Starting phenix.real_space_refine on Thu Jul 2 09:40:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wpc_32682/07_2026/7wpc_32682_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wpc_32682/07_2026/7wpc_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 { model { file = "/net/cci-nas-00/data/ceres_data/7wpc_32682/07_2026/7wpc_32682_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wpc_32682/07_2026/7wpc_32682_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wpc_32682/07_2026/7wpc_32682.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wpc_32682/07_2026/7wpc_32682.map" } resolution = 2.57 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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, 43 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {' ZN': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.77, per 1000 atoms: 0.22 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: 0.44 Conformation dependent library (CDL) restraints added in 391.0 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: 0.13 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: 0.78 Time building geometry restraints manager: 0.61 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: 7.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 7.980 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:6.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 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 8297 Z= 0.202 Angle : 0.723 9.460 11288 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.002 0.000 ARG D 514 TYR 0.013 0.001 TYR D 183 PHE 0.018 0.001 PHE B 512 TRP 0.011 0.001 TRP D 477 HIS 0.005 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.20 ( 8279) covalent geometry : angle 0.72033 / 0.42 (11247) SS BOND : bond 0.00220 / 0.09 ( 10) SS BOND : angle 0.83161 / 0.50 ( 20) hydrogen bonds : bond 0.21225 / 14.24 ( 280) hydrogen bonds : angle 7.90010 / 5.26 ( 795) metal coordination : bond 0.05708 / 3.00 ( 1) link_BETA1-4 : bond 0.00728 / 0.37 ( 2) link_BETA1-4 : angle 0.80704 / 0.41 ( 6) link_NAG-ASN : bond 0.00312 / 0.18 ( 5) link_NAG-ASN : angle 1.88729 / 1.10 ( 15) *********************** 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 : 0.243 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: 0.7451 (m-90) REVERT: D 362 THR cc_start: 0.7658 (m) cc_final: 0.7366 (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: 0.5001 time to fit residues: 109.2062 Evaluate side-chains 169 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 168 time to evaluate : 0.289 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.0170 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 0.0060 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.0000 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 0.4980 overall best weight: 0.2038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 58 ASN D 61 ASN D 154 ASN D 194 ASN D 221 GLN D 277 ASN D 300 GLN 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 = 0.4285 r_free = 0.4285 target = 0.179454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.150808 restraints weight = 11723.284| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 2.08 r_work: 0.3793 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3646 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8297 Z= 0.128 Angle : 0.558 10.080 11288 Z= 0.277 Chirality : 0.045 0.273 1197 Planarity : 0.005 0.051 1448 Dihedral : 13.577 100.332 1221 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.74 % Allowed : 14.02 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.72 (0.24), residues: 968 helix: -1.50 (0.23), residues: 402 sheet: -0.31 (0.58), residues: 72 loop : -2.32 (0.25), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 192 TYR 0.015 0.001 TYR D 202 PHE 0.018 0.001 PHE D 314 TRP 0.011 0.001 TRP D 477 HIS 0.007 0.001 HIS D 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 8279) covalent geometry : angle 0.55084 / 0.28 (11247) SS BOND : bond 0.00158 / 0.11 ( 10) SS BOND : angle 0.69547 / 0.40 ( 20) hydrogen bonds : bond 0.03863 / 2.54 ( 280) hydrogen bonds : angle 5.06846 / 3.32 ( 795) metal coordination : bond 0.00978 / 0.51 ( 1) link_BETA1-4 : bond 0.00651 / 0.31 ( 2) link_BETA1-4 : angle 2.08211 / 1.09 ( 6) link_NAG-ASN : bond 0.00438 / 0.23 ( 5) link_NAG-ASN : angle 2.19230 / 1.19 ( 15) *********************** 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 200 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 185 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 354 ARG cc_start: 0.8421 (ttp80) cc_final: 0.8042 (ttp80) REVERT: A 436 ASN cc_start: 0.8478 (t0) cc_final: 0.8278 (t160) REVERT: B 383 LYS cc_start: 0.1822 (pttp) cc_final: 0.0851 (mtmt) REVERT: D 82 MET cc_start: 0.7593 (OUTLIER) cc_final: 0.6707 (mtp) REVERT: D 117 ASN cc_start: 0.8262 (m-40) cc_final: 0.7982 (m-40) REVERT: D 145 GLU cc_start: 0.6673 (OUTLIER) cc_final: 0.6083 (pm20) outliers start: 15 outliers final: 4 residues processed: 193 average time/residue: 0.5155 time to fit residues: 105.9638 Evaluate side-chains 180 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 174 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 ARG Chi-restraints excluded: chain A residue 347 VAL 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 82 optimal weight: 0.0570 chunk 56 optimal weight: 0.9990 chunk 89 optimal weight: 0.0970 chunk 79 optimal weight: 0.4980 chunk 52 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 94 optimal weight: 0.0970 chunk 27 optimal weight: 1.9990 overall best weight: 0.3094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN A 445 ASN B 391 ASN ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 194 ASN D 378 HIS D 505 HIS D 531 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.174327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.143859 restraints weight = 11216.295| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 2.08 r_work: 0.3693 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3542 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8297 Z= 0.152 Angle : 0.587 11.136 11288 Z= 0.287 Chirality : 0.044 0.244 1197 Planarity : 0.004 0.041 1448 Dihedral : 11.726 96.883 1219 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.67 % Allowed : 15.18 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.25), residues: 968 helix: -0.73 (0.25), residues: 404 sheet: -0.01 (0.60), residues: 70 loop : -2.03 (0.25), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 192 TYR 0.029 0.001 TYR D 50 PHE 0.015 0.001 PHE D 523 TRP 0.009 0.001 TRP D 478 HIS 0.007 0.001 HIS D 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 8279) covalent geometry : angle 0.57444 / 0.28 (11247) SS BOND : bond 0.00160 / 0.12 ( 10) SS BOND : angle 0.56844 / 0.33 ( 20) hydrogen bonds : bond 0.04001 / 2.66 ( 280) hydrogen bonds : angle 4.63892 / 3.04 ( 795) metal coordination : bond 0.00266 / 0.14 ( 1) link_BETA1-4 : bond 0.00544 / 0.26 ( 2) link_BETA1-4 : angle 2.56361 / 1.28 ( 6) link_NAG-ASN : bond 0.00319 / 0.15 ( 5) link_NAG-ASN : angle 3.01765 / 1.61 ( 15) *********************** 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 202 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 179 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 354 ARG cc_start: 0.8534 (ttp80) cc_final: 0.8033 (ttp80) REVERT: A 511 SER cc_start: 0.8383 (t) cc_final: 0.8175 (p) REVERT: B 383 LYS cc_start: 0.2280 (pttp) cc_final: 0.0863 (mtmt) REVERT: D 82 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7109 (mtp) REVERT: D 117 ASN cc_start: 0.8289 (m-40) cc_final: 0.8026 (m-40) REVERT: D 271 TRP cc_start: 0.8492 (OUTLIER) cc_final: 0.8172 (m-90) REVERT: D 476 LYS cc_start: 0.8310 (tppp) cc_final: 0.7874 (tppp) REVERT: D 557 MET cc_start: 0.8791 (tmm) cc_final: 0.8451 (tmm) outliers start: 23 outliers final: 9 residues processed: 186 average time/residue: 0.5636 time to