Starting phenix.real_space_refine on Fri Sep 11 16:10:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6rai_4776/09_2026/6rai_4776.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rai_4776/09_2026/6rai_4776.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6rai_4776/09_2026/6rai_4776.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6rai_4776/09_2026/6rai_4776.cif" model { file = "/net/cci-nas-00/data/ceres_data/6rai_4776/09_2026/6rai_4776.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rai_4776/09_2026/6rai_4776.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6rai_4776/09_2026/6rai_4776.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rai_4776/09_2026/6rai_4776.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 P 6 5.49 5 Mg 2 5.21 5 S 25 5.16 5 C 6566 2.51 5 N 1797 2.21 5 O 1795 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10191 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4701 Classifications: {'peptide': 587} Link IDs: {'PTRANS': 24, 'TRANS': 562} Chain: "B" Number of atoms: 4523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4523 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 18, 'TRANS': 554} Chain: "C" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 897 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 2.13, per 1000 atoms: 0.21 Number of scatterers: 10191 At special positions: 0 Unit cell: (103.392, 81.852, 156.165, 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) S 25 16.00 P 6 15.00 Mg 2 11.99 O 1795 8.00 N 1797 7.00 C 6566 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 108 " distance=2.06 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 Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 338.1 milliseconds 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2342 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 6 sheets defined 64.9% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 13 through 23 removed outlier: 3.874A pdb=" N ARG A 20 " --> pdb=" O ALA A 16 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N TYR A 21 " --> pdb=" O ARG A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 28 removed outlier: 5.441A pdb=" N LEU A 27 " --> pdb=" O PRO A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 45 Processing helix chain 'A' and resid 46 through 55 removed outlier: 4.239A pdb=" N PHE A 50 " --> pdb=" O THR A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 120 removed outlier: 3.560A pdb=" N ARG A 69 " --> pdb=" O PRO A 65 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N PHE A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A 74 " --> pdb=" O PHE A 70 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N TRP A 75 " --> pdb=" O HIS A 71 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 97 " --> pdb=" O GLY A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 125 Processing helix chain 'A' and resid 129 through 149 removed outlier: 3.683A pdb=" N ARG A 136 " --> pdb=" O ARG A 132 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASP A 140 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N VAL A 141 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ILE A 144 " --> pdb=" O ASP A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 173 removed outlier: 3.936A pdb=" N PHE A 160 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR A 161 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE A 171 " --> pdb=" O GLY A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 182 removed outlier: 3.903A pdb=" N VAL A 179 " --> pdb=" O LYS A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 222 removed outlier: 3.894A pdb=" N SER A 200 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA A 201 " --> pdb=" O GLY A 197 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG A 203 " --> pdb=" O ARG A 199 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU A 204 " --> pdb=" O SER A 200 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG A 208 " --> pdb=" O GLU A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 229 Processing helix chain 'A' and resid 231 through 285 removed outlier: 3.526A pdb=" N GLU A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU A 242 " --> pdb=" O LYS A 238 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TRP A 256 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LEU A 259 " --> pdb=" O ARG A 255 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE A 260 " --> pdb=" O TRP A 256 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N PHE A 261 " --> pdb=" O PHE A 257 " (cutoff:3.500A) Proline residue: A 262 - end of helix removed outlier: 3.585A pdb=" N ASP A 269 " --> pdb=" O GLY A 265 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY A 281 " --> pdb=" O TYR A 277 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL A 283 " --> pdb=" O GLY A 279 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG A 285 " --> pdb=" O GLY A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 304 Processing helix chain 'A' and resid 304 through 313 Processing helix chain 'A' and resid 313 through 332 removed outlier: 3.543A pdb=" N PHE A 317 " --> pdb=" O LYS A 313 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG A 326 " --> pdb=" O ALA A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 407 removed outlier: 3.545A pdb=" N VAL A 403 " --> pdb=" O LYS A 399 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU A 405 " --> pdb=" O SER A 401 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA A 407 " --> pdb=" O VAL A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 427 No H-bonds generated for 'chain 'A' and resid 425 through 427' Processing helix chain 'A' and resid 428 through 435 removed outlier: 3.586A pdb=" N HIS A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 455 Processing helix chain 'A' and resid 462 through 473 removed outlier: 3.543A pdb=" N VAL A 466 " --> pdb=" O PRO A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 481 Processing helix chain 'A' and resid 484 through 488 Processing helix chain 'A' and resid 498 through 512 Processing helix chain 'A' and resid 529 through 544 removed outlier: 3.684A pdb=" N ALA A 539 " --> pdb=" O ARG A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 586 Processing helix chain 'A' and resid 586 through 597 removed outlier: 3.658A pdb=" N ALA A 591 " --> pdb=" O GLY A 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 18 Proline residue: B 15 - end of helix Processing helix chain 'B' and resid 20 through 39 Processing helix chain 'B' and resid 40 through 53 Processing helix chain 'B' and resid 57 through 103 removed outlier: 4.485A pdb=" N TYR B 61 " --> pdb=" O GLY B 57 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA B 62 " --> pdb=" O PHE B 58 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU B 82 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL B 85 " --> pdb=" O ARG B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 112 removed outlier: 3.680A pdb=" N LYS B 112 " --> pdb=" O ASP B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 124 removed outlier: 3.528A pdb=" N ASN B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 133 Processing helix chain 'B' and resid 134 through 156 Processing helix chain 'B' and resid 158 through 167 Processing helix chain 'B' and resid 168 through 207 removed outlier: 4.254A pdb=" N ALA B 175 " --> pdb=" O GLY B 171 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG B 177 " --> pdb=" O PHE B 173 