Starting phenix.real_space_refine on Wed Sep 17 19:17:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c7t_45292/09_2025/9c7t_45292.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c7t_45292/09_2025/9c7t_45292.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9c7t_45292/09_2025/9c7t_45292.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c7t_45292/09_2025/9c7t_45292.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9c7t_45292/09_2025/9c7t_45292.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c7t_45292/09_2025/9c7t_45292.map" } resolution = 2.7 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= 0.015 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 Fe 1 7.16 5 Zn 1 6.06 5 S 60 5.16 5 C 6744 2.51 5 N 1823 2.21 5 O 2030 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10659 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4527 Classifications: {'peptide': 581} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 554} Chain: "B" Number of atoms: 3530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3530 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 415} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2498 Classifications: {'peptide': 308} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 294} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Planarities with less than four sites: {'MLL%COO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 102 Classifications: {'peptide': 13} Link IDs: {'PTRANS': 2, 'TRANS': 10} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 1, 'FE2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.30, per 1000 atoms: 0.22 Number of scatterers: 10659 At special positions: 0 Unit cell: (102.93, 102.93, 118.26, 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) Zn 1 29.99 Fe 1 26.01 S 60 16.00 O 2030 8.00 N 1823 7.00 C 6744 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.81 Conformation dependent library (CDL) restraints added in 400.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 402 " pdb="ZN ZN C 402 " - pdb=" NE2 HIS C 59 " 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2558 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 12 sheets defined 51.6% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 10 through 20 removed outlier: 3.619A pdb=" N LEU A 20 " --> pdb=" O LEU A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 33 Processing helix chain 'A' and resid 34 through 43 Processing helix chain 'A' and resid 44 through 50 Processing helix chain 'A' and resid 50 through 57 removed outlier: 4.495A pdb=" N ASP A 57 " --> pdb=" O PRO A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 74 removed outlier: 3.655A pdb=" N GLY A 74 " --> pdb=" O ALA A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 88 removed outlier: 3.534A pdb=" N VAL A 86 " --> pdb=" O PRO A 83 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N HIS A 87 " --> pdb=" O GLU A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 97 removed outlier: 3.518A pdb=" N LEU A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 96 " --> pdb=" O PRO A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 117 removed outlier: 3.887A pdb=" N HIS A 117 " --> pdb=" O ARG A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 127 Processing helix chain 'A' and resid 127 through 137 Processing helix chain 'A' and resid 140 through 148 removed outlier: 3.510A pdb=" N CYS A 148 " --> pdb=" O ARG A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 155 removed outlier: 3.940A pdb=" N CYS A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 175 Processing helix chain 'A' and resid 178 through 194 removed outlier: 3.536A pdb=" N ARG A 182 " --> pdb=" O THR A 178 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLY A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N GLU A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 204 Processing helix chain 'A' and resid 204 through 214 Processing helix chain 'A' and resid 217 through 222 Processing helix chain 'A' and resid 223 through 233 removed outlier: 3.758A pdb=" N ALA A 227 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 241 removed outlier: 3.554A pdb=" N LEU A 240 " --> pdb=" O PRO A 236 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLU A 241 " --> pdb=" O GLN A 237 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 236 through 241' Processing helix chain 'A' and resid 244 through 253 Processing helix chain 'A' and resid 256 through 266 Processing helix chain 'A' and resid 266 through 275 Processing helix chain 'A' and resid 275 through 282 Processing helix chain 'A' and resid 282 through 292 Processing helix chain 'A' and resid 295 through 305 removed outlier: 3.618A pdb=" N LYS A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 