Starting phenix.real_space_refine on Tue May 13 03:59:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z64_39791/05_2025/8z64_39791.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z64_39791/05_2025/8z64_39791.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z64_39791/05_2025/8z64_39791.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z64_39791/05_2025/8z64_39791.map" model { file = "/net/cci-nas-00/data/ceres_data/8z64_39791/05_2025/8z64_39791.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z64_39791/05_2025/8z64_39791.cif" } resolution = 3.53 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= 0.010 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: 4 Type Number sf(0) Gaussians S 47 5.16 5 C 6176 2.51 5 N 1576 2.21 5 O 1866 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 71 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 9665 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2145 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 16, 'TRANS': 255} Chain: "C" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2369 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 15, 'TRANS': 279} 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: "B" 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: "F" 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: "G" 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: "H" 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: "I" 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: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 5.52, per 1000 atoms: 0.57 Number of scatterers: 9665 At special positions: 0 Unit cell: (134.47, 82.11, 155.89, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 47 16.00 O 1866 8.00 N 1576 7.00 C 6176 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " 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 B 1 " - " NAG B 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG B 1 " - " ASN A 331 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 149 " " NAG C1304 " - " ASN C 165 " " NAG C1305 " - " ASN C 234 " " NAG D 701 " - " ASN D 103 " " NAG D 702 " - " ASN D 322 " " NAG D 703 " - " ASN D 432 " " NAG D 704 " - " ASN D 53 " " NAG E 1 " - " ASN A 343 " " NAG F 1 " - " ASN C 17 " " NAG G 1 " - " ASN C 122 " " NAG H 1 " - " ASN D 90 " " NAG I 1 " - " ASN D 546 " Time building additional restraints: 2.61 Conformation dependent library (CDL) restraints added in 1.1 seconds 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2188 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 9 sheets defined 37.9% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 384 through 390 removed outlier: 3.727A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.788A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 removed outlier: 3.606A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'D' and resid 20 through 52 removed outlier: 3.715A pdb=" N GLU D 37 " --> pdb=" O ASN D 33 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU D 39 " --> pdb=" O GLU D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 76 Processing helix chain 'D' and resid 90 through 101 Processing helix chain 'D' and resid 109 through 130 removed outlier: 3.502A pdb=" N GLY D 130 " --> pdb=" O ILE D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 154 Processing helix chain 'D' and resid 157 through 172 removed outlier: 3.535A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (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 Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 220 through 250 removed outlier: 3.914A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) Proline residue: D 235 - end of helix removed outlier: 3.747A pdb=" N ASN D 250 " --> pdb=" O ALA D 246 " (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 277 No H-bonds generated for 'chain 'D' and resid 275 through 277' Processing helix chain 'D' and resid 278 through 283 Processing helix chain 'D' and resid 293 through 299 removed outlier: 3.555A pdb=" N VAL D 298 " --> pdb=" O THR D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 317 Processing helix chain 'D' and resid 324 through 331 removed outlier: 3.889A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU D 329 " --> pdb=" O GLN D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 386 removed outlier: 3.612A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 388 No H-bonds generated for 'chain 'D' and resid 387 through 388' Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 399 through 413 removed outlier: 3.944A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 422 Processing helix chain 'D' and resid 431 through 447 Processing helix chain 'D' and resid 448 through 466 removed outlier: 4.442A pdb=" N PHE D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 499 through 503 removed outlier: 3.612A pdb=" N LEU D 503 " --> pdb=" O PRO D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 509 removed outlier: 3.531A pdb=" N ASN D 508 " --> pdb=" O HIS D 505 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP D 509 " --> pdb=" O VAL D 506 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 505 through 509' Processing helix chain 'D' and resid 512 through 533 removed outlier: 4.161A pdb=" N TYR D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN D 524 " --> pdb=" O LEU D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.523A pdb=" N GLY D 551 " --> pdb=" O SER D 547 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 574 Processing helix chain 'D' and resid 581 through 599 Proline residue: D 590 - end of helix removed outlier: 3.571A pdb=" N TRP D 594 " --> pdb=" O PRO D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 602 No H-bonds generated for 'chain 'D' and resid 600 through 602' Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.517A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 551 through 554 removed outlier: 5.377A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N THR A 573 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ASP A 568 " --> pdb=" O THR A 573 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.030A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER C 31 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA C 263 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.512A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL C 289 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.566A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE C 119 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 9.789A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 143 through 144 removed outlier: 6.685A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.169A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 347 through 350 362 hydrogen bonds defined for protein. 