " --> pdb=" O PHE D 125 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS D 137 " --> pdb=" O SER D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 167 Processing helix chain 'D' and resid 179 through 197 removed outlier: 3.716A pdb=" N ILE D 187 " --> pdb=" O ALA D 183 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 230 removed outlier: 3.916A pdb=" N ALA D 224 " --> pdb=" O ALA D 220 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE D 225 " --> pdb=" O ILE D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 242 removed outlier: 3.804A pdb=" N THR D 242 " --> pdb=" O ASN D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 258 removed outlier: 3.637A pdb=" N ILE D 258 " --> pdb=" O LEU D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 276 removed outlier: 3.727A pdb=" N SER D 273 " --> pdb=" O LEU D 269 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TYR D 274 " --> pdb=" O MET D 270 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE D 275 " --> pdb=" O ASN D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 285 removed outlier: 3.711A pdb=" N LEU D 283 " --> pdb=" O THR D 279 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU D 284 " --> pdb=" O ALA D 280 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLN D 285 " --> pdb=" O THR D 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 279 through 285' Processing helix chain 'D' and resid 288 through 297 removed outlier: 3.735A pdb=" N THR D 292 " --> pdb=" O ALA D 288 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP D 295 " --> pdb=" O VAL D 291 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG D 296 " --> pdb=" O THR D 292 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL D 297 " --> pdb=" O PHE D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 317 removed outlier: 3.694A pdb=" N ALA D 310 " --> pdb=" O PRO D 306 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLY D 315 " --> pdb=" O PHE D 311 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA D 317 " --> pdb=" O THR D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 361 removed outlier: 3.645A pdb=" N ILE D 361 " --> pdb=" O PHE D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 366 removed outlier: 3.518A pdb=" N ILE D 366 " --> pdb=" O THR D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 395 removed outlier: 3.962A pdb=" N VAL D 375 " --> pdb=" O ILE D 371 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASN D 376 " --> pdb=" O ASN D 372 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TYR D 377 " --> pdb=" O SER D 373 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE D 380 " --> pdb=" O ASN D 376 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA D 381 " --> pdb=" O TYR D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 427 removed outlier: 3.678A pdb=" N LEU D 419 " --> pdb=" O VAL D 415 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE D 423 " --> pdb=" O LEU D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 445 Processing helix chain 'E' and resid 32 through 42 Processing helix chain 'E' and resid 50 through 60 removed outlier: 4.265A pdb=" N SER E 54 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER E 57 " --> pdb=" O LYS E 53 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASN E 58 " --> pdb=" O SER E 54 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR E 59 " --> pdb=" O VAL E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 87 removed outlier: 3.566A pdb=" N GLU E 85 " --> pdb=" O LEU E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 116 Processing helix chain 'E' and resid 120 through 137 removed outlier: 3.563A pdb=" N CYS E 129 " --> pdb=" O PHE E 125 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYS E 137 " --> pdb=" O SER E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 167 Processing helix chain 'E' and resid 179 through 197 removed outlier: 3.716A pdb=" N ILE E 187 " --> pdb=" O ALA E 183 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL E 188 " --> pdb=" O LYS E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 230 removed outlier: 3.917A pdb=" N ALA E 224 " --> pdb=" O ALA E 220 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE E 225 " --> pdb=" O ILE E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 242 removed outlier: 3.806A pdb=" N THR E 242 " --> pdb=" O ASN E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 258 removed outlier: 3.637A pdb=" N ILE E 258 " --> pdb=" O LEU E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 276 removed outlier: 3.725A pdb=" N SER E 273 " --> pdb=" O LEU E 269 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR E 274 " --> pdb=" O MET E 270 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE E 275 " --> pdb=" O ASN E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 285 removed outlier: 3.711A pdb=" N LEU E 283 " --> pdb=" O THR E 279 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU E 284 " --> pdb=" O ALA E 280 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLN E 285 " --> pdb=" O THR E 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 279 through 285' Processing helix chain 'E' and resid 288 through 297 removed outlier: 3.735A pdb=" N THR E 292 " --> pdb=" O ALA E 288 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP E 295 " --> pdb=" O VAL E 291 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG E 296 " --> pdb=" O THR E 292 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL E 297 " --> pdb=" O PHE E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 317 removed outlier: 3.694A pdb=" N ALA E 310 " --> pdb=" O PRO E 306 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLY E 315 " --> pdb=" O PHE E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 352 through 361 removed outlier: 3.645A pdb=" N ILE E 361 " --> pdb=" O PHE E 357 