Starting phenix.real_space_refine on Sun Jul 27 12:50:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nf6_12296/07_2025/7nf6_12296.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nf6_12296/07_2025/7nf6_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_2025/7nf6_12296.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nf6_12296/07_2025/7nf6_12296.map" model { file = "/net/cci-nas-00/data/ceres_data/7nf6_12296/07_2025/7nf6_12296.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nf6_12296/07_2025/7nf6_12296.cif" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 5.99, per 1000 atoms: 0.68 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: 2.36 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.92 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: 2.45 Time building geometry restraints manager: 2.78 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: 5112 26.26 - 52.52: 361 52.52 - 78.78: 42 78.78 - 105.05: 9 105.05 - 131.31: 4 Dihedral angle restraints: 5528 sinusoidal: 2383 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 5525 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: 10.910 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: 0.000 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.810 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 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 : 17.273 131.306 3498 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.017 0.001 TRP B 383 HIS 0.008 0.001 HIS A 175 PHE 0.023 0.001 PHE A 407 TYR 0.019 0.001 TYR A 65 ARG 0.002 0.000 ARG B 400 Details of bonding type rmsd link_NAG-ASN : bond 0.06082 ( 6) link_NAG-ASN : angle 6.32747 ( 18) link_BETA1-4 : bond 0.03842 ( 2) link_BETA1-4 : angle 8.34699 ( 6) hydrogen bonds : bond 0.30241 ( 371) hydrogen bonds : angle 10.10146 ( 1035) SS BOND : bond 0.02544 ( 4) SS BOND : angle 1.43327 ( 8) covalent geometry : bond 0.00611 ( 9055) covalent geometry : angle 0.74567 (12322) *********************** 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 : 0.939 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: 0.2446 time to fit residues: 67.2904 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 : 1.031 ------------------------------------------------------------------------------- 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 90 optimal weight: 0.5980 chunk 81 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 43 optimal weight: 0.0040 chunk 83 optimal weight: 0.5980 chunk 32 optimal weight: 8.9990 chunk 50 optimal weight: 0.0980 chunk 62 optimal weight: 0.0980 chunk 97 optimal weight: 0.9990 overall best weight: 0.2792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 GLN B 203 ASN B 251 ASN B 372 ASN B 456 HIS ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.152529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.100456 restraints weight = 10521.922| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.55 r_work: 0.2842 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9067 Z= 0.134 Angle : 0.676 8.769 12354 Z= 0.342 Chirality : 0.045 0.283 1400 Planarity : 0.005 0.039 1520 Dihedral : 11.315 126.568 1600 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.00 % Favored : 95.90 % Rotamer: Outliers : 5.51 % Allowed : 22.80 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.22), residues: 1074 helix: -1.83 (0.19), residues: 500 sheet: -1.89 (0.44), residues: 80 loop : -1.60 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 383 HIS 0.009 0.001 HIS A 175 PHE 0.014 0.001 PHE A 407 TYR 0.014 0.001 TYR A 65 ARG 0.006 0.000 ARG A 658 Details of bonding type rmsd link_NAG-ASN : bond 0.00581 ( 6) link_NAG-ASN : angle 3.43883 ( 18) link_BETA1-4 : bond 0.01426 ( 2) link_BETA1-4 : angle 3.75524 ( 6) hydrogen bonds : bond 0.05400 ( 371) hydrogen bonds : angle 5.10408 ( 1035) SS BOND : bond 0.00225 ( 4) SS BOND : angle 1.36546 ( 8) covalent geometry : bond 0.00284 ( 9055) covalent geometry : angle 0.65773 (12322) *********************** 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 184 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 132 time to evaluate : 1.007 Fit side-chains revert: symmetry clash REVERT: B 205 ARG cc_start: 0.6903 (ttt90) cc_final: 0.6657 (ttm-80) REVERT: B 233 ASP cc_start: 0.8481 (t70) cc_final: 0.7996 (t70) REVERT: B 278 MET cc_start: 0.8926 (ptp) cc_final: 0.8600 (ptp) REVERT: B 356 MET cc_start: 0.7540 (mmm) cc_final: 0.7051 (mmt) REVERT: B 360 MET cc_start: 0.8490 (ttp) cc_final: 0.8100 (tmm) REVERT: B 394 ILE cc_start: 0.8057 (OUTLIER) cc_final: 0.7830 (mt) REVERT: B 436 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7284 (mm-30) REVERT: B 444 MET cc_start: 0.7858 (mpp) cc_final: 0.7359 (mtt) REVERT: A 240 HIS cc_start: 0.8006 (t70) cc_final: 0.7750 (m90) REVERT: A 243 ASN cc_start: 0.8037 (m-40) cc_final: 0.7215 (p0) REVERT: A 245 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7566 (mp0) REVERT: A 250 ILE cc_start: 0.8722 (pp) cc_final: 0.8094 (mp) REVERT: A 284 ASP cc_start: 0.9135 (OUTLIER) cc_final: 0.8907 (m-30) REVERT: A 377 ARG cc_start: 0.8785 (mtp85) cc_final: 0.8538 (mtp180) REVERT: A 465 MET cc_start: 0.9216 (tpt) cc_final: 0.9000 (mmm) REVERT: A 658 ARG cc_start: 0.8721 (mmm-85) cc_final: 0.8365 (mmt180) REVERT: A 666 CYS cc_start: 0.7276 (m) cc_final: 0.7022 (m) outliers start: 52 outliers final: 26 residues processed: 172 average time/residue: 0.2543 time to fit residues: 58.0781 Evaluate side-chains 145 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 115 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 B residue 479 VAL 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 94 optimal weight: 0.6980 chunk 73 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3782 r_free = 0.3782 target = 0.152221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.098392 restraints weight = 10971.812| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.67 r_work: 0.2836 rms_B_bonded: 3.06 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: 0.8363 moved from start: 0.1847 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= 0.170 Angle : 0.654 8.679 12354 Z= 0.328 Chirality : 0.045 0.317 1400 Planarity : 0.005 0.040 1520 Dihedral : 9.706 129.501 1543 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.19 % Favored : 95.72 % Rotamer: Outliers : 5.30 % Allowed : 22.38 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.24), residues: 1074 helix: -0.80 (0.22), residues: 506 sheet: -1.69 (0.44), residues: 80 loop : -1.41 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 383 HIS 0.009 0.001 HIS A 175 PHE 0.020 0.001 PHE A 407 TYR 0.015 0.001 TYR A 65 ARG 0.003 0.000 ARG A 658 Details of bonding type rmsd link_NAG-ASN : bond 0.00600 ( 6) link_NAG-ASN : angle 2.59050 ( 18) link_BETA1-4 : bond 0.01528 ( 2) link_BETA1-4 : angle 3.72580 ( 6) hydrogen bonds : bond 0.04784 ( 371) hydrogen bonds : angle 4.72060 ( 1035) SS BOND : bond 0.00448 ( 4) SS BOND : angle 1.23903 ( 8) covalent geometry : bond 0.00398 ( 9055) covalent geometry : angle 0.64158 (12322) *********************** 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 171 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 121 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 GLU cc_start: 0.8596 (tp30) cc_final: 0.8083 (tp30) REVERT: B 175 TYR cc_start: 0.6313 (OUTLIER) cc_final: 0.5898 (m-80) REVERT: B 233 ASP cc_start: 0.8506 (t70) cc_final: 0.7915 (t70) REVERT: B 278 MET cc_start: 0.8897 (ptp) cc_final: 0.8488 (ptp) REVERT: B 356 MET cc_start: 0.7466 (mmm) cc_final: 0.7024 (mmt) REVERT: B 360 MET cc_start: 0.8524 (ttp) cc_final: 0.8176 (tmm) REVERT: B 435 TRP cc_start: 0.7346 (m-90) cc_final: 0.6200 (m-10) REVERT: B 436 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7186 (mm-30) REVERT: B 444 MET cc_start: 0.7934 (mpp) cc_final: 0.7241 (mtt) REVERT: A 240 HIS cc_start: 0.8066 (t70) cc_final: 0.7793 (t70) REVERT: A 245 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7645 (mp0) REVERT: A 273 CYS cc_start: 0.8662 (m) cc_final: 0.8453 (m) REVERT: A 284 ASP cc_start: 0.9182 (OUTLIER) cc_final: 0.8876 (m-30) REVERT: A 377 ARG cc_start: 0.8872 (mtp85) cc_final: 0.8609 (mtp180) REVERT: A 465 MET cc_start: 0.9228 (tpt) cc_final: 0.9001 (mmm) REVERT: A 546 ARG cc_start: 0.7892 (mtp180) cc_final: 0.7651 (mtp180) REVERT: A 658 ARG cc_start: 0.8749 (mmm-85) cc_final: 0.8392 (mmt180) outliers start: 50 outliers final: 30 residues processed: 159 average time/residue: 0.2550 time to fit residues: 53.1053 Evaluate side-chains 146 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 112 time to evaluate : 0.970 ------------------------------------------------------------------------------- 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 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 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 A residue 72 VAL 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 4 optimal weight: 0.6980 chunk 15 optimal weight: 0.0670 chunk 16 optimal weight: 0.6980 chunk 45 optimal weight: 0.0670 chunk 33 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 0.0770 chunk 23 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 overall best weight: 0.3214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3827 r_free = 0.3827 target = 0.156220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.101658 restraints weight = 10794.473| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.72 r_work: 0.2856 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2134 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= 0.117 Angle : 0.609 8.663 12354 Z= 0.304 Chirality : 0.043 0.316 1400 Planarity : 0.004 0.040 1520 Dihedral : 9.234 129.949 1539 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.10 % Favored : 95.81 % Rotamer: Outliers : 4.88 % Allowed : 23.33 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.25), residues: 1074 helix: -0.16 (0.24), residues: 505 sheet: -1.57 (0.44), residues: 80 loop : -1.19 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 383 HIS 0.009 0.001 HIS A 175 PHE 0.014 0.001 PHE A 407 TYR 0.016 0.001 TYR A 65 ARG 0.004 0.000 ARG B 250 Details of bonding type rmsd link_NAG-ASN : bond 0.00640 ( 6) link_NAG-ASN : angle 2.41297 ( 18) link_BETA1-4 : bond 0.01476 ( 2) link_BETA1-4 : angle 3.62673 ( 6) hydrogen bonds : bond 0.03947 ( 371) hydrogen bonds : angle 4.43409 ( 1035) SS BOND : bond 0.00443 ( 4) SS BOND : angle 1.28327 ( 8) covalent geometry : bond 0.00258 ( 9055) covalent geometry : angle 0.59665 (12322) *********************** 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 165 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 119 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 GLU cc_start: 0.8544 (tp30) cc_final: 0.8101 (tp30) REVERT: B 175 TYR cc_start: 0.6384 (OUTLIER) cc_final: 0.6006 (m-80) REVERT: B 233 ASP cc_start: 0.8484 (t70) cc_final: 0.7872 (t70) REVERT: B 356 MET cc_start: 0.7404 (mmm) cc_final: 0.6980 (mmt) REVERT: B 360 MET cc_start: 0.8326 (ttp) cc_final: 0.7959 (tmm) REVERT: B 416 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8666 (tp) REVERT: B 435 TRP cc_start: 0.7353 (m-90) cc_final: 0.6237 (m-10) REVERT: B 436 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7147 (mm-30) REVERT: B 444 MET cc_start: 0.7919 (mpp) cc_final: 0.7278 (mtt) REVERT: B 469 LEU cc_start: 0.8592 (tp) cc_final: 0.8301 (tp) REVERT: A 240 HIS cc_start: 0.8211 (t70) cc_final: 0.7997 (t70) REVERT: A 245 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7633 (mp0) REVERT: A 377 ARG cc_start: 0.8846 (mtp85) cc_final: 0.8642 (mtp180) REVERT: A 418 LYS cc_start: 0.8951 (mttp) cc_final: 0.8713 (mmmt) REVERT: A 546 ARG cc_start: 0.7954 (mtp180) cc_final: 0.7725 (mtp180) outliers start: 46 outliers final: 28 residues processed: 156 average time/residue: 0.2167 time to fit residues: 46.1495 Evaluate side-chains 143 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 