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N PHE B 178 " --> pdb=" O LEU B 174 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU B 182 " --> pdb=" O PHE B 178 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG B 185 " --> pdb=" O ARG B 181 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU B 192 " --> pdb=" O ARG B 188 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B 193 " --> pdb=" O GLU B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 214 removed outlier: 3.627A pdb=" N VAL B 211 " --> pdb=" O GLY B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 243 removed outlier: 3.709A pdb=" N LEU B 227 " --> pdb=" O TRP B 223 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU B 233 " --> pdb=" O ARG B 229 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B 238 " --> pdb=" O LYS B 234 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL B 241 " --> pdb=" O ALA B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 270 removed outlier: 3.866A pdb=" N GLY B 250 " --> pdb=" O HIS B 246 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N MET B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG B 270 " --> pdb=" O ALA B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 294 removed outlier: 4.434A pdb=" N TRP B 290 " --> pdb=" O ALA B 286 " (cutoff:3.500A) Proline residue: B 291 - end of helix removed outlier: 3.646A pdb=" N GLY B 294 " --> pdb=" O TRP B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 317 removed outlier: 3.773A pdb=" N LEU B 315 " --> pdb=" O ARG B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 335 removed outlier: 3.834A pdb=" N LEU B 335 " --> pdb=" O LEU B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 383 Processing helix chain 'B' and resid 406 through 413 removed outlier: 3.640A pdb=" N LYS B 412 " --> pdb=" O ALA B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 433 Processing helix chain 'B' and resid 440 through 451 Processing helix chain 'B' and resid 453 through 458 Processing helix chain 'B' and resid 462 through 466 removed outlier: 3.562A pdb=" N GLU B 465 " --> pdb=" O LYS B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 473 removed outlier: 3.822A pdb=" N ILE B 473 " --> pdb=" O GLU B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 491 removed outlier: 4.229A pdb=" N LYS B 491 " --> pdb=" O ARG B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 520 removed outlier: 3.888A pdb=" N THR B 519 " --> pdb=" O GLN B 515 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B 520 " --> pdb=" O GLY B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 537 Processing helix chain 'B' and resid 555 through 561 removed outlier: 3.731A pdb=" N GLN B 561 " --> pdb=" O GLU B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 575 removed outlier: 3.885A pdb=" N ALA B 567 " --> pdb=" O GLY B 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.925A pdb=" N THR C 91 " --> pdb=" O PRO C 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 374 through 382 removed outlier: 6.256A pdb=" N LEU A 360 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LYS A 377 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL A 358 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL A 379 " --> pdb=" O ARG A 356 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ARG A 356 " --> pdb=" O VAL A 379 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N PHE A 381 " --> pdb=" O GLU A 354 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLU A 354 " --> pdb=" O PHE A 381 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N PHE A 355 " --> pdb=" O PHE A 418 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N PHE A 418 " --> pdb=" O PHE A 355 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ASP A 357 " --> pdb=" O CYS A 416 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N CYS A 416 " --> pdb=" O ASP A 357 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG A 414 " --> pdb=" O TRP A 359 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 436 through 439 removed outlier: 6.508A pdb=" N LYS A 388 " --> pdb=" O ARG A 564 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N LEU A 566 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ALA A 390 " --> pdb=" O LEU A 566 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N PHE A 568 " --> pdb=" O ALA A 390 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL A 392 " --> pdb=" O PHE A 568 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU A 575 " --> pdb=" O VAL A 567 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 351 through 361 removed outlier: 6.553A pdb=" N LEU B 353 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N LYS B 347 " --> pdb=" O LEU B 353 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ARG B 355 " --> pdb=" O GLY B 345 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N GLY B 345 " --> pdb=" O ARG B 355 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N LEU B 357 " --> pdb=" O GLY B 343 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL B 344 " --> pdb=" O GLU B 392 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N GLU B 392 " --> pdb=" O VAL B 344 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 414 through 417 removed outlier: 6.370A pdb=" N GLY B 415 " --> pdb=" O ILE B 497 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ASP B 499 " --> pdb=" O GLY B 415 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ALA B 417 " --> pdb=" O ASP B 499 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N THR B 366 " --> pdb=" O TRP B 541 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N ILE B 543 " --> pdb=" O THR B 366 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLY B 368 " --> pdb=" O ILE B 543 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N LEU B 545 " --> pdb=" O GLY B 368 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N THR B 370 " --> pdb=" O LEU B 545 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU B 552 " --> pdb=" O VAL B 544 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ASP B 546 " --> pdb=" O ILE B 550 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ILE B 550 " --> pdb=" O ASP B 546 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA C 101 " --> pdb=" O VAL C 109 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.660A pdb=" N THR C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.529A pdb=" N ALA C 92 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ARG C 38 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N GLY C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) 605 hydrogen bonds defined for protein. 