Starting phenix.real_space_refine on Fri Sep 11 16:06:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6rah_4775/09_2026/6rah_4775.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rah_4775/09_2026/6rah_4775.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6rah_4775/09_2026/6rah_4775.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rah_4775/09_2026/6rah_4775.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6rah_4775/09_2026/6rah_4775.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rah_4775/09_2026/6rah_4775.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6rah_4775/09_2026/6rah_4775.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6rah_4775/09_2026/6rah_4775.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 25 5.16 5 C 6549 2.51 5 N 1792 2.21 5 O 1787 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10161 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 586, 4690 Classifications: {'peptide': 586} Link IDs: {'PTRANS': 24, 'TRANS': 561} Chain: "B" Number of atoms: 4506 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 570, 4499 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 18, 'TRANS': 551} Conformer: "B" Number of residues, atoms: 570, 4499 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 18, 'TRANS': 551} bond proxies already assigned to first conformer: 4579 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 2.94, per 1000 atoms: 0.29 Number of scatterers: 10161 At special positions: 0 Unit cell: (103.392, 85.083, 155.088, 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 1787 8.00 N 1792 7.00 C 6549 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=2.07 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.62 Conformation dependent library (CDL) restraints added in 552.0 milliseconds 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2338 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 6 sheets defined 65.2% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 12 through 23 removed outlier: 3.983A pdb=" N TYR A 21 " --> pdb=" O ARG A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 45 Processing helix chain 'A' and resid 45 through 59 Processing helix chain 'A' and resid 65 through 120 Processing helix chain 'A' and resid 121 through 128 removed outlier: 3.804A pdb=" N TYR A 125 " --> pdb=" O HIS A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 138 Processing helix chain 'A' and resid 140 through 151 removed outlier: 4.435A pdb=" N ILE A 144 " --> pdb=" O ASP A 140 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN A 145 " --> pdb=" O VAL A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 173 removed outlier: 3.789A pdb=" N PHE A 171 " --> pdb=" O GLY A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 222 removed outlier: 3.835A pdb=" N VAL A 179 " --> pdb=" O LYS A 175 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL A 183 " --> pdb=" O VAL A 179 " (cutoff:3.500A) Proline residue: A 185 - end of helix removed outlier: 3.521A pdb=" N LEU A 196 " --> pdb=" O THR A 192 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY A 197 " --> pdb=" O TRP A 193 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA A 210 " --> pdb=" O ARG A 206 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 230 removed outlier: 3.663A pdb=" N LEU A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 283 removed outlier: 3.553A pdb=" N ARG A 241 " --> pdb=" O GLU A 237 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU A 242 " --> pdb=" O LYS A 238 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE A 253 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N PHE A 261 " --> pdb=" O PHE A 257 " (cutoff:3.500A) Proline residue: A 262 - end of helix removed outlier: 3.687A pdb=" N ASP A 269 " --> pdb=" O GLY A 265 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY A 281 " --> pdb=" O TYR A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 332 removed outlier: 3.692A pdb=" N ASP A 298 " --> pdb=" O VAL A 294 " (cutoff:3.500A) Proline residue: A 306 - end of helix removed outlier: 3.977A pdb=" N ASP A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG A 326 " --> pdb=" O ALA A 322 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL A 330 " --> pdb=" O ARG A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 407 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: 3.683A 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 474 removed outlier: 3.503A 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 513 Processing helix chain 'A' and resid 529 through 544 Processing helix chain 'A' and resid 578 through 586 Processing helix chain 'A' and resid 586 through 594 removed outlier: 3.724A pdb=" N ALA A 590 " --> pdb=" O GLY A 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 19 Proline residue: B 15 - end of helix Processing helix chain 'B' and resid 20 through 55 Proline residue: B 42 - end of helix Processing helix chain 'B' and resid 57 through 103 Processing helix chain 'B' and resid 106 through 113 removed outlier: 3.567A pdb=" N TYR B 110 " --> pdb=" O ASP B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 133 removed outlier: 3.805A pdb=" N ASP B 125 " --> pdb=" O ARG B 121 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LEU B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 158 Processing helix chain 'B' and resid 158 through 167 removed outlier: 3.528A pdb=" N ALA B 162 " --> pdb=" O ASN B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 207 removed outlier: 3.587A pdb=" N ARG B 177 " --> pdb=" O PHE B 173 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N PHE B 178 " --> pdb=" O LEU B 174 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU B 179 " --> pdb=" O ALA B 175 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU B 182 " --> pdb=" O PHE B 178 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP B 184 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG B 196 " --> pdb=" O GLU B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 214 Processing helix chain 'B' and resid 216 through 264 removed outlier: 3.605A pdb=" N VAL B 241 " --> pdb=" O ALA B 237 " (cutoff:3.500A) Proline residue: B 244 - end of helix removed outlier: 4.333A pdb=" N LEU B 249 " --> pdb=" O LEU B 245 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLY B 250 " --> pdb=" O HIS B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 269 removed outlier: 3.636A pdb=" N VAL B 268 " --> pdb=" O GLY B 264 