Starting phenix.real_space_refine on Thu Jul 2 16:53:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7nf6_12296/07_2026/7nf6_12296.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nf6_12296/07_2026/7nf6_12296.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7nf6_12296/07_2026/7nf6_12296.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nf6_12296/07_2026/7nf6_12296.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7nf6_12296/07_2026/7nf6_12296.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7nf6_12296/07_2026/7nf6_12296.cif" model { file = "/net/cci-nas-00/data/ceres_data/7nf6_12296/07_2026/7nf6_12296.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nf6_12296/07_2026/7nf6_12296.cif" } resolution = 3.05 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: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 P 1 5.49 5 S 49 5.16 5 C 5754 2.51 5 N 1417 2.21 5 O 1595 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8817 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 3506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3506 Classifications: {'peptide': 455} Link IDs: {'PTRANS': 25, 'TRANS': 429} Chain: "A" Number of atoms: 5090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 5090 Classifications: {'peptide': 623} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 596} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 109 Unusual residues: {' CA': 1, 'LBN': 1, 'NAG': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 2.15, per 1000 atoms: 0.24 Number of scatterers: 8817 At special positions: 0 Unit cell: (87.8848, 95.5747, 139.517, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 49 16.00 P 1 15.00 O 1595 8.00 N 1417 7.00 C 5754 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS A 114 " distance=2.08 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=2.04 Simple disulfide: pdb=" SG CYS A 673 " - pdb=" SG CYS A 685 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A 703 " - " ASN A 513 " " NAG A 704 " - " ASN A 246 " " NAG A 705 " - " ASN A 228 " " NAG A 706 " - " ASN A 523 " " NAG C 1 " - " ASN A 332 " " NAG D 1 " - " ASN A 261 " Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 293.9 milliseconds 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2018 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 9 sheets defined 55.2% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'B' and resid 31 through 44 removed outlier: 4.440A pdb=" N ILE B 39 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY B 41 " --> pdb=" O CYS B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 60 removed outlier: 4.184A pdb=" N SER B 54 " --> pdb=" O ILE B 50 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASN B 58 " --> pdb=" O SER B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 90 removed outlier: 3.657A pdb=" N ILE B 67 " --> pdb=" O GLY B 63 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N TRP B 69 " --> pdb=" O CYS B 65 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR B 77 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU B 86 " --> pdb=" O CYS B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 104 removed outlier: 3.556A pdb=" N LEU B 100 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA B 103 " --> pdb=" O TYR B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 119 removed outlier: 4.197A pdb=" N ALA B 109 " --> pdb=" O GLY B 105 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 137 removed outlier: 3.708A pdb=" N SER B 133 " --> pdb=" O CYS B 129 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU B 134 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TYR B 135 " --> pdb=" O SER B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 142 Processing helix chain 'B' and resid 147 through 169 removed outlier: 3.506A pdb=" N ILE B 151 " --> pdb=" O PRO B 147 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA B 155 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU B 161 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA B 167 " --> pdb=" O SER B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 176 removed outlier: 3.953A pdb=" N VAL B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 201 removed outlier: 3.530A pdb=" N ALA B 182 " --> pdb=" O ASN B 178 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET B 185 " --> pdb=" O THR B 181 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU B 199 " --> pdb=" O GLY B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 231 removed outlier: 3.585A pdb=" N SER B 222 " --> pdb=" O VAL B 218 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASN B 227 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA B 231 " --> pdb=" O ASN B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 244 removed outlier: 3.921A pdb=" N ILE B 241 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU B 243 " --> pdb=" O TYR B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 258 Proline residue: B 253 - end of helix Processing helix chain 'B' and resid 259 through 276 removed outlier: 3.586A pdb=" N MET B 270 " --> pdb=" O CYS B 266 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N SER B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE B 275 " --> pdb=" O ASN B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 284 removed outlier: 4.200A pdb=" N LEU B 284 " --> pdb=" O ALA B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 298 removed outlier: 3.647A pdb=" N ARG B 296 " --> pdb=" O THR B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 323 removed outlier: 3.501A pdb=" N ALA B 310 " --> pdb=" O PRO B 306 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR B 323 " --> pdb=" O GLY B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 334 removed outlier: 4.182A pdb=" N LEU B 327 " --> pdb=" O THR B 323 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VAL B 328 " --> pdb=" O ALA B 324 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE B 329 " --> pdb=" O GLY B 325 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL B 330 " --> pdb=" O ARG B 326 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLU B 334 " --> pdb=" O VAL B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 351 through 367 removed outlier: 3.502A pdb=" N MET B 360 " --> pdb=" O MET B 356 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE B 361 " --> pdb=" O PHE B 357 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA B 362 " --> pdb=" O HIS B 358 