1041 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: 2.66 Time building geometry restraints manager: 3.05 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: 3053 1.35 - 1.47: 2589 1.47 - 1.59: 4212 1.59 - 1.71: 0 1.71 - 1.83: 70 Bond restraints: 9924 Sorted by residual: bond pdb=" C1 NAG D 701 " pdb=" O5 NAG D 701 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.21e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.17e+00 bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.04e+00 bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.04e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.03e+00 ... (remaining 9919 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 13165 1.43 - 2.87: 296 2.87 - 4.30: 28 4.30 - 5.73: 5 5.73 - 7.16: 1 Bond angle restraints: 13495 Sorted by residual: angle pdb=" CA TYR D 385 " pdb=" CB TYR D 385 " pdb=" CG TYR D 385 " ideal model delta sigma weight residual 113.90 118.01 -4.11 1.80e+00 3.09e-01 5.21e+00 angle pdb=" CA LEU A 518 " pdb=" CB LEU A 518 " pdb=" CG LEU A 518 " ideal model delta sigma weight residual 116.30 123.46 -7.16 3.50e+00 8.16e-02 4.19e+00 angle pdb=" N LYS C 150 " pdb=" CA LYS C 150 " pdb=" C LYS C 150 " ideal model delta sigma weight residual 108.63 111.72 -3.09 1.60e+00 3.91e-01 3.73e+00 angle pdb=" CA ASN C 149 " pdb=" CB ASN C 149 " pdb=" CG ASN C 149 " ideal model delta sigma weight residual 112.60 114.49 -1.89 1.00e+00 1.00e+00 3.59e+00 angle pdb=" N GLN D 139 " pdb=" CA GLN D 139 " pdb=" C GLN D 139 " ideal model delta sigma weight residual 108.34 110.74 -2.40 1.31e+00 5.83e-01 3.35e+00 ... (remaining 13490 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.68: 5913 21.68 - 43.37: 195 43.37 - 65.05: 17 65.05 - 86.73: 0 86.73 - 108.42: 8 Dihedral angle restraints: 6133 sinusoidal: 2728 harmonic: 3405 Sorted by residual: dihedral pdb=" C1 NAG F 1 " pdb=" C2 NAG F 1 " pdb=" C3 NAG F 1 " pdb=" O3 NAG F 1 " ideal model delta sinusoidal sigma weight residual -175.09 -66.67 -108.42 1 3.00e+01 1.11e-03 1.40e+01 dihedral pdb=" C1 NAG F 1 " pdb=" C2 NAG F 1 " pdb=" C3 NAG F 1 " pdb=" C4 NAG F 1 " ideal model delta sinusoidal sigma weight residual -52.39 55.10 -107.49 1 3.00e+01 1.11e-03 1.39e+01 dihedral pdb=" N2 NAG F 1 " pdb=" C2 NAG F 1 " pdb=" C3 NAG F 1 " pdb=" O3 NAG F 1 " ideal model delta sinusoidal sigma weight residual 62.25 169.68 -107.43 1 3.00e+01 1.11e-03 1.39e+01 ... (remaining 6130 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1076 0.039 - 0.078: 304 0.078 - 0.117: 118 0.117 - 0.157: 6 0.157 - 0.196: 1 Chirality restraints: 1505 Sorted by residual: chirality pdb=" C1 NAG C1303 " pdb=" ND2 ASN C 149 " pdb=" C2 NAG C1303 " pdb=" O5 NAG C1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.57e-01 chirality pdb=" CA ILE D 468 " pdb=" N ILE D 468 " pdb=" C ILE D 468 " pdb=" CB ILE D 468 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN D 90 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-01 2.50e+01 4.32e-01 ... (remaining 1502 not shown) Planarity restraints: 1733 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 336 " 0.031 5.00e-02 4.00e+02 4.74e-02 3.60e+00 pdb=" N PRO A 337 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 337 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 337 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 145 " -0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO D 146 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 146 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 146 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 582 " -0.026 5.00e-02 4.00e+02 3.98e-02 2.54e+00 pdb=" N PRO D 583 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO D 583 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 583 " -0.022 5.00e-02 4.00e+02 ... (remaining 1730 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1533 2.76 - 3.30: 9149 3.30 - 3.83: 15807 3.83 - 4.37: 18265 4.37 - 4.90: 32085 Nonbonded interactions: 76839 Sorted by model distance: nonbonded pdb=" OH TYR D 183 " pdb=" OD1 ASP D 509 " model vdw 2.227 3.040 nonbonded pdb=" OG SER A 349 " pdb=" O LEU A 452 " model vdw 2.254 3.040 nonbonded pdb=" ND2 ASN C 125 " pdb=" OG SER C 172 " model vdw 2.256 3.120 nonbonded pdb=" OE2 GLU A 406 " pdb=" OH TYR A 495 " model vdw 2.261 3.040 nonbonded pdb=" OG1 THR A 500 " pdb=" OH TYR D 41 " model vdw 2.281 3.040 ... (remaining 76834 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 'B' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.990 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 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 : 0.003 0.036 9956 Z= 0.144 Angle : 0.494 7.163 13580 Z= 0.250 Chirality : 0.041 0.196 1505 Planarity : 0.003 0.047 1718 Dihedral : 10.503 108.417 3912 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.20 % Allowed : 4.56 % Favored : 92.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.22), residues: 1156 helix: -0.42 (0.24), residues: 384 sheet: -1.67 (0.38), residues: 172 loop : -2.84 (0.21), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 610 HIS 0.003 0.000 HIS D 34 PHE 0.005 0.001 PHE D 592 TYR 0.020 0.001 TYR D 385 ARG 0.002 0.000 ARG D 219 Details of bonding type rmsd link_NAG-ASN : bond 0.00254 ( 15) link_NAG-ASN : angle 1.22846 ( 45) link_BETA1-4 : bond 0.00258 ( 6) link_BETA1-4 : angle 0.83026 ( 18) hydrogen bonds : bond 0.19602 ( 362) hydrogen bonds : angle 6.85123 ( 1041) SS BOND : bond 0.00138 ( 11) SS BOND : angle 0.50456 ( 22) covalent geometry : bond 0.00284 ( 9924) covalent geometry : angle 0.48906 (13495) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 310 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 ILE cc_start: 0.7891 (pt) cc_final: 0.7684 (pt) REVERT: A 350 VAL cc_start: 0.7791 (p) cc_final: 0.7573 (t) REVERT: A 362 VAL cc_start: 0.7618 (OUTLIER) cc_final: 0.6825 (p) REVERT: A 369 TYR cc_start: 0.6740 (t80) cc_final: 0.6388 (t80) REVERT: A 370 ASN cc_start: 0.7390 (t0) cc_final: 0.6935 (t0) REVERT: A 378 LYS cc_start: 0.7570 (mtpp) cc_final: 0.7166 (mtpp) REVERT: A 394 ASN cc_start: 0.7256 (m110) cc_final: 0.7010 (m-40) REVERT: A 396 TYR cc_start: 0.7409 (m-80) cc_final: 0.7129 (m-80) REVERT: A 403 ARG cc_start: 0.7867 (ttp-170) cc_final: 0.7651 (ttp-170) REVERT: A 406 GLU cc_start: 0.7219 (pt0) cc_final: 0.6966 (pt0) REVERT: A 414 GLN cc_start: 0.8402 (mm110) cc_final: 0.7976 (mm110) REVERT: A 434 ILE cc_start: 0.7924 (mp) cc_final: 0.7724 (mt) REVERT: A 473 TYR cc_start: 0.8184 (t80) cc_final: 0.7932 (t80) REVERT: A 512 VAL cc_start: 0.7410 (t) cc_final: 0.6971 (p) REVERT: A 536 ASN cc_start: 0.7375 (t0) cc_final: 0.6337 (p0) REVERT: A 541 PHE cc_start: 0.7754 (p90) cc_final: 0.7550 (p90) REVERT: A 542 ASN cc_start: 0.7001 (t0) cc_final: 0.6777 (t0) REVERT: A 558 LYS cc_start: 0.7835 (mtpt) cc_final: 0.7546 (mtpt) REVERT: A 576 VAL cc_start: 0.8386 (m) cc_final: 0.8067 (p) REVERT: A 584 ILE cc_start: 0.7858 (OUTLIER) cc_final: 0.7649 (pp) REVERT: C 41 LYS cc_start: 0.8145 (mttp) cc_final: 0.7620 (mttp) REVERT: C 