fit residues: 111.0535 Evaluate side-chains 184 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 173 time to evaluate : 0.328 ------------------------------------------------------------------------------- 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 465 ILE Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 271 TRP Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain D residue 347 THR 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 91 optimal weight: 0.0670 chunk 12 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 81 optimal weight: 0.4980 chunk 44 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 37 optimal weight: 0.3980 chunk 73 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 13 optimal weight: 0.3980 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN B 503 GLN ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 493 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.171089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.139660 restraints weight = 11418.604| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.14 r_work: 0.3632 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3477 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 8297 Z= 0.184 Angle : 0.560 7.736 11288 Z= 0.281 Chirality : 0.046 0.250 1197 Planarity : 0.004 0.039 1448 Dihedral : 10.831 97.030 1219 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 4.17 % Allowed : 16.34 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.26), residues: 968 helix: -0.33 (0.26), residues: 406 sheet: 0.02 (0.61), residues: 70 loop : -1.92 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 192 TYR 0.026 0.001 TYR D 50 PHE 0.019 0.001 PHE D 523 TRP 0.010 0.001 TRP D 477 HIS 0.008 0.001 HIS D 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.18 ( 8279) covalent geometry : angle 0.55305 / 0.28 (11247) SS BOND : bond 0.00145 / 0.11 ( 10) SS BOND : angle 0.67241 / 0.38 ( 20) hydrogen bonds : bond 0.03968 / 2.64 ( 280) hydrogen bonds : angle 4.59863 / 3.02 ( 795) metal coordination : bond 0.00364 / 0.19 ( 1) link_BETA1-4 : bond 0.00215 / 0.11 ( 2) link_BETA1-4 : angle 2.20880 / 1.11 ( 6) link_NAG-ASN : bond 0.00216 / 0.12 ( 5) link_NAG-ASN : angle 1.94326 / 1.11 ( 15) *********************** 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 220 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 184 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 362 TYR cc_start: 0.8866 (m-80) cc_final: 0.8604 (m-80) REVERT: B 383 LYS cc_start: 0.3203 (pttp) cc_final: 0.0809 (mtmt) REVERT: D 60 GLN cc_start: 0.7456 (mm-40) cc_final: 0.7249 (mm-40) REVERT: D 102 GLN cc_start: 0.6478 (OUTLIER) cc_final: 0.5671 (pp30) REVERT: D 117 ASN cc_start: 0.8291 (m-40) cc_final: 0.8035 (m-40) REVERT: D 155 SER cc_start: 0.8046 (OUTLIER) cc_final: 0.7568 (m) REVERT: D 215 TYR cc_start: 0.8077 (m-80) cc_final: 0.7766 (m-80) REVERT: D 225 ASP cc_start: 0.8025 (OUTLIER) cc_final: 0.7756 (m-30) REVERT: D 266 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8630 (mt) REVERT: D 363 LYS cc_start: 0.8172 (mmpt) cc_final: 0.7949 (mmpt) REVERT: D 476 LYS cc_start: 0.8438 (tppp) cc_final: 0.8068 (tppp) REVERT: D 557 MET cc_start: 0.8775 (tmm) cc_final: 0.8511 (tmm) outliers start: 36 outliers final: 14 residues processed: 198 average time/residue: 0.5524 time to fit residues: 116.2569 Evaluate side-chains 186 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 168 time to evaluate : 0.297 ------------------------------------------------------------------------------- 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 68 LYS Chi-restraints excluded: chain D residue 102 GLN Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 527 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 79 optimal weight: 0.0770 chunk 53 optimal weight: 0.8980 chunk 89 optimal weight: 0.4980 chunk 78 optimal weight: 0.0980 chunk 40 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 