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE B 364 " --> pdb=" O MET B 360 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE B 367 " --> pdb=" O ILE B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 399 removed outlier: 3.603A pdb=" N ASN B 376 " --> pdb=" O ASN B 372 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR B 377 " --> pdb=" O SER B 373 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA B 381 " --> pdb=" O TYR B 377 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TRP B 383 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE B 385 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE B 390 " --> pdb=" O TYR B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 432 removed outlier: 3.774A pdb=" N ILE B 415 " --> pdb=" O ILE B 411 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU B 416 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE B 423 " --> pdb=" O LEU B 419 " (cutoff:3.500A) Proline residue: B 428 - end of helix Processing helix chain 'B' and resid 434 through 455 removed outlier: 4.013A pdb=" N LEU B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR B 439 " --> pdb=" O TRP B 435 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET B 444 " --> pdb=" O CYS B 440 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE B 452 " --> pdb=" O LEU B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 478 removed outlier: 3.781A pdb=" N GLN B 463 " --> pdb=" O PHE B 459 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS B 464 " --> pdb=" O GLY B 460 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE B 465 " --> pdb=" O TRP B 461 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER B 466 " --> pdb=" O ALA B 462 " (cutoff:3.500A) Proline residue: B 468 - end of helix removed outlier: 3.829A pdb=" N MET B 471 " --> pdb=" O LYS B 467 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS B 472 " --> pdb=" O PRO B 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 77 removed outlier: 3.742A pdb=" N LEU A 73 " --> pdb=" O PRO A 69 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE A 74 " --> pdb=" O LYS A 70 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLN A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N PHE A 76 " --> pdb=" O VAL A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 111 removed outlier: 3.648A pdb=" N GLU A 87 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE A 105 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE A 110 " --> pdb=" O ALA A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 121 removed outlier: 4.114A pdb=" N GLY A 121 " --> pdb=" O TRP A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 131 removed outlier: 3.975A pdb=" N PHE A 131 " --> pdb=" O PRO A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 148 removed outlier: 3.578A pdb=" N LYS A 148 " --> pdb=" O GLY A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 153 Processing helix chain 'A' and resid 185 through 188 Processing helix chain 'A' and resid 189 through 203 removed outlier: 3.600A pdb=" N LYS A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 228 removed outlier: 3.609A pdb=" N ASN A 228 " --> pdb=" O GLN A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 236 removed outlier: 3.762A pdb=" N THR A 234 " --> pdb=" O GLY A 231 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP A 235 " --> pdb=" O LYS A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 306 removed outlier: 3.890A pdb=" N GLN A 293 " --> pdb=" O ASN A 289 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS A 306 " --> pdb=" O PHE A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 344 No H-bonds generated for 'chain 'A' and resid 342 through 344' Processing helix chain 'A' and resid 356 through 368 removed outlier: 3.752A pdb=" N ILE A 360 " --> pdb=" O GLY A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 398 removed outlier: 3.522A pdb=" N VAL A 395 " --> pdb=" O GLU A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 416 removed outlier: 3.521A pdb=" N LYS A 415 " --> pdb=" O TYR A 412 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 416 " --> pdb=" O LEU A 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 412 through 416' Processing helix chain 'A' and resid 420 through 435 removed outlier: 3.664A pdb=" N VAL A 427 " --> pdb=" O SER A 423 " (cutoff:3.500A) removed outlier: 3.538A 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 472 removed outlier: 3.549A pdb=" N VAL A 469 " --> pdb=" O MET A 465 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR A 471 " --> pdb=" O MET A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 519 removed outlier: 3.504A pdb=" N ALA A 517 " --> pdb=" O SER A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 542 Processing helix chain 'A' and resid 547 through 561 removed outlier: 3.529A pdb=" N LEU A 557 " --> pdb=" O GLN A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 590 removed outlier: 3.857A pdb=" N ILE A 589 " --> pdb=" O LEU A 586 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ASN A 590 " --> pdb=" O ASP A 587 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 586 through 590' Processing helix chain 'A' and resid 606 through 611 removed outlier: 4.176A pdb=" N MET A 610 " --> pdb=" O ASN A 606 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 344 through 345 Processing sheet with id=AA2, first strand: chain 'A' and resid 407 through 409 removed outlier: 6.762A pdb=" N MET A 381 " --> pdb=" O PHE A 407 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N PHE A 409 " --> pdb=" O MET A 381 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N THR A 383 " --> pdb=" O PHE A 409 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY A 310 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 166 through 170 removed outlier: 7.137A pdb=" N LYS A 167 " --> pdb=" O GLU A 178 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA A 176 " --> pdb=" O SER A 169 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 239 through 240 removed outlier: 3.776A pdb=" N GLN A 272 " --> pdb=" O ASP A 267 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 244 through 245 Processing sheet with id=AA6, first strand: chain 'A' and resid 329 through 330 removed outlier: 4.135A pdb=" N ALA A 329 " --> pdb=" O HIS A 347 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 632 through 634 removed outlier: 3.623A pdb=" N ARG A 619 " --> pdb=" O GLU A 649 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE A 647 " --> pdb=" O ARG A 621 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N SER A 623 " --> pdb=" O GLY A 645 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLY A 645 " --> pdb=" O SER A 623 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 603 through 605 Processing sheet with id=AA9, first strand: chain 'A' and resid 673 through 675 371 hydrogen bonds defined for protein. 