Starting phenix.real_space_refine on Mon Jul 28 10:18:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6rai_4776/07_2025/6rai_4776.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rai_4776/07_2025/6rai_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6rai_4776/07_2025/6rai_4776.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rai_4776/07_2025/6rai_4776.map" model { file = "/net/cci-nas-00/data/ceres_data/6rai_4776/07_2025/6rai_4776.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rai_4776/07_2025/6rai_4776.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.01, per 1000 atoms: 0.69 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: 3.00 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.18 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: 3.60 Time building geometry restraints manager: 3.39 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 - 17.37: 5925 17.37 - 34.75: 220 34.75 - 52.12: 44 52.12 - 69.49: 9 69.49 - 86.86: 9 Dihedral angle restraints: 6207 sinusoidal: 2547 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 6204 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: 0.010 Normalize map: mean=0, sd=1: 1.840 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: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 28.460 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 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 : 10.559 86.864 3859 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 9.46 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.027 0.003 TRP B 22 HIS 0.006 0.001 HIS A 121 PHE 0.039 0.003 PHE A 304 TYR 0.028 0.003 TYR B 284 ARG 0.006 0.001 ARG B 240 Details of bonding type rmsd hydrogen bonds : bond 0.20846 ( 605) hydrogen bonds : angle 7.12252 ( 1770) SS BOND : bond 0.02206 ( 2) SS BOND : angle 2.03061 ( 4) covalent geometry : bond 0.00870 (10398) covalent geometry : angle 1.39727 (14108) *********************** 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 : 1.178 Fit side-chains REVERT: A 37 LEU cc_start: 0.8211 (tp) cc_final: 0.7975 (tp) REVERT: A 58 LEU cc_start: 0.8143 (mt) cc_final: 0.7859 (mp) REVERT: A 96 TYR cc_start: 0.8440 (t80) cc_final: 0.7886 (t80) REVERT: A 145 ASN cc_start: 0.8889 (t0) cc_final: 0.8658 (t0) REVERT: A 168 PHE cc_start: 0.8304 (t80) cc_final: 0.8080 (t80) REVERT: A 206 ARG cc_start: 0.8045 (mmt180) cc_final: 0.7685 (mpt180) REVERT: A 238 LYS cc_start: 0.8330 (mttt) cc_final: 0.7798 (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: 0.6849 (mttm) REVERT: A 425 ARG cc_start: 0.7570 (mtt180) cc_final: 0.7324 (mtm-85) REVERT: A 431 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7484 (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: 0.7619 (mtt180) REVERT: B 131 GLU cc_start: 0.7228 (mt-10) cc_final: 0.6999 (mm-30) REVERT: B 299 MET cc_start: 0.7514 (mmt) cc_final: 0.6947 (mmt) REVERT: B 510 GLU cc_start: 0.6683 (tt0) cc_final: 0.6441 (pp20) REVERT: B 532 ARG cc_start: 0.7199 (mmm160) cc_final: 0.6947 (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: 0.7712 (pttt) REVERT: C 98 THR cc_start: 0.7947 (m) cc_final: 0.7552 (p) outliers start: 0 outliers final: 1 residues processed: 271 average time/residue: 1.7471 time to fit residues: 498.0384 Evaluate side-chains 167 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 166 time to evaluate : 1.194 ------------------------------------------------------------------------------- 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 107 optimal weight: 1.9990 chunk 96 optimal weight: 0.0030 chunk 53 optimal weight: 0.4980 chunk 32 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 99 optimal weight: 0.0980 chunk 38 optimal weight: 0.0980 chunk 60 optimal weight: 0.6980 chunk 74 optimal weight: 0.3980 chunk 115 optimal weight: 0.3980 overall best weight: 0.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 503 GLN A 537 GLN B 111 HIS B 113 HIS B 191 GLN B 431 ASN B 538 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.146677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.120127 restraints weight = 11697.859| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.82 r_work: 0.3231 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10400 Z= 0.119 Angle : 0.578 7.607 14112 Z= 0.298 Chirality : 0.040 0.164 1606 Planarity : 0.005 0.040 1783 Dihedral : 7.476 75.781 1506 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.72 % Allowed : 11.45 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.22), residues: 1275 helix: -0.26 (0.18), residues: 783 sheet: 0.29 (0.47), residues: 124 loop : -1.81 (0.27), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 36 HIS 0.004 0.001 HIS B 111 PHE 0.013 0.001 PHE A 304 TYR 0.025 0.001 TYR A 589 ARG 0.007 0.001 ARG A 195 Details of bonding type rmsd hydrogen bonds : bond 0.04296 ( 605) hydrogen bonds : angle 4.40776 ( 1770) SS BOND : bond 0.00065 ( 2) SS BOND : angle 0.61067 ( 4) covalent geometry : bond 0.00239 (10398) covalent geometry : angle 0.57798 (14108) *********************** 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 226 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 208 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 TYR cc_start: 0.8650 (m-80) cc_final: 0.8382 (m-80) REVERT: A 33 LEU cc_start: 0.8588 (mp) cc_final: 0.8256 (mm) REVERT: A 41 LEU cc_start: 0.8291 (mt) cc_final: 0.7960 (mt) REVERT: A 96 TYR cc_start: 0.8567 (t80) cc_final: 0.8191 (t80) REVERT: A 104 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7887 (mtp-110) REVERT: A 146 GLN cc_start: 0.8082 (mp-120) cc_final: 0.7790 (mp-120) REVERT: A 206 ARG cc_start: 0.8294 (mmt180) cc_final: 0.7957 (mpt180) REVERT: A 334 GLU cc_start: 0.8188 (tt0) cc_final: 0.7832 (tm-30) REVERT: A 354 GLU cc_start: 0.8033 (tt0) cc_final: 0.7808 (tm-30) REVERT: A 357 ASP cc_start: 0.8501 (t70) cc_final: 0.8166 (t70) REVERT: A 425 ARG cc_start: 0.8107 (mtt180) cc_final: 0.7718 (mtt90) REVERT: A 431 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7848 (mp0) REVERT: A 467 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7640 (mp0) REVERT: B 120 ASN cc_start: 0.8859 (t0) cc_final: 0.8537 (t0) REVERT: B 209 ARG cc_start: 0.8332 (mpt-90) cc_final: 0.8127 (mpt-90) REVERT: B 219 ARG cc_start: 0.8293 (mtp85) cc_final: 0.8007 (tpp80) REVERT: B 255 PHE cc_start: 0.7851 (t80) cc_final: 0.7482 (m-80) REVERT: B 299 MET cc_start: 0.8458 (mmt) cc_final: 0.7862 (mmp) REVERT: B 342 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8136 (mm-30) REVERT: B 494 LYS cc_start: 0.8718 (mmtm) cc_final: 0.8473 (mttm) REVERT: B 510 GLU cc_start: 0.7068 (tt0) cc_final: 0.6382 (pp20) REVERT: B 515 GLN cc_start: 0.7995 (mt0) cc_final: 0.7606 (mm-40) REVERT: B 532 ARG cc_start: 0.7956 (mmm160) cc_final: 0.7599 (mmm160) REVERT: B 549 ARG cc_start: 0.8295 (mtt180) cc_final: 0.7996 (mtt180) REVERT: B 552 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8270 (mt-10) REVERT: C 39 GLN cc_start: 0.7792 (tt0) cc_final: 0.7283 (tp40) REVERT: C 65 LYS cc_start: 0.7916 (ptmm) cc_final: 0.7634 (ptpt) REVERT: C 82 GLN cc_start: 0.6724 (tp40) cc_final: 0.6304 (tp40) REVERT: C 83 MET cc_start: 0.7189 (mtm) cc_final: 0.6669 (mpp) REVERT: C 98 THR cc_start: 0.8380 (m) cc_final: 0.8145 (p) outliers start: 18 outliers final: 5 residues processed: 221 average time/residue: 1.6796 time to fit residues: 392.8039 Evaluate side-chains 171 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 164 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ARG 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 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 98 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 2 optimal weight: 0.0020 chunk 15 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN A 429 GLN B 53 GLN B 111 HIS B 113 HIS C 77 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.138298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.111287 restraints weight = 12022.227| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.82 r_work: 0.3072 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10400 Z= 0.170 Angle : 0.589 7.420 14112 Z= 0.299 Chirality : 0.041 0.168 1606 Planarity : 0.004 0.045 1783 Dihedral : 6.954 78.037 1504 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.77 % Allowed : 14.12 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.23), residues: 1275 helix: 0.47 (0.18), residues: 784 sheet: 0.30 (0.46), residues: 124 loop : -1.40 (0.28), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 22 HIS 0.004 0.001 HIS B 111 PHE 0.019 0.001 PHE A 304 TYR 0.019 0.001 TYR A 588 ARG 0.009 0.001 ARG B 218 Details of bonding type rmsd hydrogen bonds : bond 0.04632 ( 605) hydrogen bonds : angle 4.19840 ( 1770) SS BOND : bond 0.00063 ( 2) SS BOND : angle 0.54907 ( 4) covalent geometry : bond 0.00396 (10398) covalent geometry : angle 0.58923 (14108) *********************** 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 201 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 1.228 Fit side-chains revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7818 (mtt90) cc_final: 0.7424 (ttp-110) REVERT: A 33 LEU cc_start: 0.8461 (mp) cc_final: 0.8156 (mm) REVERT: A 134 MET cc_start: 0.8286 (mmm) cc_final: 0.7956 (mmm) REVERT: A 146 GLN cc_start: 0.8334 (mp-120) cc_final: 0.8008 (mp-120) REVERT: A 175 LYS cc_start: 0.8483 (mmtt) cc_final: 0.8265 (tppp) REVERT: A 234 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7515 (mp0) REVERT: A 245 ASP cc_start: 0.8292 (OUTLIER) cc_final: 0.7668 (t0) REVERT: A 255 ARG cc_start: 0.8068 (ttm-80) cc_final: 0.7837 (ttp-110) REVERT: A 309 ASP cc_start: 0.8188 (t70) cc_final: 0.7965 (t70) REVERT: A 334 GLU cc_start: 0.8296 (tt0) cc_final: 0.7924 (tm-30) REVERT: A 354 GLU cc_start: 0.8145 (tt0) cc_final: 0.7918 (tm-30) REVERT: A 357 ASP cc_start: 0.8559 (t70) cc_final: 0.8334 (t70) REVERT: A 423 ASP cc_start: 0.8059 (m-30) cc_final: 0.7838 (t70) REVERT: A 425 ARG cc_start: 0.8242 (mtt180) cc_final: 0.7725 (mtm-85) REVERT: A 431 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7996 (mp0) REVERT: A 593 TYR cc_start: 0.7388 (t80) cc_final: 0.7181 (t80) REVERT: B 63 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8260 (tp) REVERT: B 131 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7812 (mm-30) REVERT: B 219 ARG cc_start: 0.8398 (mtp85) cc_final: 0.8075 (tpp80) REVERT: B 255 PHE cc_start: 0.8042 (t80) cc_final: 0.7663 (m-80) REVERT: B 510 GLU cc_start: 0.7129 (tt0) cc_final: 0.6428 (pp20) REVERT: B 532 ARG cc_start: 0.7994 (mmm160) cc_final: 0.7659 (mmm160) REVERT: B 568 GLU cc_start: 0.7663 (tt0) cc_final: 0.7332 (tp30) REVERT: B 