137 ASN cc_start: 0.7199 (m-40) cc_final: 0.6960 (m-40) REVERT: C 191 GLU cc_start: 0.7352 (mt-10) cc_final: 0.7128 (mt-10) REVERT: C 202 LYS cc_start: 0.7997 (mttp) cc_final: 0.7782 (mttt) REVERT: C 206 LYS cc_start: 0.8307 (tptt) cc_final: 0.8097 (tppt) REVERT: C 235 ILE cc_start: 0.8499 (mm) cc_final: 0.8282 (mm) REVERT: C 236 THR cc_start: 0.7959 (p) cc_final: 0.7755 (m) REVERT: C 237 ARG cc_start: 0.7885 (ptm-80) cc_final: 0.7421 (mtp-110) REVERT: C 276 LEU cc_start: 0.8274 (tp) cc_final: 0.8039 (tp) REVERT: D 23 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6898 (mm-30) REVERT: D 44 SER cc_start: 0.8235 (m) cc_final: 0.7814 (p) REVERT: D 50 TYR cc_start: 0.8061 (t80) cc_final: 0.7726 (t80) REVERT: D 61 ASN cc_start: 0.7473 (m-40) cc_final: 0.7271 (m-40) REVERT: D 70 SER cc_start: 0.8088 (m) cc_final: 0.7636 (t) REVERT: D 82 MET cc_start: 0.6946 (mmt) cc_final: 0.6672 (mmm) REVERT: D 95 LEU cc_start: 0.7444 (mt) cc_final: 0.7241 (mt) REVERT: D 148 LEU cc_start: 0.6892 (OUTLIER) cc_final: 0.6384 (mp) REVERT: D 194 ASN cc_start: 0.8386 (OUTLIER) cc_final: 0.8173 (m-40) REVERT: D 198 ASP cc_start: 0.6592 (m-30) cc_final: 0.6367 (m-30) REVERT: D 201 ASP cc_start: 0.8063 (t70) cc_final: 0.7731 (t0) REVERT: D 207 TYR cc_start: 0.8006 (m-80) cc_final: 0.7765 (m-80) REVERT: D 234 LYS cc_start: 0.8082 (mttt) cc_final: 0.7520 (mmtt) REVERT: D 238 GLU cc_start: 0.7292 (mt-10) cc_final: 0.6871 (mt-10) REVERT: D 241 HIS cc_start: 0.6596 (t-90) cc_final: 0.6292 (t-90) REVERT: D 270 MET cc_start: 0.7756 (tpp) cc_final: 0.7428 (tpp) REVERT: D 277 ASN cc_start: 0.8190 (m110) cc_final: 0.7927 (m110) REVERT: D 288 LYS cc_start: 0.8375 (mmmt) cc_final: 0.8135 (mttp) REVERT: D 295 ASP cc_start: 0.7488 (m-30) cc_final: 0.7175 (m-30) REVERT: D 362 THR cc_start: 0.7874 (m) cc_final: 0.7394 (m) REVERT: D 375 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7177 (mm-30) REVERT: D 393 ARG cc_start: 0.8011 (mtm-85) cc_final: 0.7774 (mtt180) REVERT: D 414 THR cc_start: 0.7884 (p) cc_final: 0.7500 (p) REVERT: D 441 LYS cc_start: 0.7535 (tttt) cc_final: 0.7306 (tttp) REVERT: D 458 LYS cc_start: 0.7786 (tttp) cc_final: 0.7548 (ttpp) REVERT: D 500 PRO cc_start: 0.7840 (Cg_exo) cc_final: 0.7523 (Cg_endo) REVERT: D 518 ARG cc_start: 0.8030 (ttp80) cc_final: 0.7729 (ttp80) REVERT: D 544 ILE cc_start: 0.8006 (mt) cc_final: 0.7735 (mt) REVERT: D 549 GLU cc_start: 0.6813 (tm-30) cc_final: 0.6484 (tm-30) REVERT: D 564 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7175 (mt-10) REVERT: D 577 LYS cc_start: 0.7491 (mtpt) cc_final: 0.6806 (mtpt) REVERT: D 596 LYS cc_start: 0.7054 (mtpt) cc_final: 0.6833 (mtpp) outliers start: 33 outliers final: 13 residues processed: 334 average time/residue: 0.2450 time to fit residues: 109.0921 Evaluate side-chains 292 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 274 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain D residue 23 GLU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 194 ASN Chi-restraints excluded: chain D residue 364 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 0.9980 chunk 87 optimal weight: 0.0010 chunk 48 optimal weight: 2.9990 chunk 29 optimal weight: 0.3980 chunk 58 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 chunk 34 optimal weight: 0.3980 chunk 54 optimal weight: 0.5980 chunk 67 optimal weight: 5.9990 chunk 104 optimal weight: 0.5980 overall best weight: 0.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN A 334 ASN A 394 ASN A 414 GLN A 437 ASN A 460 ASN A 487 ASN A 493 GLN A 506 GLN ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 GLN C 115 GLN C 125 ASN C 173 GLN C 245 HIS D 24 GLN D 58 ASN D 81 GLN D 89 GLN D 101 GLN D 134 ASN D 137 ASN D 239 HIS D 437 ASN D 442 GLN D 524 GLN D 526 GLN D 531 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.131487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.112928 restraints weight = 14804.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.116306 restraints weight = 7284.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.118586 restraints weight = 4615.870| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9956 Z= 0.184 Angle : 0.588 9.475 13580 Z= 0.294 Chirality : 0.046 0.251 1505 Planarity : 0.005 0.044 1718 Dihedral : 9.310 90.985 1735 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 3.79 % Allowed : 10.29 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.24), residues: 1156 helix: 0.04 (0.26), residues: 405 sheet: -1.30 (0.37), residues: 189 loop : -2.36 (0.24), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 477 HIS 0.006 0.001 HIS C 207 PHE 0.018 0.002 PHE D 285 TYR 0.024 0.002 TYR D 385 ARG 0.005 0.001 ARG A 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00260 ( 15) link_NAG-ASN : angle 1.49839 ( 45) link_BETA1-4 : bond 0.00187 ( 6) link_BETA1-4 : angle 1.45480 ( 18) hydrogen bonds : bond 0.04509 ( 362) hydrogen bonds : angle 5.12343 ( 1041) SS BOND : bond 0.00229 ( 11) SS BOND : angle 0.81067 ( 22) covalent geometry : bond 0.00419 ( 9924) covalent geometry : angle 0.58039 (13495) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 261 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 321 GLN cc_start: 0.7146 (OUTLIER) cc_final: 0.6666 (pp30) REVERT: A 326 ILE cc_start: 0.8029 (pt) cc_final: 0.7823 (pt) REVERT: A 345 THR cc_start: 0.8031 (p) cc_final: 0.6021 (m) REVERT: A 346 ARG cc_start: 0.7044 (mmm160) cc_final: 0.6621 (mmm160) REVERT: A 350 VAL cc_start: 0.7752 (p) cc_final: 0.7541 (t) REVERT: A 362 VAL cc_start: 0.7708 (OUTLIER) cc_final: 0.7087 (p) REVERT: A 370 ASN cc_start: 0.7452 (t0) cc_final: 0.7081 (t0) REVERT: A 378 LYS cc_start: 0.7357 (mtpp) cc_final: 0.6877 (mtpp) REVERT: A 408 ARG cc_start: 0.7901 (ptm-80) cc_final: 0.7592 (ptt90) REVERT: A 414 GLN cc_start: 0.8333 (mm-40) cc_final: 0.8087 (mm-40) REVERT: A 512 VAL cc_start: 0.7606 (t) cc_final: 0.7251 (p) REVERT: A 536 ASN cc_start: 0.7542 (t0) cc_final: 0.6496 (p0) REVERT: A 541 PHE cc_start: 0.7729 (p90) cc_final: 0.7247 (p90) REVERT: A 542 ASN cc_start: 0.7164 (t0) cc_final: 0.6933 (t0) REVERT: A 558 LYS cc_start: 0.7812 (mtpt) cc_final: 0.7584 (mtpt) REVERT: A 587 ILE cc_start: 0.7687 (mt) cc_final: 0.6362 (tt) REVERT: C 41 LYS cc_start: 0.8109 (mttp) cc_final: 0.7726 (mttp) REVERT: C 133 PHE cc_start: 0.7465 (m-80) cc_final: 0.6966 (m-80) REVERT: C 191 GLU cc_start: 0.7130 (mt-10) cc_final: 0.6870 (mt-10) REVERT: C 235 ILE cc_start: 0.8746 (mm) cc_final: 0.8327 (mt) REVERT: C 237 ARG cc_start: 0.7956 (ptm-80) cc_final: 0.7653 (mtp-110) REVERT: D 44 SER cc_start: 0.8525 (m) cc_final: 0.8128 (t) REVERT: D 58 ASN cc_start: 0.7647 (m-40) cc_final: 0.7195 (m110) REVERT: D 70 SER cc_start: 0.8173 (m) cc_final: 0.7727 (t) REVERT: D 91 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7527 (mm) REVERT: D 98 GLN cc_start: 0.7870 (tt0) cc_final: 0.7577 (tt0) REVERT: D 126 ILE cc_start: 0.8221 (tt) cc_final: 0.8002 (pt) REVERT: D 148 