Starting phenix.real_space_refine on Wed Mar 12 18:10:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wpc_32682/03_2025/7wpc_32682_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wpc_32682/03_2025/7wpc_32682.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wpc_32682/03_2025/7wpc_32682.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wpc_32682/03_2025/7wpc_32682.map" model { file = "/net/cci-nas-00/data/ceres_data/7wpc_32682/03_2025/7wpc_32682_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wpc_32682/03_2025/7wpc_32682_neut.cif" } resolution = 2.57 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= 0.012 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 Zn 1 6.06 5 S 44 5.16 5 Cl 1 4.86 5 C 5162 2.51 5 N 1335 2.21 5 O 1514 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8057 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1582 Classifications: {'peptide': 197} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 183} Chain: "B" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1518 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 10, 'TRANS': 177} Chain breaks: 3 Chain: "D" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CL': 1, ' ZN': 1, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 6.79, per 1000 atoms: 0.84 Number of scatterers: 8057 At special positions: 0 Unit cell: (99.704, 98.056, 127.72, 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 Cl 1 17.00 S 44 16.00 O 1514 8.00 N 1335 7.00 C 5162 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.04 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG C 1 " - " ASN A 340 " " NAG D 903 " - " ASN D 90 " " NAG D 904 " - " ASN D 322 " " NAG D 905 " - " ASN D 546 " " NAG E 1 " - " ASN B 340 " Time building additional restraints: 2.23 Conformation dependent library (CDL) restraints added in 930.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 902 " pdb="ZN ZN D 902 " - pdb=" NE2 HIS D 374 " 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1848 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 8 sheets defined 44.5% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 334 through 340 removed outlier: 3.958A pdb=" N VAL A 338 " --> pdb=" O PRO A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 368 removed outlier: 3.992A pdb=" N ASN A 367 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU A 368 " --> pdb=" O LEU A 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 364 through 368' Processing helix chain 'A' and resid 402 through 404 No H-bonds generated for 'chain 'A' and resid 402 through 404' Processing helix chain 'A' and resid 414 through 419 Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 363 through 368 removed outlier: 3.972A pdb=" N TYR B 366 " --> pdb=" O SER B 363 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU B 368 " --> pdb=" O LEU B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.557A pdb=" N ASP B 386 " --> pdb=" O LYS B 383 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LEU B 387 " --> pdb=" O LEU B 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 383 through 387' Processing helix chain 'B' and resid 402 through 404 No H-bonds generated for 'chain 'B' and resid 402 through 404' Processing helix chain 'B' and resid 414 through 419 Processing helix chain 'D' and resid 20 through 53 removed outlier: 3.509A pdb=" N GLN D 24 " --> pdb=" O THR D 20 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLU D 37 " --> pdb=" O ASN D 33 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 80 removed outlier: 3.809A pdb=" N GLN D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN D 61 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP D 67 " --> pdb=" O ASN D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 83 No H-bonds generated for 'chain 'D' and resid 81 through 83' Processing helix chain 'D' and resid 90 through 101 Processing helix chain 'D' and resid 103 through 108 removed outlier: 4.047A pdb=" N VAL D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU D 108 " --> pdb=" O SER D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 130 removed outlier: 3.590A pdb=" N ARG D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 155 removed outlier: 3.611A pdb=" N ALA D 153 " --> pdb=" O ASN D 149 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN D 154 " --> pdb=" O GLU D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 172 removed outlier: 3.718A pdb=" N ARG D 161 " --> pdb=" O ASP D 157 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TRP D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 175 No H-bonds generated for 'chain 'D' and resid 173 through 175' Processing helix chain 'D' and resid 176 through 194 removed outlier: 3.558A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 204 removed outlier: 3.503A pdb=" N TYR D 202 " --> pdb=" O ASP D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 208 