574 LYS cc_start: 0.7640 (OUTLIER) cc_final: 0.7235 (ttpt) REVERT: C 39 GLN cc_start: 0.7839 (tt0) cc_final: 0.7258 (tp40) REVERT: C 65 LYS cc_start: 0.7979 (ptmm) cc_final: 0.7719 (pttt) REVERT: C 82 GLN cc_start: 0.6755 (tp40) cc_final: 0.6285 (tp40) REVERT: C 98 THR cc_start: 0.8151 (m) cc_final: 0.7853 (p) outliers start: 29 outliers final: 11 residues processed: 187 average time/residue: 1.5707 time to fit residues: 311.3241 Evaluate side-chains 163 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 1.052 ------------------------------------------------------------------------------- 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 163 VAL Chi-restraints excluded: chain A residue 234 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 B residue 63 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 326 ASP 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 57 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 86 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 117 optimal weight: 7.9990 chunk 27 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN A 579 HIS B 53 GLN B 120 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.137957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.111136 restraints weight = 11982.919| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.80 r_work: 0.3076 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10400 Z= 0.143 Angle : 0.537 7.208 14112 Z= 0.274 Chirality : 0.040 0.174 1606 Planarity : 0.004 0.041 1783 Dihedral : 6.749 87.569 1504 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.23), residues: 1275 helix: 0.86 (0.18), residues: 784 sheet: 0.41 (0.48), residues: 114 loop : -1.17 (0.28), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 36 HIS 0.003 0.001 HIS B 454 PHE 0.016 0.001 PHE A 304 TYR 0.014 0.001 TYR B 464 ARG 0.006 0.000 ARG A 594 Details of bonding type rmsd hydrogen bonds : bond 0.04133 ( 605) hydrogen bonds : angle 4.00926 ( 1770) SS BOND : bond 0.00062 ( 2) SS BOND : angle 0.53763 ( 4) covalent geometry : bond 0.00324 (10398) covalent geometry : angle 0.53695 (14108) *********************** 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 192 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 161 time to evaluate : 1.902 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.7880 (mt) cc_final: 0.7496 (tt) REVERT: A 20 ARG cc_start: 0.7786 (mtt90) cc_final: 0.7403 (ttp-110) REVERT: A 33 LEU cc_start: 0.8448 (mp) cc_final: 0.8171 (mm) REVERT: A 134 MET cc_start: 0.8225 (mmm) cc_final: 0.7823 (mmm) REVERT: A 146 GLN cc_start: 0.8280 (mp-120) cc_final: 0.7935 (mp-120) REVERT: A 234 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7658 (mp0) REVERT: A 309 ASP cc_start: 0.8225 (t70) cc_final: 0.7974 (t70) REVERT: A 334 GLU cc_start: 0.8303 (tt0) cc_final: 0.7908 (tm-30) REVERT: A 354 GLU cc_start: 0.8153 (tt0) cc_final: 0.7922 (tm-30) REVERT: A 357 ASP cc_start: 0.8518 (t70) cc_final: 0.8178 (t70) REVERT: A 425 ARG cc_start: 0.8262 (mtt180) cc_final: 0.7782 (mtm-85) REVERT: A 431 GLU cc_start: 0.8307 (mm-30) cc_final: 0.7993 (mp0) REVERT: A 541 TYR cc_start: 0.7199 (m-10) cc_final: 0.6915 (t80) REVERT: B 63 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8277 (tp) REVERT: B 120 ASN cc_start: 0.8982 (t0) cc_final: 0.8522 (t0) REVERT: B 173 PHE cc_start: 0.7397 (t80) cc_final: 0.6904 (m-80) REVERT: B 181 ARG cc_start: 0.8047 (mtm110) cc_final: 0.7659 (tpp80) REVERT: B 219 ARG cc_start: 0.8413 (mtp85) cc_final: 0.8051 (tpp80) REVERT: B 245 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.7261 (mm) REVERT: B 255 PHE cc_start: 0.8072 (t80) cc_final: 0.7651 (m-80) REVERT: B 401 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7390 (tm-30) REVERT: B 426 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7964 (mm-30) REVERT: B 510 GLU cc_start: 0.7170 (tt0) cc_final: 0.6405 (pp20) REVERT: B 515 GLN cc_start: 0.8010 (mt0) cc_final: 0.7634 (mm-40) REVERT: B 532 ARG cc_start: 0.7953 (mmm160) cc_final: 0.7596 (mmm160) REVERT: B 568 GLU cc_start: 0.7562 (tt0) cc_final: 0.7264 (tp30) REVERT: B 574 LYS cc_start: 0.7614 (OUTLIER) cc_final: 0.7292 (pttp) REVERT: C 18 LEU cc_start: 0.6526 (OUTLIER) cc_final: 0.6165 (tt) REVERT: C 39 GLN cc_start: 0.7947 (tt0) cc_final: 0.7294 (tp40) REVERT: C 65 LYS cc_start: 0.7972 (ptmm) cc_final: 0.7694 (pttt) REVERT: C 82 GLN cc_start: 0.6809 (tp40) cc_final: 0.6404 (tp40) REVERT: C 98 THR cc_start: 0.8136 (m) cc_final: 0.7794 (p) outliers start: 31 outliers final: 10 residues processed: 180 average time/residue: 1.7035 time to fit residues: 325.8785 Evaluate side-chains 174 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 137 VAL 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 52 VAL 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 245 LEU Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain C residue 18 LEU 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 69 optimal weight: 0.5980 chunk 106 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 114 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 126 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN B 53 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.138014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.111293 restraints weight = 