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL B 269 " --> pdb=" O GLY B 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 264 through 269' Processing helix chain 'B' and resid 274 through 317 removed outlier: 4.554A pdb=" N TRP B 290 " --> pdb=" O ALA B 286 " (cutoff:3.500A) Proline residue: B 291 - end of helix removed outlier: 4.032A pdb=" N GLY B 296 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N TRP B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 383 Processing helix chain 'B' and resid 406 through 413 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 Processing helix chain 'B' and resid 476 through 491 removed outlier: 4.243A pdb=" N LYS B 491 " --> pdb=" O ARG B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 518 Processing helix chain 'B' and resid 532 through 537 Processing helix chain 'B' and resid 555 through 562 Processing helix chain 'B' and resid 564 through 573 removed outlier: 3.511A pdb=" N GLN B 573 " --> pdb=" O MET B 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 30 removed outlier: 3.560A pdb=" N LEU C 29 " --> pdb=" O GLY C 26 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ASP C 30 " --> pdb=" O SER C 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 26 through 30' Processing helix chain 'C' and resid 87 through 91 removed outlier: 4.086A 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 383 removed outlier: 6.347A pdb=" N LEU A 360 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LYS A 377 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL A 358 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL A 379 " --> pdb=" O ARG A 356 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ARG A 356 " --> pdb=" O VAL A 379 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N PHE A 381 " --> pdb=" O GLU A 354 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLU A 354 " --> pdb=" O PHE A 381 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N PHE A 355 " --> pdb=" O PHE A 418 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N PHE A 418 " --> pdb=" O PHE A 355 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ASP A 357 " --> pdb=" O CYS A 416 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N CYS A 416 " --> pdb=" O ASP A 357 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 436 through 439 removed outlier: 6.611A pdb=" N GLY A 437 " --> pdb=" O ILE A 520 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ASP A 522 " --> pdb=" O GLY A 437 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL A 439 " --> pdb=" O ASP A 522 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LYS A 388 " --> pdb=" O ARG A 564 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N LEU A 566 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ALA A 390 " --> pdb=" O LEU A 566 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N PHE A 568 " --> pdb=" O ALA A 390 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL A 392 " --> pdb=" O PHE A 568 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU A 575 " --> pdb=" O VAL A 567 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ARG A 569 " --> pdb=" O LEU A 573 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N LEU A 573 " --> pdb=" O ARG A 569 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 351 through 361 removed outlier: 6.384A pdb=" N LEU B 353 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LYS B 347 " --> pdb=" O LEU B 353 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ARG B 355 " --> pdb=" O GLY B 345 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLY B 345 " --> pdb=" O ARG B 355 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N LEU B 357 " --> pdb=" O GLY B 343 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY B 343 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL B 344 " --> pdb=" O GLU B 392 " (cutoff:3.500A) removed outlier: 6.539A 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: 6.459A pdb=" N THR B 366 " --> pdb=" O TRP B 541 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N ILE B 543 " --> pdb=" O THR B 366 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLY B 368 " --> pdb=" O ILE B 543 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N LEU B 545 " --> pdb=" O GLY B 368 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR B 370 " --> pdb=" O LEU B 545 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU B 552 " --> pdb=" O VAL B 544 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASP B 546 " --> pdb=" O ILE B 550 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ILE B 550 " --> pdb=" O ASP B 546 " (cutoff:3.500A) removed outlier: 4.057A 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: 3.563A pdb=" N THR C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP C 73 " --> pdb=" O THR C 78 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 11 through 12 removed outlier: 5.675A pdb=" N ARG C 38 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N GLY C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) 649 hydrogen bonds defined for protein. 1907 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.69 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1602 1.29 - 1.42: 2713 1.42 - 1.55: 5982 1.55 - 1.68: 29 1.68 - 1.82: 45 Bond restraints: 10371 Sorted by residual: bond pdb=" N HIS B 111 " pdb=" CA BHIS B 111 " ideal model delta sigma weight residual 1.459 1.647 -0.187 1.21e-02 6.83e+03 2.40e+02 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 6.97e+01 bond pdb=" N PRO C 110 " pdb=" CD PRO C 110 " ideal model delta sigma weight residual 1.473 1.358 0.115 1.40e-02 5.10e+03 6.71e+01 bond pdb=" C4 ATP A 701 " pdb=" C5 ATP A 701 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.08e+01 bond pdb=" N PRO C 88 " pdb=" CD PRO C 88 " ideal model delta sigma weight residual 1.473 1.375 0.098 1.40e-02 5.10e+03 4.87e+01 ... (remaining 10366 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.76: 13585 3.76 - 7.52: 417 7.52 - 11.28: 62 11.28 - 15.03: 8 15.03 - 18.79: 3 Bond angle restraints: 14075 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 139.87 121.08 18.79 1.00e+00 1.00e+00 3.53e+02 angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 124.23 15.64 1.00e+00 1.00e+00 2.45e+02 angle pdb=" N ALA C 28 " pdb=" CA ALA C 28 " pdb=" C ALA C 28 " ideal model delta sigma weight residual 113.21 131.11 -17.90 1.15e+00 7.56e-01 2.42e+02 angle pdb=" PA ATP B 601 " pdb=" O3A ATP B 601 " pdb=" PB ATP B 601 " ideal model delta sigma