Processing helix chain 'D' and resid 219 through 221 No H-bonds generated for 'chain 'D' and resid 219 through 221' Processing helix chain 'D' and resid 222 through 227 Processing helix chain 'D' and resid 233 through 249 removed outlier: 3.646A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 279 removed outlier: 3.929A pdb=" N TYR D 279 " --> pdb=" O THR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 298 Processing helix chain 'D' and resid 303 through 316 Processing helix chain 'D' and resid 324 through 330 removed outlier: 3.640A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 383 removed outlier: 3.604A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 399 through 413 removed outlier: 3.795A pdb=" N ALA D 403 " --> pdb=" O GLY D 399 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER D 411 " --> pdb=" O ILE D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.728A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASN D 437 " --> pdb=" O GLU D 433 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 465 Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.536A pdb=" N LYS D 476 " --> pdb=" O GLN D 472 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU D 479 " --> pdb=" O LYS D 475 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARG D 482 " --> pdb=" O TRP D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 502 removed outlier: 3.501A pdb=" N SER D 502 " --> pdb=" O ASP D 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 499 through 502' Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 533 removed outlier: 3.648A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.594A pdb=" N LYS D 541 " --> pdb=" O PRO D 538 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N CYS D 542 " --> pdb=" O LEU D 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 538 through 542' Processing helix chain 'D' and resid 550 through 559 removed outlier: 3.809A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 removed outlier: 3.884A pdb=" N GLU D 571 " --> pdb=" O THR D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 588 removed outlier: 3.506A pdb=" N TYR D 587 " --> pdb=" O PRO D 583 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'A' and resid 351 through 355 removed outlier: 3.693A pdb=" N ASN A 351 " --> pdb=" O SER A 396 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER A 396 " --> pdb=" O ASN A 351 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS A 375 " --> pdb=" O VAL A 430 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AA3, first strand: chain 'A' and resid 470 through 471 removed outlier: 3.579A pdb=" N TYR A 486 " --> pdb=" O TYR A 470 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 353 through 355 removed outlier: 4.169A pdb=" N LYS B 375 " --> pdb=" O VAL B 430 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AA6, first strand: chain 'D' and resid 132 through 133 Processing sheet with id=AA7, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.772A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 347 through 352 removed outlier: 3.661A pdb=" N ARG D 357 " --> pdb=" O TRP D 349 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) 280 hydrogen bonds defined for protein. 795 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: 1.94 Time building geometry restraints manager: 2.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2559 1.35 - 1.47: 2162 1.47 - 1.59: 3493 1.59 - 1.71: 0 1.71 - 1.83: 65 Bond restraints: 8279 Sorted by residual: bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.470 -0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" N VAL B 480 " pdb=" CA VAL B 480 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.31e+00 bond pdb=" N TYR B 486 " pdb=" CA TYR B 486 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.19e-02 7.06e+03 7.59e+00 bond pdb=" N LEU B 514 " pdb=" CA LEU B 514 " ideal model delta sigma weight residual 1.456 1.485 -0.029 1.23e-02 6.61e+03 5.54e+00 bond pdb=" N CYS B 485 " pdb=" CA CYS B 485 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.29e-02 6.01e+03 5.38e+00 ... (remaining 8274 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 10925 1.89 - 3.78: 267 3.78 - 5.68: 39 5.68 - 7.57: 12 7.57 - 9.46: 4 Bond angle restraints: 11247 Sorted by residual: angle pdb=" N VAL D 339 " pdb=" CA VAL D 339 " pdb=" C VAL D 339 " ideal model delta sigma weight residual 113.71 108.44 5.27 9.50e-01 1.11e+00 3.07e+01 angle pdb=" CA GLY B 482 " pdb=" C GLY B 482 " pdb=" O GLY B 482 " ideal model delta sigma weight residual 122.01 118.07 3.94 9.70e-01 1.06e+00 1.65e+01 angle pdb=" N GLY A 499 " pdb=" CA GLY A 499 " pdb=" C GLY A 499 " ideal model delta sigma weight residual 111.34 118.64 -7.30 1.82e+00 3.02e-01 1.61e+01 angle pdb=" N GLU D 145 " pdb=" CA GLU D 145 " pdb=" C GLU D 145 " ideal model delta sigma weight residual 109.81 118.47 -8.66 2.21e+00 2.05e-01 1.54e+01 angle pdb=" CA