92 optimal weight: 0.4980 chunk 14 optimal weight: 0.0670 chunk 34 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 overall best weight: 0.2476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 GLN D 194 ASN D 388 GLN D 552 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.171648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.140571 restraints weight = 11392.167| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.13 r_work: 0.3648 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8297 Z= 0.129 Angle : 0.543 8.319 11288 Z= 0.268 Chirality : 0.044 0.244 1197 Planarity : 0.004 0.044 1448 Dihedral : 10.391 92.056 1219 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.13 % Allowed : 17.61 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.26), residues: 968 helix: -0.06 (0.27), residues: 400 sheet: 0.22 (0.61), residues: 70 loop : -1.81 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 192 TYR 0.029 0.001 TYR D 50 PHE 0.019 0.001 PHE A 389 TRP 0.011 0.001 TRP D 477 HIS 0.006 0.001 HIS D 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 8279) covalent geometry : angle 0.53345 / 0.27 (11247) SS BOND : bond 0.00197 / 0.12 ( 10) SS BOND : angle 0.59086 / 0.33 ( 20) hydrogen bonds : bond 0.03626 / 2.40 ( 280) hydrogen bonds : angle 4.47545 / 2.94 ( 795) metal coordination : bond 0.00193 / 0.10 ( 1) link_BETA1-4 : bond 0.00404 / 0.21 ( 2) link_BETA1-4 : angle 1.97098 / 1.01 ( 6) link_NAG-ASN : bond 0.00611 / 0.31 ( 5) link_NAG-ASN : angle 2.50642 / 1.37 ( 15) *********************** 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 193 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 166 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 383 LYS cc_start: 0.3041 (pttp) cc_final: 0.0803 (mtmt) REVERT: D 52 THR cc_start: 0.8222 (m) cc_final: 0.7949 (m) REVERT: D 60 GLN cc_start: 0.7462 (mm-40) cc_final: 0.7261 (mm-40) REVERT: D 102 GLN cc_start: 0.6434 (OUTLIER) cc_final: 0.5574 (pp30) REVERT: D 117 ASN cc_start: 0.8255 (m-40) cc_final: 0.8004 (m-40) REVERT: D 155 SER cc_start: 0.7906 (OUTLIER) cc_final: 0.7381 (m) REVERT: D 215 TYR cc_start: 0.8055 (m-80) cc_final: 0.7767 (m-80) REVERT: D 225 ASP cc_start: 0.8027 (OUTLIER) cc_final: 0.7751 (m-30) REVERT: D 347 THR cc_start: 0.8327 (OUTLIER) cc_final: 0.8082 (p) REVERT: D 363 LYS cc_start: 0.8216 (mmpt) cc_final: 0.7938 (mmpt) REVERT: D 557 MET cc_start: 0.8759 (tmm) cc_final: 0.8526 (tmm) outliers start: 27 outliers final: 10 residues processed: 179 average time/residue: 0.5561 time to fit residues: 105.7835 Evaluate side-chains 184 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 170 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 VAL 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 155 SER Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 330 ASN 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 18 optimal weight: 0.4980 chunk 89 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 74 optimal weight: 0.4980 chunk 72 optimal weight: 0.4980 chunk 55 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 42 optimal weight: 0.2980 chunk 19 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 46 optimal weight: 0.0770 overall best weight: 0.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 GLN D 175 GLN D 239 HIS D 599 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.170631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.139722 restraints weight = 11375.021| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.11 r_work: 0.3629 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8297 Z= 0.171 Angle : 0.565 8.299 11288 Z= 0.281 Chirality : 0.046 0.258 1197 Planarity : 0.004 0.045 1448 Dihedral : 9.999 88.207 1219 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.67 % Allowed : 18.89 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.26), residues: 968 helix: 0.03 (0.27), residues: 405 sheet: 0.35 (0.61), residues: 70 loop : -1.76 