111 time to evaluate : 0.896 ------------------------------------------------------------------------------- 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 258 ILE Chi-restraints excluded: chain B residue 283 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 416 LEU Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain A residue 72 VAL 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 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 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 70 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 54 optimal weight: 0.4980 chunk 44 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 29 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3785 r_free = 0.3785 target = 0.152541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.093391 restraints weight = 10663.012| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.55 r_work: 0.2834 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9067 Z= 0.177 Angle : 0.637 8.511 12354 Z= 0.316 Chirality : 0.045 0.318 1400 Planarity : 0.004 0.039 1520 Dihedral : 8.918 130.084 1534 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.38 % Favored : 95.53 % Rotamer: Outliers : 4.67 % Allowed : 23.86 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.25), residues: 1074 helix: 0.01 (0.24), residues: 502 sheet: -1.61 (0.43), residues: 90 loop : -1.15 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 383 HIS 0.008 0.001 HIS A 175 PHE 0.026 0.001 PHE A 407 TYR 0.015 0.001 TYR A 65 ARG 0.004 0.000 ARG A 658 Details of bonding type rmsd link_NAG-ASN : bond 0.00618 ( 6) link_NAG-ASN : angle 2.42880 ( 18) link_BETA1-4 : bond 0.01438 ( 2) link_BETA1-4 : angle 3.62460 ( 6) hydrogen bonds : bond 0.04271 ( 371) hydrogen bonds : angle 4.42349 ( 1035) SS BOND : bond 0.00340 ( 4) SS BOND : angle 1.82570 ( 8) covalent geometry : bond 0.00424 ( 9055) covalent geometry : angle 0.62374 (12322) *********************** 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 155 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 111 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 MET cc_start: 0.8505 (tpt) cc_final: 0.8267 (tpt) REVERT: B 102 GLU cc_start: 0.8535 (tp30) cc_final: 0.8124 (tp30) REVERT: B 175 TYR cc_start: 0.6397 (OUTLIER) cc_final: 0.5975 (m-80) REVERT: B 233 ASP cc_start: 0.8498 (t70) cc_final: 0.7916 (t70) REVERT: B 356 MET cc_start: 0.7417 (mmm) cc_final: 0.6988 (mmt) REVERT: B 360 MET cc_start: 0.8383 (ttp) cc_final: 0.8136 (tmm) REVERT: B 435 TRP cc_start: 0.7327 (m-90) cc_final: 0.6189 (m-10) REVERT: B 436 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7165 (mm-30) REVERT: A 240 HIS cc_start: 0.8271 (t70) cc_final: 0.8056 (t70) REVERT: A 377 ARG cc_start: 0.8872 (mtp85) cc_final: 0.8652 (mtp180) REVERT: A 418 LYS cc_start: 0.8941 (mttp) cc_final: 0.8690 (mmmt) REVERT: A 546 ARG cc_start: 0.8009 (mtp180) cc_final: 0.7780 (mtp180) outliers start: 44 outliers final: 30 residues processed: 146 average time/residue: 0.2215 time to fit residues: 44.1045 Evaluate side-chains 138 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 106 time to evaluate : 0.906 ------------------------------------------------------------------------------- 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 106 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 3 optimal weight: 0.3980 chunk 105 optimal weight: 0.2980 chunk 100 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 7 optimal weight: 0.1980 chunk 66 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN A 403 GLN A 679 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.154614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.096722 restraints weight = 10701.350| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.82 r_work: 0.2848 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9067 Z= 0.126 Angle : 0.607 8.551 12354 Z= 0.300 Chirality : 0.043 0.315 1400 Planarity : 0.004 0.038 1520 Dihedral : 8.621 127.978 1533 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.10 % Favored : 95.81 % Rotamer: Outliers : 4.45 % Allowed : 24.18 % Favored : 71.