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 366 removed outlier: 3.520A pdb=" N ILE E 366 " --> pdb=" O THR E 363 " (cutoff:3.500A) Processing helix chain 'E' and resid 371 through 395 removed outlier: 3.962A pdb=" N VAL E 375 " --> pdb=" O ILE E 371 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASN E 376 " --> pdb=" O ASN E 372 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N TYR E 377 " --> pdb=" O SER E 373 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE E 380 " --> pdb=" O ASN E 376 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA E 381 " --> pdb=" O TYR E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 427 removed outlier: 3.678A pdb=" N LEU E 419 " --> pdb=" O VAL E 415 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE E 423 " --> pdb=" O LEU E 419 " (cutoff:3.500A) Processing helix chain 'E' and resid 440 through 445 Processing sheet with id=AA1, first strand: chain 'A' and resid 123 through 125 removed outlier: 6.295A pdb=" N MET A 123 " --> pdb=" O THR A 478 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N TRP A 443 " --> pdb=" O ILE A 477 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N TYR A 479 " --> pdb=" O TRP A 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 170 removed outlier: 7.285A pdb=" N LYS A 167 " --> pdb=" O GLU A 178 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER A 169 " --> pdb=" O GLY A 176 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N GLY A 176 " --> pdb=" O SER A 169 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 209 through 211 removed outlier: 3.588A pdb=" N GLY A 382 " --> pdb=" O PHE A 311 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 239 through 240 Processing sheet with id=AA5, first strand: chain 'A' and resid 398 through 399 Processing sheet with id=AA6, first strand: chain 'A' and resid 645 through 650 Processing sheet with id=AA7, first strand: chain 'A' and resid 604 through 606 removed outlier: 3.564A pdb=" N LEU A 605 " --> pdb=" O ILE A 638 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 617 through 619 Processing sheet with id=AA9, first strand: chain 'A' and resid 673 through 674 Processing sheet with id=AB1, first strand: chain 'C' and resid 123 through 125 removed outlier: 6.296A pdb=" N MET C 123 " --> pdb=" O THR C 478 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N TRP C 443 " --> pdb=" O ILE C 477 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N TYR C 479 " --> pdb=" O TRP C 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 167 through 170 removed outlier: 7.284A pdb=" N LYS C 167 " --> pdb=" O GLU C 178 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER C 169 " --> pdb=" O GLY C 176 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N GLY C 176 " --> pdb=" O SER C 169 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 209 through 211 removed outlier: 3.588A pdb=" N GLY C 382 " --> pdb=" O PHE C 311 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 239 through 240 Processing sheet with id=AB5, first strand: chain 'C' and resid 398 through 399 Processing sheet with id=AB6, first strand: chain 'C' and resid 645 through 650 Processing sheet with id=AB7, first strand: chain 'C' and resid 604 through 606 Processing sheet with id=AB8, first strand: chain 'C' and resid 617 through 618 Processing sheet with id=AB9, first strand: chain 'C' and resid 673 through 674 549 hydrogen bonds defined for protein. 1554 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: 2.52 Time building geometry restraints manager: 1.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2330 1.31 - 1.44: 4277 1.44 - 1.56: 8413 1.56 - 1.69: 4 1.69 - 1.82: 120 Bond restraints: 15144 Sorted by residual: bond pdb=" C THR C 624 " pdb=" N ASN C 625 " ideal model delta sigma weight residual 1.333 1.507 -0.174 1.41e-02 5.03e+03 1.52e+02 bond pdb=" C THR A 624 " pdb=" N ASN A 625 " ideal model delta sigma weight residual 1.332 1.417 -0.084 1.40e-02 5.10e+03 3.62e+01 bond pdb=" C7 NAG A 702 " pdb=" N2 NAG A 702 " ideal model delta sigma weight residual 1.346 1.464 -0.118 2.00e-02 2.50e+03 3.47e+01 bond pdb=" C7 NAG C 702 " pdb=" N2 NAG C 702 " ideal model delta sigma weight residual 1.346 1.464 -0.118 2.00e-02 2.50e+03 3.47e+01 bond pdb=" C7 NAG A 701 " pdb=" N2 NAG A 701 " ideal model delta sigma weight residual 1.346 1.463 -0.117 2.00e-02 2.50e+03 3.42e+01 ... (remaining 15139 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 20374 2.44 - 4.88: 197 4.88 - 7.32: 44 7.32 - 9.76: 4 9.76 - 12.20: 1 Bond angle restraints: 20620 Sorted by residual: angle pdb=" O THR A 624 " pdb=" C THR A 624 " pdb=" N ASN A 625 " ideal model delta sigma weight residual 122.59 132.25 -9.66 1.33e+00 5.65e-01 5.27e+01 angle pdb=" CA THR A 624 " pdb=" C THR A 624 " pdb=" N ASN A 625 " ideal model delta sigma weight residual 116.84 104.64 12.20 1.71e+00 3.42e-01 5.09e+01 angle pdb=" C ILE E 107 " pdb=" CA ILE E 107 " pdb=" CB ILE E 107 " ideal model delta sigma weight residual 114.35 108.30 6.05 1.06e+00 8.90e-01 3.26e+01 angle pdb=" C ILE D 107 " pdb=" CA ILE D 107 " pdb=" CB ILE D 107 " ideal model delta sigma weight residual 114.35 108.37 5.98 1.06e+00 8.90e-01 3.18e+01 angle pdb=" N VAL E 50 " pdb=" CA VAL E 50 " pdb=" C VAL E 50 " ideal model delta sigma weight residual 113.53 108.68 4.85 9.80e-01 1.04e+00 2.45e+01 ... (remaining 20615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 8078 17.79 - 35.57: 555 35.57 - 53.36: 125 53.36 - 71.14: 20 71.14 - 88.93: 10 Dihedral angle restraints: 8788 sinusoidal: 3404 harmonic: 5384 Sorted by residual: dihedral pdb=" CB CYS C 673 " pdb=" SG CYS C 673 " pdb=" SG CYS C 685 " pdb=" CB CYS C 685 " ideal model delta sinusoidal sigma weight residual -86.00 -26.44 -59.56 1 1.00e+01 1.00e-02 4.74e+01 dihedral pdb=" CB CYS A 673 " pdb=" SG CYS A 673 " pdb=" SG CYS A 685 " pdb=" CB CYS A 685 " ideal model