Starting phenix.real_space_refine on Mon Apr 28 23:43:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wpc_32682/04_2025/7wpc_32682_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wpc_32682/04_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_32682/04_2025/7wpc_32682.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wpc_32682/04_2025/7wpc_32682.map" model { file = "/net/cci-nas-00/data/ceres_data/7wpc_32682/04_2025/7wpc_32682_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wpc_32682/04_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-5669/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: 6.59, per 1000 atoms: 0.82 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: 1.99 Conformation dependent library (CDL) restraints added in 882.2 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: 0.77 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: 2.04 Time building geometry restraints manager: 2.36 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: 29.930 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 23.700 Find NCS groups from input model: 0.160 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:12.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.250 ------------------------------------------------------------------------------- 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 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 (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 Details of bonding type rmsd link_NAG-ASN : bond 0.00312 ( 5) link_NAG-ASN : angle 1.88729 ( 15) link_BETA1-4 : bond 0.00728 ( 2) link_BETA1-4 : angle 0.80704 ( 6) hydrogen bonds : bond 0.21225 ( 280) hydrogen bonds : angle 7.90010 ( 795) metal coordination : bond 0.05708 ( 1) SS BOND : bond 0.00220 ( 10) SS BOND : angle 0.83161 ( 20) covalent geometry : bond 0.00362 ( 8279) covalent geometry : angle 0.72033 (11247) *********************** 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 : 0.874 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: 1.1111 time to fit residues: 242.6380 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 : 0.831 ------------------------------------------------------------------------------- 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: 0.0170 chunk 38 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 29 optimal weight: 0.0570 chunk 45 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 87 optimal weight: 0.0980 overall best weight: 0.1736 ------------------------------------------------------------------------------- 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 531 GLN D 599 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.180032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.151656 restraints weight = 11632.273| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 2.06 r_work: 0.3812 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3665 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8297 Z= 0.119 Angle : 0.556 10.290 11288 Z= 0.273 Chirality : 0.045 0.278 1197 Planarity : 0.005 0.049 1448 Dihedral : 13.421 99.840 1221 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.62 % Allowed : 14.25 % Favored : 84.13 % 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: -2.66 (0.24), residues: 968 helix: -1.43 (0.23), residues: 402 sheet: -0.32 (0.58), residues: 72 loop : -2.29 (0.25), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 477 HIS 0.008 0.001 HIS D 34 PHE 0.018 0.001 PHE D 314 TYR 0.015 0.001 TYR D 202 ARG 0.007 0.001 ARG D 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00213 ( 5) link_NAG-ASN : angle 2.22166 ( 15) link_BETA1-4 : bond 0.00322 ( 2) link_BETA1-4 : angle 2.16261 ( 6) hydrogen bonds : bond 0.03617 ( 280) hydrogen bonds : angle 5.01098 ( 795) metal coordination : bond 0.00432 ( 1) SS BOND : bond 0.00139 ( 10) SS BOND : angle 0.72051 ( 20) covalent geometry : bond 0.00267 ( 8279) covalent geometry : angle 0.54769 (11247) *********************** 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 201 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 187 time to evaluate : 0.751 Fit side-chains revert: symmetry clash REVERT: A 354 ARG cc_start: 0.8424 (ttp80) cc_final: 0.8059 (ttp80) REVERT: A 436 ASN cc_start: 0.8486 (t0) cc_final: 0.8278 (t160) REVERT: A 450 TYR cc_start: 0.8259 (p90) cc_final: 0.8057 (p90) REVERT: B 383 LYS cc_start: 0.1764 (pttp) cc_final: 0.0847 (mtmt) REVERT: D 82 MET cc_start: 0.7559 (OUTLIER) cc_final: 0.6651 (mtp) REVERT: D 117 ASN cc_start: 0.8277 (m-40) cc_final: 0.7990 (m-40) REVERT: D 145 GLU cc_start: 0.6651 (OUTLIER) cc_final: 0.6070 (pm20) outliers start: 14 outliers final: 4 residues processed: 195 average time/residue: 1.1214 time to fit residues: 