Starting phenix.real_space_refine on Mon Jun 9 14:49:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c7t_45292/06_2025/9c7t_45292.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c7t_45292/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9c7t_45292/06_2025/9c7t_45292.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c7t_45292/06_2025/9c7t_45292.map" model { file = "/net/cci-nas-00/data/ceres_data/9c7t_45292/06_2025/9c7t_45292.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c7t_45292/06_2025/9c7t_45292.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 7.64, per 1000 atoms: 0.72 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: 2.63 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.58 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: 3.66 Time building geometry restraints manager: 2.97 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: 4.660 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: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 30.920 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.410 ------------------------------------------------------------------------------- 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 : 4.01 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (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 TRP 0.065 0.002 TRP B 424 HIS 0.004 0.001 HIS B 38 PHE 0.023 0.002 PHE A 538 TYR 0.026 0.001 TYR A 495 ARG 0.004 0.000 ARG B 158 Details of bonding type rmsd hydrogen bonds : bond 0.16228 ( 492) hydrogen bonds : angle 5.77644 ( 1413) metal coordination : bond 0.27670 ( 1) covalent geometry : bond 0.00396 (10872) covalent geometry : angle 0.53591 (14737) *********************** 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 : 1.387 Fit side-chains revert: symmetry clash REVERT: C 144 LYS cc_start: 0.8444 (tppt) cc_final: 0.8226 (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: 1.5856 time to fit residues: 146.1296 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 : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 119 optimal weight: 10.0000 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 = 0.3594 r_free = 0.3594 target = 0.104806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.069865 restraints weight = 17252.298| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.53 r_work: 0.2878 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.0859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 10873 Z= 0.163 Angle : 0.533 7.677 14737 Z= 0.279 Chirality : 0.042 0.142 1664 Planarity : 0.004 0.045 1906 Dihedral : 4.209 23.225 1449 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.58 % Favored : 97.35 % Rotamer: Outliers : 1.01 % Allowed : 4.46 % Favored : 94.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.24), residues: 1320 helix: 1.25 (0.22), residues: 615 sheet: 0.36 (0.37), residues: 208 loop : -0.03 (0.29), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 424 HIS 0.004 0.001 HIS C 230 PHE 0.028 0.002 PHE A 538 TYR 0.012 0.001 TYR B 244 ARG 0.003 0.000 ARG A 537 Details of bonding type rmsd hydrogen bonds : bond 0.04639 ( 492) hydrogen bonds : angle 4.68220 ( 1413) metal coordination : bond 0.00476 ( 1) covalent geometry : bond 0.00386 (10872) covalent geometry : angle 0.53305 (14737) *********************** 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 76 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 1.458 Fit side-chains revert: symmetry clash REVERT: B 445 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8199 (mmmt) REVERT: C 179 HIS cc_start: 0.9190 (m170) cc_final: 0.8555 (m90) outliers start: 12 outliers final: 5 residues processed: 70 average time/residue: 2.3709 time to fit residues: 180.0623 Evaluate side-chains 62 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 1.227 ------------------------------------------------------------------------------- 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 14 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 63 optimal weight: 0.2980 chunk 2 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3606 r_free = 0.3606 target = 0.105622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.070780 restraints weight = 17507.135| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.55 r_work: 0.2896 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10873 Z= 0.119 Angle : 0.496 8.702 14737 Z= 0.259 Chirality : 0.041 0.138 1664 Planarity : 0.004 0.045 1906 Dihedral : 4.086 20.358 1449 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.20 % Favored : 97.73 % Rotamer: Outliers : 1.01 % Allowed : 5.80 % Favored : 93.