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.25), residues: 1074 helix: 0.23 (0.24), residues: 508 sheet: -1.36 (0.45), residues: 80 loop : -1.04 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 383 HIS 0.009 0.001 HIS A 175 PHE 0.024 0.001 PHE A 407 TYR 0.016 0.001 TYR A 65 ARG 0.004 0.000 ARG A 658 Details of bonding type rmsd link_NAG-ASN : bond 0.00617 ( 6) link_NAG-ASN : angle 2.36063 ( 18) link_BETA1-4 : bond 0.01493 ( 2) link_BETA1-4 : angle 3.57493 ( 6) hydrogen bonds : bond 0.03812 ( 371) hydrogen bonds : angle 4.31437 ( 1035) SS BOND : bond 0.00385 ( 4) SS BOND : angle 1.52059 ( 8) covalent geometry : bond 0.00291 ( 9055) covalent geometry : angle 0.59409 (12322) *********************** 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 158 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 116 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 MET cc_start: 0.8521 (tpt) cc_final: 0.8274 (tpt) REVERT: B 102 GLU cc_start: 0.8588 (tp30) cc_final: 0.8182 (tp30) REVERT: B 175 TYR cc_start: 0.6264 (OUTLIER) cc_final: 0.5835 (m-80) REVERT: B 233 ASP cc_start: 0.8485 (t70) cc_final: 0.7880 (t70) REVERT: B 356 MET cc_start: 0.7447 (mmm) cc_final: 0.7023 (mmt) REVERT: B 360 MET cc_start: 0.8358 (ttp) cc_final: 0.8131 (tmm) REVERT: B 390 ILE cc_start: 0.8244 (mm) cc_final: 0.7945 (mm) REVERT: B 435 TRP cc_start: 0.7177 (m-90) cc_final: 0.6081 (m-10) REVERT: B 436 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7157 (mm-30) REVERT: B 444 MET cc_start: 0.7954 (mpp) cc_final: 0.7185 (mtt) REVERT: A 245 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7560 (mp0) REVERT: A 377 ARG cc_start: 0.8849 (mtp85) cc_final: 0.8618 (mtp180) REVERT: A 418 LYS cc_start: 0.8909 (mttp) cc_final: 0.8640 (mmmt) outliers start: 42 outliers final: 30 residues processed: 150 average time/residue: 0.2209 time to fit residues: 45.4317 Evaluate side-chains 140 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 107 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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 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 272 VAL Chi-restraints excluded: chain B residue 281 THR 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 116 ASP 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 403 GLN Chi-restraints excluded: chain A residue 423 SER 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 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 50 optimal weight: 0.2980 chunk 106 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 102 optimal weight: 5.9990 chunk 78 optimal weight: 0.3980 chunk 4 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 85 optimal weight: 0.2980 chunk 29 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3813 r_free = 0.3813 target = 0.154811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.098916 restraints weight = 10760.991| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.71 r_work: 0.2887 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9067 Z= 0.130 Angle : 0.613 8.515 12354 Z= 0.302 Chirality : 0.044 0.314 1400 Planarity : 0.004 0.038 1520 Dihedral : 8.232 126.129 1526 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.91 % Favored : 96.00 % Rotamer: Outliers : 4.14 % Allowed : 24.39 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.25), residues: 1074 helix: 0.38 (0.24), residues: 508 sheet: -1.43 (0.44), residues: 90 loop : -1.01 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 383 HIS 0.009 0.001 HIS A 175 PHE 0.015 0.001 PHE A 407 TYR 0.016 0.001 TYR A 65 ARG 0.004 0.000 ARG A 658 Details of bonding type rmsd link_NAG-ASN : bond 0.00606 ( 6) link_NAG-ASN : angle 2.76103 ( 18) link_BETA1-4 : bond 0.01476 ( 2) link_BETA1-4 : angle 3.55470 ( 6) hydrogen bonds : bond 0.03740 ( 371) hydrogen bonds : angle 4.24889 ( 