11980.311| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.81 r_work: 0.3065 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10400 Z= 0.132 Angle : 0.527 7.558 14112 Z= 0.267 Chirality : 0.040 0.167 1606 Planarity : 0.004 0.040 1783 Dihedral : 6.631 85.552 1504 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.67 % Allowed : 15.94 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.23), residues: 1275 helix: 1.11 (0.19), residues: 784 sheet: 0.36 (0.47), residues: 114 loop : -0.98 (0.29), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 36 HIS 0.003 0.001 HIS B 454 PHE 0.014 0.001 PHE A 304 TYR 0.011 0.001 TYR B 464 ARG 0.004 0.000 ARG A 493 Details of bonding type rmsd hydrogen bonds : bond 0.03986 ( 605) hydrogen bonds : angle 3.92958 ( 1770) SS BOND : bond 0.00041 ( 2) SS BOND : angle 0.44086 ( 4) covalent geometry : bond 0.00301 (10398) covalent geometry : angle 0.52730 (14108) *********************** 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 200 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 1.164 Fit side-chains REVERT: A 19 LEU cc_start: 0.7856 (mt) cc_final: 0.7470 (tt) REVERT: A 20 ARG cc_start: 0.7745 (mtt90) cc_final: 0.7370 (ttp-110) REVERT: A 33 LEU cc_start: 0.8428 (mp) cc_final: 0.8150 (mm) REVERT: A 134 MET cc_start: 0.8193 (mmm) cc_final: 0.7833 (mmm) REVERT: A 146 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.7965 (mp-120) REVERT: A 232 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7036 (mp0) REVERT: A 234 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7725 (mp0) REVERT: A 245 ASP cc_start: 0.8337 (OUTLIER) cc_final: 0.7701 (t0) REVERT: A 255 ARG cc_start: 0.8023 (ttm-80) cc_final: 0.7791 (ttp-110) REVERT: A 309 ASP cc_start: 0.8201 (t70) cc_final: 0.7948 (t70) REVERT: A 334 GLU cc_start: 0.8330 (tt0) cc_final: 0.7900 (tm-30) REVERT: A 354 GLU cc_start: 0.8161 (tt0) cc_final: 0.7926 (tm-30) REVERT: A 357 ASP cc_start: 0.8503 (t70) cc_final: 0.8165 (t70) REVERT: A 365 LYS cc_start: 0.8493 (mtpt) cc_final: 0.8286 (ttpt) REVERT: A 425 ARG cc_start: 0.8329 (mtt180) cc_final: 0.7799 (mtm-85) REVERT: A 431 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7906 (mp0) REVERT: A 541 TYR cc_start: 0.7230 (m-10) cc_final: 0.6913 (t80) REVERT: B 63 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8269 (tp) REVERT: B 131 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7954 (mm-30) REVERT: B 173 PHE cc_start: 0.7389 (t80) cc_final: 0.6912 (m-80) REVERT: B 181 ARG cc_start: 0.8027 (mtm110) cc_final: 0.7635 (tpp80) REVERT: B 219 ARG cc_start: 0.8349 (mtp85) cc_final: 0.7959 (tpp80) REVERT: B 255 PHE cc_start: 0.8070 (t80) cc_final: 0.7651 (m-80) REVERT: B 401 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7304 (tm-30) REVERT: B 426 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7958 (mm-30) REVERT: B 510 GLU cc_start: 0.7160 (tt0) cc_final: 0.6432 (pp20) REVERT: B 515 GLN cc_start: 0.8007 (mt0) cc_final: 0.7636 (mm-40) REVERT: B 532 ARG cc_start: 0.7928 (mmm160) cc_final: 0.7566 (mmm160) REVERT: B 568 GLU cc_start: 0.7518 (tt0) cc_final: 0.7306 (tp30) REVERT: B 574 LYS cc_start: 0.7545 (OUTLIER) cc_final: 0.7258 (pttp) REVERT: C 39 GLN cc_start: 0.7977 (tt0) cc_final: 0.7373 (tp40) REVERT: C 65 LYS cc_start: 0.7945 (ptmm) cc_final: 0.7700 (pttt) REVERT: C 82 GLN cc_start: 0.6877 (tp40) cc_final: 0.6488 (tp40) REVERT: C 98 THR cc_start: 0.8116 (m) cc_final: 0.7789 (p) outliers start: 28 outliers final: 8 residues processed: 189 average time/residue: 1.4784 time to fit residues: 297.1608 Evaluate side-chains 177 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 162 time to evaluate : 1.057 ------------------------------------------------------------------------------- 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 146 GLN Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 245 ASP 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 179 LEU Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 574 LYS 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 28 optimal weight: 0.8980 chunk 106 optimal weight: 0.0470 chunk 52 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 105 optimal weight: 0.4980 chunk 84 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN B 53 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.138552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.111868 restraints weight = 11968.510| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.82 r_work: 0.3111 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3928 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= 0.118 Angle : 0.518 8.334 14112 Z= 0.261 Chirality : 0.039 0.169 1606 Planarity : 0.003 0.039 1783 Dihedral : 6.488 83.649 1504 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.23), residues: 1275 helix: 1.34 (0.19), residues: 783 sheet: 0.45 (0.47), residues: 114 loop : -0.85 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 36 HIS 0.002 0.001 HIS B 454 PHE 0.024 0.001 PHE A 171 TYR 0.010 0.001 TYR C 94 ARG 0.003 0.000 ARG A 493 Details of bonding type rmsd hydrogen bonds : bond 0.03803 ( 605) hydrogen bonds : angle 3.84965 ( 1770) SS BOND : bond 0.00037 ( 2) SS BOND : angle 0.46029 ( 4) covalent geometry : bond 0.00265 (10398) covalent geometry : angle 0.51760 (14108) *********************** 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 