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.6876 (mt) REVERT: D 151 ILE cc_start: 0.8439 (tt) cc_final: 0.8208 (tt) REVERT: D 152 MET cc_start: 0.7815 (tpp) cc_final: 0.6992 (mmp) REVERT: D 172 VAL cc_start: 0.8682 (OUTLIER) cc_final: 0.8418 (t) REVERT: D 277 ASN cc_start: 0.8118 (m110) cc_final: 0.7894 (m-40) REVERT: D 360 MET cc_start: 0.8226 (ttm) cc_final: 0.7996 (ttm) REVERT: D 393 ARG cc_start: 0.8202 (mtm-85) cc_final: 0.7967 (mtt180) REVERT: D 398 GLU cc_start: 0.7808 (pt0) cc_final: 0.7236 (pt0) REVERT: D 503 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7863 (tt) REVERT: D 534 LYS cc_start: 0.7620 (mtpt) cc_final: 0.7279 (mtmm) REVERT: D 549 GLU cc_start: 0.6854 (tm-30) cc_final: 0.6596 (tm-30) REVERT: D 557 MET cc_start: 0.8360 (tmm) cc_final: 0.7947 (tmm) REVERT: D 577 LYS cc_start: 0.7757 (mtpt) cc_final: 0.7134 (mtpt) REVERT: D 596 LYS cc_start: 0.6946 (mtpt) cc_final: 0.6738 (mtpp) outliers start: 39 outliers final: 23 residues processed: 286 average time/residue: 0.2375 time to fit residues: 90.7378 Evaluate side-chains 273 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 244 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 411 SER Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 608 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 33 optimal weight: 0.0270 chunk 2 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 101 optimal weight: 0.5980 chunk 68 optimal weight: 0.4980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 HIS D 24 GLN D 33 ASN D 250 ASN ** D 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 397 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.128754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.110099 restraints weight = 15143.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.113557 restraints weight = 7432.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.115800 restraints weight = 4672.567| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9956 Z= 0.216 Angle : 0.607 11.239 13580 Z= 0.303 Chirality : 0.046 0.252 1505 Planarity : 0.005 0.056 1718 Dihedral : 8.647 86.897 1722 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 3.50 % Allowed : 13.50 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.24), residues: 1156 helix: 0.27 (0.26), residues: 405 sheet: -1.05 (0.39), residues: 176 loop : -2.23 (0.24), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 477 HIS 0.008 0.001 HIS D 241 PHE 0.015 0.002 PHE C 194 TYR 0.021 0.002 TYR D 385 ARG 0.005 0.001 ARG D 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00271 ( 15) link_NAG-ASN : angle 1.52906 ( 45) link_BETA1-4 : bond 0.00172 ( 6) link_BETA1-4 : angle 1.46300 ( 18) hydrogen bonds : bond 0.04384 ( 362) hydrogen bonds : angle 4.87652 ( 1041) SS BOND : bond 0.00316 ( 11) SS BOND : angle 0.78819 ( 22) covalent geometry : bond 0.00498 ( 9924) covalent geometry : angle 0.59896 (13495) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 255 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 GLN cc_start: 0.7143 (OUTLIER) cc_final: 0.6600 (pp30) REVERT: A 326 ILE cc_start: 0.8027 (pt) cc_final: 0.7805 (pt) REVERT: A 345 THR cc_start: 0.8047 (p) cc_final: 0.5893 (m) REVERT: A 346 ARG cc_start: 0.6978 (mmm160) cc_final: 0.6663 (mmm160) REVERT: A 351 TYR cc_start: 0.8213 (p90) cc_final: 0.7998 (p90) REVERT: A 362 VAL cc_start: 0.7733 (OUTLIER) cc_final: 0.7129 (p) REVERT: A 370 ASN cc_start: 0.7476 (t0) cc_final: 0.7129 (t0) REVERT: A 378 LYS cc_start: 0.7290 (mtpp) cc_final: 0.6834 (mtpp) REVERT: A 408 ARG cc_start: 0.7934 (ptm-80) cc_final: 0.7672 (ptt90) REVERT: A 414 GLN cc_start: 0.8357 (mm-40) cc_final: 0.8114 (mm-40) REVERT: A 450 ASN cc_start: 0.8148 (m-40) cc_final: 0.7508 (m-40) REVERT: A 512 VAL cc_start: 0.7632 (t) cc_final: 0.7316 (p) REVERT: A 536 ASN cc_start: 0.7750 (t0) cc_final: 0.6870 (p0) REVERT: A 542 ASN cc_start: 0.7301 (t0) cc_final: 0.7022 (t0) REVERT: A 558 LYS cc_start: 0.7805 (mtpt) cc_final: 0.7569 (mtpt) REVERT: A 587 ILE cc_start: 0.7601 (mt) cc_final: 0.7317 (mt) REVERT: C 133 PHE cc_start: 0.7569 (m-80) cc_final: 0.6858 (m-80) REVERT: C 235 ILE cc_start: 0.8718 (mm) cc_final: 0.8365 (mt) REVERT: C 237 ARG cc_start: 0.7913 (ptm-80) cc_final: 0.7711 (mtp-110) REVERT: D 35 GLU cc_start: 0.7000 (tt0) cc_final: 0.6777 (tt0) REVERT: D 44 SER cc_start: 0.8555 (m) cc_final: 0.8212 (t) REVERT: D 50 TYR cc_start: 0.8173 (t80) cc_final: 0.7874 (t80) REVERT: D 58 ASN cc_start: 0.7707 (m-40) cc_final: 0.7256 (m110) REVERT: D 70 SER cc_start: 0.8281 (m) cc_final: 0.7880 (t) REVERT: D 76 GLN cc_start: 0.8002 (mm-40) cc_final: 0.7125 (mm-40) REVERT: D 82 MET cc_start: 0.7310 (mtm) cc_final: 0.7036 (mtm) REVERT: D 91 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7560 (mm) REVERT: D 98 GLN cc_start: 0.7919 (tt0) cc_final: 0.7613 (tt0) REVERT: D 101 GLN cc_start: 0.8407 (mt0) cc_final: 0.8155 (mt0) REVERT: D 148 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.6868 (mt) REVERT: D 151 ILE cc_start: 0.8444 (tt) cc_final: 0.8048 (tp) REVERT: D 152 MET cc_start: 0.7932 (tpp) cc_final: 0.7155 (mmp) REVERT: D 241 HIS cc_start: 0.7104 (t-90) cc_final: 0.6875 (t-90) REVERT: D 332 MET cc_start: 0.7796 (ttm) cc_final: 0.7594 (ttp) REVERT: D 393 ARG cc_start: 0.8281 (mtm-85) cc_final: 0.8038 (mtt180) REVERT: D 503 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.7955 (tt) REVERT: D 534 LYS cc_start: 0.7736 (mtpt) cc_final: 0.7333 (mtmm) REVERT: D 556 ASN cc_start: 0.8375 (m-40) cc_final: 0.7989 (m-40) REVERT: D 557 MET cc_start: 0.8319 (tmm) cc_final: 0.8100 (tmm) REVERT: D 589 GLU cc_start: 0.7244 (tt0) cc_final: 0.7029 (tt0) outliers start: 36 outliers final: 29 residues processed: 280 average time/residue: 0.2455 time to fit residues: 92.4222 Evaluate side-chains 284 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 250 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 411 SER Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 608 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 79 optimal weight: 0.9980 chunk 37 optimal weight: 0.4980 chunk 98 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 68 optimal weight: 0.5980 chunk 45 optimal weight: 0.0970 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN D 24 GLN D 42 GLN D 250 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.127508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.108412 restraints weight = 14938.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.111967 restraints weight = 7041.