1770 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.46 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1610 1.31 - 1.43: 2806 1.43 - 1.56: 5915 1.56 - 1.69: 22 1.69 - 1.81: 45 Bond restraints: 10398 Sorted by residual: bond pdb=" C4 ATP B 601 " pdb=" C5 ATP B 601 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.87e+01 bond pdb=" C4 ATP A 701 " pdb=" C5 ATP A 701 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.21e+01 bond pdb=" N PRO B 320 " pdb=" CD PRO B 320 " ideal model delta sigma weight residual 1.473 1.562 -0.089 1.40e-02 5.10e+03 4.08e+01 bond pdb=" N PRO A 443 " pdb=" CD PRO A 443 " ideal model delta sigma weight residual 1.473 1.561 -0.088 1.40e-02 5.10e+03 3.95e+01 bond pdb=" C5 ATP A 701 " pdb=" C6 ATP A 701 " ideal model delta sigma weight residual 1.409 1.471 -0.062 1.00e-02 1.00e+04 3.87e+01 ... (remaining 10393 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.75: 13708 3.75 - 7.50: 353 7.50 - 11.25: 44 11.25 - 15.00: 0 15.00 - 18.76: 3 Bond angle restraints: 14108 Sorted by residual: angle pdb=" PB ATP A 701 " pdb=" O3B ATP A 701 " pdb=" PG ATP A 701 " ideal model delta sigma weight residual 139.87 121.11 18.76 1.00e+00 1.00e+00 3.52e+02 angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 122.72 17.15 1.00e+00 1.00e+00 2.94e+02 angle pdb=" PA ATP B 601 " pdb=" O3A ATP B 601 " pdb=" PB ATP B 601 " ideal model delta sigma weight residual 136.83 120.35 16.48 1.00e+00 1.00e+00 2.72e+02 angle pdb=" PA ATP A 701 " pdb=" O3A ATP A 701 " pdb=" PB ATP A 701 " ideal model delta sigma weight residual 136.83 128.10 8.73 1.00e+00 1.00e+00 7.62e+01 angle pdb=" N LEU B 45 " pdb=" CA LEU B 45 " pdb=" C LEU B 45 " ideal model delta sigma weight residual 111.28 120.38 -9.10 1.09e+00 8.42e-01 6.97e+01 ... (remaining 14103 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 5897 17.23 - 34.46: 201 34.46 - 51.69: 34 51.69 - 68.92: 6 68.92 - 86.15: 7 Dihedral angle restraints: 6145 sinusoidal: 2485 harmonic: 3660 Sorted by residual: dihedral pdb=" C HIS A 579 " pdb=" N HIS A 579 " pdb=" CA HIS A 579 " pdb=" CB HIS A 579 " ideal model delta harmonic sigma weight residual -122.60 -138.97 16.37 0 2.50e+00 1.60e-01 4.29e+01 dihedral pdb=" N HIS A 579 " pdb=" C HIS A 579 " pdb=" CA HIS A 579 " pdb=" CB HIS A 579 " ideal model delta harmonic sigma weight residual 122.80 135.97 -13.17 0 2.50e+00 1.60e-01 2.78e+01 dihedral pdb=" C ARG A 560 " pdb=" N ARG A 560 " pdb=" CA ARG A 560 " pdb=" CB ARG A 560 " ideal model delta harmonic sigma weight residual -122.60 -134.25 11.65 0 2.50e+00 1.60e-01 2.17e+01 ... (remaining 6142 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 1374 0.108 - 0.216: 191 0.216 - 0.325: 29 0.325 - 0.433: 9 0.433 - 0.541: 3 Chirality restraints: 1606 Sorted by residual: chirality pdb=" CA HIS A 579 " pdb=" N HIS A 579 " pdb=" C HIS A 579 " pdb=" CB HIS A 579 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.32e+00 chirality pdb=" CA VAL C 109 " pdb=" N VAL C 109 " pdb=" C VAL C 109 " pdb=" CB VAL C 109 " both_signs ideal model delta sigma weight residual False 2.44 2.88 -0.44 2.00e-01 2.50e+01 4.80e+00 chirality pdb=" CA LEU C 104 " pdb=" N LEU C 104 " pdb=" C LEU C 104 " pdb=" CB LEU C 104 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.79e+00 ... (remaining 1603 not shown) Planarity restraints: 1783 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 231 " 0.019 2.00e-02 2.50e+03 3.78e-02 1.43e+01 pdb=" C LYS A 231 " -0.065 2.00e-02 2.50e+03 pdb=" O LYS A 231 " 0.025 2.00e-02 2.50e+03 pdb=" N GLU A 232 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 154 " -0.017 2.00e-02 2.50e+03 3.29e-02 1.09e+01 pdb=" C GLY A 154 " 0.057 2.00e-02 2.50e+03 pdb=" O GLY A 154 " -0.021 2.00e-02 2.50e+03 pdb=" N VAL A 155 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 287 " -0.014 2.00e-02 2.50e+03 2.93e-02 8.59e+00 pdb=" C ALA A 287 " 0.051 2.00e-02 2.50e+03 pdb=" O ALA A 287 " -0.019 2.00e-02 2.50e+03 pdb=" N VAL A 288 " -0.017 2.00e-02 2.50e+03 ... (remaining 1780 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 53 2.54 - 3.13: 7245 3.13 - 3.72: 15497 3.72 - 4.31: 22725 4.31 - 4.90: 38148 Nonbonded interactions: 83668 Sorted by model distance: nonbonded pdb="MG MG A 702 " pdb=" O HOH A 802 " model vdw 1.948 2.170 nonbonded pdb="MG MG A 702 " pdb=" O HOH A 801 " model vdw 2.077 2.170 nonbonded pdb=" OG SER B 378 " pdb="MG MG B 602 " model vdw 2.094 2.170 nonbonded pdb="MG MG B 602 " pdb=" O HOH B 701 " model vdw 2.109 2.170 nonbonded pdb=" OG1 THR A 400 " pdb="MG MG A 702 " model vdw 2.114 2.170 ... (remaining 83663 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.830 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.010 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 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 : 0.009 0.089 10400 Z= 0.544 Angle : 1.397 18.755 14112 Z= 0.971 Chirality : 0.083 0.541 1606 Planarity : 0.008 0.056 1783 Dihedral : 9.821 86.149 3797 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Cbeta Deviations : 0.51 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.24 (0.19), residues: 1275 helix: -2.17 (0.15), residues: 756 sheet: 0.02 (0.47), residues: 120 loop : -2.43 (0.24), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 240 TYR 0.028 0.003 TYR B 284 PHE 0.039 0.003 PHE A 304 TRP 0.027 0.003 TRP B 22 HIS 0.006 0.001 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00870 / 0.54 (10398) covalent geometry : angle 1.39727 / 0.97 (14108) SS BOND : bond 0.02206 / 1.05 ( 2) SS BOND : angle 2.03061 / 1.13 ( 4) hydrogen bonds : bond 0.20846 / 13.71 ( 605) hydrogen bonds : angle 7.12252 / 5.13 ( 1770) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 0.280 Fit side-chains REVERT: A 37 LEU cc_start: 0.8211 (tp) cc_final: 0.7974 (tp) REVERT: A 58 LEU cc_start: 0.8143 (mt) cc_final: 0.7858 (mp) REVERT: A 96 TYR cc_start: 0.8440 (t80) cc_final: 0.7884 (t80) REVERT: A 145 ASN cc_start: 0.8889 (t0) cc_final: 0.8657 (t0) REVERT: A 168 PHE cc_start: 0.8304 (t80) cc_final: 0.8079 (t80) REVERT: A 238 LYS cc_start: 0.8330 (mttt) cc_final: 0.7799 (mttp) REVERT: A 357 ASP cc_start: 0.7979 (t70) cc_final: 0.7552 (t0) REVERT: A 388 LYS cc_start: 0.7429 (mttt) cc_final: 0.6850 (mttm) REVERT: A 425 ARG cc_start: 0.7570 (mtt180) cc_final: 0.7325 (mtm-85) REVERT: A 431 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7485 (mp0) REVERT: A 536 LEU cc_start: 0.8038 (pp) cc_final: 0.7705 (mp) REVERT: A 555 ARG cc_start: 0.7890 (mtt180) cc_final: 0.7618 (mtt180) REVERT: B 131 GLU cc_start: 0.7228 (mt-10) cc_final: 0.6906 (mm-30) REVERT: B 299 MET cc_start: 0.7514 (mmt) cc_final: 0.6946 (mmt) REVERT: B 510 GLU cc_start: 0.6683 (tt0) cc_final: 0.6440 (pp20) REVERT: B 532 ARG cc_start: 0.7199 (mmm160) cc_final: 0.6946 (mmm160) REVERT: C 39 GLN cc_start: 0.7757 (tt0) cc_final: 0.7403 (tp40) REVERT: C 65 LYS cc_start: 0.7938 (ptmm) cc_final: 0.7711 (pttt) REVERT: C 98 THR cc_start: 0.7947 (m) cc_final: 0.7554 (p) outliers start: 0 outliers final: 1 residues processed: 271 average time/residue: 0.7350 time to fit residues: 209.6516 Evaluate side-chains 165 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 164 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 349 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 chunk 123 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 HIS A 103 GLN A 146 GLN A 302 GLN A 305 GLN A 308 GLN A 318 GLN A 429 GLN A 453 ASN A 503 GLN A 537 GLN B 111 HIS B 113 HIS B 191 GLN B 431 ASN C 77 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.143647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.116804 restraints weight = 11884.331| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.83 r_work: 0.3175 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10400 Z= 0.143 Angle : 0.600 7.860 14112 Z= 0.309 Chirality : 0.041 0.158 1606 Planarity : 0.005 0.040 1783 Dihedral : 5.456 59.413 1444 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.00 % Allowed : 11.64 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.22), residues: 1275 helix: -0.32 (0.18), residues: 786 sheet: 0.23 (0.46), residues: 124 loop : -1.87 (0.27), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 195 TYR 0.022 0.001 TYR A 589 PHE 0.017 0.001 PHE A 304 TRP 0.026 0.002 TRP C 36 HIS 0.004 0.001 HIS B 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (10398) covalent geometry : angle 0.60012 / 0.31 (14108) SS BOND : bond 0.00044 / 0.02 ( 2) SS BOND : angle 0.88030 / 0.47 ( 4) hydrogen bonds : bond 0.04645 / 3.14 ( 605) hydrogen bonds : angle 4.44568 / 3.23 ( 1770) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 200 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7704 (mtt90) cc_final: 0.7281 (ttp-110) REVERT: A 25 TYR cc_start: 0.8703 (m-80) cc_final: 0.8485 (m-80) REVERT: A 33 LEU cc_start: 0.8586 (mp) cc_final: 0.8263 (mm) REVERT: A 41 LEU cc_start: 0.8317 (mt) cc_final: 0.7973 (mt) REVERT: A 74 LEU cc_start: 0.8224 (tp) cc_final: 0.8007 (tt) REVERT: A 96 TYR cc_start: 0.8595 (t80) cc_final: 0.8187 (t80) REVERT: A 118 MET cc_start: 0.9082 (mmp) cc_final: 0.8686 (mmp) REVERT: A 234 GLU cc_start: 0.7688 (tm-30) cc_final: 0.7373 (mp0) REVERT: A 245 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.7653 (t0) REVERT: A 252 GLU cc_start: 0.8216 (tp30) cc_final: 0.7800 (tp30) REVERT: A 255 ARG cc_start: 0.8015 (ttp-110) cc_final: 0.7602 (ttp-110) REVERT: A 334 GLU cc_start: 0.8196 (tt0) cc_final: 0.7826 (tm-30) REVERT: A 354 GLU cc_start: 0.8083 (tt0) cc_final: 0.7840 (tm-30) REVERT: A 357 ASP cc_start: 0.8532 (t70) cc_final: 0.8201 (t70) REVERT: A 388 LYS cc_start: 0.7862 (mttt) cc_final: 0.7520 (mttp) REVERT: A 425 ARG cc_start: 0.8135 (mtt180) cc_final: 0.7750 (mtt90) REVERT: A 431 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7934 (mp0) REVERT: B 120 ASN cc_start: 0.8891 (t0) cc_final: 0.8558 (t0) REVERT: B 219 ARG cc_start: 0.8302 (mtp85) cc_final: 0.8004 (tpp80) REVERT: B 255 PHE cc_start: 0.7923 (t80) cc_final: 0.7573 (m-80) REVERT: B 299 MET cc_start: 0.8512 (mmt) cc_final: 0.7909 (mmp) REVERT: B 342 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8041 (mm-30) REVERT: B 401 GLU cc_start: 0.7792 (tt0) cc_final: 0.7588 (tm-30) REVERT: B 510 GLU cc_start: 0.7080 (tt0) cc_final: 0.6365 (pp20) REVERT: B 532 ARG cc_start: 0.8009 (mmm160) cc_final: 0.7685 (mmm160) REVERT: B 549 ARG cc_start: 0.8320 (mtt180) cc_final: 0.8039 (mtt180) REVERT: C 39 GLN cc_start: 0.7825 (tt0) cc_final: 0.7256 (tp40) REVERT: C 51 ILE cc_start: 0.8930 (tt) cc_final: 0.8554 (tp) REVERT: C 65 LYS cc_start: 0.7946 (ptmm) cc_final: 0.7575 (pttt) REVERT: C 82 GLN cc_start: 0.6796 (tp40) cc_final: 0.6342 (tp40) REVERT: C 98 THR cc_start: 0.8315 (m) cc_final: 0.8062 (p) outliers start: 21 outliers final: 8 residues processed: 213 average time/residue: 0.6354 time to fit residues: 143.8253 Evaluate side-chains 178 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 168 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 342 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 71 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 96 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 305 GLN ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.139313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.112341 restraints weight = 11882.822| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.82 r_work: 0.3114 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10400 Z= 0.155 Angle : 0.573 7.161 14112 Z= 0.291 Chirality : 0.041 0.175 1606 Planarity : 0.004 0.044 1783 Dihedral : 5.013 59.252 1442 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.77 % Allowed : 13.55 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.23), residues: 1275 helix: 0.49 (0.18), residues: 783 sheet: 0.25 (0.46), residues: 124 loop : -1.40 (0.28), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 218 TYR 0.018 0.001 TYR A 588 PHE 0.017 0.001 PHE A 304 TRP 0.020 0.002 TRP C 36 HIS 0.005 0.001 HIS B 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (10398) covalent geometry : angle 0.57278 / 0.29 (14108) SS BOND : bond 0.00096 / 0.05 ( 2) SS BOND : angle 0.45774 / 0.26 ( 4) hydrogen bonds : bond 0.04510 / 3.07 ( 605) hydrogen bonds : angle 4.15751 / 3.02 ( 1770) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 177 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7847 (mtt90) cc_final: 0.7449 (ttp-110) REVERT: A 33 LEU cc_start: 0.8432 (mp) cc_final: 0.8133 (mm) REVERT: A 41 LEU cc_start: 0.8194 (mt) cc_final: 0.7879 (mt) REVERT: A 94 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.8071 (tt0) REVERT: A 118 MET cc_start: 0.9089 (mmp) cc_final: 0.8801 (mmp) REVERT: A 134 MET cc_start: 0.8289 (mmm) cc_final: 0.7968 (mmm) REVERT: A 146 GLN cc_start: 0.8278 (mp-120) cc_final: 0.7941 (mp-120) REVERT: A 234 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7652 (mp0) REVERT: A 245 ASP cc_start: 0.8304 (OUTLIER) cc_final: 0.7662 (t0) REVERT: A 334 GLU cc_start: 0.8281 (tt0) cc_final: 0.7887 (tm-30) REVERT: A 354 GLU cc_start: 0.8108 (tt0) cc_final: 0.7881 (tm-30) REVERT: A 357 ASP cc_start: 0.8576 (t70) cc_final: 0.8354 (t70) REVERT: A 425 ARG cc_start: 0.8222 (mtt180) cc_final: 0.7699 (mtm-85) REVERT: A 431 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7936 (mp0) REVERT: A 541 TYR cc_start: 0.7186 (m-10) cc_final: 0.6888 (t80) REVERT: A 593 TYR cc_start: 0.7336 (t80) cc_final: 0.7134 (t80) REVERT: B 63 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8268 (tp) REVERT: B 219 ARG cc_start: 0.8330 (mtp85) cc_final: 0.8001 (tpp80) REVERT: B 245 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.7241 (mm) REVERT: B 255 PHE cc_start: 0.7974 (t80) cc_final: 0.7581 (m-80) REVERT: B 510 GLU cc_start: 0.7173 (tt0) cc_final: 0.6397 (pp20) REVERT: B 532 ARG cc_start: 0.7986 (mmm160) cc_final: 0.7586 (mmm160) REVERT: B 549 ARG cc_start: 0.8347 (mtt180) cc_final: 0.8044 (mtt180) REVERT: B 568 GLU cc_start: 0.7577 (tt0) cc_final: 0.7217 (tp30) REVERT: B 574 LYS cc_start: 0.7640 (OUTLIER) cc_final: 0.7240 (ttpt) REVERT: C 39 GLN cc_start: 0.7871 (tt0) cc_final: 0.7332 (tp40) REVERT: C 65 LYS cc_start: 0.7994 (ptmm) cc_final: 0.7711 (pttt) REVERT: C 82 GLN cc_start: 0.6793 (tp40) cc_final: 0.6437 (tp-100) REVERT: C 98 THR cc_start: 0.8102 (m) cc_final: 0.7802 (p) outliers start: 29 outliers final: 8 residues processed: 191 average time/residue: 0.6479 time to fit residues: 131.3089 Evaluate side-chains 167 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 154 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 365 LYS Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 69 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 82 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 305 GLN ** A 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 GLN B 113 HIS B 120 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.138832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.111966 restraints weight = 11930.045| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.83 r_work: 0.3110 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10400 Z= 0.149 Angle : 0.545 7.490 14112 Z= 0.277 Chirality : 0.040 0.174 1606 Planarity : 0.004 0.042 1783 Dihedral : 4.928 62.819 1442 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.63 % Allowed : 14.60 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.23), residues: 1275 helix: 0.86 (0.19), residues: 783 sheet: 0.35 (0.48), residues: 114 loop : -1.21 (0.28), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 181 TYR 0.014 0.001 TYR B 464 PHE 0.019 0.001 PHE A 171 TRP 0.021 0.001 TRP C 36 HIS 0.003 0.001 HIS B 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (10398) covalent geometry : angle 0.54530 / 0.28 (14108) SS BOND : bond 0.00010 / 0.00 ( 2) SS BOND : angle 0.52509 / 0.30 ( 4) hydrogen bonds : bond 0.04250 / 2.89 ( 605) hydrogen bonds : angle 