delta sinusoidal sigma weight residual -86.00 -26.57 -59.43 1 1.00e+01 1.00e-02 4.72e+01 dihedral pdb=" CA ASN C 261 " pdb=" C ASN C 261 " pdb=" N SER C 262 " pdb=" CA SER C 262 " ideal model delta harmonic sigma weight residual 180.00 152.14 27.86 0 5.00e+00 4.00e-02 3.10e+01 ... (remaining 8785 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.270: 2371 0.270 - 0.540: 6 0.540 - 0.809: 1 0.809 - 1.079: 0 1.079 - 1.349: 2 Chirality restraints: 2380 Sorted by residual: chirality pdb=" C1 NAG A 703 " pdb=" ND2 ASN A 575 " pdb=" C2 NAG A 703 " pdb=" O5 NAG A 703 " both_signs ideal model delta sigma weight residual False -2.40 -1.05 -1.35 2.00e-01 2.50e+01 4.55e+01 chirality pdb=" C1 NAG C 704 " pdb=" ND2 ASN C 261 " pdb=" C2 NAG C 704 " pdb=" O5 NAG C 704 " both_signs ideal model delta sigma weight residual False -2.40 -1.23 -1.17 2.00e-01 2.50e+01 3.41e+01 chirality pdb=" C1 NAG A 702 " pdb=" ND2 ASN A 513 " pdb=" C2 NAG A 702 " pdb=" O5 NAG A 702 " both_signs ideal model delta sigma weight residual False -2.40 -3.05 0.65 2.00e-01 2.50e+01 1.05e+01 ... (remaining 2377 not shown) Planarity restraints: 2566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 513 " 0.247 2.00e-02 2.50e+03 2.21e-01 6.12e+02 pdb=" CG ASN C 513 " -0.078 2.00e-02 2.50e+03 pdb=" OD1 ASN C 513 " -0.112 2.00e-02 2.50e+03 pdb=" ND2 ASN C 513 " -0.314 2.00e-02 2.50e+03 pdb=" C1 NAG C 702 " 0.258 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 261 " 0.091 2.00e-02 2.50e+03 1.09e-01 1.48e+02 pdb=" CG ASN C 261 " -0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN C 261 " -0.029 2.00e-02 2.50e+03 pdb=" ND2 ASN C 261 " -0.165 2.00e-02 2.50e+03 pdb=" C1 NAG C 704 " 0.145 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 332 " 0.088 2.00e-02 2.50e+03 1.05e-01 1.39e+02 pdb=" CG ASN C 332 " -0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN C 332 " -0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN C 332 " -0.166 2.00e-02 2.50e+03 pdb=" C1 NAG C 701 " 0.135 2.00e-02 2.50e+03 ... (remaining 2563 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 32 2.39 - 3.01: 7786 3.01 - 3.64: 22088 3.64 - 4.27: 34152 4.27 - 4.90: 56143 Nonbonded interactions: 120201 Sorted by model distance: nonbonded pdb=" NZ LYS D 152 " pdb=" O ILE D 366 " model vdw 1.758 3.120 nonbonded pdb=" OD1 ASP A 150 " pdb=" NZ LYS A 203 " model vdw 1.762 3.120 nonbonded pdb=" CB PRO C 375 " pdb=" CG2 VAL D 142 " model vdw 1.790 3.860 nonbonded pdb=" NH2 ARG C 574 " pdb=" OH TYR C 579 " model vdw 1.869 3.120 nonbonded pdb=" NH2 ARG A 574 " pdb=" OH TYR A 579 " model vdw 1.957 3.120 ... (remaining 120196 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' } 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: 2.500 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: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 14.430 Find NCS groups from input model: 0.240 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: 0.010 Load rotamer database and sin/cos tables:6.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 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 : 0.008 0.478 15158 Z= 0.411 Angle : 0.852 38.251 20656 Z= 0.405 Chirality : 0.060 1.349 2380 Planarity : 0.004 0.058 2558 Dihedral : 13.019 88.930 5306 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.39 % Allowed : 3.04 % Favored : 96.57 % Rotamer: Outliers : 1.98 % Allowed : 12.52 % Favored : 85.50 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -3.94 (0.16), residues: 1808 helix: -3.06 (0.12), residues: 748 sheet: -1.94 (0.40), residues: 152 loop : -2.27 (0.19), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 229 TYR 0.006 0.001 TYR D 110 PHE 0.009 0.001 PHE A 407 TRP 0.005 0.001 TRP D 383 HIS 0.002 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.29 (15144) covalent geometry : angle 0.59713 / 0.35 (20620) SS BOND : bond 0.06010 / 3.24 ( 6) SS BOND : angle 2.95518 / 1.23 ( 12) hydrogen bonds : bond 0.27931 / 18.10 ( 549) hydrogen bonds : angle 8.24438 / 5.71 ( 1554) link_NAG-ASN : bond 0.25073 / 11.08 ( 8) link_NAG-ASN : angle 17.72707 / 9.68 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 221 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 664 ASP cc_start: 0.6991 (p0) cc_final: 0.6779 (p0) REVERT: C 368 MET cc_start: 0.8770 (mtp) cc_final: 0.8502 (mtp) REVERT: C 664 ASP cc_start: 0.7287 (p0) cc_final: 0.6980 (p0) REVERT: C 680 ILE cc_start: 0.7680 (OUTLIER) cc_final: 0.7207 (pp) REVERT: E 303 TRP cc_start: 0.7254 (p-90) cc_final: 0.7019 (p-90) outliers start: 32 outliers final: 15 residues processed: 249 average time/residue: 0.5793 time to fit residues: 159.4263 Evaluate side-chains 146 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 680 ILE Chi-restraints excluded: chain E residue 298 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.4980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.2980 chunk 149 optimal weight: 9.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 HIS A 244 HIS A 272 GLN A 366 GLN A 510 GLN A 544 GLN A 572 HIS A 659 GLN C 220 HIS C 244 HIS C 272 GLN C 366 GLN C 510 GLN C 524 ASN C 530 ASN C 544 GLN C 609 ASN C 659 GLN E 227 ASN E 237 GLN E 287 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.130009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.088991 restraints weight = 26069.988| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.30 r_work: 0.3136 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15158 Z= 0.118 Angle : 0.577 14.936 20656 Z= 0.286 Chirality : 0.044 0.672 2380 Planarity : 0.004 0.050 2558 Dihedral : 5.247 74.488 2006 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.20 % Favored : 95.74 % Rotamer: Outliers : 3.53 % Allowed : 15.68 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 are not related in a simple way. whole: -2.30 (0.18), residues: 1808 helix: -0.91 (0.17), residues: 774 sheet: -1.36 (0.43), residues: 134 loop : -2.12 (0.19), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 665 TYR 0.015 0.001 TYR D 451 PHE 0.015 0.001 PHE E 385 TRP 0.010 0.001 TRP D 230 HIS 0.004 0.001 HIS A 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (15144) covalent geometry : angle 0.55327 / 0.28 (20620) SS BOND : bond 0.00619 / 0.32 ( 6) SS BOND : angle 0.93059 / 0.46 ( 12) hydrogen bonds : bond 0.03988 / 2.63 ( 549) hydrogen bonds : angle 4.48698 / 3.13 ( 1554) link_NAG-ASN : bond 0.01450 / 0.57 ( 8) link_NAG-ASN : angle 4.77993 / 2.99 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 145 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 334 THR cc_start: 0.9142 (OUTLIER) cc_final: 0.8866 (m) REVERT: A 610 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7598 (mtm) REVERT: A 664 ASP cc_start: 0.7908 (p0) cc_final: 0.7562 (p0) REVERT: C 658 ARG cc_start: 0.8289 (mtp85) cc_final: 0.8000 (mtt-85) REVERT: C 664 ASP cc_start: 0.8057 (p0) cc_final: 0.7647 (p0) REVERT: D 49 PHE cc_start: 0.6376 (OUTLIER) cc_final: 0.5758 (p90) REVERT: D 266 CYS cc_start: 0.7792 (OUTLIER) cc_final: 0.7432 (m) REVERT: D 287 GLN cc_start: 0.6388 (mt0) cc_final: 0.6100 (mt0) REVERT: D 298 LEU cc_start: 0.7148 (OUTLIER) cc_final: 0.6928 (pp) REVERT: D 413 ILE cc_start: 0.6755 (OUTLIER) cc_final: 0.6548 (mp) REVERT: E 72 CYS cc_start: 0.7108 (m) cc_final: 0.6880 (m) REVERT: E 266 CYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7822 (m) REVERT: E 303 TRP cc_start: 0.7821 (p-90) cc_final: 0.6715 (p-90) outliers start: 57 outliers final: 17 residues processed: 182 average time/residue: 0.5283 time to fit residues: 107.4674 Evaluate side-chains 148 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain D residue 129 CYS Chi-restraints excluded: chain D residue 266 CYS Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 370 ASP Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain E residue 298 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 46 optimal weight: 0.7980 chunk 158 optimal weight: 4.9990 chunk 146 optimal weight: 8.9990 chunk 78 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 50 optimal weight: 8.9990 chunk 91 optimal weight: 0.3980 chunk 72 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 177 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 358 HIS A 530 ASN C 358 HIS E 287 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.127345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.085825 restraints weight = 25991.420| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.42 r_work: 0.3077 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15158 Z= 0.106 Angle : 0.533 13.750 20656 Z= 0.263 Chirality : 0.042 0.527 2380 Planarity : 0.004 0.050 2558 Dihedral : 4.289 52.879 1994 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.48 % Favored : 96.46 % Rotamer: Outliers : 3.47 % Allowed : 16.67 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.42 (0.19), residues: 1808 helix: 0.12 (0.19), residues: 762 sheet: -1.30 (0.44), residues: 130 loop : -1.84 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 671 TYR 0.013 0.001 TYR D 451 PHE 0.016 0.001 PHE A 165 TRP 0.013 0.001 TRP D 69 HIS 0.003 0.001 HIS A 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (15144) covalent geometry : angle 0.51499 / 0.26 (20620) SS BOND : bond 0.00200 / 0.10 ( 6) SS BOND : angle 0.66912 / 0.38 ( 12) hydrogen bonds : bond 0.03340 / 2.16 ( 549) hydrogen bonds : angle 3.92991 / 2.73 ( 1554) link_NAG-ASN : bond 0.00798 / 0.42 ( 8) link_NAG-ASN : angle 4.09636 / 2.47 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 130 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 610 MET cc_start: 0.8185 (OUTLIER) cc_final: 0.7567 (mtm) REVERT: A 662 PHE cc_start: 0.8038 (m-80) cc_final: 0.7830 (m-80) REVERT: A 664 ASP cc_start: 0.8031 (p0) cc_final: 0.7708 (p0) REVERT: C 336 ILE cc_start: 0.8896 (OUTLIER) cc_final: 0.8590 (mm) REVERT: C 608 HIS cc_start: 0.9199 (OUTLIER) cc_final: 0.8765 (m-70) REVERT: C 658 ARG cc_start: 0.8347 (mtp85) cc_final: 0.8060 (mtt-85) REVERT: C 663 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.7517 (mmm160) REVERT: C 664 ASP cc_start: 0.8083 (p0) cc_final: 0.7761 (p0) REVERT: D 49 PHE cc_start: 0.6531 (OUTLIER) cc_final: 0.5929 (p90) REVERT: D 121 LYS cc_start: 0.7703 (tptt) cc_final: 0.7471 (tptt) REVERT: D 129 CYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7618 (p) REVERT: D 266 CYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7486 (m) REVERT: D 287 GLN cc_start: 0.6443 (mt0) cc_final: 0.6127 (mt0) REVERT: E 72 CYS cc_start: 0.7120 (m) cc_final: 0.6912 (m) REVERT: E 266 CYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7981 (m) REVERT: E 270 MET cc_start: 0.8304 (ttt) cc_final: 0.7864 (ttm) REVERT: E 303 TRP cc_start: 0.7929 (p-90) cc_final: 0.6881 (p-90) outliers start: 56 outliers final: 21 residues processed: 161 average time/residue: 0.5192 time to fit residues: 93.1956 Evaluate side-chains 153 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 261 ASN Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 444 MET Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 608 HIS Chi-restraints excluded: chain C residue 663 ARG Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain D residue 129 CYS Chi-restraints excluded: chain D residue 266 CYS Chi-restraints excluded: chain D residue 370 ASP Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain E residue 49 PHE Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain E residue 298 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 20.0000 chunk 135 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 chunk 153 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 125 optimal weight: 0.5980 chunk 85 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 chunk 70 optimal weight: 0.6980 