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.114376 restraints weight = 4368.074| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9956 Z= 0.224 Angle : 0.619 9.296 13580 Z= 0.311 Chirality : 0.047 0.264 1505 Planarity : 0.005 0.068 1718 Dihedral : 8.082 79.542 1722 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 4.56 % Allowed : 12.82 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.24), residues: 1156 helix: 0.48 (0.26), residues: 401 sheet: -1.04 (0.38), residues: 183 loop : -2.07 (0.24), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 477 HIS 0.007 0.001 HIS D 241 PHE 0.018 0.002 PHE A 541 TYR 0.029 0.002 TYR A 473 ARG 0.006 0.001 ARG D 559 Details of bonding type rmsd link_NAG-ASN : bond 0.00301 ( 15) link_NAG-ASN : angle 1.68448 ( 45) link_BETA1-4 : bond 0.00267 ( 6) link_BETA1-4 : angle 1.43730 ( 18) hydrogen bonds : bond 0.04363 ( 362) hydrogen bonds : angle 4.82471 ( 1041) SS BOND : bond 0.00219 ( 11) SS BOND : angle 0.62240 ( 22) covalent geometry : bond 0.00514 ( 9924) covalent geometry : angle 0.61097 (13495) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 272 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 GLN cc_start: 0.7127 (OUTLIER) cc_final: 0.6582 (pp30) REVERT: A 324 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.6895 (tp30) REVERT: A 326 ILE cc_start: 0.8000 (pt) cc_final: 0.7758 (pt) REVERT: A 345 THR cc_start: 0.8139 (p) cc_final: 0.7917 (m) REVERT: A 362 VAL cc_start: 0.7688 (OUTLIER) cc_final: 0.7110 (p) REVERT: A 370 ASN cc_start: 0.7597 (t0) cc_final: 0.7244 (t0) REVERT: A 414 GLN cc_start: 0.8464 (mm-40) cc_final: 0.8195 (mm-40) REVERT: A 448 ASN cc_start: 0.8354 (t0) cc_final: 0.8133 (t0) REVERT: A 450 ASN cc_start: 0.8098 (m-40) cc_final: 0.7585 (m110) REVERT: A 466 ARG cc_start: 0.8169 (ttp80) cc_final: 0.7311 (ttt-90) REVERT: A 512 VAL cc_start: 0.7563 (t) cc_final: 0.7185 (p) REVERT: A 536 ASN cc_start: 0.7979 (t0) cc_final: 0.6983 (p0) REVERT: A 542 ASN cc_start: 0.7260 (t0) cc_final: 0.6933 (t0) REVERT: A 558 LYS cc_start: 0.7851 (mtpt) cc_final: 0.7582 (mtpt) REVERT: C 133 PHE cc_start: 0.7635 (m-80) cc_final: 0.7256 (m-80) REVERT: C 182 LYS cc_start: 0.8083 (mmmt) cc_final: 0.7630 (mmmt) REVERT: C 210 ILE cc_start: 0.7987 (tt) cc_final: 0.7745 (pt) REVERT: C 235 ILE cc_start: 0.8603 (mm) cc_final: 0.8268 (mt) REVERT: D 44 SER cc_start: 0.8517 (m) cc_final: 0.8188 (t) REVERT: D 70 SER cc_start: 0.8333 (m) cc_final: 0.7973 (t) REVERT: D 76 GLN cc_start: 0.7969 (mm-40) cc_final: 0.7049 (mm-40) REVERT: D 82 MET cc_start: 0.7448 (mtm) cc_final: 0.7217 (mtm) REVERT: D 91 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7604 (mm) REVERT: D 98 GLN cc_start: 0.8042 (tt0) cc_final: 0.7739 (tt0) REVERT: D 126 ILE cc_start: 0.8141 (tt) cc_final: 0.7921 (pt) REVERT: D 127 TYR cc_start: 0.8285 (t80) cc_final: 0.7895 (t80) REVERT: D 148 LEU cc_start: 0.7302 (mm) cc_final: 0.6872 (mt) REVERT: D 151 ILE cc_start: 0.8387 (tt) cc_final: 0.8161 (tt) REVERT: D 152 MET cc_start: 0.8055 (tpp) cc_final: 0.7156 (mmp) REVERT: D 216 ASP cc_start: 0.7268 (p0) cc_final: 0.6991 (p0) REVERT: D 241 HIS cc_start: 0.7083 (t-90) cc_final: 0.6843 (t-170) REVERT: D 270 MET cc_start: 0.7927 (tpp) cc_final: 0.7641 (tpp) REVERT: D 332 MET cc_start: 0.7891 (ttm) cc_final: 0.7676 (ttp) REVERT: D 360 MET cc_start: 0.8225 (ttm) cc_final: 0.8019 (ttm) REVERT: D 376 MET cc_start: 0.7573 (ttm) cc_final: 0.7203 (mtt) REVERT: D 393 ARG cc_start: 0.8175 (mtm-85) cc_final: 0.7941 (mtt180) REVERT: D 503 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7648 (tt) REVERT: D 534 LYS cc_start: 0.7878 (mtpt) cc_final: 0.7433 (mmmm) REVERT: D 557 MET cc_start: 0.8250 (tmm) cc_final: 0.8025 (tmm) REVERT: D 577 LYS cc_start: 0.8010 (mtmm) cc_final: 0.7769 (mtmm) REVERT: D 589 GLU cc_start: 0.7281 (tt0) cc_final: 0.7062 (tt0) outliers start: 47 outliers final: 35 residues processed: 301 average time/residue: 0.2402 time to fit residues: 97.0188 Evaluate side-chains 292 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 252 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 477 TRP Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 608 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 77 optimal weight: 0.0770 chunk 5 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 16 optimal weight: 0.0670 chunk 112 optimal weight: 0.1980 chunk 38 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 106 optimal weight: 0.0970 chunk 56 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 overall best weight: 0.2474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN D 58 ASN D 175 GLN D 250 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.126969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.108273 restraints weight = 15057.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.111757 restraints weight = 7283.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.113995 restraints weight = 4543.966| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9956 Z= 0.137 Angle : 0.578 10.048 13580 Z= 0.286 Chirality : 0.045 0.259 1505 Planarity : 0.005 0.057 1718 Dihedral : 7.490 73.256 1720 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 4.08 % Allowed : 15.34 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.25), residues: 1156 helix: 0.75 (0.27), residues: 400 sheet: -0.93 (0.38), residues: 183 loop : -1.86 (0.25), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 610 HIS 0.007 0.001 HIS D 241 PHE 0.018 0.002 PHE A 541 TYR 0.034 0.002 TYR A 473 ARG 0.006 0.001 ARG D 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00239 ( 15) link_NAG-ASN : angle 1.47412 ( 45) link_BETA1-4 : bond 0.00309 ( 6) link_BETA1-4 : angle 1.39261 ( 18) hydrogen bonds : bond 0.03761 ( 362) hydrogen bonds : angle 4.73384 ( 1041) SS BOND : bond 0.00232 ( 11) SS BOND : angle 0.47620 ( 22) covalent geometry : bond 0.00313 ( 9924) covalent geometry : angle 0.57075 (13495) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 266 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 GLN cc_start: 0.7004 (OUTLIER) cc_final: 0.6533 (pp30) REVERT: A 324 GLU cc_start: 0.7277 (tp30) cc_final: 0.6715 (tp30) REVERT: A 326 ILE cc_start: 0.7888 (pt) cc_final: 0.7580 (pt) REVERT: A 345 THR cc_start: 0.8182 (p) cc_final: 0.7954 (m) REVERT: A 351 TYR cc_start: 0.8050 (p90) cc_final: 0.7847 (p90) REVERT: A 357 ARG cc_start: 0.7227 (mtp85) cc_final: 0.6908 (mtp85) REVERT: A 362 VAL cc_start: 0.7745 (OUTLIER) cc_final: 0.7194 (p) REVERT: A 370 ASN cc_start: 0.7505 (t0) cc_final: 0.7164 (t0) REVERT: A 403 ARG cc_start: 0.8175 (ttp-170) cc_final: 0.7916 (ttp80) REVERT: A 408 ARG cc_start: 0.7985 (ptm-80) cc_final: 0.7726 (ptt90) REVERT: A 414 GLN cc_start: 0.8395 (mm-40) cc_final: 0.8147 (mm-40) REVERT: A 450 ASN cc_start: 0.8019 (m-40) cc_final: 0.7423 (m-40) REVERT: A 466 ARG cc_start: 0.8148 (ttp80) cc_final: 0.7817 (ttp-170) REVERT: A 512 VAL cc_start: 0.7527 (t) cc_final: 0.7149 (p) REVERT: A 536 ASN cc_start: 0.7877 (t0) cc_final: 0.6973 (p0) REVERT: A 542 ASN cc_start: 0.7240 (t0) cc_final: 0.6969 (t0) REVERT: A 558 LYS cc_start: 0.7819 (mtpt) cc_final: 0.7569 (mtpt) REVERT: C 133 PHE cc_start: 0.7646 (m-80) cc_final: 0.7286 (m-80) REVERT: C 182 LYS cc_start: 0.8068 (mmmt) cc_final: 0.7668 (mmmt) REVERT: C 210 ILE cc_start: 0.7995 (tt) cc_final: 0.7775 (pt) REVERT: C 235 