1035 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: 1.50 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1546 1.33 - 1.45: 2438 1.45 - 1.57: 4988 1.57 - 1.70: 2 1.70 - 1.82: 81 Bond restraints: 9055 Sorted by residual: bond pdb=" C9 LBN A 701 " pdb=" O2 LBN A 701 " ideal model delta sigma weight residual 1.409 1.455 -0.046 2.00e-02 2.50e+03 5.35e+00 bond pdb=" O2 LBN A 701 " pdb=" P1 LBN A 701 " ideal model delta sigma weight residual 1.650 1.605 0.045 2.00e-02 2.50e+03 5.07e+00 bond pdb=" C1 LBN A 701 " pdb=" O1 LBN A 701 " ideal model delta sigma weight residual 1.410 1.453 -0.043 2.00e-02 2.50e+03 4.71e+00 bond pdb=" C11 LBN A 701 " pdb=" C8 LBN A 701 " ideal model delta sigma weight residual 1.530 1.493 0.037 2.00e-02 2.50e+03 3.50e+00 bond pdb=" N ALA A 66 " pdb=" CA ALA A 66 " ideal model delta sigma weight residual 1.457 1.481 -0.024 1.29e-02 6.01e+03 3.34e+00 ... (remaining 9050 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 12007 1.95 - 3.90: 269 3.90 - 5.86: 33 5.86 - 7.81: 9 7.81 - 9.76: 4 Bond angle restraints: 12322 Sorted by residual: angle pdb=" C GLU B 96 " pdb=" N TYR B 97 " pdb=" CA TYR B 97 " ideal model delta sigma weight residual 120.09 125.56 -5.47 1.25e+00 6.40e-01 1.92e+01 angle pdb=" C PHE A 173 " pdb=" N ARG A 174 " pdb=" CA ARG A 174 " ideal model delta sigma weight residual 121.54 129.78 -8.24 1.91e+00 2.74e-01 1.86e+01 angle pdb=" CA TYR A 65 " pdb=" CB TYR A 65 " pdb=" CG TYR A 65 " ideal model delta sigma weight residual 113.90 120.26 -6.36 1.80e+00 3.09e-01 1.25e+01 angle pdb=" C TYR A 65 " pdb=" N ALA A 66 " pdb=" CA ALA A 66 " ideal model delta sigma weight residual 121.54 127.72 -6.18 1.91e+00 2.74e-01 1.05e+01 angle pdb=" N LYS A 70 " pdb=" CA LYS A 70 " pdb=" C LYS A 70 " ideal model delta sigma weight residual 111.02 114.55 -3.53 1.22e+00 6.72e-01 8.35e+00 ... (remaining 12317 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.26: 4834 26.26 - 52.52: 353 52.52 - 78.78: 42 78.78 - 105.05: 7 105.05 - 131.31: 3 Dihedral angle restraints: 5239 sinusoidal: 2094 harmonic: 3145 Sorted by residual: dihedral pdb=" CA ARG A 174 " pdb=" C ARG A 174 " pdb=" N HIS A 175 " pdb=" CA HIS A 175 " ideal model delta harmonic sigma weight residual 180.00 137.18 42.82 0 5.00e+00 4.00e-02 7.33e+01 dihedral pdb=" CA GLN A 79 " pdb=" C GLN A 79 " pdb=" N ALA A 80 " pdb=" CA ALA A 80 " ideal model delta harmonic sigma weight residual -180.00 -152.31 -27.69 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA TYR A 65 " pdb=" C TYR A 65 " pdb=" N ALA A 66 " pdb=" CA ALA A 66 " ideal model delta harmonic sigma weight residual -180.00 -157.49 -22.51 0 5.00e+00 4.00e-02 2.03e+01 ... (remaining 5236 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1314 0.086 - 0.172: 82 0.172 - 0.259: 1 0.259 - 0.345: 2 0.345 - 0.431: 1 Chirality restraints: 1400 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.30e+01 chirality pdb=" C1 NAG A 704 " pdb=" ND2 ASN A 246 " pdb=" C2 NAG A 704 " pdb=" O5 NAG A 704 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.64e+00 chirality pdb=" C1 NAG A 703 " pdb=" ND2 ASN A 513 " pdb=" C2 NAG A 703 " pdb=" O5 NAG A 703 " both_signs ideal model delta sigma weight residual False -2.40 -2.72 0.32 2.00e-01 2.50e+01 2.57e+00 ... (remaining 1397 not shown) Planarity restraints: 1526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 523 " 0.233 2.00e-02 2.50e+03 3.33e-01 1.38e+03 pdb=" CG ASN A 523 " -0.117 2.00e-02 2.50e+03 pdb=" OD1 ASN A 523 " 0.026 2.00e-02 2.50e+03 pdb=" ND2 ASN A 523 " -0.559 2.00e-02 2.50e+03 pdb=" C1 NAG A 706 " 0.416 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 513 " -0.080 2.00e-02 2.50e+03 2.29e-01 6.58e+02 pdb=" CG ASN A 513 " -0.062 2.00e-02 2.50e+03 pdb=" OD1 ASN A 513 " 0.228 2.00e-02 2.50e+03 pdb=" ND2 ASN A 513 " -0.357 2.00e-02 2.50e+03 pdb=" C1 NAG A 703 " 0.271 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 246 " -0.037 2.00e-02 2.50e+03 1.67e-01 3.49e+02 pdb=" CG ASN A 246 " -0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN A 246 " 0.154 2.00e-02 2.50e+03 pdb=" ND2 ASN A 246 " -0.275 2.00e-02 2.50e+03 pdb=" C1 NAG A 704 " 0.194 2.00e-02 2.50e+03 ... (remaining 1523 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 177 2.67 - 3.23: 8456 3.23 - 3.79: 13271 3.79 - 4.34: 19237 4.34 - 4.90: 31117 Nonbonded interactions: 72258 Sorted by model distance: nonbonded pdb=" O GLY B 47 " pdb=" OG SER B 51 " model vdw 2.114 3.040 nonbonded pdb=" OG SER B 345 " pdb=" O ARG B 348 " model vdw 2.141 3.040 nonbonded pdb=" O LEU A 565 " pdb=" NH2 ARG A 584 " model vdw 2.174 3.120 nonbonded pdb=" OG1 THR A 471 " pdb=" OH TYR A 582 " model vdw 2.223 3.040 nonbonded pdb=" NE2 GLN B 474 " pdb=" O VAL B 479 " model vdw 2.281 3.120 ... (remaining 72253 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.240 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.340 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.139 9067 Z= 0.283 Angle : 0.805 16.194 12354 Z= 0.428 Chirality : 0.047 0.431 1400 Planarity : 0.005 0.043 1520 Dihedral : 17.574 131.306 3209 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.03 % Favored : 94.88 % Rotamer: Outliers : 8.17 % Allowed : 22.27 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -4.80 (0.19), residues: 1074 helix: -4.12 (0.12), residues: 486 sheet: -2.26 (0.45), residues: 88 loop : -2.20 (0.24), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 400 TYR 0.019 0.001 TYR A 65 PHE 0.023 0.001 PHE A 407 TRP 0.017 0.001 TRP B 383 HIS 0.008 0.001 HIS A 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00611 / 0.27 ( 9055) covalent geometry : angle 0.74567 / 0.42 (12322) SS BOND : bond 0.02544 / 1.34 ( 4) SS BOND : angle 1.43327 / 0.65 ( 8) hydrogen bonds : bond 0.30241 / 19.82 ( 371) hydrogen bonds : angle 10.10146 / 7.08 ( 1035) link_BETA1-4 : bond 0.03842 / 1.99 ( 2) link_BETA1-4 : angle 8.34699 / 4.61 ( 6) link_NAG-ASN : bond 0.06082 / 4.14 ( 6) link_NAG-ASN : angle 6.32747 / 3.25 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 143 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: B 71 MET cc_start: 0.7689 (ttt) cc_final: 0.7288 (ttt) REVERT: B 233 ASP cc_start: 0.8265 (t70) cc_final: 0.7786 (t70) REVERT: B 237 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.7955 (mp10) REVERT: B 244 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.7166 (tm-30) REVERT: B 338 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8751 (tp) REVERT: B 356 MET cc_start: 0.6922 (mmm) cc_final: 0.6637 (mmt) REVERT: B 360 MET cc_start: 0.7974 (ttp) cc_final: 0.7408 (tmm) REVERT: B 436 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7395 (mm-30) REVERT: B 471 MET cc_start: 0.7639 (pp-130) cc_final: 0.7432 (ppp) REVERT: A 284 ASP cc_start: 0.8778 (OUTLIER) cc_final: 0.8078 (m-30) REVERT: A 377 ARG cc_start: 0.8259 (mtp85) cc_final: 0.8020 (mtp180) REVERT: A 465 MET cc_start: 0.9099 (tpt) cc_final: 0.8816 (mmm) REVERT: A 495 ASN cc_start: 0.8308 (t0) cc_final: 0.7849 (t0) REVERT: A 524 HIS cc_start: 0.7906 (p90) cc_final: 0.7688 (p-80) REVERT: A 574 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7777 (ppp-140) REVERT: A 662 PHE cc_start: 0.8497 (m-80) cc_final: 0.7648 (m-80) outliers start: 77 outliers final: 44 residues processed: 206 average time/residue: 0.1147 time to fit residues: 31.8132 Evaluate side-chains 171 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 121 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 207 PHE Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 321 CYS Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 348 ARG Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 574 ARG Chi-restraints excluded: chain A residue 670 ASN Chi-restraints excluded: chain A residue 675 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.0870 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 148 GLN B 203 ASN B 251 ASN B 372 ASN B 456 HIS B 463 GLN B 474 GLN A 79 GLN A 146 GLN A 156 ASN A 181 GLN A 220 HIS A 224 GLN A 282 GLN A 293 GLN A 301 GLN A 335 GLN A 345 GLN A 366 GLN A 370 GLN A 403 GLN A 442 ASN A 510 GLN A 544 GLN A 561 ASN A 575 ASN A 606 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.151195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.098727 restraints weight = 10685.657| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.56 r_work: 0.2845 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9067 Z= 0.162 Angle : 0.696 8.788 12354 Z= 0.353 Chirality : 0.045 0.308 1400 Planarity : 0.005 0.040 1520 Dihedral : 11.243 122.312 1311 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.47 % Favored : 95.44 % Rotamer: Outliers : 5.83 % Allowed : 23.01 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.81 (0.22), residues: 1074 helix: -1.93 (0.19), residues: 506 sheet: -1.93 (0.44), residues: 80 loop : -1.61 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 658 TYR 0.014 0.001 TYR A 65 PHE 0.018 0.002 PHE A 407 TRP 0.015 0.001 TRP B 383 HIS 0.009 0.001 HIS A 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 ( 9055) covalent geometry : angle 0.67898 / 0.35 (12322) SS BOND : bond 0.00591 / 0.30 ( 4) SS BOND : angle 1.07124 / 0.45 ( 8) hydrogen bonds : bond 0.05497 / 3.61 ( 371) hydrogen bonds : angle 5.14971 / 3.59 ( 1035) link_BETA1-4 : bond 0.01181 / 0.62 ( 2) link_BETA1-4 : angle 3.37591 / 1.91 ( 6) link_NAG-ASN : bond 0.00622 / 0.28 ( 6) link_NAG-ASN : angle 3.55710 / 1.87 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 127 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 233 ASP cc_start: 0.8464 (t70) cc_final: 0.7981 (t70) REVERT: B 278 MET cc_start: 0.8935 (ptp) cc_final: 0.8579 (ptp) REVERT: B 343 TYR cc_start: 0.8069 (m-10) cc_final: 0.7468 (m-10) REVERT: B 356 MET cc_start: 0.7366 (mmm) cc_final: 0.6898 (mmt) REVERT: B 360 MET cc_start: 0.8422 (ttp) cc_final: 0.8017 (tmm) REVERT: B 394 ILE cc_start: 0.8097 (OUTLIER) cc_final: 0.7833 (mt) REVERT: B 436 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7232 (mm-30) REVERT: B 444 MET cc_start: 0.7834 (mpp) cc_final: 0.7236 (mtt) REVERT: A 100 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.7360 (mt) REVERT: A 240 HIS cc_start: 0.8027 (t70) cc_final: 0.7676 (m-70) REVERT: A 243 ASN cc_start: 0.8095 (m-40) cc_final: 0.7248 (p0) REVERT: A 245 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7556 (mp0) REVERT: A 284 ASP cc_start: 0.9192 (OUTLIER) cc_final: 0.8888 (m-30) REVERT: A 377 ARG cc_start: 0.8810 (mtp85) cc_final: 0.8574 (mtp180) REVERT: A 465 MET cc_start: 0.9196 (tpt) cc_final: 0.8952 (mmm) REVERT: A 495 ASN cc_start: 0.8667 (t0) cc_final: 0.8166 (t0) outliers start: 55 outliers final: 28 residues processed: 171 average time/residue: 0.1139 time to fit residues: 26.0349 Evaluate side-chains 146 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 113 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 348 ARG Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain B residue 454 PHE Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 670 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 70 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 74 optimal weight: 0.0770 chunk 95 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 73 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN A 403 GLN A 466 ASN A 561 ASN A 613 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.152517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.094800 restraints weight = 10818.663| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.74 r_work: 0.2825 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9067 Z= 0.148 Angle : 0.645 9.072 12354 Z= 0.324 Chirality : 0.044 0.317 1400 Planarity : 0.005 0.041 1520 Dihedral : 9.547 115.837 1261 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.28 % Favored : 95.62 % Rotamer: Outliers : 5.41 % Allowed : 22.59 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.79 (0.24), residues: 1074 helix: -0.81 (0.22), residues: 508 sheet: -1.69 (0.44), residues: 80 loop : -1.40 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 658 TYR 0.015 0.001 TYR A 65 PHE 0.016 0.001 PHE A 407 TRP 0.017 0.001 TRP B 383 HIS 0.009 0.001 HIS A 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 9055) covalent geometry : angle 0.63309 / 0.32 (12322) SS BOND : bond 0.00461 / 0.23 ( 4) SS BOND : angle 1.39368 / 0.67 ( 8) hydrogen bonds : bond 0.04613 / 3.06 ( 371) hydrogen bonds : angle 4.68695 / 3.27 ( 1035) link_BETA1-4 : bond 0.01474 / 0.77 ( 2) link_BETA1-4 : angle 3.52175 / 2.01 ( 6) link_NAG-ASN : bond 0.00698 / 0.38 ( 6) link_NAG-ASN : angle 2.55821 / 1.47 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 118 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 GLU cc_start: 0.8484 (tp30) cc_final: 0.7919 (tp30) REVERT: B 175 TYR cc_start: 0.6348 (OUTLIER) cc_final: 0.5930 (m-80) REVERT: B 233 ASP cc_start: 0.8521 (t70) cc_final: 0.7934 (t70) REVERT: B 278 MET cc_start: 0.8888 (ptp) cc_final: 0.8483 (ptp) REVERT: B 343 TYR cc_start: 0.8104 (m-10) cc_final: 0.7417 (m-10) REVERT: B 356 MET cc_start: 0.7461 (mmm) cc_final: 0.7024 (mmt) REVERT: B 360 MET cc_start: 0.8381 (ttp) cc_final: 0.8041 (tmm) REVERT: B 435 TRP cc_start: 0.7427 (m-90) cc_final: 0.6218 (m-10) REVERT: B 436 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7187 (mm-30) REVERT: B 444 MET cc_start: 0.7898 (mpp) cc_final: 0.7284 (mtt) REVERT: A 100 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7535 (mt) REVERT: A 240 HIS cc_start: 0.8202 (t70) cc_final: 0.7969 (t70) REVERT: A 245 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7658 (mp0) REVERT: A 273 CYS cc_start: 0.8769 (m) cc_final: 0.8539 (m) REVERT: A 284 ASP cc_start: 0.9157 (OUTLIER) cc_final: 0.8858 (m-30) REVERT: A 377 ARG cc_start: 0.8906 (mtp85) cc_final: 0.8658 (mtp180) REVERT: A 465 MET cc_start: 0.9223 (tpt) cc_final: 0.8990 (mmm) REVERT: A 546 ARG cc_start: 0.7976 (mtp180) cc_final: 0.7722 (mtp180) outliers start: 51 outliers final: 34 residues processed: 158 average time/residue: 0.1017 time to fit residues: 22.2180 Evaluate side-chains 149 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 110 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 348 ARG Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain B residue 454 PHE Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 574 ARG Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 670 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 14 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 9 optimal weight: 0.4980 chunk 62 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN A 403 GLN A 561 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.152508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.098819 restraints weight = 10879.555| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.63 r_work: 0.2836 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9067 Z= 0.166 Angle : 0.638 8.544 12354 Z= 0.318 Chirality : 0.044 0.317 1400 Planarity : 0.004 0.039 1520 Dihedral : 8.968 110.704 1256 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.19 % Favored : 95.72 % Rotamer: Outliers : 5.94 % Allowed : 22.80 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.29 (0.25), residues: 1074 helix: -0.25 (0.24), residues: 502 sheet: -1.77 (0.42), residues: 90 loop : -1.22 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 658 TYR 0.015 0.001 TYR A 65 PHE 0.019 0.001 PHE A 407 TRP 0.015 0.001 TRP B 383 HIS 0.009 0.001 HIS A 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 ( 9055) covalent geometry : angle 0.62720 / 0.32 (12322) SS BOND : bond 0.00406 / 0.21 ( 4) SS BOND : angle 1.32927 / 0.64 ( 8) hydrogen bonds : bond 0.04349 / 2.88 ( 371) hydrogen bonds : angle 4.52012 / 3.14 ( 1035) link_BETA1-4 : bond 0.01404 / 0.73 ( 2) link_BETA1-4 : angle 3.40929 / 1.94 ( 6) link_NAG-ASN : bond 0.00600 / 0.30 ( 6) link_NAG-ASN : angle 2.36346 / 1.39 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 116 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 GLU cc_start: 0.8529 (tp30) cc_final: 0.8035 (tp30) REVERT: B 175 TYR cc_start: 0.6390 (OUTLIER) cc_final: 0.6016 (m-80) REVERT: B 233 ASP cc_start: 0.8504 (t70) cc_final: 0.7901 (t70) REVERT: B 270 MET cc_start: 0.8271 (mtp) cc_final: 0.8057 (mtm) REVERT: B 343 TYR cc_start: 0.8133 (m-10) cc_final: 0.7463 (m-10) REVERT: B 356 MET cc_start: 0.7483 (mmm) cc_final: 0.7033 (mmt) REVERT: B 360 MET cc_start: 0.8380 (ttp) cc_final: 0.8152 (tmm) REVERT: B 435 TRP cc_start: 0.7339 (m-90) cc_final: 0.6192 (m-10) REVERT: B 436 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7215 (mm-30) REVERT: B 444 MET cc_start: 0.7968 (mpp) cc_final: 0.7248 (mtt) REVERT: A 100 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7499 (mt) REVERT: A 240 HIS cc_start: 0.8227 (t70) cc_final: 0.7991 (t70) REVERT: A 245 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7647 (mp0) REVERT: A 284 ASP cc_start: 0.9159 (OUTLIER) cc_final: 0.8868 (m-30) REVERT: A 377 ARG cc_start: 0.8885 (mtp85) cc_final: 0.8633 (mtp180) REVERT: A 465 MET cc_start: 0.9214 (tpt) cc_final: 0.8997 (mmm) REVERT: A 546 ARG cc_start: 0.8020 (mtp180) cc_final: 0.7778 (mtp180) outliers start: 56 outliers final: 31 residues processed: 161 average time/residue: 0.0888 time to fit residues: 19.7048 Evaluate side-chains 144 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 108 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 574 ARG Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 670 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 22 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 45 optimal weight: 6.9990 chunk 49 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 105 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN A 403 GLN A 561 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.152329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.093056 restraints weight = 10843.335| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.54 r_work: 0.2833 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9067 Z= 0.171 Angle : 0.638 8.525 12354 Z= 0.318 Chirality : 0.045 0.318 1400 Planarity : 0.004 0.040 1520 Dihedral : 8.613 106.588 1249 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.19 % Favored : 95.72 % Rotamer: Outliers : 5.83 % Allowed : 23.44 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.07 (0.25), residues: 1074 helix: -0.00 (0.24), residues: 503 sheet: -1.67 (0.43), residues: 90 loop : -1.19 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 658 TYR 0.016 0.001 TYR A 65 PHE 0.020 0.001 PHE A 407 TRP 0.013 0.001 TRP B 383 HIS 0.009 0.001 HIS A 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 ( 9055) covalent geometry : angle 0.62550 / 0.31 (12322) SS BOND : bond 0.00318 / 0.16 ( 4) SS BOND : angle 2.16385 / 1.07 ( 8) hydrogen bonds : bond 0.04264 / 2.83 ( 371) hydrogen bonds : angle 4.46352 / 3.09 ( 1035) link_BETA1-4 : bond 0.01438 / 0.75 ( 2) link_BETA1-4 : angle 3.41315 / 1.93 ( 6) link_NAG-ASN : bond 0.00600 / 0.30 ( 6) link_NAG-ASN : angle 2.32308 / 1.37 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 