233.2896 Evaluate side-chains 177 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 171 time to evaluate : 0.883 ------------------------------------------------------------------------------- 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 35 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 65 optimal weight: 0.1980 chunk 22 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 67 optimal weight: 0.0040 chunk 56 optimal weight: 0.0270 chunk 62 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 1 optimal weight: 0.0970 chunk 38 optimal weight: 0.9990 overall best weight: 0.2248 ------------------------------------------------------------------------------- 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 B 391 ASN B 503 GLN ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 194 ASN D 505 HIS D 522 GLN D 531 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.176264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.146035 restraints weight = 11522.084| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 2.15 r_work: 0.3726 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3575 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2613 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= 0.123 Angle : 0.550 11.524 11288 Z= 0.267 Chirality : 0.043 0.245 1197 Planarity : 0.004 0.039 1448 Dihedral : 11.911 96.888 1219 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.78 % Allowed : 14.83 % Favored : 82.39 % 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: -1.96 (0.25), residues: 968 helix: -0.73 (0.25), residues: 405 sheet: 0.02 (0.60), residues: 72 loop : -2.03 (0.25), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 477 HIS 0.007 0.001 HIS D 34 PHE 0.013 0.001 PHE D 314 TYR 0.021 0.001 TYR D 50 ARG 0.005 0.000 ARG D 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00232 ( 5) link_NAG-ASN : angle 2.79279 ( 15) link_BETA1-4 : bond 0.00459 ( 2) link_BETA1-4 : angle 2.45840 ( 6) hydrogen bonds : bond 0.03614 ( 280) hydrogen bonds : angle 4.55911 ( 795) metal coordination : bond 0.00222 ( 1) SS BOND : bond 0.00134 ( 10) SS BOND : angle 0.49284 ( 20) covalent geometry : bond 0.00284 ( 8279) covalent geometry : angle 0.53797 (11247) *********************** 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: 24 poor density : 178 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 354 ARG cc_start: 0.8508 (ttp80) cc_final: 0.8135 (ttp80) REVERT: B 383 LYS cc_start: 0.2030 (pttp) cc_final: 0.0819 (mtmt) REVERT: D 117 ASN cc_start: 0.8288 (m-40) cc_final: 0.8024 (m-40) REVERT: D 145 GLU cc_start: 0.6822 (OUTLIER) cc_final: 0.6578 (pm20) REVERT: D 271 TRP cc_start: 0.8458 (OUTLIER) cc_final: 0.8063 (m-90) outliers start: 24 outliers final: 8 residues processed: 185 average time/residue: 1.1400 time to fit residues: 224.4599 Evaluate side-chains 185 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 175 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 145 GLU 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 46 optimal weight: 0.4980 chunk 94 optimal weight: 0.2980 chunk 84 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 33 optimal weight: 0.0870 chunk 23 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 87 optimal weight: 0.1980 chunk 59 optimal weight: 0.9980 overall best weight: 0.3758 ------------------------------------------------------------------------------- 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 447 ASN B 385 ASN ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 194 ASN D 378 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.172122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.141199 restraints weight = 11299.098| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 2.11 r_work: 0.3647 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3491 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.3379 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= 0.173 Angle : 0.559 7.743 11288 Z= 0.280 Chirality : 0.045 0.253 1197 Planarity : 0.004 0.037 1448 Dihedral : 10.833 97.209 1219 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.36 % Allowed : 16.92 % Favored : 79.72 % 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: -1.62 (0.26), residues: 968 helix: -0.34 (0.26), residues: 408 sheet: 0.04 (0.61), residues: 70 loop : -1.91 (0.25), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 477 HIS 0.008 0.002 HIS D 34 PHE 0.018 0.001 PHE D 523 TYR 0.020 0.001 TYR D 202 ARG 0.008 0.001 ARG D 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00195 ( 5) link_NAG-ASN : angle 2.07645 ( 15) link_BETA1-4 : bond 0.00458 ( 2) link_BETA1-4 : angle 2.27630 ( 6) hydrogen bonds : bond 0.03856 ( 280) hydrogen bonds : angle 4.55666 ( 795) metal