312 Processing helix chain 'A' and resid 317 through 325 Processing helix chain 'A' and resid 326 through 335 removed outlier: 3.911A pdb=" N SER A 335 " --> pdb=" O LYS A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 350 removed outlier: 3.694A pdb=" N VAL A 348 " --> pdb=" O ALA A 344 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N MET A 350 " --> pdb=" O ALA A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 357 Processing helix chain 'A' and resid 357 through 364 Processing helix chain 'A' and resid 364 through 374 removed outlier: 4.038A pdb=" N LEU A 368 " --> pdb=" O HIS A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 387 removed outlier: 3.641A pdb=" N ASN A 387 " --> pdb=" O ASN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 393 removed outlier: 3.608A pdb=" N GLU A 393 " --> pdb=" O ASP A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 413 removed outlier: 4.001A pdb=" N LEU A 400 " --> pdb=" O GLY A 396 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N GLN A 402 " --> pdb=" O ARG A 398 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N SER A 403 " --> pdb=" O GLN A 399 " (cutoff:3.500A) Proline residue: A 406 - end of helix Processing helix chain 'A' and resid 416 through 426 removed outlier: 3.638A pdb=" N TYR A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 435 Processing helix chain 'A' and resid 435 through 442 Processing helix chain 'A' and resid 443 through 451 removed outlier: 3.763A pdb=" N LEU A 451 " --> pdb=" O CYS A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 482 removed outlier: 6.890A pdb=" N LYS A 475 " --> pdb=" O GLU A 471 " (cutoff:3.500A) removed outlier: 9.088A pdb=" N GLU A 476 " --> pdb=" O LYS A 472 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N TRP A 477 " --> pdb=" O PHE A 473 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA A 478 " --> pdb=" O GLY A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 488 removed outlier: 3.519A pdb=" N ALA A 488 " --> pdb=" O PRO A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 492 Processing helix chain 'A' and resid 494 through 513 removed outlier: 4.190A pdb=" N GLU A 510 " --> pdb=" O ASN A 506 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL A 511 " --> pdb=" O VAL A 507 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLY A 513 " --> pdb=" O SER A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 520 Processing helix chain 'A' and resid 521 through 528 Processing helix chain 'A' and resid 529 through 531 No H-bonds generated for 'chain 'A' and resid 529 through 531' Processing helix chain 'A' and resid 533 through 548 Processing helix chain 'A' and resid 552 through 559 Processing helix chain 'A' and resid 559 through 568 Processing helix chain 'A' and resid 572 through 587 Processing helix chain 'B' and resid 221 through 225 Processing helix chain 'B' and resid 326 through 330 removed outlier: 3.572A pdb=" N LEU B 329 " --> pdb=" O HIS B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 339 Processing helix chain 'B' and resid 340 through 344 removed outlier: 3.722A pdb=" N PHE B 343 " --> pdb=" O ASP B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 386 removed outlier: 3.656A pdb=" N ASN B 385 " --> pdb=" O SER B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 413 No H-bonds generated for 'chain 'B' and resid 411 through 413' Processing helix chain 'C' and resid 3 through 19 removed outlier: 3.898A pdb=" N GLU C 19 " --> pdb=" O GLU C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 40 Processing helix chain 'C' and resid 61 through 73 Processing helix chain 'C' and resid 92 through 107 Processing helix chain 'C' and resid 120 through 127 Processing helix chain 'C' and resid 128 through 138 Processing helix chain 'C' and resid 140 through 151 removed outlier: 3.738A pdb=" N ASP C 151 " --> pdb=" O THR C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 182 Processing helix chain 'C' and resid 193 through 201 removed outlier: 3.735A pdb=" N LEU C 199 " --> pdb=" O MET C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 233 Processing helix chain 'C' and resid 264 through 268 Processing sheet with id=AA1, first strand: chain 'B' and resid 390 through 391 removed outlier: 4.119A pdb=" N THR B 390 " --> pdb=" O PHE B 14 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE B 441 " --> pdb=" O SER B 15 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N VAL B 17 " --> pdb=" O LEU B 439 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU B 439 " --> pdb=" O VAL B 17 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N HIS B 421 " --> pdb=" O ALA B 434 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 31 through 36 removed outlier: 