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.24), residues: 1320 helix: 1.34 (0.22), residues: 614 sheet: 0.28 (0.37), residues: 218 loop : 0.02 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 311 HIS 0.003 0.001 HIS C 230 PHE 0.024 0.001 PHE A 538 TYR 0.012 0.001 TYR B 244 ARG 0.002 0.000 ARG A 527 Details of bonding type rmsd hydrogen bonds : bond 0.03853 ( 492) hydrogen bonds : angle 4.43554 ( 1413) metal coordination : bond 0.00546 ( 1) covalent geometry : bond 0.00276 (10872) covalent geometry : angle 0.49607 (14737) *********************** 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 77 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 1.252 Fit side-chains revert: symmetry clash REVERT: A 23 GLU cc_start: 0.8584 (mp0) cc_final: 0.8314 (mp0) REVERT: B 59 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7248 (mp-120) REVERT: B 385 ASN cc_start: 0.7384 (t0) cc_final: 0.7182 (t160) REVERT: B 445 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8215 (mmmt) REVERT: C 179 HIS cc_start: 0.9181 (m170) cc_final: 0.8575 (m90) outliers start: 12 outliers final: 3 residues processed: 71 average time/residue: 1.4475 time to fit residues: 111.1567 Evaluate side-chains 62 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 5 optimal weight: 0.0870 chunk 58 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 119 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- 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 = 0.3648 r_free = 0.3648 target = 0.106880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.072862 restraints weight = 17284.992| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.48 r_work: 0.2907 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10873 Z= 0.114 Angle : 0.487 8.823 14737 Z= 0.253 Chirality : 0.040 0.140 1664 Planarity : 0.004 0.044 1906 Dihedral : 4.013 18.613 1449 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.12 % Favored : 97.80 % Rotamer: Outliers : 1.01 % Allowed : 6.64 % Favored : 92.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.24), residues: 1320 helix: 1.38 (0.22), residues: 615 sheet: 0.25 (0.36), residues: 218 loop : 0.03 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 311 HIS 0.004 0.001 HIS B 326 PHE 0.023 0.001 PHE A 538 TYR 0.011 0.001 TYR B 244 ARG 0.002 0.000 ARG B 158 Details of bonding type rmsd hydrogen bonds : bond 0.03554 ( 492) hydrogen bonds : angle 4.31806 ( 1413) metal coordination : bond 0.00349 ( 1) covalent geometry : bond 0.00267 (10872) covalent geometry : angle 0.48709 (14737) *********************** 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 77 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 1.394 Fit side-chains revert: symmetry clash REVERT: A 23 GLU cc_start: 0.8605 (mp0) cc_final: 0.8362 (mp0) REVERT: B 59 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.6912 (mp-120) REVERT: B 385 ASN cc_start: 0.7457 (t0) cc_final: 0.7255 (t160) REVERT: B 445 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8240 (mmmt) REVERT: C 179 HIS cc_start: 0.9178 (m170) cc_final: 0.8635 (m90) REVERT: C 281 THR cc_start: 0.9228 (OUTLIER) cc_final: 0.9014 (p) outliers start: 12 outliers final: 4 residues processed: 72 average time/residue: 1.4121 time to fit residues: 110.3293 Evaluate side-chains 66 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 59 GLN Chi-restraints excluded: chain B residue 445 LYS Chi-restraints excluded: chain C residue 281 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 26 optimal weight: 0.2980 chunk 85 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 120 optimal weight: 9.9990 chunk 73 optimal weight: 0.0470 chunk 39 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.6684 ------------------------------------------------------------------------------- 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 = 0.3616 r_free = 0.3616 target = 0.106198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.071354 restraints weight = 17521.966| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.56 r_work: 0.2910 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10873 Z= 0.113 Angle : 0.483 9.720 14737 Z= 0.251 Chirality : 0.040 0.142 1664 Planarity : 0.004 0.043 1906 Dihedral : 3.968 17.227 1449 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.05 % Favored : 97.88 % Rotamer: Outliers : 1.18 % Allowed : 7.57 % Favored : 91.