coordination : bond 0.00446 ( 1) SS BOND : bond 0.00151 ( 10) SS BOND : angle 0.63456 ( 20) covalent geometry : bond 0.00405 ( 8279) covalent geometry : angle 0.55188 (11247) *********************** 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 205 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 176 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 400 ARG cc_start: 0.8594 (ptm-80) cc_final: 0.8278 (mtp180) REVERT: B 383 LYS cc_start: 0.2789 (pttp) cc_final: 0.0812 (mtmt) REVERT: D 60 GLN cc_start: 0.7561 (mm-40) cc_final: 0.7325 (mm-40) REVERT: D 82 MET cc_start: 0.8202 (OUTLIER) cc_final: 0.7435 (mtp) REVERT: D 117 ASN cc_start: 0.8278 (m-40) cc_final: 0.8020 (m-40) REVERT: D 155 SER cc_start: 0.7864 (OUTLIER) cc_final: 0.7345 (m) REVERT: D 215 TYR cc_start: 0.8007 (m-80) cc_final: 0.7769 (m-80) REVERT: D 225 ASP cc_start: 0.8018 (OUTLIER) cc_final: 0.7733 (m-30) REVERT: D 363 LYS cc_start: 0.8158 (mmpt) cc_final: 0.7944 (mmpt) REVERT: D 557 MET cc_start: 0.8791 (tmm) cc_final: 0.8500 (tmm) outliers start: 29 outliers final: 11 residues processed: 186 average time/residue: 1.1580 time to fit residues: 229.1993 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 : 0.852 ------------------------------------------------------------------------------- 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 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 155 SER Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 225 ASP 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 8 optimal weight: 0.9990 chunk 93 optimal weight: 0.3980 chunk 50 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 chunk 33 optimal weight: 0.0570 chunk 6 optimal weight: 0.4980 chunk 49 optimal weight: 0.0270 chunk 26 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 83 optimal weight: 0.5980 overall best weight: 0.3156 ------------------------------------------------------------------------------- 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** B 406 GLN ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4182 r_free = 0.4182 target = 0.171217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.140179 restraints weight = 11258.896| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.10 r_work: 0.3644 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3487 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8297 Z= 0.150 Angle : 0.535 7.897 11288 Z= 0.266 Chirality : 0.044 0.242 1197 Planarity : 0.004 0.044 1448 Dihedral : 10.388 92.160 1219 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.78 % Allowed : 18.42 % Favored : 78.79 % 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: -1.40 (0.26), residues: 968 helix: -0.06 (0.27), residues: 401 sheet: 0.16 (0.61), residues: 70 loop : -1.87 (0.25), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 477 HIS 0.007 0.001 HIS D 241 PHE 0.019 0.001 PHE A 389 TYR 0.027 0.001 TYR D 50 ARG 0.011 0.001 ARG D 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00821 ( 5) link_NAG-ASN : angle 2.52235 ( 15) link_BETA1-4 : bond 0.00491 ( 2) link_BETA1-4 : angle 1.92565 ( 6) hydrogen bonds : bond 0.03670 ( 280) hydrogen bonds : angle 4.44767 ( 795) metal coordination : bond 0.00300 ( 1) SS BOND : bond 0.00147 ( 10) SS BOND : angle 0.58740 ( 20) covalent geometry : bond 0.00353 ( 8279) covalent geometry : angle 0.52598 (11247) *********************** 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 197 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 400 ARG cc_start: 0.8605 (ptm-80) cc_final: 0.8265 (mtp180) REVERT: B 383 LYS cc_start: 0.2953 (pttp) cc_final: 0.0743 (mtmt) REVERT: D 35 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7561 (mp0) REVERT: D 52 THR cc_start: 0.8250 (m) cc_final: 0.8045 (m) REVERT: D 117 ASN cc_start: 0.8268 (m-40) cc_final: 0.8025 (m-40) REVERT: D 155 SER cc_start: 0.7980 (OUTLIER) cc_final: 0.7448 (m) REVERT: D 215 TYR cc_start: 0.8013 (m-80) cc_final: 0.7728 (m-80) REVERT: D 219 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.8344 (ttp-110) REVERT: D 225 ASP cc_start: 0.8015 (OUTLIER) cc_final: 0.7735 (m-30) REVERT: D 347 THR cc_start: 0.8325 (OUTLIER) cc_final: 0.8048 (p) REVERT: D 363 LYS cc_start: 0.8180 (mmpt) cc_final: 0.7922 (mmpt) REVERT: D 557 MET cc_start: 0.8766 (tmm) cc_final: 0.8414 (tmm) outliers start: 24 outliers final: 10 residues processed: 184 average time/residue: 1.3126 time to fit residues: 256.3117 Evaluate side-chains 181 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 166 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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 A residue 522 CYS Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 219 ARG 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 