195 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 170 time to evaluate : 1.111 Fit side-chains revert: symmetry clash REVERT: A 19 LEU cc_start: 0.7827 (mt) cc_final: 0.7469 (tt) REVERT: A 20 ARG cc_start: 0.7767 (mtt90) cc_final: 0.7391 (ttp-110) REVERT: A 21 TYR cc_start: 0.8981 (m-80) cc_final: 0.8649 (m-80) REVERT: A 33 LEU cc_start: 0.8407 (mp) cc_final: 0.8140 (mm) REVERT: A 64 ARG cc_start: 0.7396 (OUTLIER) cc_final: 0.6111 (pmt-80) REVERT: A 96 TYR cc_start: 0.8639 (t80) cc_final: 0.8439 (t80) REVERT: A 134 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.7805 (mmm) REVERT: A 146 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7928 (mp-120) REVERT: A 218 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8167 (tt0) REVERT: A 232 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7033 (mp0) REVERT: A 245 ASP cc_start: 0.8358 (OUTLIER) cc_final: 0.7735 (t0) REVERT: A 309 ASP cc_start: 0.8199 (t70) cc_final: 0.7951 (t70) REVERT: A 334 GLU cc_start: 0.8299 (tt0) cc_final: 0.7961 (tm-30) REVERT: A 354 GLU cc_start: 0.8141 (tt0) cc_final: 0.7911 (tm-30) REVERT: A 357 ASP cc_start: 0.8483 (t70) cc_final: 0.8132 (t70) REVERT: A 425 ARG cc_start: 0.8341 (mtt180) cc_final: 0.8043 (mtt90) REVERT: A 431 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7873 (mp0) REVERT: A 537 GLN cc_start: 0.7902 (mm-40) cc_final: 0.7692 (mt0) REVERT: B 63 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8233 (tp) REVERT: B 120 ASN cc_start: 0.8983 (t0) cc_final: 0.8496 (t0) REVERT: B 131 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7989 (mm-30) REVERT: B 173 PHE cc_start: 0.7231 (t80) cc_final: 0.6729 (m-80) REVERT: B 181 ARG cc_start: 0.7952 (mtm110) cc_final: 0.7622 (tpp80) REVERT: B 219 ARG cc_start: 0.8344 (mtp85) cc_final: 0.7949 (tpp80) REVERT: B 255 PHE cc_start: 0.8056 (t80) cc_final: 0.7631 (m-80) REVERT: B 401 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7264 (tm-30) REVERT: B 426 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7957 (mm-30) REVERT: B 510 GLU cc_start: 0.7167 (tt0) cc_final: 0.6402 (pp20) REVERT: B 515 GLN cc_start: 0.8050 (mt0) cc_final: 0.7659 (mm-40) REVERT: B 532 ARG cc_start: 0.7914 (mmm160) cc_final: 0.7559 (mmm160) REVERT: B 570 ASP cc_start: 0.8525 (t0) cc_final: 0.8301 (t0) REVERT: B 574 LYS cc_start: 0.7540 (ttpt) cc_final: 0.7285 (pttp) REVERT: C 39 GLN cc_start: 0.8030 (tt0) cc_final: 0.7421 (tp40) REVERT: C 65 LYS cc_start: 0.7912 (ptmm) cc_final: 0.7620 (pttt) REVERT: C 82 GLN cc_start: 0.6776 (tp40) cc_final: 0.6363 (tp40) REVERT: C 98 THR cc_start: 0.8060 (m) cc_final: 0.7732 (p) outliers start: 25 outliers final: 5 residues processed: 186 average time/residue: 1.4493 time to fit residues: 287.1272 Evaluate side-chains 176 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 162 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 146 GLN 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 511 LEU Chi-restraints excluded: chain A residue 549 SER 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 63 optimal weight: 0.0370 chunk 51 optimal weight: 0.8980 chunk 109 optimal weight: 0.0070 chunk 64 optimal weight: 1.9990 chunk 111 optimal weight: 0.4980 chunk 72 optimal weight: 0.6980 chunk 74 optimal weight: 0.1980 chunk 107 optimal weight: 0.0570 chunk 119 optimal weight: 4.9990 chunk 114 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 overall best weight: 0.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN B 53 GLN B 287 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.143948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.117242 restraints weight = 12037.567| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.84 r_work: 0.3184 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10400 Z= 0.094 Angle : 0.501 8.285 14112 Z= 0.251 Chirality : 0.038 0.166 1606 Planarity : 0.003 0.037 1783 Dihedral : 6.044 79.648 1504 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.91 % Allowed : 18.13 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.23), residues: 1275 helix: 1.66 (0.19), residues: 783 sheet: 0.62 (0.47), residues: 115 loop : -0.67 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP C 36 HIS 0.001 0.000 HIS B 531 PHE 0.011 0.001 PHE A 304 TYR 0.014 0.001 TYR B 164 ARG 0.006 0.000 ARG A 255 Details of bonding type rmsd hydrogen bonds : bond 0.03234 ( 605) hydrogen bonds : angle 3.67574 ( 1770) SS BOND : bond 0.00052 ( 2) SS BOND : angle 0.38466 ( 4) covalent geometry : bond 0.00194 (10398) covalent geometry : angle 0.50089 (14108) *********************** 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 200 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 1.115 Fit side-chains revert: symmetry clash REVERT: A 19 LEU cc_start: 0.7839 (mt) cc_final: 0.7457 (tt) REVERT: A 20 ARG cc_start: 0.7909 (mtt90) cc_final: 0.7570 (ttp-110) REVERT: A 25 TYR cc_start: 0.8699 (m-80) cc_final: 0.8383 (m-80) REVERT: A 134 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7913 (mmm) REVERT: A 146 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7860 (mp-120) REVERT: A 165 LEU cc_start: 0.7808 (tt) cc_final: 0.7599 (pp) REVERT: A 245 ASP cc_start: 0.8244 (OUTLIER) cc_final: 0.7643 (t0) REVERT: A 255 ARG cc_start: 0.8005 (ttm-80) cc_final: 0.7785 (ttp-110) REVERT: A 309 