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.24), residues: 1320 helix: 1.42 (0.22), residues: 615 sheet: 0.26 (0.36), residues: 218 loop : 0.02 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 311 HIS 0.004 0.001 HIS B 326 PHE 0.022 0.001 PHE A 538 TYR 0.011 0.001 TYR B 244 ARG 0.002 0.000 ARG B 158 Details of bonding type rmsd hydrogen bonds : bond 0.03433 ( 492) hydrogen bonds : angle 4.24549 ( 1413) metal coordination : bond 0.00323 ( 1) covalent geometry : bond 0.00263 (10872) covalent geometry : angle 0.48339 (14737) *********************** 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 79 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 1.323 Fit side-chains revert: symmetry clash REVERT: A 23 GLU cc_start: 0.8609 (mp0) cc_final: 0.8341 (mp0) REVERT: B 59 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.6799 (mp-120) REVERT: B 445 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8244 (mmmt) REVERT: C 179 HIS cc_start: 0.9158 (m170) cc_final: 0.8624 (m90) REVERT: C 281 THR cc_start: 0.9229 (OUTLIER) cc_final: 0.8968 (p) outliers start: 14 outliers final: 5 residues processed: 73 average time/residue: 1.2367 time to fit residues: 98.3009 Evaluate side-chains 68 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 323 MET 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 445 LYS Chi-restraints excluded: chain C residue 281 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 116 optimal weight: 4.9990 chunk 99 optimal weight: 0.0770 chunk 13 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 83 optimal weight: 0.0670 overall best weight: 0.9480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 385 ASN C 230 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.105525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.070570 restraints weight = 17351.994| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.55 r_work: 0.2895 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10873 Z= 0.137 Angle : 0.506 10.320 14737 Z= 0.262 Chirality : 0.041 0.150 1664 Planarity : 0.004 0.042 1906 Dihedral : 4.013 16.898 1449 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.12 % Favored : 97.80 % Rotamer: Outliers : 1.35 % Allowed : 8.07 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.24), residues: 1320 helix: 1.41 (0.22), residues: 615 sheet: 0.26 (0.36), residues: 218 loop : 0.00 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 350 HIS 0.009 0.001 HIS C 230 PHE 0.023 0.001 PHE A 538 TYR 0.011 0.001 TYR B 244 ARG 0.002 0.000 ARG B 303 Details of bonding type rmsd hydrogen bonds : bond 0.03578 ( 492) hydrogen bonds : angle 4.25205 ( 1413) metal coordination : bond 0.00407 ( 1) covalent geometry : bond 0.00329 (10872) covalent geometry : angle 0.50591 (14737) *********************** 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 79 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 1.371 Fit side-chains revert: symmetry clash REVERT: A 23 GLU cc_start: 0.8625 (mp0) cc_final: 0.8370 (mp0) REVERT: B 59 GLN cc_start: 0.7557 (OUTLIER) cc_final: 0.7083 (mp10) REVERT: B 158 ARG cc_start: 0.8937 (mmt-90) cc_final: 0.8338 (mmt-90) REVERT: B 409 SER cc_start: 0.8919 (t) cc_final: 0.8686 (p) REVERT: B 445 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8241 (mmmt) REVERT: C 179 HIS cc_start: 0.9158 (m170) cc_final: 0.8602 (m90) outliers start: 16 outliers final: 6 residues processed: 73 average time/residue: 1.4691 time to fit residues: 116.7677 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 : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 445 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 26 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 31 optimal weight: 0.0370 chunk 74 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 overall best weight: 1.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN B 385 ASN C 230 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.104134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.069122 restraints weight = 17642.482| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.52 r_work: 0.2862 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10873 Z= 0.179 Angle : 0.529 10.700 14737 Z= 0.273 Chirality : 0.042 0.161 1664 Planarity : 0.004 0.042 1906 Dihedral : 4.149 16.606 1449 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.27 % Favored : 97.65 % Rotamer: Outliers : 1.09 % Allowed : 8.66 % Favored : 90.