Chi-restraints excluded: chain D residue 527 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 64 optimal weight: 0.0000 chunk 44 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 14 optimal weight: 0.0870 chunk 94 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 92 optimal weight: 0.0170 chunk 42 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 overall best weight: 0.2800 ------------------------------------------------------------------------------- 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** ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 GLN D 239 HIS D 599 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.171580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.140646 restraints weight = 11212.452| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.09 r_work: 0.3643 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3488 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8297 Z= 0.138 Angle : 0.535 8.098 11288 Z= 0.266 Chirality : 0.044 0.262 1197 Planarity : 0.004 0.044 1448 Dihedral : 9.806 87.274 1219 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.43 % Allowed : 18.89 % Favored : 78.68 % 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: 0.12 (0.27), residues: 402 sheet: 0.35 (0.61), residues: 70 loop : -1.77 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 477 HIS 0.007 0.001 HIS D 34 PHE 0.020 0.001 PHE A 389 TYR 0.030 0.001 TYR D 50 ARG 0.011 0.001 ARG D 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00533 ( 5) link_NAG-ASN : angle 2.45616 ( 15) link_BETA1-4 : bond 0.00455 ( 2) link_BETA1-4 : angle 1.90818 ( 6) hydrogen bonds : bond 0.03640 ( 280) hydrogen bonds : angle 4.37722 ( 795) metal coordination : bond 0.00237 ( 1) SS BOND : bond 0.00148 ( 10) SS BOND : angle 0.57513 ( 20) covalent geometry : bond 0.00327 ( 8279) covalent geometry : angle 0.52642 (11247) *********************** 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 189 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 168 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 383 LYS cc_start: 0.2926 (pttp) cc_final: 0.0772 (mtmt) REVERT: D 82 MET cc_start: 0.8270 (OUTLIER) cc_final: 0.7500 (mtp) REVERT: D 117 ASN cc_start: 0.8264 (m-40) cc_final: 0.8017 (m-40) REVERT: D 215 TYR cc_start: 0.8062 (m-80) cc_final: 0.7768 (m-80) REVERT: D 225 ASP cc_start: 0.8052 (OUTLIER) cc_final: 0.7775 (m-30) REVERT: D 347 THR cc_start: 0.8367 (OUTLIER) cc_final: 0.8134 (p) REVERT: D 363 LYS cc_start: 0.8186 (mmpt) cc_final: 0.7897 (mmpt) REVERT: D 557 MET cc_start: 0.8749 (tmm) cc_final: 0.8449 (tmm) outliers start: 21 outliers final: 10 residues processed: 178 average time/residue: 1.3436 time to fit residues: 255.1855 Evaluate side-chains 181 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 168 time to evaluate : 0.918 ------------------------------------------------------------------------------- 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 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 145 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 527 GLU Chi-restraints excluded: chain D residue 574 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.0116 > 50: distance: 25 - 29: 35.024 distance: 30 - 31: 56.903 distance: 31 - 32: 63.465 distance: 31 - 33: 57.304 distance: 33 - 34: 54.807 distance: 34 - 35: 53.281 distance: 35 - 36: 39.868 distance: 35 - 40: 39.992 distance: 37 - 38: 17.736 distance: 37 - 39: 56.513 distance: 40 - 41: 40.051 distance: 41 - 42: 40.054 distance: 41 - 44: 39.541 distance: 42 - 46: 57.060 distance: 46 - 47: 38.707 distance: 47 - 50: 57.178 distance: 48 - 53: 39.804 distance: 50 - 51: 43.332 distance: 51 - 52: 46.247 distance: 53 - 54: 40.895 distance: 54 - 55: 7.043 distance: 54 - 57: 38.883 distance: 55 - 56: 40.357 distance: 55 - 60: 6.697 distance: 57 - 58: 38.978 distance: 60 - 61: 39.335 distance: 61 - 62: 52.616 distance: 61 - 64: 56.468 distance: 62 - 63: 7.503 distance: 62 - 69: 40.268 distance: 64 - 65: 15.131 distance: 65 - 66: 46.349 distance: 67 - 68: 39.547 distance: 69 - 70: 40.342 distance: 73 - 74: 57.876 distance: 74 - 75: 30.879 distance: 74 - 76: 34.712 distance: 77 - 78: 59.118 distance: 78 - 79: 46.490 distance: 78 - 81: 23.642 distance: 81 - 82: 35.475 distance: 82 - 83: 5.839 distance: 82 - 84: 65.524 distance: 85 - 86: 49.370 distance: 86 - 87: 41.023 distance: 86 - 89: 25.963 distance: 87 - 88: 24.590 distance: 87 - 93: 34.533 distance: 89 - 90: 8.014 distance: 90 - 91: 30.186 distance: 90 - 92: 30.685 distance: 93 - 94: 32.460 distance: 94 - 95: 48.964 distance: 94 - 97: 52.120 distance: 95 - 96: 7.985 distance: 95 - 101: 28.580 distance: 97 - 98: 36.540 distance: 98 - 99: 36.338 distance: 98 - 100: 34.798