4.370A pdb=" N ARG B 51 " --> pdb=" O ASP B 47 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL B 52 " --> pdb=" O THR B 76 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N THR B 76 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE B 54 " --> pdb=" O TYR B 74 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AA4, first strand: chain 'B' and resid 98 through 101 removed outlier: 6.792A pdb=" N ILE B 119 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ILE B 171 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU B 121 " --> pdb=" O ARG B 169 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N LYS B 129 " --> pdb=" O ASP B 161 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ASP B 161 " --> pdb=" O LYS B 129 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 180 through 185 removed outlier: 6.589A pdb=" N ALA B 195 " --> pdb=" O ASN B 181 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ILE B 183 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU B 193 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N ILE B 185 " --> pdb=" O THR B 191 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N THR B 191 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ARG B 199 " --> pdb=" O ASP B 196 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE B 200 " --> pdb=" O ILE B 214 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N HIS B 204 " --> pdb=" O ARG B 210 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ARG B 210 " --> pdb=" O HIS B 204 " (cutoff:3.500A) removed outlier: 9.001A pdb=" N HIS C 299 " --> pdb=" O ILE B 207 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N ASP B 209 " --> pdb=" O HIS C 299 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N THR C 301 " --> pdb=" O ASP B 209 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N SER B 211 " --> pdb=" O THR C 301 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.697A pdb=" N ALA B 231 " --> pdb=" O SER B 245 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 290 through 293 removed outlier: 3.519A pdb=" N ASP B 290 " --> pdb=" O ARG B 303 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 348 through 350 removed outlier: 3.596A pdb=" N ARG B 375 " --> pdb=" O ASP B 370 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 397 through 398 Processing sheet with id=AB1, first strand: chain 'C' and resid 45 through 48 removed outlier: 6.083A pdb=" N PHE C 164 " --> pdb=" O SER C 238 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL C 237 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ILE C 259 " --> pdb=" O VAL C 237 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ARG C 239 " --> pdb=" O ILE C 259 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 111 through 113 Processing sheet with id=AB3, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.934A pdb=" N ASP C 202 " --> pdb=" O PHE C 220 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 492 hydrogen bonds defined for protein. 1413 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: 1.85 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3535 1.34 - 1.46: 1760 1.46 - 1.57: 5490 1.57 - 1.69: 0 1.69 - 1.81: 87 Bond restraints: 10872 Sorted by residual: bond pdb=" C MLL C 309 " pdb=" OXT MLL C 309 " ideal model delta sigma weight residual 1.231 1.363 -0.132 2.00e-02 2.50e+03 4.32e+01 bond pdb=" C LEU A 522 " pdb=" N PRO A 523 " ideal model delta sigma weight residual 1.335 1.351 -0.017 1.28e-02 6.10e+03 1.68e+00 bond pdb=" C LEU A 327 " pdb=" N PRO A 328 " ideal model delta sigma weight residual 1.335 1.350 -0.015 1.28e-02 6.10e+03 1.46e+00 bond pdb=" CB ILE B 431 " pdb=" CG2 ILE B 431 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.19e+00 bond pdb=" CG PRO C 51 " pdb=" CD PRO C 51 " ideal model delta sigma weight residual 1.512 1.484 0.028 2.70e-02 1.37e+03 1.06e+00 ... (remaining 10867 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 14428 1.50 - 2.99: 245 2.99 - 4.49: 43 4.49 - 5.99: 15 5.99 - 7.48: 6 Bond angle restraints: 14737 Sorted by residual: angle pdb=" N HIS C 241 " pdb=" CA HIS C 241 " pdb=" CB HIS C 241 " ideal model delta sigma weight residual 114.27 109.44 4.83 1.64e+00 3.72e-01 8.67e+00 angle pdb=" N GLU C 15 " pdb=" CA GLU C 15 " pdb=" CB GLU C 15 " ideal model delta sigma weight residual 110.12 114.15 -4.03 1.47e+00 4.63e-01 7.51e+00 angle pdb=" C PRO B 146 " pdb=" N THR B 147 " pdb=" CA THR B 147 " ideal model delta sigma weight residual 121.54 126.74 -5.20 1.91e+00 2.74e-01 7.40e+00 angle pdb=" CA MLL C 309 " pdb=" C MLL C 309 " pdb=" OXT MLL C 309 " ideal model delta sigma weight residual 121.00 113.52 7.48 3.00e+00 1.11e-01 6.22e+00 angle pdb=" C ARG A 537 " pdb=" N PHE A 538 " pdb=" CA PHE A 538 " ideal model delta