weight residual 136.83 121.95 14.88 1.00e+00 1.00e+00 2.21e+02 angle pdb=" PA ATP A 701 " pdb=" O3A ATP A 701 " pdb=" PB ATP A 701 " ideal model delta sigma weight residual 136.83 123.70 13.13 1.00e+00 1.00e+00 1.73e+02 ... (remaining 14070 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.25: 5849 16.25 - 32.50: 218 32.50 - 48.75: 47 48.75 - 65.00: 11 65.00 - 81.25: 6 Dihedral angle restraints: 6131 sinusoidal: 2477 harmonic: 3654 Sorted by residual: dihedral pdb=" C VAL A 59 " pdb=" N VAL A 59 " pdb=" CA VAL A 59 " pdb=" CB VAL A 59 " ideal model delta harmonic sigma weight residual -122.00 -137.97 15.97 0 2.50e+00 1.60e-01 4.08e+01 dihedral pdb=" N VAL C 99 " pdb=" C VAL C 99 " pdb=" CA VAL C 99 " pdb=" CB VAL C 99 " ideal model delta harmonic sigma weight residual 123.40 109.91 13.49 0 2.50e+00 1.60e-01 2.91e+01 dihedral pdb=" CA GLY A 151 " pdb=" C GLY A 151 " pdb=" N LEU A 152 " pdb=" CA LEU A 152 " ideal model delta harmonic sigma weight residual -180.00 -153.09 -26.91 0 5.00e+00 4.00e-02 2.90e+01 ... (remaining 6128 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1298 0.096 - 0.193: 214 0.193 - 0.289: 62 0.289 - 0.385: 24 0.385 - 0.482: 6 Chirality restraints: 1604 Sorted by residual: chirality pdb=" CA ILE A 54 " pdb=" N ILE A 54 " pdb=" C ILE A 54 " pdb=" CB ILE A 54 " both_signs ideal model delta sigma weight residual False 2.43 2.92 -0.48 2.00e-01 2.50e+01 5.80e+00 chirality pdb=" CA VAL C 99 " pdb=" N VAL C 99 " pdb=" C VAL C 99 " pdb=" CB VAL C 99 " both_signs ideal model delta sigma weight residual False 2.44 2.92 -0.48 2.00e-01 2.50e+01 5.79e+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 ... (remaining 1601 not shown) Planarity restraints: 1778 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 226 " -0.020 2.00e-02 2.50e+03 4.03e-02 1.62e+01 pdb=" C ASP B 226 " 0.070 2.00e-02 2.50e+03 pdb=" O ASP B 226 " -0.027 2.00e-02 2.50e+03 pdb=" N LEU B 227 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 69 " -0.019 2.00e-02 2.50e+03 3.89e-02 1.51e+01 pdb=" C ARG A 69 " 0.067 2.00e-02 2.50e+03 pdb=" O ARG A 69 " -0.026 2.00e-02 2.50e+03 pdb=" N PHE A 70 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 223 " -0.021 2.00e-02 2.50e+03 2.12e-02 1.12e+01 pdb=" CG TRP B 223 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP B 223 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP B 223 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 223 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 223 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 223 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 223 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 223 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP B 223 " -0.000 2.00e-02 2.50e+03 ... (remaining 1775 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 63 2.60 - 3.17: 8040 3.17 - 3.75: 15536 3.75 - 4.32: 22067 4.32 - 4.90: 36913 Nonbonded interactions: 82619 Sorted by model distance: nonbonded pdb="MG MG A 702 " pdb=" O HOH A 802 " model vdw 2.022 2.170 nonbonded pdb=" OG1 THR A 400 " pdb="MG MG A 702 " model vdw 2.047 2.170 nonbonded pdb=" O2B ATP B 601 " pdb="MG MG B 602 " model vdw 2.094 2.170 nonbonded pdb=" O2G ATP A 701 " pdb="MG MG A 702 " model vdw 2.102 2.170 nonbonded pdb=" O2B ATP A 701 " pdb="MG MG A 702 " model vdw 2.110 2.170 ... (remaining 82614 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.220 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.187 10373 Z= 0.568 Angle : 1.575 44.635 14079 Z= 1.096 Chirality : 0.091 0.482 1604 Planarity : 0.007 0.060 1778 Dihedral : 9.898 81.253 3787 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.12 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Cbeta Deviations : 0.77 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.51 (0.20), residues: 1272 helix: -1.58 (0.15), residues: 778 sheet: -0.29 (0.43), residues: 127 loop : -1.92 (0.27), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG B 88 TYR 0.019 0.002 TYR A 299 PHE 0.038 0.003 PHE A 229 TRP 0.055 0.003 TRP B 223 HIS 0.008 0.002 HIS A 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00813 / 0.57 (10371) covalent geometry : angle 1.52933 / 1.08 (14075) SS BOND : bond 0.02729 / 1.30 ( 2) SS BOND : angle 22.38824 / 9.44 ( 4) hydrogen bonds : bond 0.18035 / 12.20 ( 649) hydrogen bonds : angle 6.47260 / 4.65 ( 1907) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7814 (mtm-85) cc_final: 0.7570 (mtm110) REVERT: A 259 LEU cc_start: 0.8379 (tt) cc_final: 0.8174 (tp) REVERT: A 467 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7681 (mt-10) REVERT: A 477 GLU cc_start: 0.7534 (pt0) cc_final: 0.7120 (pt0) REVERT: A 534 LYS cc_start: 0.8332 (tttm) cc_final: 0.8128 (ttmt) REVERT: A 537 GLN cc_start: 0.7706 (mt0) cc_final: 0.7496 (mt0) REVERT: A 558 THR cc_start: 0.8439 (m) cc_final: 0.8143 (m) REVERT: B 50 ASP cc_start: 0.7870 (m-30) cc_final: 0.7661 (m-30) REVERT: B 63 LEU cc_start: 0.8027 (mt) cc_final: 0.7797 (mt) REVERT: B 164 TYR cc_start: 0.7160 (m-10) cc_final: 0.6876 (m-10) REVERT: B 184 ASP cc_start: 0.8204 (t0) cc_final: 0.7986 (t0) REVERT: B 299 MET cc_start: 0.7626 (mtm) cc_final: 0.7249 (mtt) REVERT: B 481 GLN cc_start: 0.8438 (mt0) cc_final: 0.8221 (mt0) REVERT: B 510 GLU cc_start: 0.7519 (tt0) cc_final: 0.7090 (tt0) REVERT: B 568 GLU cc_start: 0.7921 (tp30) cc_final: 0.7559 (tp30) outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.7730 time to fit residues: 205.3976 Evaluate side-chains 178 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 123 optimal weight: 7.