110 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 MET cc_start: 0.8528 (tpt) cc_final: 0.8230 (tpt) REVERT: B 102 GLU cc_start: 0.8567 (tp30) cc_final: 0.8061 (tp30) REVERT: B 175 TYR cc_start: 0.6414 (OUTLIER) cc_final: 0.5989 (m-80) REVERT: B 233 ASP cc_start: 0.8485 (t70) cc_final: 0.7886 (t70) REVERT: B 270 MET cc_start: 0.8257 (mtp) cc_final: 0.8018 (mtm) REVERT: B 356 MET cc_start: 0.7410 (mmm) cc_final: 0.6956 (mmt) REVERT: B 360 MET cc_start: 0.8368 (ttp) cc_final: 0.8118 (tmm) REVERT: B 435 TRP cc_start: 0.7318 (m-90) cc_final: 0.6172 (m-10) REVERT: B 436 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7155 (mm-30) REVERT: B 444 MET cc_start: 0.7972 (mpp) cc_final: 0.7241 (mtt) REVERT: A 99 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7491 (tt) REVERT: A 284 ASP cc_start: 0.9167 (OUTLIER) cc_final: 0.8842 (m-30) REVERT: A 377 ARG cc_start: 0.8872 (mtp85) cc_final: 0.8650 (mtp180) REVERT: A 418 LYS cc_start: 0.8940 (mttp) cc_final: 0.8677 (mmmt) REVERT: A 465 MET cc_start: 0.9201 (tpt) cc_final: 0.8981 (mmm) REVERT: A 546 ARG cc_start: 0.8073 (mtp180) cc_final: 0.7834 (mtp180) REVERT: A 574 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7365 (ttp80) REVERT: A 679 ASN cc_start: 0.8486 (t0) cc_final: 0.8188 (t0) outliers start: 55 outliers final: 39 residues processed: 155 average time/residue: 0.1027 time to fit residues: 22.0859 Evaluate side-chains 151 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 107 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 348 ARG Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 574 ARG Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 670 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 93 optimal weight: 0.3980 chunk 44 optimal weight: 0.2980 chunk 95 optimal weight: 0.0570 chunk 40 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 70 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 77 optimal weight: 0.2980 chunk 21 optimal weight: 0.1980 chunk 13 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 overall best weight: 0.2498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN A 403 GLN A 561 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.153985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.101373 restraints weight = 10731.194| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.59 r_work: 0.2876 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9067 Z= 0.107 Angle : 0.592 8.562 12354 Z= 0.293 Chirality : 0.043 0.316 1400 Planarity : 0.004 0.037 1520 Dihedral : 8.074 96.538 1248 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.82 % Favored : 96.09 % Rotamer: Outliers : 4.45 % Allowed : 24.50 % Favored : 71.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.70 (0.26), residues: 1074 helix: 0.35 (0.24), residues: 508 sheet: -1.53 (0.42), residues: 90 loop : -1.06 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 658 TYR 0.017 0.001 TYR A 65 PHE 0.020 0.001 PHE A 407 TRP 0.012 0.001 TRP B 383 HIS 0.009 0.001 HIS A 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 ( 9055) covalent geometry : angle 0.58007 / 0.29 (12322) SS BOND : bond 0.00151 / 0.08 ( 4) SS BOND : angle 1.57381 / 0.78 ( 8) hydrogen bonds : bond 0.03584 / 2.38 ( 371) hydrogen bonds : angle 4.26437 / 2.95 ( 1035) link_BETA1-4 : bond 0.01387 / 0.73 ( 2) link_BETA1-4 : angle 3.31494 / 1.88 ( 6) link_NAG-ASN : bond 0.00623 / 0.31 ( 6) link_NAG-ASN : angle 2.29658 / 1.36 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 121 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 MET cc_start: 0.8605 (tpt) cc_final: 0.8279 (tpt) REVERT: B 102 GLU cc_start: 0.8536 (tp30) cc_final: 0.8100 (tp30) REVERT: B 175 TYR cc_start: 0.6242 (OUTLIER) cc_final: 0.5837 (m-80) REVERT: B 233 ASP cc_start: 0.8468 (t70) cc_final: 0.7858 (t70) REVERT: B 270 MET cc_start: 0.8203 (mtp) cc_final: 0.7994 (mtt) REVERT: B 356 MET cc_start: 0.7436 (mmm) cc_final: 0.7015 (mmt) REVERT: B 360 MET cc_start: 0.8348 (ttp) cc_final: 0.8108 (tmm) REVERT: B 390 ILE cc_start: 0.8265 (mm) cc_final: 0.8011 (mm) REVERT: B 405 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7857 (mtt90) REVERT: B 435 TRP cc_start: 0.7185 (m-90) cc_final: 0.6096 (m-10) REVERT: B 436 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7163 (mm-30) REVERT: B 444 MET cc_start: 0.7957 (mpp) cc_final: 0.7173 (mtt) REVERT: A 377 ARG cc_start: 0.8839 (mtp85) cc_final: 0.8611 (mtp180) REVERT: A 418 LYS cc_start: 0.8909 (mttp) cc_final: 0.8656 (mmmt) REVERT: A 574 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7299 (ttp80) REVERT: A 679 ASN cc_start: 0.8420 (t0) cc_final: 0.8150 (t0) outliers start: 42 outliers final: 24 residues processed: 152 average time/residue: 0.0937 time to fit residues: 19.4189 Evaluate side-chains 139 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 405 ARG Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 574 ARG Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 670 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 51 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 79 optimal weight: 0.9990 chunk 54 optimal weight: 0.0970 chunk 59 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 0.4980 chunk 11 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 45 optimal weight: 0.0370 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 GLN A 561 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.154002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.096866 restraints weight = 10742.250| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.72 r_work: 0.2867 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9067 Z= 0.122 Angle : 0.600 8.598 12354 Z= 0.296 Chirality : 0.043 0.319 1400 Planarity : 0.004 0.038 1520 Dihedral : 7.313 89.653 1237 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.00 % Favored : 95.90 % Rotamer: Outliers : 4.14 % Allowed : 24.71 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.48 (0.26), residues: 1074 helix: 0.59 (0.25), residues: 503 sheet: -1.39 (0.44), residues: 90 loop : -1.01 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 658 TYR 0.016 0.001 TYR A 65 PHE 0.018 0.001 PHE A 407 TRP 0.010 0.001 TRP B 383 HIS 0.009 0.001 HIS A 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 9055) covalent geometry : angle 0.58735 / 0.29 (12322) SS BOND : bond 0.00172 / 0.09 ( 4) SS BOND : angle 1.83642 / 0.88 ( 8) hydrogen bonds : bond 0.03623 / 2.41 ( 371) hydrogen bonds : angle 4.20723 / 2.91 ( 