PHE B 512 " pdb=" CB PHE B 512 " pdb=" CG PHE B 512 " ideal model delta sigma weight residual 113.80 117.43 -3.63 1.00e+00 1.00e+00 1.32e+01 ... (remaining 11242 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.38: 4594 22.38 - 44.76: 320 44.76 - 67.15: 35 67.15 - 89.53: 7 89.53 - 111.91: 25 Dihedral angle restraints: 4981 sinusoidal: 2101 harmonic: 2880 Sorted by residual: dihedral pdb=" CA PHE A 372 " pdb=" C PHE A 372 " pdb=" N THR A 373 " pdb=" CA THR A 373 " ideal model delta harmonic sigma weight residual 180.00 159.39 20.61 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" C3 NAG E 1 " pdb=" C1 NAG E 1 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sinusoidal sigma weight residual -55.55 56.36 -111.91 1 3.00e+01 1.11e-03 1.46e+01 dihedral pdb=" N2 NAG E 1 " pdb=" C1 NAG E 1 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sinusoidal sigma weight residual -178.19 -66.52 -111.67 1 3.00e+01 1.11e-03 1.46e+01 ... (remaining 4978 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1033 0.064 - 0.129: 152 0.129 - 0.193: 6 0.193 - 0.258: 4 0.258 - 0.322: 2 Chirality restraints: 1197 Sorted by residual: chirality pdb=" CA LEU B 515 " pdb=" N LEU B 515 " pdb=" C LEU B 515 " pdb=" CB LEU B 515 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.43 0.03 2.00e-02 2.50e+03 2.35e+00 chirality pdb=" CA ASN B 484 " pdb=" N ASN B 484 " pdb=" C ASN B 484 " pdb=" CB ASN B 484 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 1194 not shown) Planarity restraints: 1453 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D 564 " 0.042 5.00e-02 4.00e+02 6.34e-02 6.44e+00 pdb=" N PRO D 565 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO D 565 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 565 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 499 " -0.040 5.00e-02 4.00e+02 5.98e-02 5.73e+00 pdb=" N PRO D 500 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO D 500 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 500 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 582 " -0.037 5.00e-02 4.00e+02 5.51e-02 4.86e+00 pdb=" N PRO D 583 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO D 583 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 583 " -0.031 5.00e-02 4.00e+02 ... (remaining 1450 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1689 2.78 - 3.31: 6569 3.31 - 3.84: 13351 3.84 - 4.37: 15369 4.37 - 4.90: 26616 Nonbonded interactions: 63594 Sorted by model distance: nonbonded pdb=" OE2 GLU D 402 " pdb="ZN ZN D 902 " model vdw 2.253 2.230 nonbonded pdb=" O THR D 118 " pdb=" OG1 THR D 122 " model vdw 2.303 3.040 nonbonded pdb=" OG1 THR B 412 " pdb=" OD2 ASP B 417 " model vdw 2.337 3.040 nonbonded pdb=" OG SER D 109 " pdb=" OD1 ASP D 111 " model vdw 2.349 3.040 nonbonded pdb=" OG SER B 466 " pdb=" OE1 GLU B 468 " model vdw 2.354 3.040 ... (remaining 63589 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 329 through 369 or resid 372 through 499 or resid 501 thro \ ugh 515 or resid 523 through 525)) selection = (chain 'B' and resid 329 through 525) } ncs_group { reference = chain 'C' selection = chain 'E' } 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: 270.420 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: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.680 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 306.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 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 : 0.004 0.064 8279 Z= 0.237 Angle : 0.720 9.460 11247 Z= 0.420 Chirality : 0.048 0.322 1197 Planarity : 0.006 0.063 1448 Dihedral : 17.016 111.911 3103 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.12 % Allowed : 4.52 % Favored : 95.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.11 % 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: -4.19 (0.20), residues: 968 helix: -2.98 (0.17), residues: 385 sheet: -0.65 (0.53), residues: 69 loop : -2.98 (0.22), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 477 HIS 0.005 0.001 HIS D 374 PHE 0.018 0.001 PHE B 512 TYR 0.013 0.001 TYR D 183 ARG 0.002 0.000 ARG D 514 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 204 time to evaluate : 0.805 Fit side-chains REVERT: A 362 TYR cc_start: 0.8789 (m-80) cc_final: 0.8561 (m-80) REVERT: A 436 ASN cc_start: 0.8211 (t0) cc_final: 0.8009 (t0) REVERT: B 383 LYS cc_start: 0.1328 (pttp) cc_final: 0.0891 (mtmt) REVERT: B 415 ILE cc_start: 0.7493 (mm) cc_final: 0.7243 (pp) REVERT: D 126 ILE cc_start: 0.7831 (mt) cc_final: 0.7627 (mt) REVERT: D 271 TRP cc_start: 0.8191 (m-90) cc_final: 0.7452 (m-90) REVERT: D 362 THR cc_start: 0.7658 (m) cc_final: 0.7363 (m) REVERT: D 527 GLU cc_start: 0.7125 (tm-30) cc_final: 0.6923 (tm-30) outliers start: 1 outliers final: 1 residues processed: 205 average time/residue: 1.2271 time to fit residues: 267.7248 Evaluate side-chains 170 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 