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 454 HIS B 524 GLN B 573 GLN C 57 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.143275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.108060 restraints weight = 24682.833| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.71 r_work: 0.3086 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2905 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2905 r_free = 0.2905 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2905 r_free = 0.2905 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (6 function evaluations) r_final: 0.2905 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10373 Z= 0.159 Angle : 0.617 8.196 14079 Z= 0.320 Chirality : 0.041 0.149 1604 Planarity : 0.005 0.036 1778 Dihedral : 5.634 89.558 1439 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.68 % Allowed : 12.24 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.22), residues: 1272 helix: 0.47 (0.18), residues: 792 sheet: 0.11 (0.43), residues: 129 loop : -1.19 (0.30), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 512 TYR 0.014 0.001 TYR A 427 PHE 0.025 0.002 PHE B 36 TRP 0.028 0.002 TRP B 223 HIS 0.005 0.001 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (10371) covalent geometry : angle 0.61709 / 0.32 (14075) SS BOND : bond 0.00077 / 0.04 ( 2) SS BOND : angle 1.00290 / 0.65 ( 4) hydrogen bonds : bond 0.05249 / 3.45 ( 649) hydrogen bonds : angle 4.30799 / 3.20 ( 1907) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 192 time to evaluate : 0.438 Fit side-chains revert: symmetry clash REVERT: A 99 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.8262 (mt0) REVERT: A 183 VAL cc_start: 0.8436 (OUTLIER) cc_final: 0.8195 (p) REVERT: A 334 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7768 (tp30) REVERT: A 354 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8213 (tt0) REVERT: A 477 GLU cc_start: 0.8197 (pt0) cc_final: 0.7743 (pt0) REVERT: A 481 ARG cc_start: 0.8542 (mtt-85) cc_final: 0.8134 (mtt-85) REVERT: A 534 LYS cc_start: 0.8473 (tttm) cc_final: 0.8231 (ttmt) REVERT: B 164 TYR cc_start: 0.7633 (m-10) cc_final: 0.7383 (m-10) REVERT: B 185 ARG cc_start: 0.8514 (ttt-90) cc_final: 0.8289 (mtp85) REVERT: B 189 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8115 (mt-10) REVERT: B 274 SER cc_start: 0.6810 (t) cc_final: 0.6384 (p) REVERT: B 299 MET cc_start: 0.8439 (mtm) cc_final: 0.8006 (mtt) REVERT: B 338 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7617 (mt-10) REVERT: B 532 ARG cc_start: 0.8169 (mtm180) cc_final: 0.7940 (mtm180) REVERT: B 549 ARG cc_start: 0.8494 (pmm-80) cc_final: 0.8105 (ptm-80) REVERT: B 568 GLU cc_start: 0.8243 (tp30) cc_final: 0.8023 (tp30) REVERT: C 80 HIS cc_start: 0.6502 (m-70) cc_final: 0.6247 (m-70) REVERT: C 98 THR cc_start: 0.8069 (p) cc_final: 0.7728 (p) REVERT: C 107 ARG cc_start: 0.8475 (tpp80) cc_final: 0.7479 (tpt90) outliers start: 28 outliers final: 7 residues processed: 204 average time/residue: 0.6913 time to fit residues: 149.7393 Evaluate side-chains 183 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 171 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 365 LYS Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 585 LYS Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 99 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 115 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 104 optimal weight: 0.1980 chunk 71 optimal weight: 1.9990 chunk 84 optimal weight: 0.0980 chunk 34 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 537 GLN B 524 GLN C 57 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.141571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.106683 restraints weight = 16691.342| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.19 r_work: 0.3075 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2959 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2959 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10373 Z= 0.134 Angle : 0.550 8.534 14079 Z= 0.282 Chirality : 0.039 0.141 1604 Planarity : 0.004 0.037 1778 Dihedral : 5.192 88.803 1439 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 2.49 % Allowed : 13.96 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.23), residues: 1272 helix: 1.38 (0.18), residues: 793 sheet: 0.36 (0.44), residues: 129 loop : -0.87 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 512 TYR 0.011 0.001 TYR A 427 PHE 0.022 0.001 PHE B 36 TRP 0.023 0.002 TRP B 223 HIS 0.005 0.001 HIS B 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (10371) covalent geometry : angle 0.54999 / 0.28 (14075) SS BOND : bond 0.00131 / 0.07 ( 2) SS BOND : angle 0.71827 / 0.39 ( 4) hydrogen bonds : bond 0.04625 / 3.06 ( 649) hydrogen bonds : angle 3.94033 / 2.95 ( 1907) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 189 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: A 52 TRP cc_start: 0.5522 (m-10) cc_final: 0.5319 (m-10) REVERT: A 72 LEU cc_start: 0.7610 (mm) cc_final: 0.7371 (mt) REVERT: A 127 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.7306 (mpp-170) REVERT: A 301 ARG cc_start: 0.8050 (mmm-85) cc_final: 0.7816 (mmm-85) REVERT: A 305 GLN cc_start: 0.8200 (mm110) cc_final: 0.7946 (mp10) REVERT: A 356 ARG cc_start: 0.8530 (mtp180) cc_final: 0.6892 (ptt90) REVERT: A 477 GLU cc_start: 0.8159 (pt0) cc_final: 0.7802 (pt0) REVERT: A 481 ARG cc_start: 0.8620 (mtt-85) cc_final: 0.8226 (mtt-85) REVERT: A 534 LYS cc_start: 0.8670 (tttm) cc_final: 0.8418 (ttmt) REVERT: A 585 LYS cc_start: 0.7138 (OUTLIER) cc_final: 0.6563 (ptmm) REVERT: B 164 TYR cc_start: 0.7716 (m-10) cc_final: 0.7459 (m-10) REVERT: B 274 SER cc_start: 0.6714 (t) cc_final: 0.6309 (p) REVERT: B 510 GLU cc_start: 0.7793 (tt0) cc_final: 0.7357 (tt0) REVERT: B 532 ARG cc_start: 0.8420 (mtm180) cc_final: 0.8071 (mtm180) REVERT: B 549 ARG cc_start: 0.8549 (pmm-80) cc_final: 0.8268 (ptm-80) REVERT: B 568 GLU cc_start: 0.8260 (tp30) cc_final: 0.8045 (tp30) REVERT: C 98 THR cc_start: 0.8154 (p) cc_final: 0.7772 (p) REVERT: C 103 LEU cc_start: 0.7888 (mp) cc_final: 0.7681 (mp) REVERT: C 107 ARG cc_start: 0.8340 (tpp80) cc_final: 0.7433 (tpt90) outliers start: 26 outliers final: 9 residues processed: 205 average time/residue: 0.7326 time to fit residues: 159.1145 Evaluate side-chains 176 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 165 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 585 LYS Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain C residue 93 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 40 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 109 optimal weight: 0.0370 chunk 53 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.9060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 537 GLN ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.139339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.104393 restraints weight = 14744.827| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.07 r_work: 0.3065 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2843 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2843 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10373 Z= 0.165 Angle : 0.573 9.499 14079 Z= 0.291 Chirality : 0.041 0.140 1604 Planarity : 0.004 0.046 1778 Dihedral : 5.177 89.140 1439 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 2.96 % Allowed : 14.53 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.23), residues: 