sigma weight residual 120.72 116.64 4.08 1.67e+00 3.59e-01 5.97e+00 ... (remaining 14732 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 6130 17.90 - 35.79: 414 35.79 - 53.69: 51 53.69 - 71.58: 12 71.58 - 89.48: 7 Dihedral angle restraints: 6614 sinusoidal: 2685 harmonic: 3929 Sorted by residual: dihedral pdb=" CA THR B 114 " pdb=" C THR B 114 " pdb=" N ASN B 115 " pdb=" CA ASN B 115 " ideal model delta harmonic sigma weight residual 180.00 162.72 17.28 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA GLU C 297 " pdb=" C GLU C 297 " pdb=" N PRO C 298 " pdb=" CA PRO C 298 " ideal model delta harmonic sigma weight residual 180.00 163.51 16.49 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CB GLU B 316 " pdb=" CG GLU B 316 " pdb=" CD GLU B 316 " pdb=" OE1 GLU B 316 " ideal model delta sinusoidal sigma weight residual 0.00 89.48 -89.48 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 6611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 952 0.029 - 0.059: 459 0.059 - 0.088: 155 0.088 - 0.117: 79 0.117 - 0.147: 19 Chirality restraints: 1664 Sorted by residual: chirality pdb=" CA ILE B 99 " pdb=" N ILE B 99 " pdb=" C ILE B 99 " pdb=" CB ILE B 99 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.37e-01 chirality pdb=" CA PHE A 538 " pdb=" N PHE A 538 " pdb=" C PHE A 538 " pdb=" CB PHE A 538 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.88e-01 chirality pdb=" CA TRP B 424 " pdb=" N TRP B 424 " pdb=" C TRP B 424 " pdb=" CB TRP B 424 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.74e-01 ... (remaining 1661 not shown) Planarity restraints: 1906 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 424 " -0.016 2.00e-02 2.50e+03 2.68e-02 1.79e+01 pdb=" CG TRP B 424 " 0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP B 424 " -0.048 2.00e-02 2.50e+03 pdb=" CD2 TRP B 424 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 424 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP B 424 " 0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP B 424 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 424 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 424 " -0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP B 424 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 522 " 0.028 5.00e-02 4.00e+02 4.22e-02 2.85e+00 pdb=" N PRO A 523 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 523 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 523 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 297 " 0.026 5.00e-02 4.00e+02 3.98e-02 2.53e+00 pdb=" N PRO C 298 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO C 298 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 298 " 0.022 5.00e-02 4.00e+02 ... (remaining 1903 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.12: 6 2.12 - 2.81: 3027 2.81 - 3.51: 14586 3.51 - 4.20: 25897 4.20 - 4.90: 46719 Nonbonded interactions: 90235 Sorted by model distance: nonbonded pdb=" OXT MLL C 309 " pdb=" C10 MLL C 309 " model vdw 1.425 3.460 nonbonded pdb=" OD2 ASP C 85 " pdb="ZN ZN C 402 " model vdw 1.988 2.230 nonbonded pdb=" OD2 ASP C 85 " pdb="FE FE2 C 401 " model vdw 2.002 3.000 nonbonded pdb=" ND1 HIS C 241 " pdb="FE FE2 C 401 " model vdw 2.047 3.080 nonbonded pdb=" NE2 HIS C 167 " pdb="FE FE2 C 401 " model vdw 2.062 3.080 ... (remaining 90230 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.730 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 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 : 0.005 0.277 10873 Z= 0.193 Angle : 0.536 7.482 14737 Z= 0.288 Chirality : 0.042 0.147 1664 Planarity : 0.004 0.042 1906 Dihedral : 12.309 89.477 4056 Min Nonbonded Distance : 1.425 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.65 % Favored : 97.27 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: 0.68 (0.24), residues: 1320 helix: 1.08 (0.23), residues: 609 sheet: 0.24 (0.37), residues: 212 loop : -0.09 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 158 TYR 0.026 0.001 TYR A 495 PHE 0.023 0.002 PHE A 538 TRP 0.065 0.002 TRP B 424 HIS 0.004 0.001 HIS B 38 Details of bonding type rmsd covalent geometry : bond 0.00396 (10872) covalent geometry : angle 0.53591 (14737) hydrogen bonds : bond 0.16228 ( 492) hydrogen bonds : angle 5.77644 ( 1413) metal coordination : bond 0.27670 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: C 144 LYS cc_start: 0.8444 (tppt) cc_final: 0.8216 (tppt) REVERT: C 179 HIS cc_start: 0.8910 (m170) cc_final: 0.8602 (m90) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.6749 time to fit residues: 61.5274 Evaluate side-chains 56 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.0570 chunk 124 optimal weight: 0.0010 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 overall best weight: 