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 287 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.123177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.080596 restraints weight = 25958.375| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.31 r_work: 0.2979 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15158 Z= 0.142 Angle : 0.558 12.740 20656 Z= 0.279 Chirality : 0.044 0.512 2380 Planarity : 0.004 0.049 2558 Dihedral : 4.496 55.950 1991 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.70 % Favored : 95.24 % Rotamer: Outliers : 3.47 % Allowed : 16.91 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 are not related in a simple way. whole: -0.98 (0.20), residues: 1808 helix: 0.47 (0.19), residues: 770 sheet: -1.21 (0.45), residues: 130 loop : -1.57 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 671 TYR 0.013 0.001 TYR A 166 PHE 0.019 0.001 PHE C 407 TRP 0.010 0.001 TRP A 161 HIS 0.005 0.001 HIS A 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (15144) covalent geometry : angle 0.54324 / 0.28 (20620) SS BOND : bond 0.00327 / 0.16 ( 6) SS BOND : angle 0.82953 / 0.40 ( 12) hydrogen bonds : bond 0.03297 / 2.14 ( 549) hydrogen bonds : angle 3.77982 / 2.63 ( 1554) link_NAG-ASN : bond 0.00699 / 0.40 ( 8) link_NAG-ASN : angle 3.80549 / 2.28 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 130 time to evaluate : 0.569 Fit side-chains revert: symmetry clash REVERT: A 265 HIS cc_start: 0.7744 (OUTLIER) cc_final: 0.7130 (m90) REVERT: A 610 MET cc_start: 0.8362 (OUTLIER) cc_final: 0.7800 (mtm) REVERT: A 662 PHE cc_start: 0.8140 (m-80) cc_final: 0.7839 (m-80) REVERT: A 664 ASP cc_start: 0.8052 (p0) cc_final: 0.7778 (p0) REVERT: A 684 SER cc_start: 0.7675 (m) cc_final: 0.7446 (m) REVERT: C 658 ARG cc_start: 0.8271 (mtp85) cc_final: 0.7977 (mtt-85) REVERT: C 664 ASP cc_start: 0.8041 (p0) cc_final: 0.7749 (p0) REVERT: C 684 SER cc_start: 0.7831 (m) cc_final: 0.7520 (m) REVERT: D 49 PHE cc_start: 0.6658 (OUTLIER) cc_final: 0.6246 (p90) REVERT: D 121 LYS cc_start: 0.7809 (tptt) cc_final: 0.7582 (tptt) REVERT: D 266 CYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7594 (m) REVERT: D 287 GLN cc_start: 0.6554 (mt0) cc_final: 0.6328 (mt0) REVERT: E 72 CYS cc_start: 0.7253 (m) cc_final: 0.7040 (m) REVERT: E 266 CYS cc_start: 0.8292 (OUTLIER) cc_final: 0.8028 (m) REVERT: E 303 TRP cc_start: 0.7937 (p-90) cc_final: 0.7030 (p-90) outliers start: 56 outliers final: 24 residues processed: 165 average time/residue: 0.4982 time to fit residues: 91.8600 Evaluate side-chains 149 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 120 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 261 ASN Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 444 MET Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain D residue 129 CYS Chi-restraints excluded: chain D residue 266 CYS Chi-restraints excluded: chain D residue 370 ASP Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain E residue 49 PHE Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 266 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 142 optimal weight: 6.9990 chunk 78 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 61 optimal weight: 0.0570 chunk 156 optimal weight: 10.0000 chunk 81 optimal weight: 0.6980 chunk 44 optimal weight: 6.9990 chunk 157 optimal weight: 0.9980 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 287 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.124538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.082228 restraints weight = 25858.916| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.31 r_work: 0.3016 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15158 Z= 0.104 Angle : 0.522 11.924 20656 Z= 0.256 Chirality : 0.042 0.436 2380 Planarity : 0.004 0.050 2558 Dihedral : 4.038 57.633 1986 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.98 % Favored : 95.96 % Rotamer: Outliers : 2.54 % Allowed : 17.97 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.74 (0.20), residues: 1808 helix: 0.77 (0.19), residues: 774 sheet: -0.74 (0.47), residues: 114 loop : -1.60 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 619 TYR 0.009 0.001 TYR A 582 PHE 0.028 0.001 PHE E 161 TRP 0.009 0.001 TRP A 431 HIS 0.003 0.001 HIS C 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 (15144) covalent geometry : angle 0.51089 / 0.25 (20620) SS BOND : bond 0.00167 / 0.08 ( 6) SS BOND : angle 0.51236 / 0.28 ( 12) hydrogen bonds : bond 0.02818 / 1.84 ( 549) hydrogen bonds : angle 3.61758 / 2.50 ( 1554) link_NAG-ASN : bond 0.01080 / 0.50 ( 8) link_NAG-ASN : angle 3.24731 / 2.18 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 131 time to evaluate : 0.573 Fit side-chains REVERT: A 265 HIS cc_start: 0.7696 (OUTLIER) cc_final: 0.7083 (m90) REVERT: A 610 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.7692 (mtm) REVERT: A 662 PHE cc_start: 0.8086 (m-80) cc_final: 0.7878 (m-80) REVERT: A 664 ASP cc_start: 0.8103 (p0) cc_final: 0.7854 (p0) REVERT: A 684 SER cc_start: 0.7760 (m) cc_final: 0.7552 (m) REVERT: C 658 ARG cc_start: 0.8255 (mtp85) cc_final: 0.7943 (mtt-85) REVERT: C 664 ASP cc_start: 0.8004 (p0) cc_final: 0.7724 (p0) REVERT: D 121 LYS cc_start: 0.7828 (tptt) cc_final: 0.7566 (tptt) REVERT: D 266 CYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7566 (m) REVERT: E 53 LYS cc_start: 0.8601 (tmmm) cc_final: 0.8299 (ttmm) REVERT: E 72 CYS cc_start: 0.7198 (m) cc_final: 0.6973 (m) REVERT: E 145 LYS cc_start: 0.8179 (mmtt) cc_final: 0.7952 (mmtt) REVERT: E 266 CYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7971 (m) REVERT: E 303 TRP cc_start: 0.7931 (p-90) cc_final: 0.7097 (p-90) outliers start: 41 outliers final: 15 residues processed: 159 average time/residue: 0.5669 time to fit residues: 99.8900 Evaluate side-chains 145 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain C residue 444 