1272 helix: 1.50 (0.18), residues: 804 sheet: 0.57 (0.44), residues: 129 loop : -0.80 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 185 TYR 0.016 0.001 TYR A 541 PHE 0.026 0.002 PHE A 49 TRP 0.023 0.002 TRP B 223 HIS 0.005 0.001 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 (10371) covalent geometry : angle 0.57318 / 0.29 (14075) SS BOND : bond 0.00062 / 0.03 ( 2) SS BOND : angle 0.37512 / 0.17 ( 4) hydrogen bonds : bond 0.04908 / 3.24 ( 649) hydrogen bonds : angle 3.96533 / 2.96 ( 1907) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 174 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: A 52 TRP cc_start: 0.5603 (m-10) cc_final: 0.5358 (m-10) REVERT: A 72 LEU cc_start: 0.7739 (mm) cc_final: 0.7391 (OUTLIER) REVERT: A 94 GLU cc_start: 0.8493 (tm-30) cc_final: 0.8282 (tt0) REVERT: A 127 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.7410 (mpp-170) REVERT: A 199 ARG cc_start: 0.8285 (ttp-170) cc_final: 0.7317 (tpp80) REVERT: A 334 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7767 (tp30) REVERT: A 354 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8003 (tt0) REVERT: A 356 ARG cc_start: 0.8641 (mtp180) cc_final: 0.6775 (ptt90) REVERT: A 477 GLU cc_start: 0.8123 (pt0) cc_final: 0.7885 (pt0) REVERT: A 534 LYS cc_start: 0.8450 (tttm) cc_final: 0.8235 (ttmt) REVERT: A 576 GLU cc_start: 0.7860 (tt0) cc_final: 0.7467 (tm-30) REVERT: B 35 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7745 (mp) REVERT: B 164 TYR cc_start: 0.7742 (m-10) cc_final: 0.7487 (m-10) REVERT: B 267 MET cc_start: 0.6814 (mmm) cc_final: 0.6310 (mmm) REVERT: B 274 SER cc_start: 0.6763 (t) cc_final: 0.6334 (p) REVERT: B 319 LYS cc_start: 0.8649 (mtpp) cc_final: 0.8386 (tppt) REVERT: B 549 ARG cc_start: 0.8520 (pmm-80) cc_final: 0.8188 (ptm-80) REVERT: B 568 GLU cc_start: 0.8268 (tp30) cc_final: 0.8032 (tp30) REVERT: C 83 MET cc_start: 0.6603 (mtm) cc_final: 0.6296 (mtm) REVERT: C 107 ARG cc_start: 0.8253 (tpp80) cc_final: 0.7370 (tpt90) outliers start: 31 outliers final: 17 residues processed: 192 average time/residue: 0.7143 time to fit residues: 145.5492 Evaluate side-chains 188 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 168 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 365 LYS Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 585 LYS Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain C residue 93 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 22 optimal weight: 0.5980 chunk 83 optimal weight: 0.0270 chunk 67 optimal weight: 0.9990 chunk 106 optimal weight: 0.5980 chunk 100 optimal weight: 0.9990 chunk 75 optimal weight: 0.0670 chunk 109 optimal weight: 0.4980 chunk 30 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 ASN B 538 HIS C 77 ASN C 80 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.142163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.106830 restraints weight = 15946.518| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.18 r_work: 0.3075 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2924 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2924 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10373 Z= 0.113 Angle : 0.519 8.134 14079 Z= 0.264 Chirality : 0.038 0.139 1604 Planarity : 0.004 0.052 1778 Dihedral : 4.896 87.985 1439 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 2.39 % Allowed : 15.30 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.23), residues: 1272 helix: 1.89 (0.18), residues: 799 sheet: 0.72 (0.44), residues: 129 loop : -0.61 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 185 TYR 0.015 0.001 TYR A 541 PHE 0.025 0.001 PHE B 36 TRP 0.019 0.001 TRP C 36 HIS 0.003 0.001 HIS B 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (10371) covalent geometry : angle 0.51918 / 0.26 (14075) SS BOND : bond 0.00131 / 0.07 ( 2) SS BOND : angle 0.31015 / 0.15 ( 4) hydrogen bonds : bond 0.04173 / 2.76 ( 649) hydrogen bonds : angle 3.77074 / 2.82 ( 1907) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 175 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: A 72 LEU cc_start: 0.7713 (mm) cc_final: 0.7388 (OUTLIER) REVERT: A 94 GLU cc_start: 0.8516 (tm-30) cc_final: 0.8284 (tt0) REVERT: A 127 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.7237 (mpp-170) REVERT: A 199 ARG cc_start: 0.8320 (ttp-170) cc_final: 0.7320 (tpp80) REVERT: A 356 ARG cc_start: 0.8641 (mtp180) cc_final: 0.6843 (ptt90) REVERT: A 371 GLU cc_start: 0.8123 (tp30) cc_final: 0.7853 (tp30) REVERT: A 464 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7747 (mp0) REVERT: A 477 GLU cc_start: 0.8089 (pt0) cc_final: 0.7813 (pt0) REVERT: A 534 LYS cc_start: 0.8435 (tttm) cc_final: 0.8202 (ttmt) REVERT: A 576 GLU cc_start: 0.7801 (tt0) cc_final: 0.7449 (tm-30) REVERT: A 585 LYS cc_start: 0.7159 (OUTLIER) cc_final: 0.6666 (ptmm) REVERT: B 35 ILE cc_start: 0.8008 (OUTLIER) cc_final: 0.7572 (mp) REVERT: B 76 SER cc_start: 0.8361 (t) cc_final: 0.8023 (m) REVERT: B 164 TYR cc_start: 0.7727 (m-10) cc_final: 0.7504 (m-10) REVERT: B 248 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.7084 (tt) REVERT: B 267 MET cc_start: 0.6885 (mmm) cc_final: 0.6458 (mmm) REVERT: B 274 SER cc_start: 0.6652 (t) cc_final: 0.6315 (p) REVERT: B 319 LYS cc_start: 0.8609 (mtpp) cc_final: 0.8245 (tppt) REVERT: B 323 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.6905 (ptp-170) REVERT: B 325 GLU cc_start: 0.7621 (mp0) cc_final: 0.7374 (mp0) REVERT: B 549 ARG cc_start: 0.8559 (pmm-80) cc_final: 0.8157 (ptm-80) REVERT: C 83 MET cc_start: 0.6552 (mtm) cc_final: 0.6289 (mtm) REVERT: C 107 ARG cc_start: 0.8169 (tpp80) cc_final: 0.7300 (tpt90) outliers start: 25 outliers final: 10 residues processed: 191 average time/residue: 0.7194 time to fit residues: 145.7307 Evaluate side-chains 176 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 161 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 585 LYS Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain C residue 93 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 27 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 24 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 191 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.140038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.104074 restraints weight = 19566.771| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.42 r_work: 0.3048 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2880 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2880 r_free = 0.2880 