ASP cc_start: 0.8286 (t70) cc_final: 0.8075 (t70) REVERT: A 334 GLU cc_start: 0.8321 (tt0) cc_final: 0.7975 (tm-30) REVERT: A 342 ASP cc_start: 0.7687 (t0) cc_final: 0.7425 (t0) REVERT: A 357 ASP cc_start: 0.8483 (t70) cc_final: 0.8140 (t70) REVERT: A 425 ARG cc_start: 0.8327 (mtt180) cc_final: 0.7896 (mtm110) REVERT: A 431 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7853 (mp0) REVERT: A 537 GLN cc_start: 0.8011 (mm-40) cc_final: 0.7645 (mt0) REVERT: B 63 LEU cc_start: 0.8417 (mp) cc_final: 0.8182 (tp) REVERT: B 119 MET cc_start: 0.8708 (mmm) cc_final: 0.8228 (mmm) REVERT: B 120 ASN cc_start: 0.8929 (t0) cc_final: 0.8520 (t0) REVERT: B 131 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7913 (mm-30) REVERT: B 173 PHE cc_start: 0.7253 (t80) cc_final: 0.6763 (m-80) REVERT: B 181 ARG cc_start: 0.7940 (mtm110) cc_final: 0.7714 (tpp80) REVERT: B 219 ARG cc_start: 0.8336 (mtp85) cc_final: 0.7963 (tpp80) REVERT: B 255 PHE cc_start: 0.8018 (t80) cc_final: 0.7605 (m-80) REVERT: B 401 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7222 (tm-30) REVERT: B 510 GLU cc_start: 0.7147 (tt0) cc_final: 0.6402 (pp20) REVERT: B 515 GLN cc_start: 0.8072 (mt0) cc_final: 0.7750 (mm-40) REVERT: B 532 ARG cc_start: 0.7900 (mmm160) cc_final: 0.7572 (mmm160) REVERT: C 39 GLN cc_start: 0.7965 (tt0) cc_final: 0.7477 (tp-100) REVERT: C 65 LYS cc_start: 0.7815 (ptmm) cc_final: 0.7557 (pttt) REVERT: C 82 GLN cc_start: 0.6797 (tp40) cc_final: 0.6336 (tp40) REVERT: C 98 THR cc_start: 0.8069 (m) cc_final: 0.7791 (p) outliers start: 20 outliers final: 4 residues processed: 191 average time/residue: 1.4086 time to fit residues: 286.7530 Evaluate side-chains 173 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 165 time to evaluate : 1.244 ------------------------------------------------------------------------------- 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 146 GLN Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 588 TYR Chi-restraints excluded: chain B residue 401 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 44 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 53 optimal weight: 0.0870 chunk 42 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 47 optimal weight: 0.4980 chunk 33 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN B 53 GLN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.140476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.113531 restraints weight = 11961.179| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.84 r_work: 0.3142 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10400 Z= 0.122 Angle : 0.544 9.372 14112 Z= 0.267 Chirality : 0.040 0.172 1606 Planarity : 0.004 0.056 1783 Dihedral : 6.292 80.491 1504 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.91 % Allowed : 18.42 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.23), residues: 1275 helix: 1.65 (0.19), residues: 785 sheet: 0.62 (0.47), residues: 115 loop : -0.69 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP C 36 HIS 0.002 0.001 HIS B 454 PHE 0.027 0.001 PHE A 171 TYR 0.014 0.001 TYR B 164 ARG 0.012 0.000 ARG B 218 Details of bonding type rmsd hydrogen bonds : bond 0.03716 ( 605) hydrogen bonds : angle 3.76019 ( 1770) SS BOND : bond 0.00046 ( 2) SS BOND : angle 0.39180 ( 4) covalent geometry : bond 0.00280 (10398) covalent geometry : angle 0.54363 (14108) *********************** 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 190 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 170 time to evaluate : 1.089 Fit side-chains revert: symmetry clash REVERT: A 19 LEU cc_start: 0.7852 (mt) cc_final: 0.7482 (tt) REVERT: A 20 ARG cc_start: 0.7883 (mtt90) cc_final: 0.7538 (ttp-110) REVERT: A 33 LEU cc_start: 0.8437 (mp) cc_final: 0.8176 (mm) REVERT: A 134 MET cc_start: 0.8203 (mmm) cc_final: 0.7856 (mmm) REVERT: A 146 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.7939 (mp-120) REVERT: A 165 LEU cc_start: 0.7904 (tt) cc_final: 0.7698 (pp) REVERT: A 166 LEU cc_start: 0.7530 (tm) cc_final: 0.7235 (tp) REVERT: A 234 GLU cc_start: 0.8103 (tt0) cc_final: 0.7861 (mp0) REVERT: A 245 ASP cc_start: 0.8285 (OUTLIER) cc_final: 0.7711 (t0) REVERT: A 255 ARG cc_start: 0.8060 (ttm-80) cc_final: 0.7838 (ttp-110) REVERT: A 309 ASP cc_start: 0.8257 (t70) cc_final: 0.8036 (t70) REVERT: A 334 GLU cc_start: 0.8271 (tt0) cc_final: 0.7936 (tm-30) REVERT: A 342 ASP cc_start: 0.7651 (t0) cc_final: 0.7386 (t0) REVERT: A 357 ASP cc_start: 0.8484 (t70) cc_final: 0.8145 (t70) REVERT: A 425 ARG cc_start: 0.8367 (mtt180) cc_final: 0.7919 (mtm110) REVERT: A 431 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7910 (mp0) REVERT: A 537 GLN cc_start: 0.8059 (mm-40) cc_final: 0.7681 (mt0) REVERT: B 63 LEU cc_start: 0.8500 (mp) cc_final: 0.8270 (tp) REVERT: B 131 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7903 (mm-30) REVERT: B 173 PHE cc_start: 0.7291 (t80) cc_final: 0.6788 (m-80) REVERT: B 181 ARG cc_start: 0.7950 (mtm110) cc_final: 0.7647 (tpp80) REVERT: B 219 ARG cc_start: 0.8313 (mtp85) cc_final: 0.7902 (tpp80) REVERT: B 255 PHE cc_start: 0.8064 (t80) cc_final: 0.7613 (m-80) REVERT: B 401 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7246 (tm-30) REVERT: B 510 GLU cc_start: 0.7139 (tt0) cc_final: 0.6350 (pp20) REVERT: B 515 GLN cc_start: 0.7960 (mt0) cc_final: 