1.0108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN ** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 385 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.105221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.070247 restraints weight = 17372.727| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.55 r_work: 0.2886 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.0909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 10873 Z= 0.150 Angle : 0.527 7.892 14737 Z= 0.275 Chirality : 0.042 0.139 1664 Planarity : 0.004 0.047 1906 Dihedral : 4.190 22.931 1449 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.50 % Favored : 97.42 % Rotamer: Outliers : 1.01 % Allowed : 4.54 % Favored : 94.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: 0.89 (0.24), residues: 1320 helix: 1.26 (0.22), residues: 615 sheet: 0.38 (0.37), residues: 208 loop : -0.02 (0.29), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 537 TYR 0.011 0.001 TYR B 244 PHE 0.028 0.002 PHE A 538 TRP 0.023 0.002 TRP B 424 HIS 0.003 0.001 HIS B 38 Details of bonding type rmsd covalent geometry : bond 0.00355 (10872) covalent geometry : angle 0.52710 (14737) hydrogen bonds : bond 0.04361 ( 492) hydrogen bonds : angle 4.62619 ( 1413) metal coordination : bond 0.01370 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.451 Fit side-chains revert: symmetry clash REVERT: B 445 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8235 (mmmt) REVERT: C 179 HIS cc_start: 0.9191 (m170) cc_final: 0.8553 (m90) outliers start: 12 outliers final: 5 residues processed: 71 average time/residue: 0.7096 time to fit residues: 54.0170 Evaluate side-chains 61 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 272 LYS Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 445 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 4 optimal weight: 0.1980 chunk 101 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 chunk 119 optimal weight: 7.9990 chunk 66 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN B 326 HIS B 385 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.105075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.070194 restraints weight = 17414.488| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.55 r_work: 0.2886 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10873 Z= 0.139 Angle : 0.505 8.477 14737 Z= 0.264 Chirality : 0.041 0.144 1664 Planarity : 0.004 0.046 1906 Dihedral : 4.127 19.900 1449 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.12 % Favored : 97.80 % Rotamer: Outliers : 1.01 % Allowed : 6.06 % Favored : 92.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: 0.92 (0.24), residues: 1320 helix: 1.31 (0.22), residues: 615 sheet: 0.27 (0.37), residues: 218 loop : 0.02 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 537 TYR 0.012 0.001 TYR B 244 PHE 0.025 0.002 PHE A 538 TRP 0.012 0.001 TRP B 350 HIS 0.003 0.001 HIS B 38 Details of bonding type rmsd covalent geometry : bond 0.00329 (10872) covalent geometry : angle 0.50538 (14737) hydrogen bonds : bond 0.03997 ( 492) hydrogen bonds : angle 4.45882 ( 1413) metal coordination : bond 0.00614 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: A 23 GLU cc_start: 0.8592 (mp0) cc_final: 0.8330 (mp0) REVERT: B 59 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7246 (mp-120) REVERT: B 385 ASN cc_start: 0.7381 (t0) cc_final: 0.7179 (t160) REVERT: B 445 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8208 (mmmt) REVERT: C 179 HIS cc_start: 0.9179 (m170) cc_final: 0.8587 (m90) outliers start: 12 outliers final: 4 residues processed: 70 average time/residue: 0.7175 time to fit residues: 53.8948 Evaluate side-chains 63 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 445 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 85 optimal weight: 0.4980 chunk 79 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.104439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.069428 restraints weight = 17464.538| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 2.54 r_work: 0.2870 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10873 Z= 0.163 Angle : 0.513 9.041 14737 Z= 0.268 Chirality : 0.042 0.152 1664 Planarity : 0.004 0.046 1906 Dihedral : 4.162 18.349 1449 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.12 % Favored : 97.80 % Rotamer: Outliers : 1.18 % Allowed : 6.56 % Favored : 92.