MET Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 266 CYS Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 370 ASP Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain E residue 49 PHE Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 266 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 77 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 146 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 155 optimal weight: 8.9990 chunk 43 optimal weight: 7.9990 chunk 59 optimal weight: 20.0000 chunk 171 optimal weight: 0.6980 chunk 119 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 ASN A 215 HIS A 277 GLN C 215 HIS C 277 GLN D 287 GLN E 287 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.120281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.077396 restraints weight = 25654.972| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.30 r_work: 0.2920 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8992 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15158 Z= 0.167 Angle : 0.584 12.748 20656 Z= 0.290 Chirality : 0.044 0.418 2380 Planarity : 0.004 0.051 2558 Dihedral : 4.218 28.184 1984 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.09 % Favored : 94.86 % Rotamer: Outliers : 3.22 % Allowed : 17.97 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.74 (0.20), residues: 1808 helix: 0.74 (0.19), residues: 794 sheet: -1.32 (0.41), residues: 152 loop : -1.53 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 574 TYR 0.012 0.001 TYR A 259 PHE 0.020 0.002 PHE C 407 TRP 0.010 0.001 TRP E 383 HIS 0.006 0.001 HIS A 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (15144) covalent geometry : angle 0.57619 / 0.29 (20620) SS BOND : bond 0.00258 / 0.13 ( 6) SS BOND : angle 1.14815 / 0.66 ( 12) hydrogen bonds : bond 0.03550 / 2.30 ( 549) hydrogen bonds : angle 3.71057 / 2.58 ( 1554) link_NAG-ASN : bond 0.00770 / 0.39 ( 8) link_NAG-ASN : angle 2.82869 / 1.83 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 131 time to evaluate : 0.552 Fit side-chains REVERT: A 265 HIS cc_start: 0.7686 (OUTLIER) cc_final: 0.7090 (m90) REVERT: A 415 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.7859 (mmp) REVERT: A 610 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.7875 (mtm) REVERT: A 664 ASP cc_start: 0.8055 (p0) cc_final: 0.7836 (p0) REVERT: C 368 MET cc_start: 0.8747 (mtm) cc_final: 0.8525 (mtp) REVERT: C 415 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.7864 (mmp) REVERT: C 658 ARG cc_start: 0.8245 (mtp85) cc_final: 0.7964 (mtt-85) REVERT: C 664 ASP cc_start: 0.7962 (p0) cc_final: 0.7690 (p0) REVERT: D 53 LYS cc_start: 0.8684 (tmtp) cc_final: 0.8438 (tmmm) REVERT: D 266 CYS cc_start: 0.7974 (OUTLIER) cc_final: 0.7705 (m) REVERT: D 298 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7666 (pp) REVERT: E 72 CYS cc_start: 0.7299 (m) cc_final: 0.7059 (m) REVERT: E 303 TRP cc_start: 0.7984 (p-90) cc_final: 0.7144 (p-90) outliers start: 52 outliers final: 21 residues processed: 162 average time/residue: 0.5370 time to fit residues: 96.5732 Evaluate side-chains 152 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 444 MET Chi-restraints excluded: chain C residue 449 ASP Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 266 CYS Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 370 ASP Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain E residue 49 PHE Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain E residue 165 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 176 optimal weight: 6.9990 chunk 36 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 145 optimal weight: 5.9990 chunk 23 optimal weight: 0.2980 chunk 46 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 133 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 282 GLN D 287 GLN E 148 GLN E 287 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.121648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.079502 restraints weight = 25686.544| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.29 r_work: 0.2960 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15158 Z= 0.114 Angle : 0.534 11.694 20656 Z= 0.262 Chirality : 0.042 0.368 2380 Planarity : 0.004 0.050 2558 Dihedral : 4.011 26.905 1984 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.42 % Allowed : 19.70 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.64 (0.20), residues: 1808 helix: 0.86 (0.19), residues: 800 sheet: -1.23 (0.42), residues: 152 loop : -1.54 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 574 TYR 0.013 0.001 TYR A 166 PHE 0.018 0.001 PHE E 161 TRP 0.009 0.001 TRP A 431 HIS 0.004 0.001 HIS C 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (15144) covalent geometry : angle 0.52760 / 0.26 (20620) SS BOND : bond 0.00193 / 0.10 ( 6) SS BOND : angle 0.72319 / 0.41 ( 12) hydrogen bonds : bond 0.02948 / 1.93 ( 549) hydrogen bonds : angle 3.55216 / 2.46 ( 1554) link_NAG-ASN : bond 0.00574 / 0.28 ( 8) link_NAG-ASN : angle 2.49167 / 1.56 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 126 time to evaluate : 0.468 Fit side-chains REVERT: A 265 HIS cc_start: 0.7637 (OUTLIER) cc_final: 0.7078 (m90) REVERT: A 415 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.7717 (mmp) REVERT: A 610 MET cc_start: 0.8337 (OUTLIER) cc_final: 0.7774 (mtm) REVERT: C 280 LYS cc_start: 0.8501 (tptp) cc_final: 0.8244 (tttt) REVERT: C 415 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.7732 (mmp) REVERT: C 658 ARG cc_start: 0.8264 (mtp85) cc_final: 0.7970 (mtt-85) REVERT: C 664 ASP cc_start: 0.7911 (p0) cc_final: 0.7671 (p0) REVERT: D 53 LYS cc_start: 0.8710 (tmtp) cc_final: 0.8471 (tmmm) REVERT: D 266 CYS cc_start: 0.7979 (OUTLIER) cc_final: 0.7729 (m) REVERT: D 298 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7699 (pp) REVERT: E 53 LYS cc_start: 0.8561 (tmmm) cc_final: 0.8175 (ttmm) REVERT: E 72 CYS cc_start: 0.7320 (m) cc_final: 0.7080 (m) REVERT: E 233 ASP cc_start: 0.8157 (t70) cc_final: 0.7826 (m-30) REVERT: E 303 TRP cc_start: 0.7977 (p-90) cc_final: 0.7137 (p-90) REVERT: E 445 LEU cc_start: 0.6191 (mp) cc_final: 0.5544 (tt) outliers start: 39 outliers final: 20 residues processed: 147 average time/residue: 0.5831 time to fit residues: 94.5086 Evaluate side-chains 150 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 444 MET Chi-restraints excluded: chain C residue 685 CYS Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 266 CYS Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain E residue 49 PHE Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 370 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 105 optimal weight: 2.9990 chunk 174 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 57 optimal weight: 6.9990 chunk 136 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 180 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 195 ASN D 227 ASN D 287 GLN E 287 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.117922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.075596 restraints weight = 25945.612| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.32 r_work: 0.2877 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.4420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15158 Z= 0.168 Angle : 0.575 12.141 20656 Z= 0.285 Chirality : 0.044 0.372 2380 Planarity : 0.004 0.053 2558 Dihedral : 4.161 26.188 1983 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.42 % Allowed : 20.01 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.60 (0.20), residues: 1808 helix: 0.89 (0.19), residues: 796 sheet: -1.23 (0.42), residues: 152 loop : -1.50 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 574 TYR 0.010 0.001 TYR C 582 PHE 0.018 0.001 PHE C 407 TRP 0.013 0.001 TRP D 383 HIS 0.006 0.001 HIS A 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 (15144) covalent geometry : angle 0.56812 / 0.28 (20620) SS BOND : bond 0.00371 / 0.19 ( 6) SS BOND : angle 0.98015 / 0.56 ( 12) hydrogen bonds : bond 0.03429 / 2.23 ( 549) hydrogen bonds : angle 3.62099 / 2.51 ( 1554) link_NAG-ASN : bond 0.00437 / 0.20 ( 8) link_NAG-ASN : angle 2.60522 / 1.61 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 129 time to evaluate : 0.575 Fit side-chains REVERT: A 265 HIS cc_start: 0.7624 (OUTLIER) cc_final: 0.6921 (m90) REVERT: A 415 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.7863 (mmp) REVERT: A 610 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.7839 (mtm) REVERT: C 415 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.7860 (mmp) REVERT: C 658 ARG cc_start: 0.8186 (mtp85) cc_final: 0.7896 (mtt-85) REVERT: C 664 ASP cc_start: 0.7922 (p0) cc_final: 0.7690 (p0) REVERT: D 53 LYS cc_start: 0.8641 (tmtp) cc_final: 0.8402 (tmmm) REVERT: D 72 CYS cc_start: 0.7242 (m) cc_final: 0.7005 (m) REVERT: D 137 CYS cc_start: 0.8082 (p) cc_final: 0.7875 (p) REVERT: D 298 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7659 (pp) REVERT: E 72 CYS cc_start: 0.7243 (m) cc_final: 0.6980 (m) REVERT: E 303 TRP cc_start: 0.7989 (p-90) cc_final: 0.7139 (p-90) REVERT: E 445 LEU cc_start: 0.6312 (OUTLIER) cc_final: 0.5658 (tt) outliers start: 39 outliers final: 22 residues processed: 151 average time/residue: 0.6105 time to fit residues: 101.6452 Evaluate side-chains 151 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 444 MET Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 685 CYS Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain E residue 49 PHE Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 370 ASP Chi-restraints excluded: chain E residue 445 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 30 optimal weight: 0.8980 chunk 143 optimal weight: 0.3980 chunk 13 optimal weight: 1.9990 chunk 174 optimal weight: 5.9990 chunk 104 optimal weight: 0.4980 chunk 3 optimal weight: 0.0070 chunk 139 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 chunk 159 optimal weight: 0.7980 chunk 112 optimal weight: 0.0670 chunk 142 optimal weight: 7.9990 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 578 HIS C 265 HIS C 282 GLN D 287 GLN E 287 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.123095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.081153 restraints weight = 25894.376| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.31 r_work: 0.2996 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15158 Z= 0.096 Angle : 0.521 11.842 20656 Z= 0.256 Chirality : 0.041 0.326 2380 Planarity : 0.004 0.054 2558 Dihedral : 3.731 16.899 1982 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.55 % Allowed : 20.69 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.20), residues: 1808 helix: 1.13 (0.19), residues: 794 sheet: -1.01 (0.49), residues: 112 loop : -1.48 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 619 TYR 0.009 0.001 TYR A 151 PHE 0.016 0.001 PHE E 161 TRP 0.012 0.001 TRP D 383 HIS 0.003 0.001 HIS A 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.10 (15144) covalent geometry : angle 0.51685 / 0.25 (20620) SS BOND : bond 0.00115 / 0.06 ( 6) SS BOND : angle 0.42774 / 0.24 ( 12) hydrogen bonds : bond 0.02594 / 1.71 ( 549) hydrogen bonds : angle 3.44597 / 2.38 ( 1554) link_NAG-ASN : bond 0.00496 / 0.24 ( 8) link_NAG-ASN : angle 2.11019 / 1.31 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 0.619 Fit side-chains REVERT: A 265 HIS cc_start: 0.7643 (OUTLIER) cc_final: 0.7104 (m90) REVERT: A 437 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8291 (mp0) REVERT: A 610 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.7755 (mtm) REVERT: A 663 ARG cc_start: 0.7609 (tpt170) cc_final: 0.7146 (mmm160) REVERT: C 658 ARG cc_start: 0.8246 (mtp85) cc_final: 0.7964 (mtt-85) REVERT: C 664 ASP cc_start: 0.7877 (p0) cc_final: 0.7642 (p0) REVERT: D 53 LYS cc_start: 0.8711 (tmtp) cc_final: 