ILE cc_start: 0.8676 (mm) cc_final: 0.8351 (mt) REVERT: D 44 SER cc_start: 0.8531 (m) cc_final: 0.8200 (t) REVERT: D 70 SER cc_start: 0.8361 (m) cc_final: 0.7992 (t) REVERT: D 76 GLN cc_start: 0.7846 (mm-40) cc_final: 0.7004 (mm-40) REVERT: D 91 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7666 (mm) REVERT: D 98 GLN cc_start: 0.8027 (tt0) cc_final: 0.7716 (tt0) REVERT: D 127 TYR cc_start: 0.8157 (t80) cc_final: 0.7872 (t80) REVERT: D 148 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.6941 (mt) REVERT: D 151 ILE cc_start: 0.8428 (tt) cc_final: 0.8137 (tt) REVERT: D 152 MET cc_start: 0.8020 (tpp) cc_final: 0.7179 (mmp) REVERT: D 168 TRP cc_start: 0.8098 (t-100) cc_final: 0.7892 (t-100) REVERT: D 203 TRP cc_start: 0.8461 (OUTLIER) cc_final: 0.8180 (m-10) REVERT: D 216 ASP cc_start: 0.7252 (p0) cc_final: 0.7010 (p0) REVERT: D 231 GLU cc_start: 0.6439 (mm-30) cc_final: 0.6208 (mm-30) REVERT: D 241 HIS cc_start: 0.7095 (t-90) cc_final: 0.6832 (t-90) REVERT: D 270 MET cc_start: 0.7847 (tpp) cc_final: 0.7642 (tpp) REVERT: D 323 MET cc_start: 0.8729 (mmm) cc_final: 0.7804 (mmm) REVERT: D 332 MET cc_start: 0.7844 (ttm) cc_final: 0.7643 (ttp) REVERT: D 376 MET cc_start: 0.7488 (ttm) cc_final: 0.7270 (mmm) REVERT: D 393 ARG cc_start: 0.8149 (mtm-85) cc_final: 0.7898 (mtt180) REVERT: D 503 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7715 (tt) REVERT: D 534 LYS cc_start: 0.7815 (mtpt) cc_final: 0.7414 (mmmm) REVERT: D 557 MET cc_start: 0.8210 (tmm) cc_final: 0.7999 (tmm) REVERT: D 577 LYS cc_start: 0.7872 (mtmm) cc_final: 0.7639 (mtmm) outliers start: 42 outliers final: 33 residues processed: 292 average time/residue: 0.2742 time to fit residues: 106.7861 Evaluate side-chains 292 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 253 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 300 GLN Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 477 TRP Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 608 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 72 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 105 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN A 556 ASN A 580 GLN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN D 58 ASN D 81 GLN D 250 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.124390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.105669 restraints weight = 15060.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.109077 restraints weight = 7371.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.111253 restraints weight = 4625.930| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 9956 Z= 0.275 Angle : 0.672 9.732 13580 Z= 0.335 Chirality : 0.050 0.272 1505 Planarity : 0.005 0.072 1718 Dihedral : 7.283 65.247 1720 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 5.05 % Allowed : 14.85 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.24), residues: 1156 helix: 0.53 (0.26), residues: 402 sheet: -1.02 (0.37), residues: 189 loop : -1.88 (0.25), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 477 HIS 0.008 0.001 HIS C 207 PHE 0.032 0.002 PHE D 285 TYR 0.040 0.002 TYR A 473 ARG 0.006 0.001 ARG D 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00365 ( 15) link_NAG-ASN : angle 1.79728 ( 45) link_BETA1-4 : bond 0.00282 ( 6) link_BETA1-4 : angle 1.62931 ( 18) hydrogen bonds : bond 0.04498 ( 362) hydrogen bonds : angle 4.84775 ( 1041) SS BOND : bond 0.00227 ( 11) SS BOND : angle 0.58937 ( 22) covalent geometry : bond 0.00630 ( 9924) covalent geometry : angle 0.66305 (13495) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 264 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 GLN cc_start: 0.7164 (OUTLIER) cc_final: 0.6758 (pp30) REVERT: A 324 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.6962 (tp30) REVERT: A 326 ILE cc_start: 0.8049 (pt) cc_final: 0.7812 (pt) REVERT: A 345 THR cc_start: 0.8177 (p) cc_final: 0.7969 (m) REVERT: A 357 ARG cc_start: 0.7231 (mtp85) cc_final: 0.6734 (mtp85) REVERT: A 362 VAL cc_start: 0.7748 (OUTLIER) cc_final: 0.7196 (p) REVERT: A 370 ASN cc_start: 0.7585 (t0) cc_final: 0.7250 (t0) REVERT: A 414 GLN cc_start: 0.8449 (mm-40) cc_final: 0.8192 (mm-40) REVERT: A 450 ASN cc_start: 0.8015 (m-40) cc_final: 0.7441 (m-40) REVERT: A 466 ARG cc_start: 0.8212 (ttp80) cc_final: 0.8009 (ttp80) REVERT: A 512 VAL cc_start: 0.7593 (t) cc_final: 0.7273 (p) REVERT: A 536 ASN cc_start: 0.8127 (t0) cc_final: 0.7338 (p0) REVERT: A 542 ASN cc_start: 0.7328 (t0) cc_final: 0.7040 (t0) REVERT: A 558 LYS cc_start: 0.7900 (mtpt) cc_final: 0.7666 (mtpt) REVERT: C 133 PHE cc_start: 0.7676 (m-80) cc_final: 0.7271 (m-80) REVERT: C 182 LYS cc_start: 0.8147 (mmmt) cc_final: 0.7758 (mmmt) REVERT: C 235 ILE cc_start: 0.8649 (mm) cc_final: 0.8339 (mt) REVERT: D 44 SER cc_start: 0.8610 (m) cc_final: 0.8257 (t) REVERT: D 70 SER cc_start: 0.8389 (m) cc_final: 0.8031 (t) REVERT: D 76 GLN cc_start: 0.7843 (mm-40) cc_final: 0.7046 (mm-40) REVERT: D 91 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7763 (mm) REVERT: D 98 GLN cc_start: 0.8063 (tt0) cc_final: 0.7707 (tt0) REVERT: D 127 TYR cc_start: 0.8210 (t80) cc_final: 0.7853 (t80) REVERT: D 148 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7217 (mt) REVERT: D 151 ILE cc_start: 0.8500 (tt) cc_final: 0.8082 (tp) REVERT: D 203 TRP cc_start: 0.8500 (OUTLIER) cc_final: 0.8185 (m-10) REVERT: D 216 ASP cc_start: 0.7267 (p0) cc_final: 0.7026 (p0) REVERT: D 231 GLU cc_start: 0.6503 (mm-30) cc_final: 0.6230 (mm-30) REVERT: D 376 MET cc_start: 0.7559 (ttm) cc_final: 0.7247 (ttm) REVERT: D 460 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.6882 (mtt90) REVERT: D 503 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7728 (tt) REVERT: D 534 LYS cc_start: 0.7940 (mtpt) cc_final: 0.7561 (mmmm) REVERT: D 557 MET cc_start: 0.8245 (tmm) cc_final: 0.7992 (tmm) outliers start: 52 outliers final: 39 residues processed: 298 average time/residue: 0.2408 time to fit residues: 95.7924 Evaluate side-chains 306 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 259 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 300 GLN Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 460 ARG Chi-restraints excluded: chain D residue 477 TRP Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 608 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 80 optimal weight: 0.0770 chunk 48 optimal weight: 3.9990 chunk 18 optimal weight: 0.0970 chunk 91 optimal weight: 0.1980 chunk 6 optimal weight: 0.0670 chunk 112 optimal weight: 0.2980 chunk 7 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 81 optimal weight: 0.3980 chunk 77 optimal weight: 0.0970 overall best weight: 0.1072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN D 58 ASN D 250 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.130649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.112246 restraints weight = 15027.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.115811 restraints weight = 7147.