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: 0.87 (0.24), residues: 1320 helix: 1.28 (0.22), residues: 614 sheet: 0.21 (0.36), residues: 218 loop : -0.00 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 158 TYR 0.012 0.001 TYR B 244 PHE 0.025 0.002 PHE A 538 TRP 0.012 0.001 TRP B 350 HIS 0.007 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00393 (10872) covalent geometry : angle 0.51313 (14737) hydrogen bonds : bond 0.03999 ( 492) hydrogen bonds : angle 4.44651 ( 1413) metal coordination : bond 0.00553 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: A 23 GLU cc_start: 0.8635 (mp0) cc_final: 0.8375 (mp0) REVERT: B 59 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.6951 (mp10) REVERT: B 385 ASN cc_start: 0.7424 (t0) cc_final: 0.7220 (t160) REVERT: B 409 SER cc_start: 0.8932 (t) cc_final: 0.8710 (p) REVERT: B 445 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8212 (mmmt) REVERT: C 179 HIS cc_start: 0.9160 (m170) cc_final: 0.8563 (m90) outliers start: 14 outliers final: 6 residues processed: 75 average time/residue: 0.6378 time to fit residues: 51.5698 Evaluate side-chains 67 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 445 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 56 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 119 optimal weight: 8.9990 chunk 80 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 63 optimal weight: 0.0980 chunk 92 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 116 optimal weight: 0.2980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.104255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.069260 restraints weight = 17526.477| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.52 r_work: 0.2864 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10873 Z= 0.168 Angle : 0.516 9.327 14737 Z= 0.269 Chirality : 0.042 0.152 1664 Planarity : 0.004 0.045 1906 Dihedral : 4.191 17.477 1449 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.20 % Favored : 97.73 % Rotamer: Outliers : 1.01 % Allowed : 8.33 % Favored : 90.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: 0.83 (0.24), residues: 1320 helix: 1.29 (0.22), residues: 613 sheet: 0.17 (0.36), residues: 218 loop : -0.08 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 303 TYR 0.012 0.001 TYR B 244 PHE 0.025 0.002 PHE A 538 TRP 0.013 0.001 TRP B 350 HIS 0.006 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00406 (10872) covalent geometry : angle 0.51563 (14737) hydrogen bonds : bond 0.03997 ( 492) hydrogen bonds : angle 4.42827 ( 1413) metal coordination : bond 0.00546 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.425 Fit side-chains revert: symmetry clash REVERT: A 23 GLU cc_start: 0.8640 (mp0) cc_final: 0.8404 (mp0) REVERT: B 59 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7119 (mp-120) REVERT: B 385 ASN cc_start: 0.7500 (t0) cc_final: 0.7299 (t160) REVERT: B 389 ARG cc_start: 0.8561 (mtm-85) cc_final: 0.7775 (mtp180) REVERT: B 409 SER cc_start: 0.8959 (t) cc_final: 0.8740 (p) REVERT: C 179 HIS cc_start: 0.9146 (m170) cc_final: 0.8568 (m90) outliers start: 12 outliers final: 8 residues processed: 72 average time/residue: 0.5996 time to fit residues: 46.7632 Evaluate side-chains 67 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 390 CYS Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain C residue 134 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 38 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 chunk 123 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 130 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN C 230 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.104294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.069346 restraints weight = 17588.692| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.52 r_work: 0.2867 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10873 Z= 0.152 Angle : 0.509 10.491 14737 Z= 0.265 Chirality : 0.042 0.148 1664 Planarity : 0.004 0.045 1906 Dihedral : 4.160 17.149 1449 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.20 % Favored : 97.73 % Rotamer: Outliers : 1.01 % Allowed : 8.92 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: 0.84 (0.24), residues: 1320 helix: 1.29 (0.22), residues: 615 sheet: 0.18 (0.36), residues: 218 loop : -0.06 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 527 TYR 0.012 0.001 TYR B 244 PHE 0.024 0.001 PHE A 538 TRP 0.013 0.001 TRP B 350 HIS 0.009 0.001 HIS C 230 Details of bonding type rmsd covalent geometry : bond 0.00368 (10872) covalent geometry : angle 0.50919 (14737) hydrogen bonds : bond 0.03840 ( 492) hydrogen bonds : angle 4.36321 ( 1413) metal coordination : bond 0.00480 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.457 Fit side-chains revert: symmetry clash REVERT: A 23 GLU cc_start: 0.8686 (mp0) cc_final: 0.8460 (mp0) REVERT: B 385 ASN cc_start: 0.7568 (t0) cc_final: 0.7357 (t160) REVERT: B 389 ARG cc_start: 0.8573 (mtm-85) cc_final: 0.7801 (mtp180) REVERT: B 409 SER cc_start: 0.8961 (t) cc_final: 0.8759 (p) outliers start: 12 outliers final: 8 residues processed: 69 average time/residue: 