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 192 TYR 0.026 0.001 TYR D 50 PHE 0.018 0.001 PHE A 389 TRP 0.011 0.001 TRP D 477 HIS 0.007 0.001 HIS D 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 ( 8279) covalent geometry : angle 0.55678 / 0.28 (11247) SS BOND : bond 0.00150 / 0.11 ( 10) SS BOND : angle 0.63567 / 0.36 ( 20) hydrogen bonds : bond 0.03861 / 2.59 ( 280) hydrogen bonds : angle 4.48920 / 2.96 ( 795) metal coordination : bond 0.00384 / 0.20 ( 1) link_BETA1-4 : bond 0.00380 / 0.20 ( 2) link_BETA1-4 : angle 1.93551 / 1.00 ( 6) link_NAG-ASN : bond 0.00462 / 0.24 ( 5) link_NAG-ASN : angle 2.46151 / 1.37 ( 15) *********************** 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 196 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 173 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 383 LYS cc_start: 0.3171 (pttp) cc_final: 0.0823 (mtmt) REVERT: D 82 MET cc_start: 0.8342 (OUTLIER) cc_final: 0.7568 (mtp) REVERT: D 87 GLU cc_start: 0.7247 (mp0) cc_final: 0.6969 (mm-30) REVERT: D 102 GLN cc_start: 0.6469 (OUTLIER) cc_final: 0.5619 (pp30) REVERT: D 117 ASN cc_start: 0.8266 (m-40) cc_final: 0.7993 (m-40) REVERT: D 155 SER cc_start: 0.8163 (OUTLIER) cc_final: 0.7654 (m) REVERT: D 215 TYR cc_start: 0.8144 (m-80) cc_final: 0.7826 (m-80) REVERT: D 225 ASP cc_start: 0.8068 (OUTLIER) cc_final: 0.7790 (m-30) REVERT: D 347 THR cc_start: 0.8360 (OUTLIER) cc_final: 0.8109 (p) REVERT: D 363 LYS cc_start: 0.8217 (mmpt) cc_final: 0.7939 (mmpt) REVERT: D 557 MET cc_start: 0.8783 (tmm) cc_final: 0.8449 (tmm) outliers start: 23 outliers final: 12 residues processed: 185 average time/residue: 0.5683 time to fit residues: 111.5984 Evaluate side-chains 180 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 163 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 VAL 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 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 155 SER Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 330 ASN Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 487 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 93 optimal weight: 0.0270 chunk 82 optimal weight: 0.3980 chunk 81 optimal weight: 0.3980 chunk 55 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 chunk 30 optimal weight: 9.9990 chunk 70 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 59 optimal weight: 0.4980 chunk 94 optimal weight: 0.8980 overall best weight: 0.3838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 599 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.170121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.137854 restraints weight = 11342.844| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.23 r_work: 0.3618 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8297 Z= 0.174 Angle : 0.578 8.861 11288 Z= 0.286 Chirality : 0.046 0.270 1197 Planarity : 0.004 0.048 1448 Dihedral : 9.505 83.138 1219 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.43 % Allowed : 19.35 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.26), residues: 968 helix: 0.07 (0.27), residues: 402 sheet: 0.44 (0.61), residues: 70 loop : -1.69 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 192 TYR 0.026 0.001 TYR D 50 PHE 0.020 0.001 PHE A 389 TRP 0.010 0.001 TRP D 477 HIS 0.007 0.001 HIS D 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.17 ( 8279) covalent geometry : angle 0.56965 / 0.28 (11247) SS BOND : bond 0.00161 / 0.12 ( 10) SS BOND : angle 0.65966 / 0.38 ( 20) hydrogen bonds : bond 0.03868 / 2.59 ( 280) hydrogen bonds : angle 4.51287 / 2.98 ( 795) metal coordination : bond 0.00384 / 0.20 ( 1) link_BETA1-4 : bond 0.00545 / 0.28 ( 2) link_BETA1-4 : angle 1.90417 / 0.99 ( 6) link_NAG-ASN : bond 0.00475 / 0.24 ( 5) link_NAG-ASN : angle 2.50124 / 1.40 ( 15) *********************** 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 192 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 171 