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2880 r_free = 0.2880 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2880 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10373 Z= 0.137 Angle : 0.542 7.426 14079 Z= 0.274 Chirality : 0.039 0.138 1604 Planarity : 0.004 0.053 1778 Dihedral : 4.909 88.857 1439 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 2.77 % Allowed : 15.49 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.23), residues: 1272 helix: 1.93 (0.18), residues: 799 sheet: 0.83 (0.44), residues: 129 loop : -0.55 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 185 TYR 0.014 0.001 TYR A 541 PHE 0.024 0.001 PHE B 36 TRP 0.019 0.001 TRP B 223 HIS 0.004 0.001 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (10371) covalent geometry : angle 0.54251 / 0.27 (14075) SS BOND : bond 0.00192 / 0.09 ( 2) SS BOND : angle 0.42289 / 0.34 ( 4) hydrogen bonds : bond 0.04478 / 2.96 ( 649) hydrogen bonds : angle 3.80339 / 2.85 ( 1907) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: A 72 LEU cc_start: 0.7753 (mm) cc_final: 0.7410 (OUTLIER) REVERT: A 94 GLU cc_start: 0.8565 (tm-30) cc_final: 0.8316 (tt0) REVERT: A 127 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.7308 (mpp-170) REVERT: A 199 ARG cc_start: 0.8396 (ttp-170) cc_final: 0.7345 (tpp80) REVERT: A 354 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7839 (tp30) REVERT: A 356 ARG cc_start: 0.8679 (mtp180) cc_final: 0.6800 (ptt90) REVERT: A 371 GLU cc_start: 0.8128 (tp30) cc_final: 0.7889 (tp30) REVERT: A 464 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7760 (mp0) REVERT: A 477 GLU cc_start: 0.8145 (pt0) cc_final: 0.7935 (pt0) REVERT: A 525 THR cc_start: 0.8804 (p) cc_final: 0.8447 (p) REVERT: A 533 GLU cc_start: 0.8178 (tt0) cc_final: 0.7893 (tt0) REVERT: A 534 LYS cc_start: 0.8499 (tttm) cc_final: 0.8246 (ttmt) REVERT: A 537 GLN cc_start: 0.8203 (mt0) cc_final: 0.8002 (mt0) REVERT: A 576 GLU cc_start: 0.7892 (tt0) cc_final: 0.7578 (tm-30) REVERT: A 585 LYS cc_start: 0.7397 (OUTLIER) cc_final: 0.6912 (ptmm) REVERT: B 35 ILE cc_start: 0.7912 (OUTLIER) cc_final: 0.7437 (mp) REVERT: B 164 TYR cc_start: 0.7779 (m-10) cc_final: 0.7517 (m-10) REVERT: B 181 ARG cc_start: 0.8033 (ptp90) cc_final: 0.7740 (mtm-85) REVERT: B 248 LEU cc_start: 0.7322 (OUTLIER) cc_final: 0.7093 (tt) REVERT: B 274 SER cc_start: 0.6620 (t) cc_final: 0.6282 (p) REVERT: B 319 LYS cc_start: 0.8648 (mtpp) cc_final: 0.8350 (tppt) REVERT: B 481 GLN cc_start: 0.9095 (mt0) cc_final: 0.8751 (mt0) REVERT: B 549 ARG cc_start: 0.8606 (pmm-80) cc_final: 0.8165 (ptm-80) REVERT: C 65 LYS cc_start: 0.8737 (ttpp) cc_final: 0.8427 (ttpt) REVERT: C 83 MET cc_start: 0.6554 (mtm) cc_final: 0.6224 (mtm) REVERT: C 107 ARG cc_start: 0.8267 (tpp80) cc_final: 0.7421 (tpt90) outliers start: 29 outliers final: 14 residues processed: 191 average time/residue: 0.7356 time to fit residues: 148.8716 Evaluate side-chains 181 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 162 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 585 LYS Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 93 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 20 optimal weight: 1.9990 chunk 90 optimal weight: 0.0670 chunk 1 optimal weight: 1.9990 chunk 39 optimal weight: 0.3980 chunk 48 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.139932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.106357 restraints weight = 19509.706| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.27 r_work: 0.3057 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2878 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2878 r_free = 0.2878 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2878 r_free = 0.2878 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2878 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10373 Z= 0.132 Angle : 0.551 11.841 14079 Z= 0.278 Chirality : 0.039 0.139 1604 Planarity : 0.004 0.060 1778 Dihedral : 4.875 88.742 1439 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 2.58 % Allowed : 16.06 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.23), residues: 1272 helix: 2.00 (0.18), residues: 801 sheet: 0.89 (0.44), residues: 129 loop : -0.49 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 560 TYR 0.013 0.001 TYR A 541 PHE 0.024 0.001 PHE B 36 TRP 0.020 0.001 TRP C 36 HIS 0.004 0.001 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (10371) covalent geometry : angle 0.55117 / 0.28 (14075) SS BOND : bond 0.00087 / 0.04 ( 2) SS BOND : angle 0.83645 / 0.83 ( 4) hydrogen bonds : bond 0.04446 / 2.95 ( 649) hydrogen bonds : angle 3.77869 / 2.82 ( 1907) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 170 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: A 72 LEU cc_start: 0.7806 (mm) cc_final: 0.7463 (OUTLIER) REVERT: A 94 GLU cc_start: 0.8565 (tm-30) cc_final: 0.8312 (tt0) REVERT: A 127 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.7310 (mpp-170) REVERT: A 199 ARG cc_start: 0.8395 (ttp-170) cc_final: 0.7311 (tpp80) REVERT: A 354 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8072 (tt0) REVERT: A 356 ARG cc_start: 0.8635 (mtp180) cc_final: 0.6832 (ptt90) REVERT: A 371 GLU cc_start: 0.8129 (tp30) cc_final: 0.7887 (tp30) REVERT: A 525 THR cc_start: 0.8822 (p) cc_final: 0.8501 (p) REVERT: A 534 LYS cc_start: 0.8451 (tttm) cc_final: 0.8217 (ttmt) REVERT: A 585 LYS cc_start: 0.7308 (OUTLIER) cc_final: 0.6803 (ptmm) REVERT: B 164 TYR cc_start: 0.7791 (m-10) cc_final: 0.7519 (m-10) REVERT: B 177 ARG cc_start: 0.7908 (mmm160) cc_final: 0.7557 (mmm-85) REVERT: B 181 ARG cc_start: 0.8031 (ptp90) cc_final: 0.7738 (mtm-85) REVERT: B 253 MET cc_start: 0.6470 (ttm) cc_final: 0.6172 (ppp) REVERT: B 267 MET cc_start: 0.6823 (mmm) cc_final: 0.6155 (mmm) REVERT: B 319 LYS cc_start: 0.8623 (mtpp) cc_final: 0.8334 (tppt) REVERT: B 549 ARG cc_start: 0.8590 (pmm-80) cc_final: 0.8206 (ptm-80) REVERT: C 65 LYS cc_start: 0.8739 (ttpp) cc_final: 0.8440 (ttpt) REVERT: C 83 MET cc_start: 0.6579 (mtm) cc_final: 0.6269 (mtm) REVERT: C 107 ARG cc_start: 0.8115 (tpp80) cc_final: 0.7298 (tpt90) outliers start: 27 outliers final: 14 residues processed: 187 average time/residue: 0.7752 time to fit residues: 153.2946 Evaluate side-chains 179 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 163 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 585 LYS Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 93 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 15 optimal