1035) SS BOND : bond 0.00260 ( 4) SS BOND : angle 1.59072 ( 8) covalent geometry : bond 0.00300 ( 9055) covalent geometry : angle 0.59850 (12322) *********************** 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 153 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 114 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 MET cc_start: 0.8515 (tpt) cc_final: 0.8290 (tpt) REVERT: B 102 GLU cc_start: 0.8529 (tp30) cc_final: 0.8165 (tp30) REVERT: B 175 TYR cc_start: 0.6247 (OUTLIER) cc_final: 0.5899 (m-80) REVERT: B 233 ASP cc_start: 0.8507 (t70) cc_final: 0.7910 (t70) REVERT: B 356 MET cc_start: 0.7513 (mmm) cc_final: 0.7104 (mmt) REVERT: B 360 MET cc_start: 0.8403 (ttp) cc_final: 0.8158 (tmm) REVERT: B 390 ILE cc_start: 0.8266 (mm) cc_final: 0.8006 (mm) REVERT: B 435 TRP cc_start: 0.7230 (m-90) cc_final: 0.6135 (m-10) REVERT: B 436 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7228 (mm-30) REVERT: A 377 ARG cc_start: 0.8870 (mtp85) cc_final: 0.8644 (mtp180) REVERT: A 418 LYS cc_start: 0.8905 (mttp) cc_final: 0.8669 (mmmt) outliers start: 39 outliers final: 29 residues processed: 146 average time/residue: 0.2299 time to fit residues: 46.0239 Evaluate side-chains 140 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 109 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 ILE 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 272 VAL Chi-restraints excluded: chain B residue 281 THR 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 116 ASP Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 423 SER 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 536 VAL Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 603 SER 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 43 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 49 optimal weight: 0.1980 chunk 58 optimal weight: 0.9990 chunk 67 optimal weight: 0.0980 chunk 73 optimal weight: 0.7980 chunk 91 optimal weight: 0.0170 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.154343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.102297 restraints weight = 10667.194| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.53 r_work: 0.2878 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9067 Z= 0.119 Angle : 0.597 8.511 12354 Z= 0.294 Chirality : 0.043 0.316 1400 Planarity : 0.004 0.038 1520 Dihedral : 8.127 122.251 1526 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.72 % Favored : 96.18 % Rotamer: Outliers : 3.50 % Allowed : 25.03 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.26), residues: 1074 helix: 0.58 (0.24), residues: 509 sheet: -1.31 (0.44), residues: 90 loop : -0.97 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 383 HIS 0.009 0.001 HIS A 175 PHE 0.019 0.001 PHE A 407 TYR 0.016 0.001 TYR A 65 ARG 0.004 0.000 ARG A 658 Details of bonding type rmsd link_NAG-ASN : bond 0.00608 ( 6) link_NAG-ASN : angle 2.45480 ( 18) link_BETA1-4 : bond 0.01513 ( 2) link_BETA1-4 : angle 3.54668 ( 6) hydrogen bonds : bond 0.03560 ( 371) hydrogen bonds : angle 4.17985 ( 1035) SS BOND : bond 0.00258 ( 4) SS BOND : angle 1.60150 ( 8) covalent geometry : bond 0.00275 ( 9055) covalent geometry : angle 0.58323 (12322) *********************** 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 152 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 119 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 MET cc_start: 0.8488 (tpt) cc_final: 0.8217 (tpt) REVERT: B 102 GLU cc_start: 0.8529 (tp30) cc_final: 0.8093 (tp30) REVERT: B 175 TYR cc_start: 0.6154 (OUTLIER) cc_final: 0.5902 (m-80) REVERT: B 233 ASP cc_start: 0.8446 (t70) cc_final: 0.7836 (t70) REVERT: B 356 MET cc_start: 0.7305 (mmm) cc_final: 0.6900 (mmt) REVERT: B 360 MET cc_start: 0.8264 (ttp) cc_final: 0.7977 (tmm) REVERT: B 390 ILE cc_start: 0.8188 (mm) cc_final: 0.7900 (mm) REVERT: B 435 TRP cc_start: 0.7104 (m-90) cc_final: 0.6014 (m-10) REVERT: B 436 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7098 (mm-30) REVERT: B 445 