0.7591 (mm-40) REVERT: B 532 ARG cc_start: 0.7911 (mmm160) cc_final: 0.7562 (mmm160) REVERT: C 39 GLN cc_start: 0.7988 (tt0) cc_final: 0.7415 (tp40) REVERT: C 65 LYS cc_start: 0.7840 (ptmm) cc_final: 0.7563 (pttt) REVERT: C 82 GLN cc_start: 0.6728 (tp40) cc_final: 0.6340 (tp-100) REVERT: C 98 THR cc_start: 0.8069 (m) cc_final: 0.7705 (p) outliers start: 20 outliers final: 5 residues processed: 183 average time/residue: 1.4116 time to fit residues: 274.8264 Evaluate side-chains 163 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 155 time to evaluate : 1.079 ------------------------------------------------------------------------------- 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 146 GLN Chi-restraints excluded: chain A residue 245 ASP 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 401 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 0 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 2 optimal weight: 0.0770 chunk 67 optimal weight: 0.3980 chunk 76 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 73 optimal weight: 0.5980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN A 554 HIS B 53 GLN B 120 ASN ** B 280 GLN ** 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 = 0.3610 r_free = 0.3610 target = 0.141314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.114314 restraints weight = 11914.337| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.84 r_work: 0.3142 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.4257 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= 0.115 Angle : 0.538 8.766 14112 Z= 0.266 Chirality : 0.039 0.177 1606 Planarity : 0.003 0.035 1783 Dihedral : 6.305 81.003 1504 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.53 % Allowed : 18.99 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.24), residues: 1275 helix: 1.66 (0.19), residues: 785 sheet: 0.72 (0.48), residues: 115 loop : -0.62 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP C 36 HIS 0.002 0.001 HIS B 454 PHE 0.013 0.001 PHE A 304 TYR 0.014 0.001 TYR B 164 ARG 0.004 0.000 ARG A 255 Details of bonding type rmsd hydrogen bonds : bond 0.03649 ( 605) hydrogen bonds : angle 3.74643 ( 1770) SS BOND : bond 0.00043 ( 2) SS BOND : angle 0.37784 ( 4) covalent geometry : bond 0.00258 (10398) covalent geometry : angle 0.53775 (14108) *********************** 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 180 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 164 time to evaluate : 1.092 Fit side-chains revert: symmetry clash REVERT: A 19 LEU cc_start: 0.7858 (mt) cc_final: 0.7478 (tt) REVERT: A 20 ARG cc_start: 0.7901 (mtt90) cc_final: 0.7562 (ttp-110) REVERT: A 21 TYR cc_start: 0.8936 (m-80) cc_final: 0.8445 (m-80) REVERT: A 33 LEU cc_start: 0.8433 (mp) cc_final: 0.8169 (mm) REVERT: A 134 MET cc_start: 0.8243 (mmm) cc_final: 0.7908 (mmm) REVERT: A 146 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7930 (mp-120) REVERT: A 165 LEU cc_start: 0.7897 (tt) cc_final: 0.7674 (pp) REVERT: A 166 LEU cc_start: 0.7595 (tm) cc_final: 0.7314 (tp) REVERT: A 234 GLU cc_start: 0.8110 (tt0) cc_final: 0.7851 (mp0) REVERT: A 245 ASP cc_start: 0.8276 (OUTLIER) cc_final: 0.7672 (t0) REVERT: A 255 ARG cc_start: 0.8018 (ttm-80) cc_final: 0.7778 (ttp-110) REVERT: A 309 ASP cc_start: 0.8258 (t70) cc_final: 0.8036 (t70) REVERT: A 334 GLU cc_start: 0.8310 (tt0) cc_final: 0.7962 (tm-30) REVERT: A 357 ASP cc_start: 0.8486 (t70) cc_final: 0.8133 (t70) REVERT: A 425 ARG cc_start: 0.8355 (mtt180) cc_final: 0.7910 (mtm110) REVERT: A 431 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7929 (mp0) REVERT: A 537 GLN cc_start: 0.7981 (mm-40) cc_final: 0.7629 (mt0) REVERT: B 63 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8230 (tp) REVERT: B 120 ASN cc_start: 0.8966 (t0) cc_final: 0.8571 (t0) REVERT: B 131 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7945 (mm-30) REVERT: B 173 PHE cc_start: 0.7313 (t80) cc_final: 0.6749 (m-80) REVERT: B 181 ARG cc_start: 0.7902 (mtm110) cc_final: 0.7621 (tpp80) REVERT: B 218 ARG cc_start: 0.8280 (mtp85) cc_final: 0.8042 (mtm-85) REVERT: B 219 ARG cc_start: 0.8346 (mtp85) cc_final: 0.7944 (tpp80) REVERT: B 255 PHE cc_start: 0.7985 (t80) cc_final: 0.7506 (m-80) REVERT: B 349 ASP cc_start: 0.8053 (t70) cc_final: 0.7745 (t0) REVERT: B 401 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7225 (tm-30) REVERT: B 510 GLU cc_start: 0.7141 (tt0) cc_final: 0.6344 (pp20) REVERT: B 515 GLN cc_start: 0.7961 (mt0) cc_final: 0.7582 (mm-40) REVERT: B 532 ARG cc_start: 0.7921 (mmm160) cc_final: 0.7570 (mmm160) REVERT: C 39 GLN cc_start: 0.7967 (tt0) cc_final: 0.7417 (tp40) REVERT: C 65 LYS cc_start: 0.7847 (ptmm) cc_final: 0.7550 (pttm) REVERT: C 82 GLN cc_start: 0.6741 (tp40) cc_final: 0.6348 (tp-100) REVERT: C 98 THR cc_start: 0.8050 (m) cc_final: 0.7696 (p) outliers start: 16 outliers final: 4 residues processed: 175 average time/residue: 1.5383 time to fit residues: 287.8407 Evaluate side-chains 163 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 155 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 146 GLN Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 365 LYS Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 401 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 52 optimal weight: 0.9990 chunk 47 optimal