weight: 2.9990 chunk 115 optimal weight: 0.0770 chunk 99 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 80 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 537 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.139572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.105169 restraints weight = 14312.937| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.03 r_work: 0.3053 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2905 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2905 r_free = 0.2905 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2905 r_free = 0.2905 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2905 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10373 Z= 0.133 Angle : 0.561 11.065 14079 Z= 0.281 Chirality : 0.039 0.138 1604 Planarity : 0.004 0.058 1778 Dihedral : 4.853 88.650 1439 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.10 % Allowed : 16.63 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.23), residues: 1272 helix: 2.02 (0.18), residues: 805 sheet: 0.91 (0.44), residues: 129 loop : -0.50 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 547 TYR 0.013 0.001 TYR A 125 PHE 0.024 0.001 PHE B 36 TRP 0.018 0.001 TRP B 223 HIS 0.004 0.001 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (10371) covalent geometry : angle 0.56134 / 0.28 (14075) SS BOND : bond 0.00105 / 0.06 ( 2) SS BOND : angle 0.72012 / 0.72 ( 4) hydrogen bonds : bond 0.04444 / 2.94 ( 649) hydrogen bonds : angle 3.76754 / 2.82 ( 1907) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 170 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 84 ARG cc_start: 0.8010 (mmm160) cc_final: 0.7706 (mmm160) REVERT: A 94 GLU cc_start: 0.8495 (tm-30) cc_final: 0.8261 (tt0) REVERT: A 127 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.7313 (mpp-170) REVERT: A 199 ARG cc_start: 0.8251 (ttp-170) cc_final: 0.7236 (tpp80) REVERT: A 356 ARG cc_start: 0.8612 (mtp180) cc_final: 0.6821 (ptt90) REVERT: A 371 GLU cc_start: 0.8129 (tp30) cc_final: 0.7884 (tp30) REVERT: A 464 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7771 (mp0) REVERT: A 477 GLU cc_start: 0.8086 (pt0) cc_final: 0.7833 (pt0) REVERT: A 481 ARG cc_start: 0.8418 (mtt-85) cc_final: 0.8205 (mtt-85) REVERT: A 525 THR cc_start: 0.8830 (p) cc_final: 0.8521 (p) REVERT: A 534 LYS cc_start: 0.8486 (tttm) cc_final: 0.8235 (ttmt) REVERT: A 538 GLU cc_start: 0.7930 (pt0) cc_final: 0.7704 (pt0) REVERT: A 585 LYS cc_start: 0.7483 (OUTLIER) cc_final: 0.7009 (ptmm) REVERT: B 11 ARG cc_start: 0.8219 (ptp-170) cc_final: 0.7891 (ptp-110) REVERT: B 164 TYR cc_start: 0.7803 (m-10) cc_final: 0.7497 (m-10) REVERT: B 177 ARG cc_start: 0.7902 (mmm160) cc_final: 0.7545 (mmm-85) REVERT: B 181 ARG cc_start: 0.8017 (ptp90) cc_final: 0.7741 (mtm-85) REVERT: B 253 MET cc_start: 0.6474 (ttm) cc_final: 0.6170 (ppp) REVERT: B 267 MET cc_start: 0.6870 (mmm) cc_final: 0.6141 (mmm) REVERT: B 319 LYS cc_start: 0.8603 (mtpp) cc_final: 0.8238 (mmtm) REVERT: B 481 GLN cc_start: 0.9077 (mt0) cc_final: 0.8726 (mt0) REVERT: B 549 ARG cc_start: 0.8548 (pmm-80) cc_final: 0.8189 (ptm-80) REVERT: C 65 LYS cc_start: 0.8745 (ttpp) cc_final: 0.8451 (ttpt) REVERT: C 83 MET cc_start: 0.6580 (mtm) cc_final: 0.6262 (mtm) REVERT: C 107 ARG cc_start: 0.8160 (tpp80) cc_final: 0.7361 (tpt90) outliers start: 22 outliers final: 17 residues processed: 186 average time/residue: 0.7264 time to fit residues: 143.1111 Evaluate side-chains 187 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 167 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 585 LYS Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 93 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 112 optimal weight: 0.9980 chunk 73 optimal weight: 0.1980 chunk 0 optimal weight: 3.9990 chunk 27 optimal weight: 0.1980 chunk 97 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 103 optimal weight: 0.5980 chunk 96 optimal weight: 0.7980 chunk 120 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 537 GLN C 57 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.140911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.105486 restraints weight = 19488.738| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.39 r_work: 0.3045 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2889 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2889 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10373 Z= 0.118 Angle : 0.550 10.867 14079 Z= 0.275 Chirality : 0.038 0.138 1604 Planarity : 0.004 0.060 1778 Dihedral : 4.741 87.249 1439 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 2.10 % Allowed : 17.40 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.24), residues: 1272 helix: 2.13 (0.18), residues: 802 sheet: 1.05 (0.46), residues: 124 loop : -0.30 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 547 TYR 0.012 0.001 TYR A 125 PHE 0.026 0.001 PHE B 36 TRP 0.017 0.001 TRP B 223 HIS 0.003 0.001 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (10371) covalent geometry : angle 0.55005 / 0.28 (14075) SS BOND : bond 0.00061 / 0.03 ( 2) SS BOND : angle 0.53099 / 0.53 ( 4) hydrogen bonds : bond 0.04178 / 2.77 ( 649) hydrogen bonds : angle 3.68531 / 2.75 ( 1907) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 174 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: A 72 LEU cc_start: 0.7688 (mm) cc_final: 0.7426 (OUTLIER) REVERT: A 84 ARG cc_start: 0.8018 (mmm160) cc_final: 0.7727 (mmm160) REVERT: A 94 GLU cc_start: 0.8512 (tm-30) cc_final: 0.8264 (tt0) REVERT: A 127 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.7301 (mpp-170) REVERT: A 199 ARG cc_start: 0.8304 (ttp-170) cc_final: 0.7315 (tpp80) REVERT: A 277 TYR cc_start: 0.7729 (t80) cc_final: 0.7334 (t80) REVERT: A 356 ARG cc_start: 0.8663 (mtp180) cc_final: 0.6872 (ptt90) REVERT: A 371 GLU cc_start: 0.8178 (tp30) cc_final: 0.7932 (tp30) REVERT: A 387 GLU cc_start: 0.8691 (tt0) cc_final: 0.8311 (tt0) REVERT: A 464 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7843 (mp0) REVERT: A 525 THR cc_start: 0.8853 (p) cc_final: 0.8524 (p) REVERT: A 534 LYS cc_start: 0.8491 (tttm) cc_final: 0.8258 (ttmt) REVERT: A 576 GLU cc_start: 0.7782 (tt0) cc_final: 0.7526 (tm-30) REVERT: A 585 LYS cc_start: 0.7397 (OUTLIER) cc_final: 0.6777 (ptmm) REVERT: B 11 ARG cc_start: 0.8186 (ptp-170) cc_final: 0.7876 (ptp-110) REVERT: B 35 ILE cc_start: 0.7819 (OUTLIER) cc_final: 0.7327 (mp) REVERT: B 164 TYR cc_start: 0.7823 (m-10) cc_final: 0.7561 (m-10) REVERT: B 177 ARG cc_start: 0.7874 (mmm160) cc_final: 0.7585 (mmm-85) REVERT: B 248 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.7174 (tt) REVERT: B 253 MET cc_start: 0.6611 (ttm) cc_final: 0.6363 (ppp) REVERT: B 267 MET cc_start: 0.6918 (mmm) cc_final: 0.6212 (mmm) REVERT: B 319 LYS cc_start: 0.8583 (mtpp) cc_final: 0.8305 (tppt) REVERT: B 549 ARG cc_start: 0.8543 (pmm-80) cc_final: 0.8186 (ptm-80) REVERT: C 65 LYS cc_start: 0.8753 (ttpp) cc_final: 0.8482 (ttpt) REVERT: C 83 MET cc_start: 0.6570 (mtm) cc_final: 0.6276 (mtm) REVERT: C 107 ARG cc_start: 0.8134 (tpp80) cc_final: 0.7346 (tpt90) outliers start: 22 outliers final: 14 residues processed: 187 average time/residue: 0.7752 time to fit residues: 153.1271 Evaluate side-chains 189 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 171 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 585 LYS Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 93 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 6 optimal weight: 4.9990 chunk 123 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 40 optimal weight: 0.0980 chunk 30 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 71 optimal weight: 0.3980 chunk 41 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 537 GLN C 57 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.140429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.106088 restraints weight = 14613.554| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.05 r_work: 0.3093 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2953 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2953 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10373 Z= 0.126 Angle : 0.575 10.685 14079 Z= 0.285 Chirality : 0.039 0.138 1604 Planarity : 0.004 0.060 1778 Dihedral : 4.759 87.593 1439 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.82 % Allowed : 18.16 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.24), residues: 1272 helix: 2.11 (0.18), residues: 802 sheet: 1.05 (0.46), residues: 124 loop : -0.27 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 547 TYR 0.014 0.001 TYR A 125 PHE 0.026 0.001 PHE B 36 TRP 0.017 0.001 TRP B 223 HIS 0.004 0.001 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (10371) covalent geometry : angle 0.57368 / 0.28 (14075) SS BOND : bond 0.00073 / 0.04 ( 2) SS BOND : angle 2.36793 / 1.38 ( 4) hydrogen bonds : bond 0.04268 / 2.83 ( 649) hydrogen bonds : angle 3.68741 / 2.75 ( 1907) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 176 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: A 72 LEU cc_start: 0.7658 (mm) cc_final: 0.7390 (OUTLIER) REVERT: A 84 ARG cc_start: 0.8012 (mmm160) cc_final: 0.7714 (mmm160) REVERT: A 94 GLU cc_start: 0.8444 (tm-30) cc_final: 0.8202 (tt0) REVERT: A 127 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.7314 (mpp-170) REVERT: A 199 ARG cc_start: 0.8221 (ttp-170) cc_final: 0.7254 (tpp80) REVERT: A 277 TYR cc_start: 0.7723 (t80) cc_final: 0.7321 (t80) REVERT: A 356 ARG cc_start: 0.8624 (mtp180) cc_final: 0.6872 (ptt90) REVERT: A 371 GLU cc_start: 0.8126 (tp30) cc_final: 0.7885 (tp30) REVERT: A 387 GLU cc_start: 0.8656 (tt0) cc_final: 0.8255 (tt0) REVERT: A 464 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7789 (mp0) REVERT: A 525 THR cc_start: 0.8828 (p) cc_final: 0.8525 (p) REVERT: A 534 LYS cc_start: 0.8494 (tttm) cc_final: 0.8202 (tttp) REVERT: A 537 GLN cc_start: 0.8116 (mt0) cc_final: 0.7871 (mt0) REVERT: A 560 ARG cc_start: 0.6227 (mmm160) cc_final: 0.5766 (mtm-85) REVERT: A 576 GLU cc_start: 0.7760 (tt0) cc_final: 0.7496 (tm-30) REVERT: A 585 LYS cc_start: 0.7411 (OUTLIER) cc_final: 0.6789 (ptmm) REVERT: B 11 ARG cc_start: 0.8185 (ptp-170) cc_final: 0.7871 (ptp-110) REVERT: B 35 ILE cc_start: 0.7874 (OUTLIER) cc_final: 0.7372 (mp) REVERT: B 164 TYR cc_start: 0.7812 (m-10) cc_final: 0.7546 (m-10) REVERT: B 177 ARG cc_start: 0.7835 (mmm160) cc_final: 0.7540 (mmm-85) REVERT: B 248 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.7196 (tt) REVERT: B 253 MET cc_start: 0.6898 (ttm) cc_final: 0.6552 (ppp) REVERT: B 267 MET cc_start: 0.6855 (mmm) cc_final: 0.6176 (mmm) REVERT: B 319 LYS cc_start: 0.8577 (mtpp) cc_final: 0.8307 (tppt) REVERT: B 549 ARG cc_start: 0.8505 (pmm-80) cc_final: 0.8172 (ptm-80) REVERT: C 65 LYS cc_start: 0.8755 (ttpp) cc_final: 0.8483 (ttpt) REVERT: C 83 MET cc_start: 0.6535 (mtm) cc_final: 0.6243 (mtm) REVERT: C 107 ARG cc_start: 0.8133 (tpp80) cc_final: 0.7334 (tpt90) outliers start: 19 outliers final: 13 residues processed: 187 average time/residue: 0.7596 time to fit residues: 150.3373 Evaluate side-chains 189 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 172 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 585 LYS Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 323 ARG Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 93 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 32 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 75 optimal weight: 0.1980 chunk 81 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 1 optimal weight: 0.4980 chunk 79 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 57 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.139835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.105601 restraints weight = 14347.796| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.03 r_work: 0.3074 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2900 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2900 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 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 0.038 10373 Z= 0.130 Angle : 0.565 10.516 14079 Z= 0.281 Chirality : 0.039 0.138 1604 Planarity : 0.004 0.058 1778 Dihedral : 4.802 88.020 1439 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.01 % Allowed : 17.88 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.24), residues: 1272 helix: 2.10 (0.18), residues: 802 sheet: 1.10 (0.46), residues: 124 loop : -0.28 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 547 TYR 0.014 0.001 TYR A 125 PHE 0.027 0.001 PHE B 36 TRP 0.017 0.001 TRP B 223 HIS 0.004 0.001 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (10371) covalent geometry : angle 0.56364 / 0.28 (14075) SS BOND : bond 0.00028 / 0.01 ( 2) SS BOND : angle 2.02412 / 1.21 ( 4) hydrogen bonds : bond 0.04332 / 2.87 ( 649) hydrogen bonds : angle 3.70797 / 2.77 ( 1907) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5121.71 seconds wall clock time: 87 minutes 31.09 seconds (5251.09 seconds total)