0.5958 time to fit residues: 44.4693 Evaluate side-chains 63 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 390 CYS Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain C residue 134 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 94 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 119 optimal weight: 0.3980 chunk 117 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN C 230 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.105370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.070481 restraints weight = 17599.956| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.52 r_work: 0.2888 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10873 Z= 0.118 Angle : 0.493 10.857 14737 Z= 0.255 Chirality : 0.041 0.139 1664 Planarity : 0.004 0.043 1906 Dihedral : 4.058 17.045 1449 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.12 % Favored : 97.80 % Rotamer: Outliers : 0.93 % Allowed : 9.34 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: 0.91 (0.24), residues: 1320 helix: 1.36 (0.22), residues: 615 sheet: 0.17 (0.36), residues: 220 loop : -0.02 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 527 TYR 0.012 0.001 TYR B 244 PHE 0.022 0.001 PHE A 538 TRP 0.031 0.002 TRP C 209 HIS 0.010 0.001 HIS C 230 Details of bonding type rmsd covalent geometry : bond 0.00277 (10872) covalent geometry : angle 0.49331 (14737) hydrogen bonds : bond 0.03477 ( 492) hydrogen bonds : angle 4.25256 ( 1413) metal coordination : bond 0.00304 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.586 Fit side-chains REVERT: A 23 GLU cc_start: 0.8652 (mp0) cc_final: 0.8424 (mp0) REVERT: B 158 ARG cc_start: 0.8976 (mmt-90) cc_final: 0.8572 (mmt-90) REVERT: B 385 ASN cc_start: 0.7650 (t0) cc_final: 0.7417 (t160) REVERT: B 389 ARG cc_start: 0.8576 (mtm-85) cc_final: 0.7810 (mtp180) REVERT: C 179 HIS cc_start: 0.9151 (m170) cc_final: 0.8603 (m90) outliers start: 11 outliers final: 5 residues processed: 66 average time/residue: 0.6471 time to fit residues: 46.0458 Evaluate side-chains 64 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain C residue 134 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 28 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 40 optimal weight: 0.0470 chunk 116 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 121 optimal weight: 0.9980 overall best weight: 0.7878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN C 230 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.105344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.070438 restraints weight = 17559.862| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.52 r_work: 0.2887 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10873 Z= 0.124 Angle : 0.500 11.329 14737 Z= 0.259 Chirality : 0.041 0.148 1664 Planarity : 0.004 0.044 1906 Dihedral : 4.040 16.950 1449 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.97 % Favored : 97.95 % Rotamer: Outliers : 1.01 % Allowed : 10.01 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: 0.93 (0.24), residues: 1320 helix: 1.37 (0.22), residues: 615 sheet: 0.21 (0.36), residues: 220 loop : -0.04 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 527 TYR 0.012 0.001 TYR B 244 PHE 0.022 0.001 PHE A 538 TRP 0.018 0.001 TRP C 209 HIS 0.013 0.001 HIS C 230 Details of bonding type rmsd covalent geometry : bond 0.00293 (10872) covalent geometry : angle 0.50019 (14737) hydrogen bonds : bond 0.03460 ( 492) hydrogen bonds : angle 4.22314 ( 1413) metal coordination : bond 0.00315 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.457 Fit side-chains REVERT: A 23 GLU cc_start: 0.8646 (mp0) cc_final: 0.8426 (mp0) REVERT: B 158 ARG cc_start: 0.9003 (OUTLIER) cc_final: 0.8641 (mmt-90) REVERT: B 224 GLU cc_start: 0.9004 (mt-10) cc_final: 0.8712 (mt-10) REVERT: B 385 ASN cc_start: 0.7625 (t0) cc_final: 0.7421 (t160) REVERT: B 389 ARG cc_start: 0.8572 (mtm-85) cc_final: 0.7811 (mtp180) REVERT: C 179 HIS cc_start: 0.9161 (m170) cc_final: 0.8638 (m90) outliers start: 12 outliers final: 9 residues processed: 67 average time/residue: 0.6698 time to fit residues: 48.3741 Evaluate side-chains 69 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 390 CYS Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 230 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 41 optimal weight: 0.6980 chunk 121 optimal weight: 6.9990 chunk 46 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 126 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN C 230 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.105195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.070292 restraints weight = 17578.725| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.52 r_work: 0.2883 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10873 