4.04463 / 2.93 ( 1770) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 163 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: A 19 LEU cc_start: 0.7873 (mt) cc_final: 0.7511 (tt) REVERT: A 20 ARG cc_start: 0.7812 (mtt90) cc_final: 0.7430 (ttp-110) REVERT: A 33 LEU cc_start: 0.8458 (mp) cc_final: 0.8185 (mm) REVERT: A 64 ARG cc_start: 0.7549 (tmm-80) cc_final: 0.7310 (pmt170) REVERT: A 118 MET cc_start: 0.9088 (mmp) cc_final: 0.8791 (mmp) REVERT: A 134 MET cc_start: 0.8246 (mmm) cc_final: 0.7854 (mmm) REVERT: A 146 GLN cc_start: 0.8294 (mp-120) cc_final: 0.7988 (mp-120) REVERT: A 234 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7774 (mp0) REVERT: A 244 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7299 (mtp85) REVERT: A 245 ASP cc_start: 0.8310 (OUTLIER) cc_final: 0.7641 (t0) REVERT: A 309 ASP cc_start: 0.8275 (t70) cc_final: 0.8031 (t70) REVERT: A 334 GLU cc_start: 0.8301 (tt0) cc_final: 0.7884 (tm-30) REVERT: A 354 GLU cc_start: 0.8179 (tt0) cc_final: 0.7952 (tm-30) REVERT: A 357 ASP cc_start: 0.8565 (t70) cc_final: 0.8349 (t70) REVERT: A 425 ARG cc_start: 0.8343 (mtt180) cc_final: 0.7811 (mtm-85) REVERT: A 431 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7953 (mp0) REVERT: A 541 TYR cc_start: 0.7201 (m-10) cc_final: 0.6884 (t80) REVERT: B 63 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8310 (tp) REVERT: B 131 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7970 (mm-30) REVERT: B 173 PHE cc_start: 0.7402 (t80) cc_final: 0.6968 (m-80) REVERT: B 181 ARG cc_start: 0.8060 (mtm110) cc_final: 0.7629 (tpp80) REVERT: B 219 ARG cc_start: 0.8278 (mtp85) cc_final: 0.7910 (tpp80) REVERT: B 255 PHE cc_start: 0.8066 (t80) cc_final: 0.7629 (m-80) REVERT: B 401 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7430 (tm-30) REVERT: B 426 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7937 (mm-30) REVERT: B 510 GLU cc_start: 0.7134 (tt0) cc_final: 0.6334 (pp20) REVERT: B 515 GLN cc_start: 0.7975 (mt0) cc_final: 0.7582 (mm110) REVERT: B 532 ARG cc_start: 0.7953 (mmm160) cc_final: 0.7561 (mmm160) REVERT: B 568 GLU cc_start: 0.7561 (tt0) cc_final: 0.7285 (tp30) REVERT: B 574 LYS cc_start: 0.7637 (OUTLIER) cc_final: 0.7312 (pttp) REVERT: C 39 GLN cc_start: 0.7989 (tt0) cc_final: 0.7334 (tp40) REVERT: C 65 LYS cc_start: 0.8000 (ptmm) cc_final: 0.7716 (pttt) REVERT: C 82 GLN cc_start: 0.6826 (tp40) cc_final: 0.6500 (tp-100) REVERT: C 98 THR cc_start: 0.8125 (m) cc_final: 0.7788 (p) outliers start: 38 outliers final: 11 residues processed: 186 average time/residue: 0.6514 time to fit residues: 128.8636 Evaluate side-chains 173 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 156 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 588 TYR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain C residue 69 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 80 optimal weight: 1.9990 chunk 120 optimal weight: 0.0050 chunk 68 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 33 optimal weight: 0.0570 overall best weight: 0.5314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 305 GLN ** A 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.140317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.113471 restraints weight = 11899.690| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.84 r_work: 0.3128 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10400 Z= 0.117 Angle : 0.516 7.934 14112 Z= 0.262 Chirality : 0.040 0.256 1606 Planarity : 0.003 0.040 1783 Dihedral : 4.713 62.668 1442 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.39 % Allowed : 15.36 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.23), residues: 1275 helix: 1.15 (0.19), residues: 783 sheet: 0.44 (0.48), residues: 114 loop : -0.99 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 209 TYR 0.011 0.001 TYR B 164 PHE 0.012 0.001 PHE A 304 TRP 0.026 0.001 TRP C 36 HIS 0.003 0.001 HIS B 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (10398) covalent geometry : angle 0.51572 / 0.26 (14108) SS BOND : bond 0.00058 / 0.03 ( 2) SS BOND : angle 0.52129 / 0.30 ( 4) hydrogen bonds : bond 0.03865 / 2.62 ( 605) hydrogen bonds : angle 3.89816 / 2.82 ( 1770) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 174 time to evaluate : 0.372 Fit side-chains REVERT: A 19 LEU cc_start: 0.7836 (mt) cc_final: 0.7453 (tt) REVERT: A 20 ARG cc_start: 0.7834 (mtt90) cc_final: 0.7457 (ttp-110) REVERT: A 21 TYR cc_start: 0.9001 (m-80) cc_final: 0.8622 (m-80) REVERT: A 33 LEU cc_start: 0.8453 (mp) cc_final: 0.8182 (mm) REVERT: A 64 ARG cc_start: 0.7528 (tmm-80) cc_final: 0.7279 (pmt170) REVERT: A 118 MET cc_start: 0.9075 (mmp) cc_final: 0.8586 (mmp) REVERT: A 134 MET cc_start: 0.8174 (mmm) cc_final: 0.7836 (mmm) REVERT: A 146 GLN cc_start: 0.8294 (mp-120) cc_final: 0.7956 (mp-120) REVERT: A 232 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.6894 (mp0) REVERT: A 234 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7691 (mp0) REVERT: A 245 ASP cc_start: 0.8326 (OUTLIER) cc_final: 0.7663 (t0) REVERT: A 309 ASP cc_start: 0.8233 (t70) cc_final: 0.7983 (t70) REVERT: A 334 GLU cc_start: 0.8283 (tt0) cc_final: 0.7947 (tm-30) REVERT: A 354 GLU cc_start: 0.8136 (tt0) cc_final: 0.7902 (tm-30) REVERT: A 357 ASP cc_start: 0.8531 (t70) cc_final: 0.8191 (t70) REVERT: A 388 LYS cc_start: 0.7598 (mttt) cc_final: 0.7336 (mtmt) REVERT: A 425 ARG cc_start: 0.8332 (mtt180) cc_final: 0.7827 (mtm-85) REVERT: A 431 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7900 (mp0) REVERT: A 537 GLN cc_start: 0.7907 (mm-40) cc_final: 0.7684 (mm-40) REVERT: A 541 TYR cc_start: 0.7230 (m-10) cc_final: 0.6954 (t80) REVERT: B 63 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8273 (tp) REVERT: B 120 ASN cc_start: 0.8989 (t0) cc_final: 0.8501 (t0) REVERT: B 131 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7941 (mm-30) REVERT: B 173 PHE cc_start: 0.7383 (t80) cc_final: 0.6954 (m-80) REVERT: B 181 ARG cc_start: 0.7998 (mtm110) cc_final: 0.7609 (tpp80) REVERT: B 219 ARG cc_start: 0.8299 (mtp85) cc_final: 0.7971 (tpp80) REVERT: B 255 PHE cc_start: 0.8067 (t80) cc_final: 0.7645 (m-80) REVERT: B 401 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7379 (tm-30) REVERT: B 426 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7966 (mm-30) REVERT: B 510 GLU cc_start: 0.7149 (tt0) cc_final: 0.6367 (pp20) REVERT: B 515 GLN cc_start: 0.7983 (mt0) cc_final: 0.7588 (mm110) REVERT: B 532 ARG cc_start: 0.7927 (mmm160) cc_final: 0.7541 (mmm160) REVERT: B 570 ASP cc_start: 0.8540 (t0) cc_final: 0.8312 (t0) REVERT: B 574 LYS cc_start: 0.7529 (ttpt) cc_final: 0.7211 (pttp) REVERT: C 39 GLN cc_start: 0.7980 (tt0) cc_final: 0.7301 (tp40) REVERT: C 65 LYS cc_start: 0.7919 (ptmm) cc_final: 0.7615 (pttt) REVERT: C 82 GLN cc_start: 0.6626 (tp40) cc_final: 0.6203 (tp40) REVERT: C 98 THR cc_start: 0.8060 (m) cc_final: 0.7760 (p) outliers start: 25 outliers final: 10 residues processed: 188 average time/residue: 0.6182 time to fit residues: 123.6973 Evaluate side-chains 176 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 161 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 69 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 32 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 120 optimal weight: 0.9980 chunk 90 optimal weight: 0.0010 chunk 11 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 111 optimal weight: 0.2980 chunk 40 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 305 GLN A 429 GLN B 53 