0.8441 (tmmm) REVERT: D 72 CYS cc_start: 0.7301 (m) cc_final: 0.7051 (m) REVERT: D 262 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7881 (tp) REVERT: E 72 CYS cc_start: 0.7317 (m) cc_final: 0.7074 (m) REVERT: E 233 ASP cc_start: 0.8178 (t70) cc_final: 0.7802 (m-30) REVERT: E 303 TRP cc_start: 0.7964 (p-90) cc_final: 0.7100 (p-90) REVERT: E 445 LEU cc_start: 0.6310 (OUTLIER) cc_final: 0.5665 (tt) outliers start: 25 outliers final: 14 residues processed: 148 average time/residue: 0.6203 time to fit residues: 101.2691 Evaluate side-chains 147 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 685 CYS Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain E residue 49 PHE Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 370 ASP Chi-restraints excluded: chain E residue 445 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 121 optimal weight: 0.4980 chunk 120 optimal weight: 0.0670 chunk 128 optimal weight: 4.9990 chunk 180 optimal weight: 8.9990 chunk 10 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 140 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 overall best weight: 1.0922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 578 HIS C 578 HIS D 287 GLN E 287 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.121612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.079269 restraints weight = 25698.224| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.29 r_work: 0.2959 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.4479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15158 Z= 0.121 Angle : 0.543 12.771 20656 Z= 0.267 Chirality : 0.042 0.333 2380 Planarity : 0.004 0.060 2558 Dihedral : 3.816 17.010 1982 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.36 % Allowed : 20.94 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.20), residues: 1808 helix: 1.16 (0.19), residues: 796 sheet: -1.34 (0.45), residues: 132 loop : -1.40 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 574 TYR 0.009 0.001 TYR A 582 PHE 0.015 0.001 PHE E 161 TRP 0.018 0.001 TRP D 383 HIS 0.004 0.001 HIS A 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (15144) covalent geometry : angle 0.53770 / 0.27 (20620) SS BOND : bond 0.00229 / 0.12 ( 6) SS BOND : angle 0.73717 / 0.42 ( 12) hydrogen bonds : bond 0.02891 / 1.89 ( 549) hydrogen bonds : angle 3.45203 / 2.39 ( 1554) link_NAG-ASN : bond 0.00454 / 0.20 ( 8) link_NAG-ASN : angle 2.22200 / 1.37 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.598 Fit side-chains REVERT: A 265 HIS cc_start: 0.7634 (OUTLIER) cc_final: 0.7088 (m90) REVERT: A 610 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.7807 (mtm) REVERT: A 663 ARG cc_start: 0.7693 (tpt170) cc_final: 0.7226 (mmm160) REVERT: C 415 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.7831 (mmp) REVERT: C 658 ARG cc_start: 0.8261 (mtp85) cc_final: 0.7985 (mtt-85) REVERT: C 664 ASP cc_start: 0.7885 (p0) cc_final: 0.7632 (p0) REVERT: D 53 LYS cc_start: 0.8698 (tmtp) cc_final: 0.8429 (tmmm) REVERT: D 72 CYS cc_start: 0.7299 (m) cc_final: 0.7034 (m) REVERT: E 53 LYS cc_start: 0.8606 (tmmm) cc_final: 0.8331 (ttmm) REVERT: E 72 CYS cc_start: 0.7298 (m) cc_final: 0.7046 (m) REVERT: E 233 ASP cc_start: 0.8172 (t70) cc_final: 0.7828 (m-30) REVERT: E 287 GLN cc_start: 0.6947 (mt0) cc_final: 0.6681 (mt0) REVERT: E 303 TRP cc_start: 0.7975 (p-90) cc_final: 0.7117 (p-90) REVERT: E 445 LEU cc_start: 0.6285 (OUTLIER) cc_final: 0.5669 (tt) outliers start: 22 outliers final: 15 residues processed: 145 average time/residue: 0.6076 time to fit residues: 97.4693 Evaluate side-chains 148 residues out of total 1614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 444 MET Chi-restraints excluded: chain C residue 685 CYS Chi-restraints excluded: chain D residue 49 PHE Chi-restraints excluded: chain D residue 82 CYS Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain E residue 49 PHE Chi-restraints excluded: chain E residue 82 CYS Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 370 ASP Chi-restraints excluded: chain E residue 445 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 131 optimal weight: 6.9990 chunk 157 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 181 optimal weight: 0.0010 chunk 52 optimal weight: 6.9990 chunk 134 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 148 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 overall best weight: 2.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 354 GLN A 578 HIS C 282 GLN D 287 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.118885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.075969 restraints weight = 25559.774| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.29 r_work: 0.2893 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9012 moved from start: 0.4744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 15158 Z= 0.197 Angle : 0.600 13.561 20656 Z= 0.299 Chirality : 0.045 0.358 2380 Planarity : 0.004 0.058 2558 Dihedral : 4.233 19.249 1982 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.67 % Allowed : 20.63 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.20), residues: 1808 helix: 1.09 (0.19), residues: 792 sheet: -1.14 (0.43), residues: 152 loop : -1.38 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 574 TYR 0.011 0.001 TYR C 582 PHE 0.019 0.002 PHE C 165 TRP 0.019 0.001 TRP D 383 HIS 0.007 0.001 HIS A 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.20 (15144) covalent geometry : angle 0.59383 / 0.30 (20620) SS BOND : bond 0.00340 / 0.17 ( 6) SS BOND : angle 1.11084 / 0.63 ( 12) hydrogen bonds : bond 0.03587 / 2.33 ( 549) hydrogen bonds : angle 3.64388 / 2.53 ( 1554) link_NAG-ASN : bond 0.00326 / 0.14 ( 8) link_NAG-ASN : angle 2.55299 / 1.57 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5201.82 seconds wall clock time: 89 minutes 29.31 seconds (5369.31 seconds total)