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 ARG cc_start: 0.8408 (ttp80) cc_final: 0.7875 (ttp80) REVERT: B 383 LYS cc_start: 0.3127 (pttp) cc_final: 0.0827 (mttp) REVERT: D 82 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.8162 (mtm) REVERT: D 87 GLU cc_start: 0.7356 (mp0) cc_final: 0.7098 (mm-30) REVERT: D 102 GLN cc_start: 0.6544 (OUTLIER) cc_final: 0.5656 (pp30) REVERT: D 117 ASN cc_start: 0.8277 (m-40) cc_final: 0.8011 (m-40) REVERT: D 215 TYR cc_start: 0.8210 (m-80) cc_final: 0.7880 (m-80) REVERT: D 225 ASP cc_start: 0.8091 (OUTLIER) cc_final: 0.7822 (m-30) REVERT: D 347 THR cc_start: 0.8391 (OUTLIER) cc_final: 0.8142 (p) REVERT: D 363 LYS cc_start: 0.8259 (mmpt) cc_final: 0.7979 (mmpt) REVERT: D 557 MET cc_start: 0.8802 (tmm) cc_final: 0.8497 (tmm) outliers start: 21 outliers final: 13 residues processed: 181 average time/residue: 0.5818 time to fit residues: 111.6777 Evaluate side-chains 191 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 174 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 VAL 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 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 Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 574 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 3 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 63 optimal weight: 0.3980 chunk 40 optimal weight: 0.2980 chunk 48 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4137 r_free = 0.4137 target = 0.168379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.136108 restraints weight = 11229.264| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.22 r_work: 0.3596 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3440 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 8297 Z= 0.233 Angle : 0.629 9.212 11288 Z= 0.311 Chirality : 0.048 0.273 1197 Planarity : 0.004 0.056 1448 Dihedral : 9.127 76.927 1219 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.32 % Allowed : 19.58 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.26), residues: 968 helix: -0.03 (0.27), residues: 404 sheet: 0.33 (0.60), residues: 72 loop : -1.67 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 192 TYR 0.034 0.002 TYR D 50 PHE 0.022 0.002 PHE A 389 TRP 0.014 0.002 TRP D 477 HIS 0.008 0.001 HIS D 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00558 / 0.23 ( 8279) covalent geometry : angle 0.62041 / 0.31 (11247) SS BOND : bond 0.00185 / 0.14 ( 10) SS BOND : angle 0.85257 / 0.48 ( 20) hydrogen bonds : bond 0.04250 / 2.87 ( 280) hydrogen bonds : angle 4.70014 / 3.12 ( 795) metal coordination : bond 0.00459 / 0.24 ( 1) link_BETA1-4 : bond 0.00534 / 0.27 ( 2) link_BETA1-4 : angle 2.02509 / 1.08 ( 6) link_NAG-ASN : bond 0.00487 / 0.24 ( 5) link_NAG-ASN : angle 2.62336 / 1.50 ( 15) *********************** 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 195 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 175 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 383 LYS cc_start: 0.3212 (pttp) cc_final: 0.0632 (mttp) REVERT: D 87 GLU cc_start: 0.7387 (mp0) cc_final: 0.7157 (mm-30) REVERT: D 102 GLN cc_start: 0.6704 (OUTLIER) cc_final: 0.5835 (pp30) REVERT: D 117 ASN cc_start: 0.8291 (m-40) cc_final: 0.8036 (m-40) REVERT: D 215 TYR cc_start: 0.8303 (m-80) cc_final: 0.7935 (m-80) REVERT: D 225 ASP cc_start: 0.8113 (OUTLIER) cc_final: 0.7832 (m-30) REVERT: D 347 THR cc_start: 0.8381 (OUTLIER) cc_final: 0.8159 (p) REVERT: D 363 LYS cc_start: 0.8247 (mmpt) cc_final: 0.7962 (mmpt) REVERT: D 557 MET cc_start: 0.8830 (tmm) cc_final: 0.8526 (tmm) outliers start: 20 outliers final: 14 residues processed: 184 average time/residue: 0.5936 time to fit residues: 115.7503 Evaluate side-chains 190 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 173 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 VAL 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 329 ILE Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain D residue 68 LYS 