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.24), residues: 1320 helix: 1.37 (0.22), residues: 613 sheet: 0.21 (0.36), residues: 218 loop : -0.08 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 350 HIS 0.009 0.001 HIS C 230 PHE 0.025 0.002 PHE A 538 TYR 0.012 0.001 TYR B 244 ARG 0.003 0.000 ARG B 158 Details of bonding type rmsd hydrogen bonds : bond 0.03956 ( 492) hydrogen bonds : angle 4.34899 ( 1413) metal coordination : bond 0.00533 ( 1) covalent geometry : bond 0.00436 (10872) covalent geometry : angle 0.52864 (14737) *********************** 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 75 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 1.181 Fit side-chains REVERT: A 23 GLU cc_start: 0.8658 (mp0) cc_final: 0.8424 (mp0) REVERT: B 59 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7021 (mp-120) REVERT: B 158 ARG cc_start: 0.9006 (mmt-90) cc_final: 0.8600 (mmt-90) REVERT: B 389 ARG cc_start: 0.8571 (mtm-85) cc_final: 0.7828 (mtp180) REVERT: C 179 HIS cc_start: 0.9161 (m170) cc_final: 0.8617 (m90) outliers start: 13 outliers final: 6 residues processed: 69 average time/residue: 1.3006 time to fit residues: 97.6146 Evaluate side-chains 65 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 1.315 ------------------------------------------------------------------------------- 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 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 C residue 134 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 123 optimal weight: 9.9990 chunk 7 optimal weight: 0.6980 chunk 118 optimal weight: 0.7980 chunk 93 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 127 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 90 optimal weight: 0.0270 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN B 385 ASN C 230 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.105241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.070580 restraints weight = 17516.117| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.54 r_work: 0.2892 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10873 Z= 0.108 Angle : 0.490 11.200 14737 Z= 0.253 Chirality : 0.040 0.142 1664 Planarity : 0.004 0.042 1906 Dihedral : 4.014 17.122 1449 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.05 % Favored : 97.88 % Rotamer: Outliers : 0.76 % Allowed : 9.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.24), residues: 1320 helix: 1.44 (0.22), residues: 615 sheet: 0.17 (0.36), residues: 220 loop : -0.01 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 209 HIS 0.012 0.001 HIS C 230 PHE 0.021 0.001 PHE A 538 TYR 0.012 0.001 TYR B 244 ARG 0.002 0.000 ARG A 527 Details of bonding type rmsd hydrogen bonds : bond 0.03377 ( 492) hydrogen bonds : angle 4.19870 ( 1413) metal coordination : bond 0.00250 ( 1) covalent geometry : bond 0.00250 (10872) covalent geometry : angle 0.48951 (14737) *********************** 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 69 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 1.266 Fit side-chains REVERT: A 23 GLU cc_start: 0.8685 (mp0) cc_final: 0.8440 (mp0) REVERT: B 158 ARG cc_start: 0.9008 (mmt-90) cc_final: 0.8632 (mmt-90) REVERT: B 389 ARG cc_start: 0.8568 (mtm-85) cc_final: 0.7821 (mtp180) REVERT: C 179 HIS cc_start: 0.9168 (m170) cc_final: 0.8635 (m90) outliers start: 9 outliers final: 4 residues processed: 65 average time/residue: 1.4178 time to fit residues: 100.0825 Evaluate side-chains 58 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 390 CYS Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain C residue 134 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 114 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 128 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 112 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN B 385 ASN C 230 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.105105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.070214 restraints weight = 17783.645| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.53 r_work: 0.2884 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.1444 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= 0.132 Angle : 0.499 11.535 14737 Z= 0.257 Chirality : 0.041 0.149 1664 Planarity : 0.004 0.042 1906 Dihedral : 4.021 16.788 1449 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.93 % Allowed : 9.59 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.24), residues: 1320 helix: 1.43 (0.22), residues: 615 sheet: 0.20 (0.36), residues: 218 loop : -0.02 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 209 HIS 0.012 0.001 HIS C 230 PHE 0.022 0.001 PHE A 538 TYR 0.011 0.001 TYR B 244 ARG 0.003 0.000 ARG A 527 Details of bonding type rmsd hydrogen bonds : bond 0.03516 ( 492) hydrogen