169 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 515 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 24 optimal weight: 0.0980 chunk 49 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 29 optimal weight: 0.0570 chunk 45 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 87 optimal weight: 0.0970 overall best weight: 0.3096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN A 445 ASN A 471 GLN A 478 ASN B 357 ASN B 457 ASN B 484 ASN D 33 ASN D 51 ASN ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 ASN D 154 ASN D 194 ASN D 221 GLN D 277 ASN D 300 GLN D 378 HIS D 505 HIS D 522 GLN D 531 GLN D 599 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.175604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.146358 restraints weight = 11488.328| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 2.06 r_work: 0.3742 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3593 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8279 Z= 0.242 Angle : 0.585 10.549 11247 Z= 0.291 Chirality : 0.046 0.298 1197 Planarity : 0.005 0.053 1448 Dihedral : 13.198 98.705 1221 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.85 % Allowed : 13.79 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.11 % 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: -2.68 (0.24), residues: 968 helix: -1.43 (0.23), residues: 403 sheet: -0.47 (0.58), residues: 72 loop : -2.29 (0.25), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 433 HIS 0.008 0.001 HIS D 34 PHE 0.018 0.002 PHE D 314 TYR 0.017 0.002 TYR A 393 ARG 0.007 0.001 ARG D 192 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 188 time to evaluate : 0.912 Fit side-chains revert: symmetry clash REVERT: A 354 ARG cc_start: 0.8505 (ttp80) cc_final: 0.8152 (ttp80) REVERT: B 383 LYS cc_start: 0.2064 (pttp) cc_final: 0.0968 (mtmt) REVERT: D 82 MET cc_start: 0.7883 (OUTLIER) cc_final: 0.7045 (mtp) REVERT: D 117 ASN cc_start: 0.8289 (m-40) cc_final: 0.7999 (m-40) REVERT: D 145 GLU cc_start: 0.6828 (OUTLIER) cc_final: 0.6255 (pm20) REVERT: D 152 MET cc_start: 0.6347 (OUTLIER) cc_final: 0.6131 (ttp) REVERT: D 571 GLU cc_start: 0.7505 (pt0) cc_final: 0.7301 (pt0) outliers start: 16 outliers final: 6 residues processed: 196 average time/residue: 1.1603 time to fit residues: 241.5288 Evaluate side-chains 193 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 184 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 ARG Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 474 ASN Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 401 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 35 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 67 optimal weight: 0.1980 chunk 56 optimal weight: 0.0870 chunk 62 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN B 391 ASN B 503 GLN ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 194 ASN D 239 HIS D 505 HIS D 531 GLN D 599 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.171931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.141136 restraints weight = 11402.089| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.09 r_work: 0.3648 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 8279 Z= 0.292 Angle : 0.589 9.195 11247 Z= 0.296 Chirality : 0.046 0.233 1197 Planarity : 0.005 0.044 1448 Dihedral : 11.479 97.244 1219 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.13 % Allowed : 15.53 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.11 % 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: -2.04 (0.25), residues: 968 helix: -0.78 (0.25), residues: 413 sheet: -0.14 (0.60), residues: 70 loop : -2.07 (0.25), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 477 HIS 0.009 0.002 HIS D 34 PHE 0.021 0.002 PHE D 523 TYR 0.021 0.001 TYR D 183 ARG 0.006 0.001 ARG A 495 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 187 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 365 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7568 (pt) REVERT: B 383 LYS cc_start: 0.2995 (pttp) cc_final: 0.0878 (mtmt) REVERT: D 52 THR cc_start: 0.8348 (m) cc_final: 0.8125 (m) REVERT: D 87 GLU cc_start: 0.7495 (mp0) cc_final: 0.7269 (mm-30) REVERT: D 117 ASN cc_start: 0.8281 (m-40) cc_final: 0.8019 (m-40) REVERT: D 215 TYR cc_start: 0.8130 (m-80) cc_final: 0.7748 (m-80) REVERT: D 225 ASP cc_start: 0.7966 (OUTLIER) cc_final: 0.7686 (m-30) REVERT: D 363 LYS cc_start: 0.8120 (mmpt) cc_final: 0.7868 (mmpt) REVERT: D 557 MET cc_start: 0.8751 (tmm) cc_final: 0.8497 (tmm) REVERT: D 571 GLU cc_start: 0.7829 (pt0) cc_final: 0.7377 (pt0) outliers start: 27 outliers final: 8 residues processed: 195 average time/residue: 1.1513 time to fit residues: 238.3600 Evaluate side-chains 172 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 162 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 ARG Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 474 ASN Chi-restraints excluded: chain B residue 385 ASN Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain D residue 401 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 46 optimal weight: 0.3980 chunk 94 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 33 optimal weight: 0.0370 chunk 23 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 87 optimal weight: 0.2980 chunk 59 optimal weight: 0.7980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 GLN ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 GLN D 194 ASN D 388 GLN D 552 GLN D 599 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.166789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.134491 restraints weight = 11153.974| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.16 r_work: 0.3622 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 8279 Z= 0.297 Angle : 0.574 7.526 11247 Z= 0.287 Chirality : 0.047 0.247 1197 Planarity : 0.004 0.040 1448 Dihedral : 10.969 96.046 1219 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.36 % Allowed : 17.15 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.11 % 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: -1.67 (0.26), residues: 968 helix: -0.32 (0.26), residues: 403 sheet: -0.07 (0.60), residues: 70 loop : -1.97 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 477 HIS 0.007 0.002 HIS D 241 PHE 0.017 0.001 PHE D 523 TYR 0.019 0.001 TYR D 385 ARG 0.008 0.001 ARG D 192 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 170 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7148 (pt) REVERT: A 463 ARG cc_start: 0.8118 (ttt-90) cc_final: 0.7870 (ttp80) REVERT: D 87 GLU cc_start: 0.7548 (mp0) cc_final: 0.7348 (mm-30) REVERT: D 102 GLN cc_start: 0.6511 (OUTLIER) cc_final: 0.5701 (pp30) REVERT: D 117 ASN cc_start: 0.8271 (m-40) cc_final: 0.8021 (m-40) REVERT: D 215 TYR cc_start: 0.8193 (m-80) cc_final: 0.7830 (m-80) REVERT: D 225 ASP cc_start: 0.8012 (OUTLIER) cc_final: 0.7745 (m-30) REVERT: D 234 LYS cc_start: 0.8681 (mtmm) cc_final: 0.8373 (mtmm) REVERT: D 363 LYS cc_start: 0.8171 (mmpt) cc_final: 0.7928 (mmpt) REVERT: D 557 MET cc_start: 0.8764 (tmm) cc_final: 0.8474 (tmm) REVERT: D 571 GLU cc_start: 0.7877 (pt0) cc_final: 0.7505 (pt0) outliers start: 29 outliers final: 9 residues processed: 184 average time/residue: 1.1438 time to fit residues: 224.1213 Evaluate side-chains 183 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 171 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 ARG Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 474 ASN Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain D residue 102 GLN Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 522 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 8 optimal weight: 0.9980 chunk 93 optimal weight: 0.1980 chunk 50 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 33 optimal weight: 0.0670 chunk 6 optimal weight: 0.3980 chunk 49 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 18 optimal weight: 0.3980 chunk 61 optimal weight: 0.9980 chunk 83 optimal weight: 0.0970 overall best weight: 0.2316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 GLN D 175 GLN D 194 ASN D 522 GLN D 599 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.170277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.138454 restraints weight = 11193.957| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.20 r_work: 0.3645 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3486 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8279 Z= 0.191 Angle : 0.527 7.812 11247 Z= 0.263 Chirality : 0.044 0.240 1197 Planarity : 0.004 0.055 1448 Dihedral : 10.498 92.596 1219 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.01 % Allowed : 17.61 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.11 % 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: -1.34 (0.26), residues: 968 helix: -0.00 (0.27), residues: 398 sheet: 0.18 (0.61), residues: 70 loop : -1.84 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 477 HIS 0.007 0.001 HIS D 34 PHE 0.018 0.001 PHE A 389 TYR 0.026 0.001 TYR D 50 ARG 0.011 0.001 ARG A 354 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 176 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8547 (ttmm) REVERT: A 400 ARG cc_start: 0.8615 (ptm-80) cc_final: 0.8277 (mtp180) REVERT: A 463 ARG cc_start: 0.8108 (ttt-90) cc_final: 0.7875 (ttp80) REVERT: B 383 LYS cc_start: 0.3176 (pttp) cc_final: 0.1015 (mtmt) REVERT: D 87 GLU cc_start: 0.7538 (mp0) cc_final: 0.7307 (mp0) REVERT: D 102 GLN cc_start: 0.6422 (OUTLIER) cc_final: 0.5570 (pp30) REVERT: D 117 ASN cc_start: 0.8252 (m-40) cc_final: 0.7994 (m-40) REVERT: D 215 TYR cc_start: 0.8170 (m-80) cc_final: 0.7829 (m-80) REVERT: D 225 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7749 (m-30) REVERT: D 347 THR cc_start: 0.8323 (OUTLIER) cc_final: 0.8095 (p) REVERT: D 363 LYS cc_start: 0.8156 (mmpt) cc_final: 0.7847 (mmpt) REVERT: D 557 