LEU cc_start: 0.7508 (mt) cc_final: 0.7288 (mm) REVERT: A 377 ARG cc_start: 0.8846 (mtp85) cc_final: 0.8594 (mtp180) REVERT: A 418 LYS cc_start: 0.8914 (mttp) cc_final: 0.8645 (mmmt) REVERT: A 679 ASN cc_start: 0.8476 (t0) cc_final: 0.8201 (t0) outliers start: 33 outliers final: 26 residues processed: 144 average time/residue: 0.2305 time to fit residues: 45.7235 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 : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 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 272 VAL Chi-restraints excluded: chain B residue 281 THR 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 116 ASP Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 423 SER 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 536 VAL Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 603 SER 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 38 optimal weight: 0.5980 chunk 85 optimal weight: 0.0670 chunk 20 optimal weight: 0.0670 chunk 83 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 0.0000 chunk 27 optimal weight: 0.0670 chunk 76 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 61 optimal weight: 0.2980 overall best weight: 0.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 358 HIS ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN A 243 ASN A 561 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.158704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.101519 restraints weight = 10750.866| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.93 r_work: 0.2905 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9067 Z= 0.100 Angle : 0.581 8.853 12354 Z= 0.285 Chirality : 0.042 0.329 1400 Planarity : 0.004 0.037 1520 Dihedral : 7.865 115.180 1526 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.28 % Favored : 95.62 % Rotamer: Outliers : 2.23 % Allowed : 26.09 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.26), residues: 1074 helix: 0.94 (0.25), residues: 496 sheet: -1.21 (0.46), residues: 89 loop : -0.94 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 383 HIS 0.009 0.001 HIS A 175 PHE 0.011 0.001 PHE B 132 TYR 0.017 0.001 TYR A 65 ARG 0.005 0.000 ARG A 658 Details of bonding type rmsd link_NAG-ASN : bond 0.00758 ( 6) link_NAG-ASN : angle 2.45376 ( 18) link_BETA1-4 : bond 0.01408 ( 2) link_BETA1-4 : angle 3.44482 ( 6) hydrogen bonds : bond 0.03031 ( 371) hydrogen bonds : angle 4.05179 ( 1035) SS BOND : bond 0.00197 ( 4) SS BOND : angle 1.34975 ( 8) covalent geometry : bond 0.00214 ( 9055) covalent geometry : angle 0.56856 (12322) *********************** 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 144 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 101 MET cc_start: 0.8274 (tpt) cc_final: 0.7784 (tpt) REVERT: B 102 GLU cc_start: 0.8439 (tp30) cc_final: 0.8031 (tp30) REVERT: B 233 ASP cc_start: 0.8342 (t70) cc_final: 0.7721 (t70) REVERT: B 343 TYR cc_start: 0.7995 (m-10) cc_final: 0.7320 (m-10) REVERT: B 360 MET cc_start: 0.8201 (ttp) cc_final: 0.7945 (tmm) REVERT: B 435 TRP cc_start: 0.6994 (m-90) cc_final: 0.5925 (m-10) REVERT: B 436 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7017 (mm-30) REVERT: A 377 ARG cc_start: 0.8636 (mtp85) cc_final: 0.8414 (mtp180) REVERT: A 679 ASN cc_start: 0.8478 (t0) cc_final: 0.8252 (t0) outliers start: 21 outliers final: 13 residues processed: 140 average time/residue: 0.2192 time to fit residues: 42.0361 Evaluate side-chains 126 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 254 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 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 536 VAL Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 603 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 102 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 23 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 80 optimal weight: 0.2980 chunk 44 optimal weight: 7.9990 chunk 19 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.155121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.099670 restraints weight = 10782.234| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.88 r_work: 0.2850 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9067 Z= 0.146 Angle : 0.618 8.592 12354 Z= 0.305 Chirality : 0.045 0.322 1400 Planarity : 0.004 0.040 1520 Dihedral : 7.734 112.361 1522 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.54 % Favored : 96.37 % Rotamer: Outliers : 1.38 % Allowed : 27.