Z= 0.131 Angle : 0.503 11.626 14737 Z= 0.260 Chirality : 0.041 0.154 1664 Planarity : 0.004 0.043 1906 Dihedral : 4.042 16.845 1449 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.18 % Allowed : 9.92 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: 0.91 (0.24), residues: 1320 helix: 1.38 (0.22), residues: 615 sheet: 0.20 (0.36), residues: 220 loop : -0.06 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 527 TYR 0.012 0.001 TYR B 244 PHE 0.022 0.001 PHE A 538 TRP 0.016 0.001 TRP C 209 HIS 0.015 0.001 HIS C 230 Details of bonding type rmsd covalent geometry : bond 0.00312 (10872) covalent geometry : angle 0.50311 (14737) hydrogen bonds : bond 0.03496 ( 492) hydrogen bonds : angle 4.21815 ( 1413) metal coordination : bond 0.00332 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.453 Fit side-chains revert: symmetry clash REVERT: A 23 GLU cc_start: 0.8643 (mp0) cc_final: 0.8430 (mp0) REVERT: B 224 GLU cc_start: 0.9013 (mt-10) cc_final: 0.8722 (mt-10) REVERT: B 385 ASN cc_start: 0.7625 (t0) cc_final: 0.7409 (t160) REVERT: B 389 ARG cc_start: 0.8574 (mtm-85) cc_final: 0.7817 (mtp180) REVERT: C 179 HIS cc_start: 0.9162 (m170) cc_final: 0.8640 (m90) outliers start: 14 outliers final: 8 residues processed: 68 average time/residue: 0.6622 time to fit residues: 48.6155 Evaluate side-chains 66 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 390 CYS Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain C residue 134 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 44 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN C 230 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.104589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.069683 restraints weight = 17518.297| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.51 r_work: 0.2873 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10873 Z= 0.151 Angle : 0.516 11.789 14737 Z= 0.267 Chirality : 0.042 0.158 1664 Planarity : 0.004 0.045 1906 Dihedral : 4.088 16.571 1449 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.93 % Allowed : 10.01 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: 0.88 (0.24), residues: 1320 helix: 1.34 (0.22), residues: 615 sheet: 0.22 (0.36), residues: 213 loop : -0.08 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 527 TYR 0.012 0.001 TYR B 244 PHE 0.023 0.001 PHE A 538 TRP 0.016 0.002 TRP C 209 HIS 0.013 0.001 HIS C 230 Details of bonding type rmsd covalent geometry : bond 0.00364 (10872) covalent geometry : angle 0.51589 (14737) hydrogen bonds : bond 0.03674 ( 492) hydrogen bonds : angle 4.26333 ( 1413) metal coordination : bond 0.00379 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.491 Fit side-chains revert: symmetry clash REVERT: A 23 GLU cc_start: 0.8677 (mp0) cc_final: 0.8467 (mp0) REVERT: B 224 GLU cc_start: 0.9005 (mt-10) cc_final: 0.8697 (mt-10) REVERT: B 385 ASN cc_start: 0.7660 (t0) cc_final: 0.7426 (t160) REVERT: B 389 ARG cc_start: 0.8576 (mtm-85) cc_final: 0.7827 (mtp180) REVERT: C 179 HIS cc_start: 0.9169 (m170) cc_final: 0.8630 (m90) outliers start: 11 outliers final: 10 residues processed: 66 average time/residue: 0.6799 time to fit residues: 48.4721 Evaluate side-chains 69 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 390 CYS Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 230 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 119 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 105 optimal weight: 0.0040 chunk 104 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN C 230 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.105354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.070487 restraints weight = 17597.901| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.53 r_work: 0.2888 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10873 Z= 0.116 Angle : 0.500 11.831 14737 Z= 0.258 Chirality : 0.041 0.150 1664 Planarity : 0.004 0.045 1906 Dihedral : 4.039 16.921 1449 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.93 % Allowed : 10.09 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 aren not related in a simple way. whole: 0.91 (0.24), residues: 1320 helix: 1.39 (0.22), residues: 615 sheet: 0.11 (0.36), residues: 222 loop : -0.03 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 527 TYR 0.012 0.001 TYR B 244 PHE 0.021 0.001 PHE A 538 TRP 0.014 0.001 TRP C 209 HIS 0.007 0.001 HIS C 230 Details of bonding type rmsd covalent geometry : bond 0.00271 (10872) covalent geometry : angle 0.49991 (14737) hydrogen bonds : bond 0.03423 ( 492) hydrogen bonds : angle 4.20775 ( 1413) metal coordination : bond 0.00260 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3944.49 seconds wall clock time: 68 minutes 2.42 seconds (4082.42 seconds total)