weight: 0.0670 chunk 33 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 114 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN B 53 GLN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.137476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.110547 restraints weight = 12014.332| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.83 r_work: 0.3090 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10400 Z= 0.164 Angle : 0.584 8.719 14112 Z= 0.289 Chirality : 0.041 0.177 1606 Planarity : 0.004 0.034 1783 Dihedral : 6.817 81.924 1504 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.62 % Allowed : 18.70 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.23), residues: 1275 helix: 1.46 (0.19), residues: 787 sheet: 0.56 (0.48), residues: 115 loop : -0.72 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP C 36 HIS 0.003 0.001 HIS B 454 PHE 0.032 0.001 PHE A 171 TYR 0.013 0.001 TYR B 164 ARG 0.003 0.000 ARG A 555 Details of bonding type rmsd hydrogen bonds : bond 0.04228 ( 605) hydrogen bonds : angle 3.93798 ( 1770) SS BOND : bond 0.00026 ( 2) SS BOND : angle 0.47330 ( 4) covalent geometry : bond 0.00385 (10398) covalent geometry : angle 0.58354 (14108) ********************** 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 176 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 159 time to evaluate : 1.592 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.7890 (mt) cc_final: 0.7512 (tt) REVERT: A 20 ARG cc_start: 0.7863 (mtt90) cc_final: 0.7505 (ttp-110) REVERT: A 21 TYR cc_start: 0.8967 (m-80) cc_final: 0.8632 (m-80) REVERT: A 33 LEU cc_start: 0.8477 (mp) cc_final: 0.8224 (mm) REVERT: A 134 MET cc_start: 0.8220 (OUTLIER) cc_final: 0.7863 (mmm) REVERT: A 146 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.7960 (mp-120) REVERT: A 166 LEU cc_start: 0.7567 (tm) cc_final: 0.7301 (tp) REVERT: A 234 GLU cc_start: 0.8158 (tt0) cc_final: 0.7920 (mp0) REVERT: A 245 ASP cc_start: 0.8326 (OUTLIER) cc_final: 0.7741 (t0) REVERT: A 309 ASP cc_start: 0.8249 (t70) cc_final: 0.7997 (t70) REVERT: A 334 GLU cc_start: 0.8367 (tt0) cc_final: 0.7913 (tm-30) REVERT: A 357 ASP cc_start: 0.8530 (t70) cc_final: 0.8195 (t70) REVERT: A 425 ARG cc_start: 0.8384 (mtt180) cc_final: 0.7932 (mtm110) REVERT: A 431 GLU cc_start: 0.8331 (mm-30) cc_final: 0.7992 (mp0) REVERT: A 442 GLU cc_start: 0.7853 (tt0) cc_final: 0.7443 (tm-30) REVERT: A 537 GLN cc_start: 0.8120 (mm-40) cc_final: 0.7726 (mt0) REVERT: B 63 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8324 (tp) REVERT: B 120 ASN cc_start: 0.8978 (t0) cc_final: 0.8531 (t0) REVERT: B 131 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7943 (mm-30) REVERT: B 173 PHE cc_start: 0.7315 (t80) cc_final: 0.6825 (m-80) REVERT: B 181 ARG cc_start: 0.7904 (mtm110) cc_final: 0.7580 (tpp80) REVERT: B 219 ARG cc_start: 0.8304 (mtp85) cc_final: 0.7951 (tpp80) REVERT: B 255 PHE cc_start: 0.8048 (t80) cc_final: 0.7614 (m-80) REVERT: B 349 ASP cc_start: 0.8116 (t70) cc_final: 0.7761 (t0) REVERT: B 401 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7191 (tm-30) REVERT: B 426 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7981 (mm-30) REVERT: B 510 GLU cc_start: 0.7167 (tt0) cc_final: 0.6361 (pp20) REVERT: B 532 ARG cc_start: 0.7943 (mmm160) cc_final: 0.7536 (mmm160) REVERT: C 39 GLN cc_start: 0.7993 (tt0) cc_final: 0.7522 (tp-100) REVERT: C 82 GLN cc_start: 0.6769 (tp40) cc_final: 0.6374 (tp-100) outliers start: 17 outliers final: 5 residues processed: 170 average time/residue: 1.5216 time to fit residues: 274.6487 Evaluate side-chains 167 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 156 time to evaluate : 1.086 ------------------------------------------------------------------------------- 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 146 GLN Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 365 LYS Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 426 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 17 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 104 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3571 r_free = 0.3571 target = 0.138202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.111403 restraints weight = 11965.235| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.82 r_work: 0.3092 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.4269 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= 0.142 Angle : 0.584 8.897 14112 Z= 0.289 Chirality : 0.041 0.177 1606 Planarity : 0.004 0.063 1783 Dihedral : 6.707 82.569 1504 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.72 % Allowed : 19.08 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.23), residues: 1275 helix: 1.49 (0.19), residues: 787 sheet: 0.57 (0.48), residues: 115 loop : -0.69 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP C 36 HIS 0.002 0.001 HIS B 454 PHE 0.030 0.001 PHE A 171 TYR 0.024 0.001 TYR B 164 ARG 0.013 0.000 ARG B 218 Details of bonding type rmsd hydrogen bonds : bond 0.03962 ( 605) hydrogen bonds : angle 3.91976 ( 1770) SS BOND : bond 0.00016 ( 2) SS BOND : angle 0.44394 ( 4) covalent geometry : bond 0.00332 (10398) covalent geometry : angle 0.58374 (14108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9278.01 seconds wall clock time: 162 minutes 44.92 seconds (9764.92 seconds total)