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 Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 574 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 35 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 65 optimal weight: 0.2980 chunk 57 optimal weight: 0.3980 chunk 84 optimal weight: 0.1980 chunk 36 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 85 optimal weight: 0.5980 chunk 22 optimal weight: 0.0970 chunk 42 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 overall best weight: 0.3178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 502 HIS D 86 GLN D 121 ASN D 599 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.166893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.134732 restraints weight = 11126.027| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.16 r_work: 0.3623 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.4362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8297 Z= 0.156 Angle : 0.593 10.343 11288 Z= 0.291 Chirality : 0.045 0.264 1197 Planarity : 0.004 0.061 1448 Dihedral : 8.639 70.121 1219 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.09 % Allowed : 20.51 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.26), residues: 968 helix: 0.10 (0.27), residues: 406 sheet: 0.39 (0.61), residues: 72 loop : -1.62 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 192 TYR 0.025 0.001 TYR D 50 PHE 0.021 0.001 PHE A 389 TRP 0.011 0.001 TRP D 477 HIS 0.006 0.001 HIS D 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 ( 8279) covalent geometry : angle 0.58346 / 0.29 (11247) SS BOND : bond 0.00164 / 0.11 ( 10) SS BOND : angle 0.65249 / 0.37 ( 20) hydrogen bonds : bond 0.03783 / 2.51 ( 280) hydrogen bonds : angle 4.59306 / 3.05 ( 795) metal coordination : bond 0.00249 / 0.13 ( 1) link_BETA1-4 : bond 0.00568 / 0.29 ( 2) link_BETA1-4 : angle 2.07273 / 1.11 ( 6) link_NAG-ASN : bond 0.00470 / 0.24 ( 5) link_NAG-ASN : angle 2.61312 / 1.51 ( 15) *********************** 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 190 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 172 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 ARG cc_start: 0.8364 (ttp80) cc_final: 0.7861 (ttp80) REVERT: A 514 LEU cc_start: 0.7552 (tp) cc_final: 0.7318 (tp) REVERT: B 383 LYS cc_start: 0.3044 (pttp) cc_final: 0.0585 (mttp) REVERT: D 87 GLU cc_start: 0.7342 (mp0) cc_final: 0.7084 (mm-30) REVERT: D 117 ASN cc_start: 0.8266 (m-40) cc_final: 0.8011 (m-40) REVERT: D 215 TYR cc_start: 0.8259 (m-80) cc_final: 0.7952 (m-80) REVERT: D 225 ASP cc_start: 0.8080 (OUTLIER) cc_final: 0.7813 (m-30) REVERT: D 347 THR cc_start: 0.8393 (OUTLIER) cc_final: 0.8186 (p) REVERT: D 363 LYS cc_start: 0.8236 (mmpt) cc_final: 0.7960 (mmpt) REVERT: D 557 MET cc_start: 0.8810 (tmm) cc_final: 0.8537 (tmm) outliers start: 18 outliers final: 11 residues processed: 182 average time/residue: 0.5760 time to fit residues: 111.2848 Evaluate side-chains 183 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 170 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 VAL 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 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 574 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 87 optimal weight: 0.6980 chunk 63 optimal weight: 0.0470 chunk 3 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 67 optimal weight: 0.0770 chunk 72 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 61 optimal weight: 0.1980 chunk 56 optimal weight: 0.8980 chunk 92 optimal weight: 0.6980 overall best weight: 0.3236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4150 r_free = 0.4150 target = 0.169021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.136965 restraints weight = 11261.569| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.22 r_work: 0.3619 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.4429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8297 Z= 0.158 Angle : 