MET cc_start: 0.8765 (tmm) cc_final: 0.8454 (tmm) REVERT: D 571 GLU cc_start: 0.7890 (pt0) cc_final: 0.7527 (pt0) outliers start: 26 outliers final: 11 residues processed: 188 average time/residue: 1.3789 time to fit residues: 275.6215 Evaluate side-chains 187 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 172 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 ARG Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 474 ASN Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain D residue 102 GLN Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 574 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 64 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 14 optimal weight: 0.0980 chunk 94 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 92 optimal weight: 0.0670 chunk 42 optimal weight: 0.3980 chunk 18 optimal weight: 0.6980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 GLN D 194 ASN ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 599 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.169378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.137048 restraints weight = 11164.146| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.21 r_work: 0.3613 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3458 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 8279 Z= 0.292 Angle : 0.571 8.040 11247 Z= 0.285 Chirality : 0.046 0.258 1197 Planarity : 0.004 0.045 1448 Dihedral : 10.169 88.217 1219 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.24 % Allowed : 18.19 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.11 % 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: -1.27 (0.26), residues: 968 helix: -0.01 (0.27), residues: 407 sheet: 0.31 (0.61), residues: 70 loop : -1.78 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 477 HIS 0.007 0.001 HIS D 241 PHE 0.018 0.001 PHE A 389 TYR 0.029 0.002 TYR D 50 ARG 0.011 0.001 ARG D 192 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.7374 (ptm160) REVERT: B 383 LYS cc_start: 0.3377 (pttp) cc_final: 0.1042 (mtmt) REVERT: D 82 MET cc_start: 0.8374 (OUTLIER) cc_final: 0.8168 (mtm) REVERT: D 87 GLU cc_start: 0.7606 (mp0) cc_final: 0.7336 (mp0) REVERT: D 102 GLN cc_start: 0.6485 (OUTLIER) cc_final: 0.5628 (pp30) REVERT: D 117 ASN cc_start: 0.8271 (m-40) cc_final: 0.8007 (m-40) REVERT: D 215 TYR cc_start: 0.8269 (m-80) cc_final: 0.7962 (m-80) REVERT: D 225 ASP cc_start: 0.8029 (OUTLIER) cc_final: 0.7759 (m-30) REVERT: D 347 THR cc_start: 0.8384 (OUTLIER) cc_final: 0.8143 (p) REVERT: D 363 LYS cc_start: 0.8182 (mmpt) cc_final: 0.7874 (mmpt) REVERT: D 557 MET cc_start: 0.8815 (tmm) cc_final: 0.8502 (tmm) outliers start: 28 outliers final: 12 residues processed: 186 average time/residue: 1.2330 time to fit residues: 242.9490 Evaluate side-chains 182 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 165 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 ARG Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 474 ASN Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 102 GLN Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 401 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 1 optimal weight: 0.2980 chunk 70 optimal weight: 0.2980 chunk 53 optimal weight: 0.4980 chunk 73 optimal weight: 0.4980 chunk 9 optimal weight: 0.9980 chunk 5 optimal weight: 0.0770 chunk 88 optimal weight: 1.9990 overall best weight: 0.3338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 GLN D 175 GLN D 599 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.168613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.136452 restraints weight = 11151.113| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.19 r_work: 0.3623 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.4094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8279 Z= 0.240 Angle : 0.562 8.895 11247 Z= 0.279 Chirality : 0.045 0.268 1197 Planarity : 0.004 0.052 1448 Dihedral : 9.795 84.255 1219 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.67 % Allowed : 19.47 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.11 % 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: -1.19 (0.26), residues: 968 helix: 0.06 (0.27), residues: 406 sheet: 0.43 (0.61), residues: 70 loop : -1.74 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 477 HIS 0.006 0.001 HIS D 241 PHE 0.021 0.001 PHE A 389 TYR 0.029 0.001 TYR D 50 ARG 0.011 0.001 ARG D 192 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 165 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8598 (ttmm) REVERT: A 400 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.8267 (mtp180) REVERT: B 383 LYS cc_start: 0.3426 (pttp) cc_final: 0.1069 (mtmt) REVERT: D 82 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.8144 (mtm) REVERT: D 87 GLU cc_start: 0.7624 (mp0) cc_final: 0.7344 (mp0) REVERT: D 102 GLN cc_start: 0.6533 (OUTLIER) cc_final: 0.5657 (pp30) REVERT: D 117 ASN cc_start: 