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.26), residues: 1074 helix: 0.72 (0.24), residues: 515 sheet: -1.17 (0.47), residues: 88 loop : -0.93 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 443 HIS 0.009 0.001 HIS A 175 PHE 0.020 0.001 PHE A 407 TYR 0.016 0.001 TYR A 65 ARG 0.004 0.000 ARG A 658 Details of bonding type rmsd link_NAG-ASN : bond 0.00602 ( 6) link_NAG-ASN : angle 2.34911 ( 18) link_BETA1-4 : bond 0.01544 ( 2) link_BETA1-4 : angle 3.49123 ( 6) hydrogen bonds : bond 0.03687 ( 371) hydrogen bonds : angle 4.15307 ( 1035) SS BOND : bond 0.00210 ( 4) SS BOND : angle 1.91821 ( 8) covalent geometry : bond 0.00347 ( 9055) covalent geometry : angle 0.60577 (12322) ********************** 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 128 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 2.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 101 MET cc_start: 0.8287 (tpt) cc_final: 0.7788 (tpt) REVERT: B 102 GLU cc_start: 0.8366 (tp30) cc_final: 0.8043 (tp30) REVERT: B 233 ASP cc_start: 0.8328 (t70) cc_final: 0.7697 (t70) REVERT: B 343 TYR cc_start: 0.8081 (m-10) cc_final: 0.7398 (m-10) REVERT: B 360 MET cc_start: 0.8239 (ttp) cc_final: 0.7928 (tmm) REVERT: B 435 TRP cc_start: 0.7181 (m-90) cc_final: 0.6090 (m-10) REVERT: B 436 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7146 (mm-30) REVERT: A 377 ARG cc_start: 0.8652 (mtp85) cc_final: 0.8407 (mtp180) REVERT: A 389 SER cc_start: 0.8276 (t) cc_final: 0.7980 (p) REVERT: A 679 ASN cc_start: 0.8484 (t0) cc_final: 0.8222 (t0) outliers start: 13 outliers final: 11 residues processed: 123 average time/residue: 0.3246 time to fit residues: 55.1201 Evaluate side-chains 119 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 436 GLU Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 210 ASP 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 603 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 25 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 98 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 85 optimal weight: 0.0570 chunk 27 optimal weight: 1.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.156252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.095228 restraints weight = 10780.680| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.62 r_work: 0.2855 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2795 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= 0.153 Angle : 0.625 8.596 12354 Z= 0.309 Chirality : 0.045 0.320 1400 Planarity : 0.004 0.045 1520 Dihedral : 7.727 109.721 1522 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.10 % Favored : 95.81 % Rotamer: Outliers : 2.12 % Allowed : 27.47 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.26), residues: 1074 helix: 0.73 (0.24), residues: 508 sheet: -1.29 (0.47), residues: 90 loop : -0.94 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 383 HIS 0.009 0.001 HIS A 175 PHE 0.024 0.001 PHE A 407 TYR 0.016 0.001 TYR A 65 ARG 0.005 0.000 ARG A 546 Details of bonding type rmsd link_NAG-ASN : bond 0.00606 ( 6) link_NAG-ASN : angle 2.32772 ( 18) link_BETA1-4 : bond 0.01448 ( 2) link_BETA1-4 : angle 3.48455 ( 6) hydrogen bonds : bond 0.03778 ( 371) hydrogen bonds : angle 4.18517 ( 1035) SS BOND : bond 0.00255 ( 4) SS BOND : angle 2.02418 ( 8) covalent geometry : bond 0.00366 ( 9055) covalent geometry : angle 0.61248 (12322) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6339.57 seconds wall clock time: 109 minutes 30.76 seconds (6570.76 seconds total)