bonds : angle 4.20773 ( 1413) metal coordination : bond 0.00321 ( 1) covalent geometry : bond 0.00315 (10872) covalent geometry : angle 0.49866 (14737) *********************** 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 69 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 1.217 Fit side-chains REVERT: A 23 GLU cc_start: 0.8651 (mp0) cc_final: 0.8427 (mp0) REVERT: B 158 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.8719 (mmt-90) REVERT: B 340 ASP cc_start: 0.8836 (OUTLIER) cc_final: 0.8612 (t0) REVERT: B 389 ARG cc_start: 0.8591 (mtm-85) cc_final: 0.7856 (mtp180) REVERT: C 179 HIS cc_start: 0.9164 (m170) cc_final: 0.8653 (m90) outliers start: 11 outliers final: 5 residues processed: 62 average time/residue: 1.2775 time to fit residues: 86.2065 Evaluate side-chains 64 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 390 CYS Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 340 ASP 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 68 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 101 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN B 385 ASN C 230 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.106425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.072073 restraints weight = 17508.029| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.51 r_work: 0.2890 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.1467 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= 0.128 Angle : 0.498 11.821 14737 Z= 0.257 Chirality : 0.041 0.150 1664 Planarity : 0.004 0.042 1906 Dihedral : 4.010 16.859 1449 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.01 % Allowed : 9.59 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.24), residues: 1320 helix: 1.45 (0.22), residues: 615 sheet: 0.11 (0.36), residues: 220 loop : -0.00 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 209 HIS 0.009 0.001 HIS C 230 PHE 0.022 0.001 PHE A 538 TYR 0.012 0.001 TYR B 244 ARG 0.003 0.000 ARG A 527 Details of bonding type rmsd hydrogen bonds : bond 0.03476 ( 492) hydrogen bonds : angle 4.20138 ( 1413) metal coordination : bond 0.00307 ( 1) covalent geometry : bond 0.00306 (10872) covalent geometry : angle 0.49791 (14737) ********************** 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 69 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 1.339 Fit side-chains REVERT: A 23 GLU cc_start: 0.8666 (mp0) cc_final: 0.8446 (mp0) REVERT: B 158 ARG cc_start: 0.9018 (OUTLIER) cc_final: 0.8702 (mmt-90) REVERT: B 340 ASP cc_start: 0.8825 (OUTLIER) cc_final: 0.8601 (t0) REVERT: B 389 ARG cc_start: 0.8592 (mtm-85) cc_final: 0.7861 (mtp180) REVERT: C 179 HIS cc_start: 0.9160 (m170) cc_final: 0.8636 (m90) outliers start: 12 outliers final: 8 residues processed: 64 average time/residue: 1.3109 time to fit residues: 91.4178 Evaluate side-chains 66 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 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 B residue 340 ASP 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 110 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 88 optimal weight: 0.0020 chunk 26 optimal weight: 0.0060 chunk 69 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 109 optimal weight: 5.9990 chunk 84 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 overall best weight: 0.5604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN B 385 ASN C 230 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.105623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.070989 restraints weight = 17358.264| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.51 r_work: 0.2905 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10873 Z= 0.106 Angle : 0.487 11.786 14737 Z= 0.251 Chirality : 0.040 0.144 1664 Planarity : 0.004 0.042 1906 Dihedral : 3.958 17.168 1449 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.93 % Allowed : 9.67 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.24), residues: 1320 helix: 1.48 (0.22), residues: 616 sheet: 0.10 (0.36), residues: 222 loop : 0.01 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 209 HIS 0.012 0.001 HIS C 230 PHE 0.020 0.001 PHE A 538 TYR 0.012 0.001 TYR B 244 ARG 0.003 0.000 ARG A 527 Details of bonding type rmsd hydrogen bonds : bond 0.03258 ( 492) hydrogen bonds : angle 4.14252 ( 1413) metal coordination : bond 0.00208 ( 1) covalent geometry : bond 0.00245 (10872) covalent geometry : angle 0.48704 (14737) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8706.58 seconds wall clock time: 153 minutes 45.48 seconds (9225.48 seconds total)