0.8262 (m-40) cc_final: 0.8003 (m-40) REVERT: D 215 TYR cc_start: 0.8262 (m-80) cc_final: 0.7958 (m-80) REVERT: D 225 ASP cc_start: 0.8002 (OUTLIER) cc_final: 0.7733 (m-30) REVERT: D 266 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8705 (mt) REVERT: D 347 THR cc_start: 0.8408 (OUTLIER) cc_final: 0.8191 (p) REVERT: D 363 LYS cc_start: 0.8180 (mmpt) cc_final: 0.7860 (mmpt) REVERT: D 557 MET cc_start: 0.8801 (tmm) cc_final: 0.8508 (tmm) outliers start: 23 outliers final: 11 residues processed: 175 average time/residue: 1.2663 time to fit residues: 234.8901 Evaluate side-chains 189 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 171 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 474 ASN Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 102 GLN Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 401 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 79 optimal weight: 0.6980 chunk 80 optimal weight: 0.3980 chunk 50 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 8 optimal weight: 0.1980 chunk 10 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 84 optimal weight: 0.3980 chunk 45 optimal weight: 0.6980 chunk 38 optimal weight: 0.2980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 599 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.168536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.136435 restraints weight = 11325.976| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 2.21 r_work: 0.3614 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3456 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8279 Z= 0.277 Angle : 0.582 9.418 11247 Z= 0.288 Chirality : 0.046 0.273 1197 Planarity : 0.004 0.055 1448 Dihedral : 9.409 79.092 1219 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.32 % Allowed : 20.39 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.11 % 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: -1.13 (0.27), residues: 968 helix: 0.07 (0.27), residues: 412 sheet: 0.31 (0.60), residues: 72 loop : -1.67 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 477 HIS 0.007 0.001 HIS D 241 PHE 0.020 0.001 PHE A 389 TYR 0.030 0.001 TYR D 50 ARG 0.014 0.001 ARG D 192 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 170 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8620 (ttmm) REVERT: B 383 LYS cc_start: 0.3388 (pttp) cc_final: 0.1042 (mtmt) REVERT: D 82 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.8198 (mtm) REVERT: D 87 GLU cc_start: 0.7671 (mp0) cc_final: 0.7383 (mp0) REVERT: D 102 GLN cc_start: 0.6654 (OUTLIER) cc_final: 0.5794 (pp30) REVERT: D 117 ASN cc_start: 0.8276 (m-40) cc_final: 0.8014 (m-40) REVERT: D 215 TYR cc_start: 0.8285 (m-80) cc_final: 0.7966 (m-80) REVERT: D 225 ASP cc_start: 0.8030 (OUTLIER) cc_final: 0.7770 (m-30) REVERT: D 347 THR cc_start: 0.8421 (OUTLIER) cc_final: 0.8214 (p) REVERT: D 363 LYS cc_start: 0.8215 (mmpt) cc_final: 0.7875 (mmpt) REVERT: D 557 MET cc_start: 0.8832 (tmm) cc_final: 0.8541 (tmm) outliers start: 20 outliers final: 11 residues processed: 178 average time/residue: 1.2565 time to fit residues: 236.5672 Evaluate side-chains 183 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 167 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 474 ASN Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 102 GLN Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 476 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 68 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 46 optimal weight: 0.4980 chunk 91 optimal weight: 0.2980 chunk 66 optimal weight: 0.0970 chunk 29 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 599 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.165052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.133684 restraints weight = 11371.525| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.12 r_work: 0.3609 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3452 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.4359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 8279 Z= 0.316 Angle : 0.596 9.982 11247 Z= 0.296 Chirality : 0.047 0.269 1197 Planarity : 0.004 0.061 1448 Dihedral : 8.998 72.377 1219 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.43 % Allowed : 20.39 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.11 % 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: -1.15 (0.27), residues: 968 helix: 0.06 (0.27), residues: 415 sheet: 0.26 (0.60), residues: 70 loop : -1.68 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 477 HIS 0.008 0.001 HIS D 241 PHE 0.022 0.001 PHE A 389 TYR 0.022 0.002 TYR D 202 ARG 0.015 0.001 ARG D 192 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 163 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8609 (ttmm) REVERT: A 400 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.7369 (ptm160) REVERT: A 514 LEU cc_start: 0.7551 (tp) cc_final: 0.7318 (tp) REVERT: D 82 