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.140604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.113722 restraints weight = 11962.624| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.84 r_work: 0.3148 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10400 Z= 0.111 Angle : 0.516 8.405 14112 Z= 0.258 Chirality : 0.039 0.217 1606 Planarity : 0.003 0.039 1783 Dihedral : 4.629 61.952 1442 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.96 % Allowed : 15.27 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.23), residues: 1275 helix: 1.37 (0.19), residues: 784 sheet: 0.48 (0.49), residues: 114 loop : -0.91 (0.29), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 12 TYR 0.011 0.001 TYR B 164 PHE 0.023 0.001 PHE A 171 TRP 0.029 0.001 TRP C 36 HIS 0.002 0.000 HIS B 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (10398) covalent geometry : angle 0.51572 / 0.26 (14108) SS BOND : bond 0.00049 / 0.02 ( 2) SS BOND : angle 0.39572 / 0.23 ( 4) hydrogen bonds : bond 0.03741 / 2.54 ( 605) hydrogen bonds : angle 3.85050 / 2.79 ( 1770) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 168 time to evaluate : 0.388 Fit side-chains REVERT: A 19 LEU cc_start: 0.7834 (mt) cc_final: 0.7440 (tt) REVERT: A 20 ARG cc_start: 0.7821 (mtt90) cc_final: 0.7453 (ttp-110) REVERT: A 33 LEU cc_start: 0.8436 (mp) cc_final: 0.8170 (mm) REVERT: A 64 ARG cc_start: 0.7544 (tmm-80) cc_final: 0.7234 (pmt170) REVERT: A 118 MET cc_start: 0.9029 (mmp) cc_final: 0.8731 (mmp) REVERT: A 134 MET cc_start: 0.8179 (OUTLIER) cc_final: 0.7841 (mmm) REVERT: A 146 GLN cc_start: 0.8283 (mp-120) cc_final: 0.7941 (mp-120) REVERT: A 218 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8169 (tt0) REVERT: A 232 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.6878 (mp0) REVERT: A 234 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7815 (mp0) REVERT: A 245 ASP cc_start: 0.8360 (OUTLIER) cc_final: 0.7730 (t0) REVERT: A 309 ASP cc_start: 0.8265 (t70) cc_final: 0.8031 (t70) REVERT: A 334 GLU cc_start: 0.8308 (tt0) cc_final: 0.7938 (tm-30) REVERT: A 354 GLU cc_start: 0.8129 (tt0) cc_final: 0.7909 (tm-30) REVERT: A 357 ASP cc_start: 0.8497 (t70) cc_final: 0.8145 (t70) REVERT: A 425 ARG cc_start: 0.8338 (mtt180) cc_final: 0.8071 (mtt90) REVERT: A 431 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7918 (mp0) REVERT: A 537 GLN cc_start: 0.7907 (mm-40) cc_final: 0.7595 (mt0) REVERT: A 541 TYR cc_start: 0.7223 (m-10) cc_final: 0.6929 (t80) REVERT: B 63 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8258 (tp) REVERT: B 120 ASN cc_start: 0.8958 (t0) cc_final: 0.8478 (t0) REVERT: B 131 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7962 (mm-30) REVERT: B 173 PHE cc_start: 0.7318 (t80) cc_final: 0.6915 (m-80) REVERT: B 181 ARG cc_start: 0.7987 (mtm110) cc_final: 0.7651 (tpp80) REVERT: B 219 ARG cc_start: 0.8341 (mtp85) cc_final: 0.8025 (tpp80) REVERT: B 255 PHE cc_start: 0.8049 (t80) cc_final: 0.7606 (m-80) REVERT: B 401 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7317 (tm-30) REVERT: B 426 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7972 (mm-30) REVERT: B 510 GLU cc_start: 0.7152 (tt0) cc_final: 0.6370 (pp20) REVERT: B 515 GLN cc_start: 0.7967 (mt0) cc_final: 0.7574 (mm-40) REVERT: B 532 ARG cc_start: 0.7938 (mmm160) cc_final: 0.7549 (mmm160) REVERT: B 570 ASP cc_start: 0.8508 (t0) cc_final: 0.8301 (t0) REVERT: B 574 LYS cc_start: 0.7529 (OUTLIER) cc_final: 0.7280 (pttp) REVERT: C 39 GLN cc_start: 0.8012 (tt0) cc_final: 0.7406 (tp40) REVERT: C 65 LYS cc_start: 0.7855 (ptmm) cc_final: 0.7555 (pttt) REVERT: C 82 GLN cc_start: 0.6765 (tp40) cc_final: 0.6374 (tp-100) REVERT: C 98 THR cc_start: 0.8094 (m) cc_final: 0.7799 (p) outliers start: 31 outliers final: 11 residues processed: 186 average time/residue: 0.6397 time to fit residues: 126.7854 Evaluate side-chains 179 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 365 LYS Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain C residue 69 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 67 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 305 GLN A 579 HIS B 53 GLN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.137640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.110845 restraints weight = 11907.464| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.82 r_work: 0.3100 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10400 Z= 0.145 Angle : 0.548 8.470 14112 Z= 0.273 Chirality : 0.040 0.195 1606 Planarity : 0.003 0.038 1783 Dihedral : 4.732 63.436 1442 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.15 % Allowed : 15.36 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.23), residues: 1275 helix: 1.36 (0.19), residues: 784 sheet: 0.44 (0.49), residues: 115 loop : -0.90 (0.29), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 244 TYR 0.017 0.001 TYR B 164 PHE 0.015 0.001 PHE A 304 TRP 0.033 0.001 TRP C 36 HIS 0.003 0.001 HIS B 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (10398) covalent geometry : angle 0.54755 / 0.27 (14108) SS BOND : bond 0.00028 / 0.01 ( 2) SS BOND : angle 0.48712 / 0.29 ( 4) hydrogen bonds : bond 0.04068 / 2.77 ( 605) hydrogen bonds : angle 3.91483 / 2.84 ( 1770) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 166 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 19 LEU cc_start: 0.7880 (mt) cc_final: 0.7498 (tt) REVERT: A 20 ARG cc_start: 0.7856 (mtt90) cc_final: 0.7495 (ttp-110) REVERT: A 33 LEU cc_start: 0.8462 (mp) cc_final: 0.8199 (mm) REVERT: A 134 MET cc_start: 0.8175 (OUTLIER) cc_final: 0.7854 (mmm) REVERT: A 146 GLN cc_start: 0.8334 (mp-120) cc_final: 0.7972 (mp-120) REVERT: A 218 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8202 (tt0) REVERT: A 232 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.6921 (mp0) REVERT: A 234 GLU cc_start: 0.8110 (tm-30) cc_final: 0.7840 (mp0) REVERT: A 245 ASP cc_start: 0.8317 (OUTLIER) cc_final: 0.7691 (t0) REVERT: A 334 GLU cc_start: 0.8323 (tt0) cc_final: 0.7958 (tm-30) REVERT: A 354 GLU cc_start: 0.8205 (tt0) cc_final: 0.7938 (tm-30) REVERT: A 356 ARG cc_start: 0.8358 (ttm-80) cc_final: 0.7177 (ttp-170) REVERT: A 357 ASP cc_start: 0.8535 (t70) cc_final: 0.8206 (t70) REVERT: A 425 ARG cc_start: 0.8357 (mtt180) cc_final: 0.8087 (mtt90) REVERT: A 431 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7884 (mp0) REVERT: A 537 GLN cc_start: 0.7872 (mm-40) cc_final: 0.7589 (mt0) REVERT: A 541 TYR cc_start: 0.7161 (m-10) cc_final: 0.6933 (t80) REVERT: B 63 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8296 (tp) REVERT: B 131 GLU cc_start: 0.8287 (mt-10) cc_final: 0.8005 (mm-30) REVERT: B 138 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8564 (mt) REVERT: B 173 PHE cc_start: 0.7294 (t80) cc_final: 0.6949 (m-80) REVERT: B 181 ARG cc_start: 0.7999 (mtm110) cc_final: 0.7669 (tpp80) REVERT: B 219 ARG cc_start: 0.8354 (mtp85) cc_final: 0.8008 (tpp80) REVERT: B 255 PHE cc_start: 0.8096 (t80) cc_final: 0.7650 (m-80) REVERT: B 349 ASP cc_start: 0.8106 (t70) cc_final: 0.7768 (t0) REVERT: B 401 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7340 (tm-30) REVERT: B 426 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7953 (mm-30) REVERT: B 510 GLU cc_start: 0.7159 (tt0) cc_final: 0.6380 (pp20) REVERT: B 532 ARG cc_start: 0.7929 (mmm160) cc_final: 0.7547 (mmm160) REVERT: B 570 ASP cc_start: 0.8517 (t0) cc_final: 0.8290 (t0) REVERT: B 574 LYS cc_start: 0.7576 (OUTLIER) cc_final: 0.7317 (pttp) REVERT: C 18 LEU cc_start: 0.6460 (OUTLIER) cc_final: 