0.602 10.237 11288 Z= 0.295 Chirality : 0.046 0.234 1197 Planarity : 0.004 0.064 1448 Dihedral : 8.173 61.763 1219 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.62 % Allowed : 21.44 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.27), residues: 968 helix: 0.15 (0.27), residues: 405 sheet: 0.39 (0.60), residues: 72 loop : -1.59 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 192 TYR 0.023 0.001 TYR D 202 PHE 0.021 0.001 PHE A 389 TRP 0.011 0.001 TRP D 477 HIS 0.006 0.001 HIS D 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 ( 8279) covalent geometry : angle 0.59224 / 0.29 (11247) SS BOND : bond 0.00157 / 0.11 ( 10) SS BOND : angle 0.66503 / 0.38 ( 20) hydrogen bonds : bond 0.03799 / 2.52 ( 280) hydrogen bonds : angle 4.60888 / 3.05 ( 795) metal coordination : bond 0.00284 / 0.15 ( 1) link_BETA1-4 : bond 0.00691 / 0.35 ( 2) link_BETA1-4 : angle 2.08459 / 1.14 ( 6) link_NAG-ASN : bond 0.00476 / 0.24 ( 5) link_NAG-ASN : angle 2.68347 / 1.57 ( 15) ********************** 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 186 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 172 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 514 LEU cc_start: 0.7587 (tp) cc_final: 0.7340 (tp) REVERT: B 383 LYS cc_start: 0.3094 (pttp) cc_final: 0.0743 (mttp) REVERT: D 87 GLU cc_start: 0.7345 (mp0) cc_final: 0.7088 (mm-30) REVERT: D 117 ASN cc_start: 0.8270 (m-40) cc_final: 0.8013 (m-40) REVERT: D 215 TYR cc_start: 0.8359 (m-80) cc_final: 0.8018 (m-80) REVERT: D 225 ASP cc_start: 0.8033 (OUTLIER) cc_final: 0.7743 (m-30) REVERT: D 347 THR cc_start: 0.8422 (OUTLIER) cc_final: 0.8210 (p) REVERT: D 363 LYS cc_start: 0.8241 (mmpt) cc_final: 0.7960 (mmpt) REVERT: D 557 MET cc_start: 0.8800 (tmm) cc_final: 0.8528 (tmm) outliers start: 14 outliers final: 11 residues processed: 179 average time/residue: 0.5605 time to fit residues: 106.3648 Evaluate side-chains 179 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 166 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 VAL 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 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 574 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 64 optimal weight: 0.6980 chunk 78 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 9 optimal weight: 0.4980 chunk 89 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 65 optimal weight: 0.5980 chunk 15 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 599 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.166788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.134663 restraints weight = 11245.403| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.21 r_work: 0.3594 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.4613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 8297 Z= 0.247 Angle : 0.652 10.416 11288 Z= 0.320 Chirality : 0.048 0.209 1197 Planarity : 0.005 0.053 1448 Dihedral : 7.903 57.334 1219 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.74 % Allowed : 21.55 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.26), residues: 968 helix: 0.05 (0.27), residues: 405 sheet: 0.32 (0.60), residues: 72 loop : -1.61 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 192 TYR 0.023 0.002 TYR D 202 PHE 0.022 0.002 PHE A 389 TRP 0.012 0.002 TRP D 477 HIS 0.009 0.001 HIS D 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00590 / 0.25 ( 8279) covalent geometry : angle 0.64217 / 0.32 (11247) SS BOND : bond 0.00186 / 0.15 ( 10) SS BOND : angle 0.90118 / 0.51 ( 20) hydrogen bonds : bond 0.04299 / 2.91 ( 280) hydrogen bonds : angle 4.77264 / 3.16 ( 795) metal coordination : bond 0.00465 / 0.24 ( 1) link_BETA1-4 : bond 0.00666 / 0.33 ( 2) link_BETA1-4 : angle 2.15695 / 1.19 ( 6) link_NAG-ASN : bond 0.00482 / 0.24 ( 5) link_NAG-ASN : angle 2.79778 / 1.67 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4328.19 seconds wall clock time: 74 minutes 28.69 seconds (4468.69 seconds total)