1035) link_BETA1-4 : bond 0.01415 / 0.74 ( 2) link_BETA1-4 : angle 3.33492 / 1.89 ( 6) link_NAG-ASN : bond 0.00614 / 0.30 ( 6) link_NAG-ASN : angle 2.37813 / 1.39 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 111 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 MET cc_start: 0.8515 (tpt) cc_final: 0.8242 (tpt) REVERT: B 102 GLU cc_start: 0.8556 (tp30) cc_final: 0.8115 (tp30) REVERT: B 175 TYR cc_start: 0.6224 (OUTLIER) cc_final: 0.5852 (m-80) REVERT: B 233 ASP cc_start: 0.8488 (t70) cc_final: 0.7886 (t70) REVERT: B 270 MET cc_start: 0.8212 (mtp) cc_final: 0.7993 (mtt) REVERT: B 343 TYR cc_start: 0.8080 (m-10) cc_final: 0.7410 (m-10) REVERT: B 356 MET cc_start: 0.7472 (mmm) cc_final: 0.7053 (mmt) REVERT: B 360 MET cc_start: 0.8378 (ttp) cc_final: 0.8121 (tmm) REVERT: B 390 ILE cc_start: 0.8177 (mm) cc_final: 0.7937 (mm) REVERT: B 435 TRP cc_start: 0.7167 (m-90) cc_final: 0.6074 (m-10) REVERT: B 436 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7175 (mm-30) REVERT: A 100 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7545 (mt) REVERT: A 377 ARG cc_start: 0.8856 (mtp85) cc_final: 0.8635 (mtp180) REVERT: A 418 LYS cc_start: 0.8897 (mttp) cc_final: 0.8642 (mmmt) REVERT: A 679 ASN cc_start: 0.8466 (t0) cc_final: 0.8182 (t0) outliers start: 39 outliers final: 30 residues processed: 140 average time/residue: 0.0987 time to fit residues: 19.1085 Evaluate side-chains 144 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 111 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 348 ARG Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 574 ARG Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 670 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 58 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 37 optimal weight: 0.4980 chunk 53 optimal weight: 0.6980 chunk 24 optimal weight: 0.0980 chunk 27 optimal weight: 0.1980 chunk 8 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.156351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.101219 restraints weight = 10721.455| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.83 r_work: 0.2868 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9067 Z= 0.122 Angle : 0.599 8.614 12354 Z= 0.296 Chirality : 0.043 0.319 1400 Planarity : 0.004 0.038 1520 Dihedral : 7.238 86.069 1237 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.82 % Favored : 96.09 % Rotamer: Outliers : 4.03 % Allowed : 25.34 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 (0.26), residues: 1074 helix: 0.68 (0.25), residues: 503 sheet: -1.30 (0.44), residues: 90 loop : -0.99 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 658 TYR 0.016 0.001 TYR A 65 PHE 0.018 0.001 PHE B 398 TRP 0.010 0.001 TRP B 383 HIS 0.009 0.001 HIS A 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 9055) covalent geometry : angle 0.58670 / 0.29 (12322) SS BOND : bond 0.00282 / 0.14 ( 4) SS BOND : angle 1.90646 / 0.89 ( 8) hydrogen bonds : bond 0.03573 / 2.37 ( 371) hydrogen bonds : angle 4.20605 / 2.90 ( 1035) link_BETA1-4 : bond 0.01388 / 0.73 ( 2) link_BETA1-4 : angle 3.30958 / 1.87 ( 6) link_NAG-ASN : bond 0.00615 / 0.30 ( 6) link_NAG-ASN : angle 2.32046 / 1.37 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 116 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 MET cc_start: 0.8560 (tpt) cc_final: 0.8290 (tpt) REVERT: B 102 GLU cc_start: 0.8570 (tp30) cc_final: 0.8152 (tp30) REVERT: B 175 TYR cc_start: 0.6221 (OUTLIER) cc_final: 0.5872 (m-80) REVERT: B 233 ASP cc_start: 0.8482 (t70) cc_final: 0.7845 (t70) REVERT: B 270 MET cc_start: 0.8088 (mtp) cc_final: 0.7864 (mtt) REVERT: B 343 TYR cc_start: 0.8069 (m-10) cc_final: 0.7414 (m-10) REVERT: B 356 MET cc_start: 0.7288 (mmm) cc_final: 0.6884 (mmt) REVERT: B 360 MET cc_start: 0.8287 (ttp) cc_final: 0.8011 (tmm) REVERT: B 390 ILE cc_start: 0.8121 (mm) cc_final: 0.7851 (mm) REVERT: B 405 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7822 (mtt90) REVERT: B 435 TRP cc_start: 0.7116 (m-90) cc_final: 0.6019 (m-10) REVERT: B 436 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7098 (mm-30) REVERT: A 100 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7456 (mt) REVERT: A 243 ASN cc_start: 0.7574 (t0) cc_final: 0.7361 (t0) REVERT: A 377 ARG cc_start: 0.8832 (mtp85) cc_final: 0.8593 (mtp180) REVERT: A 418 LYS cc_start: 0.8892 (mttp) cc_final: 0.8620 (mmmt) REVERT: A 546 ARG cc_start: 0.8120 (mtp180) cc_final: 0.7807 (mtp180) outliers start: 38 outliers final: 29 residues processed: 145 average time/residue: 0.0893 time to fit residues: 17.7423 Evaluate side-chains 147 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 114 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 348 ARG Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 405 ARG Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 670 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 74 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 91 optimal weight: 0.1980 chunk 42 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 87 optimal weight: 0.4980 chunk 45 optimal weight: 7.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN A 403 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.154592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.095742 restraints weight = 10749.157| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.46 r_work: 0.2870 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9067 Z= 0.148 Angle : 0.613 8.529 12354 Z= 0.303 Chirality : 0.044 0.320 1400 Planarity : 0.004 0.043 1520 Dihedral : 7.253 84.330 1237 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.10 % Favored : 95.81 % Rotamer: Outliers : 4.24 % Allowed : 25.03 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.42 (0.26), residues: 1074 helix: 0.66 (0.24), residues: 506 sheet: -1.33 (0.44), residues: 90 loop : -1.03 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 658 TYR 0.016 0.001 TYR A 65 PHE 0.019 0.001 PHE B 398 TRP 0.009 0.001 TRP A 443 HIS 0.009 0.001 HIS A 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 9055) covalent geometry : angle 0.60044 / 0.30 (12322) SS BOND : bond 0.00314 / 0.16 ( 4) SS BOND : angle 2.18157 / 1.01 ( 8) hydrogen bonds : bond 0.03741 / 2.48 ( 371) hydrogen bonds : angle 4.21936 / 2.91 ( 1035) link_BETA1-4 : bond 0.01433 / 0.75 ( 2) link_BETA1-4 : angle 3.34037 / 1.89 ( 6) link_NAG-ASN : bond 0.00602 / 0.30 ( 6) link_NAG-ASN : angle 2.28889 / 1.35 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 114 