0.6073 (tm) REVERT: C 39 GLN cc_start: 0.8022 (tt0) cc_final: 0.7470 (tp40) REVERT: C 65 LYS cc_start: 0.7967 (ptmm) cc_final: 0.7678 (pttt) REVERT: C 82 GLN cc_start: 0.6784 (tp40) cc_final: 0.6368 (tp-100) REVERT: C 98 THR cc_start: 0.8105 (m) cc_final: 0.7736 (p) outliers start: 33 outliers final: 13 residues processed: 185 average time/residue: 0.6380 time to fit residues: 125.3045 Evaluate side-chains 181 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 158 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 365 LYS Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 53 LYS Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 79 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 105 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 83 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 305 GLN B 53 GLN B 120 ASN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.137491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.110706 restraints weight = 11946.195| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.82 r_work: 0.3097 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10400 Z= 0.141 Angle : 0.548 8.740 14112 Z= 0.272 Chirality : 0.040 0.186 1606 Planarity : 0.003 0.037 1783 Dihedral : 4.753 64.751 1442 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.96 % Allowed : 15.94 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.23), residues: 1275 helix: 1.42 (0.19), residues: 783 sheet: 0.43 (0.49), residues: 115 loop : -0.85 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 493 TYR 0.018 0.001 TYR B 164 PHE 0.030 0.001 PHE A 171 TRP 0.039 0.001 TRP C 36 HIS 0.003 0.001 HIS B 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (10398) covalent geometry : angle 0.54769 / 0.27 (14108) SS BOND : bond 0.00022 / 0.01 ( 2) SS BOND : angle 0.42709 / 0.26 ( 4) hydrogen bonds : bond 0.04041 / 2.75 ( 605) hydrogen bonds : angle 3.91841 / 2.84 ( 1770) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 156 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: A 19 LEU cc_start: 0.7869 (mt) cc_final: 0.7499 (tt) REVERT: A 20 ARG cc_start: 0.7859 (mtt90) cc_final: 0.7505 (ttp-110) REVERT: A 33 LEU cc_start: 0.8458 (mp) cc_final: 0.8196 (mm) REVERT: A 96 TYR cc_start: 0.8636 (t80) cc_final: 0.8427 (t80) REVERT: A 134 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7849 (mmm) REVERT: A 146 GLN cc_start: 0.8342 (mp-120) cc_final: 0.7972 (mp-120) REVERT: A 166 LEU cc_start: 0.7526 (tp) cc_final: 0.7296 (tm) REVERT: A 218 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8199 (tt0) REVERT: A 232 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.6902 (mp0) REVERT: A 234 GLU cc_start: 0.8082 (tm-30) cc_final: 0.7852 (mp0) REVERT: A 244 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7872 (mmp80) REVERT: A 245 ASP cc_start: 0.8337 (OUTLIER) cc_final: 0.7712 (t0) REVERT: A 334 GLU cc_start: 0.8322 (tt0) cc_final: 0.7941 (tm-30) REVERT: A 354 GLU cc_start: 0.8219 (tt0) cc_final: 0.7948 (tm-30) REVERT: A 356 ARG cc_start: 0.8371 (ttm-80) cc_final: 0.7158 (ttp-170) REVERT: A 357 ASP cc_start: 0.8512 (t70) cc_final: 0.8173 (t70) REVERT: A 425 ARG cc_start: 0.8351 (mtt180) cc_final: 0.8088 (mtt90) REVERT: A 431 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7924 (mp0) REVERT: A 537 GLN cc_start: 0.7888 (mm-40) cc_final: 0.7620 (mt0) REVERT: A 541 TYR cc_start: 0.7168 (m-10) cc_final: 0.6927 (t80) REVERT: B 63 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8319 (tp) REVERT: B 120 ASN cc_start: 0.8989 (t0) cc_final: 0.8552 (t0) REVERT: B 131 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7992 (mm-30) REVERT: B 138 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8559 (mt) REVERT: B 173 PHE cc_start: 0.7281 (t80) cc_final: 0.6880 (m-80) REVERT: B 181 ARG cc_start: 0.7934 (mtm110) cc_final: 0.7606 (tpp80) REVERT: B 219 ARG cc_start: 0.8308 (mtp85) cc_final: 0.7988 (tpp80) REVERT: B 255 PHE cc_start: 0.8102 (t80) cc_final: 0.7650 (m-80) REVERT: B 349 ASP cc_start: 0.8107 (t70) cc_final: 0.7758 (t0) REVERT: B 401 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7248 (tm-30) REVERT: B 426 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7957 (mm-30) REVERT: B 510 GLU cc_start: 0.7163 (tt0) cc_final: 0.6379 (pp20) REVERT: B 515 GLN cc_start: 0.7953 (mt0) cc_final: 0.7569 (mm110) REVERT: B 532 ARG cc_start: 0.7915 (mmm160) cc_final: 0.7539 (mmm160) REVERT: B 557 GLU cc_start: 0.8016 (mp0) cc_final: 0.7780 (mp0) REVERT: B 570 ASP cc_start: 0.8527 (t0) cc_final: 0.8299 (t0) REVERT: B 574 LYS cc_start: 0.7553 (OUTLIER) cc_final: 0.7281 (pttp) REVERT: C 18 LEU cc_start: 0.6396 (OUTLIER) cc_final: 0.5971 (tm) REVERT: C 39 GLN cc_start: 0.8029 (tt0) cc_final: 0.7475 (tp40) REVERT: C 65 LYS cc_start: 0.7979 (ptmm) cc_final: 0.7692 (pttt) REVERT: C 82 GLN cc_start: 0.6771 (tp40) cc_final: 0.6379 (tp-100) REVERT: C 98 THR cc_start: 0.8003 (m) cc_final: 0.7643 (p) outliers start: 31 outliers final: 10 residues processed: 176 average time/residue: 0.6585 time to fit residues: 123.0758 Evaluate side-chains 178 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 157 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 79 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 109 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 305 GLN B 53 GLN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.137554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.110775 restraints weight = 11869.864| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.82 r_work: 0.3110 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10400 Z= 0.136 Angle : 0.551 8.857 14112 Z= 0.275 Chirality : 0.040 0.174 1606 Planarity : 0.003 0.037 1783 Dihedral : 4.742 64.779 1442 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.48 % Allowed : 16.60 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.23), residues: 1275 helix: 1.42 (0.19), residues: 790 sheet: 0.41 (0.49), residues: 115 loop : -0.83 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 493 TYR 0.017 0.001 TYR B 164 PHE 0.014 0.001 PHE A 304 TRP 0.046 0.001 TRP C 36 HIS 0.003 0.001 HIS B 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (10398) covalent geometry : angle 0.55093 / 0.27 (14108) SS BOND : bond 0.00012 / 0.01 ( 2) SS BOND : angle 0.52897 / 0.32 ( 4) hydrogen bonds : bond 0.03988 / 2.72 ( 605) hydrogen bonds : angle 3.90592 / 2.83 ( 1770) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 161 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 19 LEU cc_start: 0.7865 (mt) cc_final: 0.7496 (tt) REVERT: A 20 ARG cc_start: 0.7854 (mtt90) cc_final: 0.7499 (ttp-110) REVERT: A 33 LEU cc_start: 0.8468 (mp) cc_final: 0.8203 (mm) REVERT: A 96 TYR cc_start: 0.8623 (t80) cc_final: 0.8417 (t80) REVERT: A 134 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7858 (mmm) REVERT: A 146 GLN cc_start: 0.8340 (mp-120) cc_final: 0.8000 (mp-120) REVERT: A 166 LEU cc_start: 0.7535 (tp) cc_final: 0.7317 (tm) REVERT: A 218 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8201 (tt0) REVERT: A 232 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.6940 (mp0) REVERT: A 234 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7860 (mp0) REVERT: A 245 ASP cc_start: 0.8367 (OUTLIER) cc_final: 0.7753 (t0) REVERT: A 334 GLU cc_start: 0.8308 (tt0) cc_final: 0.7922 (tm-30) REVERT: A 354 GLU cc_start: 0.8252 (tt0) cc_final: 0.8004 (tm-30) REVERT: A 356 ARG cc_start: 0.8360 (ttm-80) cc_final: 0.7148 (ttp-170) REVERT: A 357 ASP cc_start: 0.8498 (t70) cc_final: 0.8161 (t70) REVERT: A 425 ARG cc_start: 0.8342 (mtt180) cc_final: 0.8080 (mtt90) REVERT: A 431 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7949 (mp0) REVERT: A 541 TYR cc_start: 0.7135 (m-10) cc_final: 0.6925 (t80) REVERT: B 63 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8312 (tp) REVERT: B 120 ASN cc_start: 0.8986 (t0) cc_final: 0.8529 (t0) REVERT: B 131 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7966 (mm-30) REVERT: B 138 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8549 (mt) REVERT: B 173 PHE cc_start: 0.7228 (t80) cc_final: 0.6791 (m-80) REVERT: B 181 ARG cc_start: 0.7907 (mtm110) cc_final: 0.7589 (tpp80) REVERT: B 219 ARG cc_start: 0.8302 (mtp85) cc_final: 0.7986 (tpp80) REVERT: B 255 PHE cc_start: 0.8087 (t80) cc_final: 0.7633 (m-80) REVERT: B 349 ASP cc_start: 0.8116 (t70) cc_final: 0.7765 (t0) REVERT: B 401 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7241 (tm-30) REVERT: B 426 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7963 (mm-30) REVERT: B 510 GLU cc_start: 0.7157 (tt0) cc_final: 0.6384 (pp20) REVERT: B 515 GLN cc_start: 0.7925 (mt0) cc_final: 0.7580 (mm-40) REVERT: B 532 ARG cc_start: 0.7951 (mmm160) cc_final: 0.7528 (mmm160) REVERT: B 557 GLU cc_start: 0.8011 (mp0) cc_final: 0.7776 (mp0) REVERT: B 570 ASP cc_start: 0.8524 (t0) cc_final: 0.8304 (t0) REVERT: B 574 LYS cc_start: 0.7548 (OUTLIER) cc_final: 0.7282 (pttp) REVERT: C 18 LEU cc_start: 0.6362 (OUTLIER) cc_final: 0.6031 (tm) REVERT: C 39 GLN cc_start: 0.8023 (tt0) cc_final: 0.7496 (tp40) REVERT: C 65 LYS cc_start: 0.7976 (ptmm) cc_final: 0.7696 (pttt) REVERT: C 82 GLN cc_start: 0.6778 (tp40) cc_final: 0.6385 (tp-100) REVERT: C 98 THR cc_start: 0.8031 (m) cc_final: 0.7667 (p) outliers start: 26 outliers final: 10 residues processed: 178 average time/residue: 0.6365 time to fit residues: 120.4537 Evaluate side-chains 176 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 79 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 101 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 114 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 305 GLN A 537 GLN B 53 GLN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.136258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.109476 restraints weight = 11840.916| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.81 r_work: 0.3085 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10400 Z= 0.145 Angle : 0.565 8.836 14112 Z= 0.280 Chirality : 0.041 0.182 1606 Planarity : 0.004 0.036 1783 Dihedral : 4.796 65.448 1442 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.39 % Allowed : 17.08 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.23), residues: 1275 helix: 1.43 (0.19), residues: 790 sheet: 0.38 (0.49), residues: 115 loop : -0.82 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 351 TYR 0.017 0.001 TYR B 164 PHE 0.030 0.001 PHE A 171 TRP 0.051 0.002 TRP C 36 HIS 0.003 0.001 HIS B 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 (10398) covalent geometry : angle 0.56511 / 0.28 (14108) SS BOND : bond 0.00026 / 0.01 ( 2) SS BOND : angle 0.55691 / 0.33 ( 4) hydrogen bonds : bond 0.04050 / 2.75 ( 605) hydrogen bonds : angle 3.94218 / 2.86 ( 1770) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.7875 (mt) cc_final: 0.7514 (tt) REVERT: A 20 ARG cc_start: 0.7835 (mtt90) cc_final: 0.7477 (ttp-110) REVERT: A 33 LEU cc_start: 0.8464 (mp) cc_final: 0.8201 (mm) REVERT: A 96 TYR cc_start: 0.8628 (t80) cc_final: 0.8425 (t80) REVERT: A 134 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7861 (mmm) REVERT: A 146 GLN cc_start: 0.8367 (mp-120) cc_final: 0.8024 (mp-120) REVERT: A 166 LEU cc_start: 0.7538 (tp) cc_final: 0.7328 (tm) REVERT: A 218 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8189 (tt0) REVERT: A 232 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.6895 (mp0) REVERT: A 234 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7791 (mp0) REVERT: A 245 ASP cc_start: 0.8332 (OUTLIER) cc_final: 0.7709 (t0) REVERT: A 334 GLU cc_start: 0.8289 (tt0) cc_final: 0.7928 (tm-30) REVERT: A 354 GLU cc_start: 0.8258 (tt0) cc_final: 0.8005 (tm-30) REVERT: A 356 ARG cc_start: 0.8350 (ttm-80) cc_final: 0.7141 (ttp-170) REVERT: A 357 ASP cc_start: 0.8503 (t70) cc_final: 0.8164 (t70) REVERT: A 425 ARG cc_start: 0.8345 (mtt180) cc_final: 0.8084 (mtt90) REVERT: A 431 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7955 (mp0) REVERT: B 63 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8326 (tp) REVERT: B 120 ASN cc_start: 0.9006 (t0) cc_final: 0.8538 (t0) REVERT: B 131 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7962 (mm-30) REVERT: B 138 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8553 (mt) REVERT: B 173 PHE cc_start: 0.7141 (t80) cc_final: 0.6661 (m-80) REVERT: B 181 ARG cc_start: 0.7947 (mtm110) cc_final: 0.7596 (tpp80) REVERT: B 219 ARG cc_start: 0.8224 (mtp85) cc_final: 0.7930 (tpp80) REVERT: B 255 PHE cc_start: 0.8087 (t80) cc_final: 0.7605 (m-80) REVERT: B 349 ASP cc_start: 0.8118 (t70) cc_final: 0.7770 (t0) REVERT: B 401 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7215 (tm-30) REVERT: B 426 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7976 (mm-30) REVERT: B 510 GLU cc_start: 0.7182 (tt0) cc_final: 0.6398 (pp20) REVERT: B 515 GLN cc_start: 0.7897 (mt0) cc_final: 0.7564 (mm-40) REVERT: B 532 ARG cc_start: 0.7953 (mmm160) cc_final: 0.7517 (mmm160) REVERT: B 557 GLU cc_start: 0.8029 (mp0) cc_final: 0.7785 (mp0) REVERT: B 570 ASP cc_start: 0.8539 (t0) cc_final: 0.8317 (t0) REVERT: B 574 LYS cc_start: 0.7544 (OUTLIER) cc_final: 0.7270 (pttp) REVERT: C 18 LEU cc_start: 0.6294 (OUTLIER) cc_final: 0.6010 (tm) REVERT: C 39 GLN cc_start: 0.8062 (tt0) cc_final: 0.7579 (tp40) REVERT: C 82 GLN cc_start: 0.6761 (tp40) cc_final: 0.6333 (tp-100) REVERT: C 98 THR cc_start: 0.8010 (m) cc_final: 0.7639 (p) outliers start: 25 outliers final: 10 residues processed: 175 average time/residue: 0.6481 time to fit residues: 120.3661 Evaluate side-chains 175 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 79 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 99 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 115 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 305 GLN A 537 GLN A 554 HIS B 53 GLN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.137165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.110484 restraints weight = 11966.412| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.83 r_work: 0.3093 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10400 Z= 0.148 Angle : 0.575 8.959 14112 Z= 0.285 Chirality : 0.041 0.176 1606 Planarity : 0.004 0.060 1783 Dihedral : 4.826 65.868 1442 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.39 % Allowed : 16.98 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.23), residues: 1275 helix: 1.43 (0.19), residues: 790 sheet: 0.40 (0.49), residues: 115 loop : -0.82 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 233 TYR 0.017 0.001 TYR B 164 PHE 0.031 0.001 PHE A 171 TRP 0.049 0.002 TRP C 36 HIS 0.003 0.001 HIS B 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (10398) covalent geometry : angle 0.57506 / 0.29 (14108) SS BOND : bond 0.00028 / 0.01 ( 2) SS BOND : angle 0.57165 / 0.34 ( 4) hydrogen bonds : bond 0.04058 / 2.76 ( 605) hydrogen bonds : angle 3.94515 / 2.86 ( 1770) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3568.33 seconds wall clock time: 61 minutes 21.02 seconds (3681.02 seconds total)