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.8234 (mtm) REVERT: D 87 GLU cc_start: 0.7661 (mp0) cc_final: 0.7428 (mm-30) REVERT: D 102 GLN cc_start: 0.6701 (OUTLIER) cc_final: 0.5838 (pp30) REVERT: D 117 ASN cc_start: 0.8300 (m-40) cc_final: 0.8028 (m-40) REVERT: D 215 TYR cc_start: 0.8307 (m-80) cc_final: 0.8006 (m-80) REVERT: D 225 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7826 (m-30) REVERT: D 347 THR cc_start: 0.8403 (OUTLIER) cc_final: 0.8187 (p) REVERT: D 363 LYS cc_start: 0.8212 (mmpt) cc_final: 0.7886 (mmpt) REVERT: D 557 MET cc_start: 0.8816 (tmm) cc_final: 0.8512 (tmm) outliers start: 21 outliers final: 11 residues processed: 170 average time/residue: 1.4623 time to fit residues: 263.4244 Evaluate side-chains 177 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 160 time to evaluate : 1.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 474 ASN Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 102 GLN Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 578 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 3 optimal weight: 0.6980 chunk 93 optimal weight: 0.0980 chunk 92 optimal weight: 0.0070 chunk 81 optimal weight: 0.4980 chunk 45 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 27 optimal weight: 0.1980 chunk 0 optimal weight: 0.0980 chunk 80 optimal weight: 0.1980 chunk 49 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 overall best weight: 0.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 ASN D 599 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.170630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.138902 restraints weight = 11227.082| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 2.20 r_work: 0.3650 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8279 Z= 0.159 Angle : 0.557 9.767 11247 Z= 0.274 Chirality : 0.043 0.246 1197 Planarity : 0.004 0.056 1448 Dihedral : 8.356 64.645 1219 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.74 % Allowed : 20.63 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.11 % 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 (0.27), residues: 968 helix: 0.27 (0.27), residues: 407 sheet: 0.42 (0.61), residues: 72 loop : -1.64 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 271 HIS 0.006 0.001 HIS D 34 PHE 0.023 0.001 PHE A 389 TYR 0.023 0.001 TYR D 202 ARG 0.017 0.001 ARG D 192 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 170 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8565 (ttmm) REVERT: A 514 LEU cc_start: 0.7526 (tp) cc_final: 0.7295 (tp) REVERT: B 383 LYS cc_start: 0.3126 (pttp) cc_final: 0.0931 (mtmt) REVERT: D 87 GLU cc_start: 0.7551 (mp0) cc_final: 0.7288 (mp0) REVERT: D 117 ASN cc_start: 0.8246 (m-40) cc_final: 0.7990 (m-40) REVERT: D 215 TYR cc_start: 0.8226 (m-80) cc_final: 0.7886 (m-80) REVERT: D 225 ASP cc_start: 0.8052 (OUTLIER) cc_final: 0.7754 (m-30) REVERT: D 363 LYS cc_start: 0.8185 (mmpt) cc_final: 0.7854 (mmpt) REVERT: D 401 HIS cc_start: 0.8935 (OUTLIER) cc_final: 0.8383 (m-70) REVERT: D 557 MET cc_start: 0.8765 (tmm) cc_final: 0.8477 (tmm) outliers start: 15 outliers final: 7 residues processed: 178 average time/residue: 1.1861 time to fit residues: 223.6913 Evaluate side-chains 172 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 162 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 401 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 35 optimal weight: 2.9990 chunk 94 optimal weight: 0.3980 chunk 71 optimal weight: 0.8980 chunk 58 optimal weight: 0.2980 chunk 70 optimal weight: 0.0980 chunk 47 optimal weight: 0.7980 chunk 26 optimal weight: 0.4980 chunk 40 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 93 optimal weight: 0.0370 overall best weight: 0.2658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 86 GLN D 599 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.170906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.140450 restraints weight = 11402.637| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.10 r_work: 0.3637 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3482 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.4356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8279 Z= 0.214 Angle : 0.569 10.822 11247 Z= 0.280 Chirality : 0.045 0.216 1197 Planarity : 0.004 0.063 1448 Dihedral : 7.991 57.571 1219 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.39 % Allowed : 22.02 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.11 % 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: -0.93 (0.27), residues: 968 helix: 0.27 (0.27), residues: 410 sheet: 0.44 (0.61), residues: 72 loop : -1.59 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 433 HIS 0.005 0.001 HIS D 34 PHE 0.018 0.001 PHE A 389 TYR 0.025 0.001 TYR D 50 ARG 0.015 0.001 ARG D 192 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9619.73 seconds wall clock time: 167 minutes 47.57 seconds (10067.57 seconds total)