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 MET cc_start: 0.8570 (tpt) cc_final: 0.8273 (tpt) REVERT: B 102 GLU cc_start: 0.8537 (tp30) cc_final: 0.8087 (tp30) REVERT: B 175 TYR cc_start: 0.6275 (OUTLIER) cc_final: 0.5998 (m-80) REVERT: B 233 ASP cc_start: 0.8512 (t70) cc_final: 0.7890 (t70) REVERT: B 270 MET cc_start: 0.8190 (mtp) cc_final: 0.7971 (mtt) REVERT: B 343 TYR cc_start: 0.8091 (m-10) cc_final: 0.7439 (m-10) REVERT: B 356 MET cc_start: 0.7373 (mmm) cc_final: 0.6950 (mmt) REVERT: B 360 MET cc_start: 0.8367 (ttp) cc_final: 0.8094 (tmm) REVERT: B 390 ILE cc_start: 0.8175 (mm) cc_final: 0.7898 (mm) REVERT: B 405 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7827 (mtt90) REVERT: B 435 TRP cc_start: 0.7137 (m-90) cc_final: 0.6021 (m-10) REVERT: B 436 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7173 (mm-30) REVERT: B 445 LEU cc_start: 0.7553 (mt) cc_final: 0.7318 (mm) REVERT: A 100 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7561 (mt) REVERT: A 240 HIS cc_start: 0.8110 (t70) cc_final: 0.7793 (t70) REVERT: A 377 ARG cc_start: 0.8841 (mtp85) cc_final: 0.8611 (mtp180) REVERT: A 418 LYS cc_start: 0.8875 (mttp) cc_final: 0.8629 (mmmt) REVERT: A 546 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7791 (mtp180) REVERT: A 679 ASN cc_start: 0.8493 (t0) cc_final: 0.8218 (t0) outliers start: 40 outliers final: 31 residues processed: 144 average time/residue: 0.0868 time to fit residues: 17.0953 Evaluate side-chains 148 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 112 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 348 ARG Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 405 ARG Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 670 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 94 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.153405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.093858 restraints weight = 10766.919| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.56 r_work: 0.2840 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9067 Z= 0.177 Angle : 0.632 8.782 12354 Z= 0.313 Chirality : 0.045 0.328 1400 Planarity : 0.004 0.046 1520 Dihedral : 7.355 84.420 1237 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.19 % Favored : 95.72 % Rotamer: Outliers : 3.92 % Allowed : 25.13 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.46 (0.26), residues: 1074 helix: 0.62 (0.24), residues: 506 sheet: -1.40 (0.44), residues: 90 loop : -1.04 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 574 TYR 0.016 0.001 TYR A 65 PHE 0.023 0.001 PHE A 407 TRP 0.011 0.001 TRP A 443 HIS 0.009 0.001 HIS A 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 ( 9055) covalent geometry : angle 0.61976 / 0.31 (12322) SS BOND : bond 0.00216 / 0.11 ( 4) SS BOND : angle 2.23292 / 1.01 ( 8) hydrogen bonds : bond 0.03960 / 2.63 ( 371) hydrogen bonds : angle 4.27602 / 2.94 ( 1035) link_BETA1-4 : bond 0.01376 / 0.72 ( 2) link_BETA1-4 : angle 3.35203 / 1.89 ( 6) link_NAG-ASN : bond 0.00654 / 0.32 ( 6) link_NAG-ASN : angle 2.34935 / 1.38 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 110 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 MET cc_start: 0.8513 (tpt) cc_final: 0.8020 (tpt) REVERT: B 102 GLU cc_start: 0.8543 (tp30) cc_final: 0.8089 (tp30) REVERT: B 175 TYR cc_start: 0.6158 (OUTLIER) cc_final: 0.5930 (m-80) REVERT: B 233 ASP cc_start: 0.8522 (t70) cc_final: 0.7933 (t70) REVERT: B 270 MET cc_start: 0.8199 (mtp) cc_final: 0.7972 (mtt) REVERT: B 343 TYR cc_start: 0.8098 (m-10) cc_final: 0.7422 (m-10) REVERT: B 356 MET cc_start: 0.7429 (mmm) cc_final: 0.7004 (mmt) REVERT: B 360 MET cc_start: 0.8365 (ttp) cc_final: 0.8094 (tmm) REVERT: B 390 ILE cc_start: 0.8103 (mm) cc_final: 0.7854 (mm) REVERT: B 405 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7823 (mtt90) REVERT: B 435 TRP cc_start: 0.7143 (m-90) cc_final: 0.6006 (m-10) REVERT: B 436 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7177 (mm-30) REVERT: B 445 LEU cc_start: 0.7611 (mt) cc_final: 0.7364 (mm) REVERT: A 99 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7415 (tt) REVERT: A 240 HIS cc_start: 0.8115 (t70) cc_final: 0.7827 (t70) REVERT: A 377 ARG cc_start: 0.8862 (mtp85) cc_final: 0.8625 (mtp180) REVERT: A 418 LYS cc_start: 0.8864 (mttp) cc_final: 0.8608 (mmmt) REVERT: A 546 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7815 (mtp180) REVERT: A 679 ASN cc_start: 0.8490 (t0) cc_final: 0.8221 (t0) outliers start: 37 outliers final: 31 residues processed: 138 average time/residue: 0.0907 time to fit residues: 16.9814 Evaluate side-chains 145 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 109 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 348 ARG Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 405 ARG Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 670 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 93 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 14 optimal weight: 0.2980 chunk 22 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 27 optimal weight: 0.0010 chunk 50 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.154756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.095639 restraints weight = 10638.496| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.53 r_work: 0.2869 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9067 Z= 0.126 Angle : 0.612 9.100 12354 Z= 0.302 Chirality : 0.043 0.333 1400 Planarity : 0.004 0.047 1520 Dihedral : 7.281 80.653 1237 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.19 % Favored : 95.72 % Rotamer: Outliers : 3.82 % Allowed : 25.45 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.35 (0.26), residues: 1074 helix: 0.69 (0.24), residues: 513 sheet: -1.31 (0.44), residues: 90 loop : -0.99 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 574 TYR 0.016 0.001 TYR A 65 PHE 0.021 0.001 PHE B 398 TRP 0.011 0.001 TRP B 383 HIS 0.009 0.001 HIS A 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 9055) covalent geometry : angle 0.59970 / 0.30 (12322) SS BOND : bond 0.00183 / 0.09 ( 4) SS BOND : angle 1.97544 / 0.90 ( 8) hydrogen bonds : bond 0.03633 / 2.41 ( 371) hydrogen bonds : angle 4.20500 / 2.89 ( 1035) link_BETA1-4 : bond 0.01302 / 0.68 ( 2) link_BETA1-4 : angle 3.29567 / 1.86 ( 6) link_NAG-ASN : bond 0.00673 / 0.33 ( 6) link_NAG-ASN : angle 2.40465 / 1.42 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2910.29 seconds wall clock time: 50 minutes 22.11 seconds (3022.11 seconds total)