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.118087 restraints weight = 4402.699| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9956 Z= 0.113 Angle : 0.594 10.035 13580 Z= 0.293 Chirality : 0.044 0.256 1505 Planarity : 0.004 0.047 1718 Dihedral : 6.560 55.961 1720 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 4.66 % Allowed : 15.63 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.25), residues: 1156 helix: 0.84 (0.27), residues: 403 sheet: -0.85 (0.39), residues: 182 loop : -1.67 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 610 HIS 0.010 0.001 HIS D 241 PHE 0.031 0.001 PHE D 285 TYR 0.035 0.001 TYR A 473 ARG 0.005 0.000 ARG D 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00313 ( 15) link_NAG-ASN : angle 1.37950 ( 45) link_BETA1-4 : bond 0.00394 ( 6) link_BETA1-4 : angle 1.48113 ( 18) hydrogen bonds : bond 0.03484 ( 362) hydrogen bonds : angle 4.69011 ( 1041) SS BOND : bond 0.00141 ( 11) SS BOND : angle 0.51304 ( 22) covalent geometry : bond 0.00256 ( 9924) covalent geometry : angle 0.58731 (13495) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 261 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 GLN cc_start: 0.7003 (OUTLIER) cc_final: 0.6597 (pp30) REVERT: A 324 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6737 (tp30) REVERT: A 326 ILE cc_start: 0.7852 (pt) cc_final: 0.7604 (pt) REVERT: A 345 THR cc_start: 0.8210 (p) cc_final: 0.7987 (m) REVERT: A 362 VAL cc_start: 0.7775 (OUTLIER) cc_final: 0.7262 (p) REVERT: A 370 ASN cc_start: 0.7480 (t0) cc_final: 0.7149 (t0) REVERT: A 378 LYS cc_start: 0.7177 (mtpp) cc_final: 0.6724 (mtpp) REVERT: A 403 ARG cc_start: 0.8175 (ttp-170) cc_final: 0.7946 (ttp80) REVERT: A 405 ASP cc_start: 0.7112 (p0) cc_final: 0.6896 (p0) REVERT: A 414 GLN cc_start: 0.8367 (mm-40) cc_final: 0.8118 (mm-40) REVERT: A 450 ASN cc_start: 0.7970 (m-40) cc_final: 0.7397 (m-40) REVERT: A 466 ARG cc_start: 0.8155 (ttp80) cc_final: 0.7924 (ttp80) REVERT: A 512 VAL cc_start: 0.7603 (t) cc_final: 0.7153 (p) REVERT: A 536 ASN cc_start: 0.7875 (t0) cc_final: 0.6939 (p0) REVERT: A 542 ASN cc_start: 0.7202 (t0) cc_final: 0.6939 (t0) REVERT: C 41 LYS cc_start: 0.8002 (mttp) cc_final: 0.7786 (mttp) REVERT: C 116 SER cc_start: 0.7967 (m) cc_final: 0.7439 (t) REVERT: C 133 PHE cc_start: 0.7644 (m-80) cc_final: 0.7294 (m-80) REVERT: C 182 LYS cc_start: 0.8071 (mmmt) cc_final: 0.7717 (mmmt) REVERT: C 202 LYS cc_start: 0.8182 (mttt) cc_final: 0.7869 (mttm) REVERT: C 235 ILE cc_start: 0.8693 (mm) cc_final: 0.8360 (mt) REVERT: D 44 SER cc_start: 0.8534 (m) cc_final: 0.8183 (t) REVERT: D 70 SER cc_start: 0.8380 (m) cc_final: 0.8009 (t) REVERT: D 76 GLN cc_start: 0.7708 (mm-40) cc_final: 0.6994 (mm-40) REVERT: D 98 GLN cc_start: 0.8008 (tt0) cc_final: 0.7653 (tt0) REVERT: D 148 LEU cc_start: 0.7421 (OUTLIER) cc_final: 0.6911 (mt) REVERT: D 151 ILE cc_start: 0.8405 (OUTLIER) cc_final: 0.7952 (tp) REVERT: D 152 MET cc_start: 0.8035 (tpp) cc_final: 0.7172 (mmp) REVERT: D 203 TRP cc_start: 0.8455 (OUTLIER) cc_final: 0.8070 (m-10) REVERT: D 208 GLU cc_start: 0.7368 (tt0) cc_final: 0.6914 (mt-10) REVERT: D 216 ASP cc_start: 0.7241 (p0) cc_final: 0.7007 (p0) REVERT: D 231 GLU cc_start: 0.6384 (mm-30) cc_final: 0.6136 (mm-30) REVERT: D 393 ARG cc_start: 0.8123 (mtm-85) cc_final: 0.7879 (mtt180) REVERT: D 460 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.6538 (mtt90) REVERT: D 500 PRO cc_start: 0.7985 (Cg_exo) cc_final: 0.7686 (Cg_endo) REVERT: D 503 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.7957 (tt) REVERT: D 534 LYS cc_start: 0.7806 (mtpt) cc_final: 0.7408 (mmmm) REVERT: D 574 VAL cc_start: 0.8649 (t) cc_final: 0.8240 (p) outliers start: 48 outliers final: 34 residues processed: 290 average time/residue: 0.2556 time to fit residues: 97.8871 Evaluate side-chains 294 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 252 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 271 TRP Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 460 ARG Chi-restraints excluded: chain D residue 477 TRP Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 608 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 83 optimal weight: 0.2980 chunk 23 optimal weight: 0.2980 chunk 108 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 86 optimal weight: 0.3980 chunk 20 optimal weight: 0.5980 chunk 25 optimal weight: 0.1980 chunk 4 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 101 optimal weight: 0.3980 chunk 51 optimal weight: 2.9990 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN D 101 GLN D 250 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.125606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.107137 restraints weight = 15252.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.110538 restraints weight = 7343.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.112788 restraints weight = 4572.964| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9956 Z= 0.160 Angle : 0.616 9.738 13580 Z= 0.305 Chirality : 0.046 0.258 1505 Planarity : 0.005 0.051 1718 Dihedral : 6.317 52.170 1720 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 4.85 % Allowed : 16.89 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.25), residues: 1156 helix: 0.83 (0.27), residues: 404 sheet: -0.79 (0.39), residues: 181 loop : -1.63 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 610 HIS 0.011 0.001 HIS D 241 PHE 0.032 0.002 PHE D 285 TYR 0.031 0.002 TYR A 473 ARG 0.005 0.001 ARG D 518 Details of bonding type rmsd link_NAG-ASN : bond 0.00216 ( 15) link_NAG-ASN : angle 1.48169 ( 45) link_BETA1-4 : bond 0.00284 ( 6) link_BETA1-4 : angle 1.55761 ( 18) hydrogen bonds : bond 0.03822 ( 362) hydrogen bonds : angle 4.72479 ( 1041) SS BOND : bond 0.00191 ( 11) SS BOND : angle 0.42198 ( 22) covalent geometry : bond 0.00368 ( 9924) covalent geometry : angle 0.60912 (13495) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 258 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 GLN cc_start: 0.7061 (OUTLIER) cc_final: 0.6675 (pp30) REVERT: A 324 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.6841 (tp30) REVERT: A 326 ILE cc_start: 0.7821 (pt) cc_final: 0.7606 (pt) REVERT: A 328 ARG cc_start: 0.8529 (mtt-85) cc_final: 0.8298 (mtp180) REVERT: A 345 THR cc_start: 0.8207 (p) cc_final: 0.7975 (m) REVERT: A 362 VAL cc_start: 0.7775 (OUTLIER) cc_final: 0.7270 (p) REVERT: A 370 ASN cc_start: 0.7516 (t0) cc_final: 0.7186 (t0) REVERT: A 378 LYS cc_start: 0.7184 (mtpp) cc_final: 0.6715 (mtpp) REVERT: A 403 ARG cc_start: 0.8125 (ttp-170) cc_final: 0.7695 (ttp-170) REVERT: A 408 ARG cc_start: 0.7974 (ptm-80) cc_final: 0.7708 (ptt90) REVERT: A 414 GLN cc_start: 0.8398 (mm-40) cc_final: 0.8115 (mm-40) REVERT: A 442 ASP cc_start: 0.7370 (t0) cc_final: 0.6975 (t0) REVERT: A 450 ASN cc_start: 0.7945 (m-40) cc_final: 0.7372 (m-40) REVERT: A 466 ARG cc_start: 0.8168 (ttp80) cc_final: 0.7928 (ttp80) REVERT: A 536 ASN cc_start: 0.7971 (t0) cc_final: 0.7024 (p0) REVERT: A 542 ASN cc_start: 0.7205 (t0) cc_final: 0.6965 (t0) REVERT: C 116 SER cc_start: 0.7979 (m) cc_final: 0.7439 (t) REVERT: C 133 PHE cc_start: 0.7655 (m-80) cc_final: 0.7287 (m-80) REVERT: C 182 LYS cc_start: 0.8091 (mmmt) cc_final: 0.7741 (mmmt) REVERT: C 235 ILE cc_start: 0.8670 (mm) cc_final: 0.8361 (mt) REVERT: D 44 SER cc_start: 0.8585 (m) cc_final: 0.8238 (t) REVERT: D 50 TYR cc_start: 0.8065 (t80) cc_final: 0.7768 (t80) REVERT: D 70 SER cc_start: 0.8378 (m) cc_final: 0.8015 (t) REVERT: D 76 GLN cc_start: 0.7798 (mm-40) cc_final: 0.7014 (mm-40) REVERT: D 98 GLN cc_start: 0.8009 (tt0) cc_final: 0.7668 (tt0) REVERT: D 101 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8245 (mt0) REVERT: D 148 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7133 (mt) REVERT: D 151 ILE cc_start: 0.8470 (OUTLIER) cc_final: 0.8025 (tp) REVERT: D 152 MET cc_start: 0.8077 (tpp) cc_final: 0.7211 (mmp) REVERT: D 203 TRP cc_start: 0.8488 (OUTLIER) cc_final: 0.8091 (m-10) REVERT: D 208 GLU cc_start: 0.7401 (tt0) cc_final: 0.6895 (mt-10) REVERT: D 231 GLU cc_start: 0.6432 (mm-30) cc_final: 0.6222 (mm-30) REVERT: D 376 MET cc_start: 0.7503 (ttm) cc_final: 0.7194 (mtt) REVERT: D 393 ARG cc_start: 0.8163 (mtm-85) cc_final: 0.7928 (mtt180) REVERT: D 435 GLU cc_start: 0.5370 (mp0) cc_final: 0.4983 (mp0) REVERT: D 460 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.6694 (mtt90) REVERT: D 470 LYS cc_start: 0.7761 (tppt) cc_final: 0.7211 (tppt) REVERT: D 479 GLU cc_start: 0.6227 (tm-30) cc_final: 0.5815 (tp30) REVERT: D 500 PRO cc_start: 0.7981 (Cg_exo) cc_final: 0.7731 (Cg_endo) REVERT: D 503 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7929 (tt) REVERT: D 534 LYS cc_start: 0.7837 (mtpt) cc_final: 0.7451 (mmmm) REVERT: D 557 MET cc_start: 0.8138 (tmm) cc_final: 0.7884 (tmm) REVERT: D 574 VAL cc_start: 0.8667 (t) cc_final: 0.8244 (p) outliers start: 50 outliers final: 40 residues processed: 286 average time/residue: 0.2678 time to fit residues: 101.1589 Evaluate side-chains 304 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 255 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 101 GLN Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 271 TRP Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 300 GLN Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 460 ARG Chi-restraints excluded: chain D residue 477 TRP Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 608 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 102 optimal weight: 0.5980 chunk 90 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 85 optimal weight: 0.4980 chunk 9 optimal weight: 0.0670 chunk 5 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 106 optimal weight: 0.3980 chunk 25 optimal weight: 0.3980 chunk 43 optimal weight: 2.9990 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN D 101 GLN D 250 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.125526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.106995 restraints weight = 15065.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.110287 restraints weight = 7307.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.112638 restraints weight = 4594.600| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9956 Z= 0.183 Angle : 0.634 9.817 13580 Z= 0.315 Chirality : 0.047 0.261 1505 Planarity : 0.005 0.055 1718 Dihedral : 6.194 52.141 1720 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 5.44 % Allowed : 16.80 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.25), residues: 1156 helix: 0.76 (0.27), residues: 402 sheet: -0.77 (0.38), residues: 183 loop : -1.57 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 610 HIS 0.005 0.001 HIS C 207 PHE 0.032 0.002 PHE D 285 TYR 0.031 0.002 TYR A 473 ARG 0.006 0.001 ARG D 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00236 ( 15) link_NAG-ASN : angle 1.53295 ( 45) link_BETA1-4 : bond 0.00283 ( 6) link_BETA1-4 : angle 1.55632 ( 18) hydrogen bonds : bond 0.03951 ( 362) hydrogen bonds : angle 4.73962 ( 1041) SS BOND : bond 0.00196 ( 11) SS BOND : angle 0.45951 ( 22) covalent geometry : bond 0.00421 ( 9924) covalent geometry : angle 0.62694 (13495) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 262 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 GLN cc_start: 0.7032 (OUTLIER) cc_final: 0.6621 (pp30) REVERT: A 324 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.6859 (tp30) REVERT: A 326 ILE cc_start: 0.7860 (pt) cc_final: 0.7653 (pt) REVERT: A 328 ARG cc_start: 0.8530 (mtt-85) cc_final: 0.8295 (mtp180) REVERT: A 345 THR cc_start: 0.8212 (p) cc_final: 0.7977 (m) REVERT: A 362 VAL cc_start: 0.7804 (OUTLIER) cc_final: 0.7296 (p) REVERT: A 370 ASN cc_start: 0.7526 (t0) cc_final: 0.7198 (t0) REVERT: A 394 ASN cc_start: 0.7681 (OUTLIER) cc_final: 0.7351 (m110) REVERT: A 403 ARG cc_start: 0.8137 (ttp-170) cc_final: 0.7709 (ttp-170) REVERT: A 408 ARG cc_start: 0.7977 (ptm-80) cc_final: 0.7715 (ptt90) REVERT: A 414 GLN cc_start: 0.8363 (mm-40) cc_final: 0.8104 (mm-40) REVERT: A 442 ASP cc_start: 0.7442 (t0) cc_final: 0.7043 (t0) REVERT: A 450 ASN cc_start: 0.7949 (m-40) cc_final: 0.7369 (m-40) REVERT: A 536 ASN cc_start: 0.8015 (t0) cc_final: 0.7071 (p0) REVERT: A 542 ASN cc_start: 0.7235 (t0) cc_final: 0.7019 (t0) REVERT: C 41 LYS cc_start: 0.8017 (mttp) cc_final: 0.7793 (mttp) REVERT: C 116 SER cc_start: 0.7983 (m) cc_final: 0.7464 (t) REVERT: C 133 PHE cc_start: 0.7675 (m-80) cc_final: 0.7302 (m-80) REVERT: C 182 LYS cc_start: 0.8094 (mmmt) cc_final: 0.7761 (mmmt) REVERT: C 235 ILE cc_start: 0.8682 (mm) cc_final: 0.8355 (mt) REVERT: D 44 SER cc_start: 0.8583 (m) cc_final: 0.8242 (t) REVERT: D 50 TYR cc_start: 0.8148 (t80) cc_final: 0.7816 (t80) REVERT: D 70 SER cc_start: 0.8387 (m) cc_final: 0.8027 (t) REVERT: D 76 GLN cc_start: 0.7784 (mm-40) cc_final: 0.7043 (mm-40) REVERT: D 98 GLN cc_start: 0.7991 (tt0) cc_final: 0.7588 (tt0) REVERT: D 148 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7226 (mt) REVERT: D 151 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.8028 (tp) REVERT: D 152 MET cc_start: 0.8064 (tpp) cc_final: 0.7271 (mmp) REVERT: D 203 TRP cc_start: 0.8498 (OUTLIER) cc_final: 0.8097 (m-10) REVERT: D 208 GLU cc_start: 0.7401 (tt0) cc_final: 0.6875 (mt-10) REVERT: D 231 GLU cc_start: 0.6424 (mm-30) cc_final: 0.6172 (mm-30) REVERT: D 341 LYS cc_start: 0.7592 (mmmt) cc_final: 0.7270 (mmmt) REVERT: D 376 MET cc_start: 0.7519 (ttm) cc_final: 0.7216 (mtt) REVERT: D 393 ARG cc_start: 0.8179 (mtm-85) cc_final: 0.7927 (mtt180) REVERT: D 435 GLU cc_start: 0.5402 (mp0) cc_final: 0.4968 (mp0) REVERT: D 455 MET cc_start: 0.6413 (tmm) cc_final: 0.6079 (ttp) REVERT: D 460 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.6731 (mtt90) REVERT: D 470 LYS cc_start: 0.7832 (tppt) cc_final: 0.7207 (tppt) REVERT: D 479 GLU cc_start: 0.6255 (tm-30) cc_final: 0.5862 (tp30) REVERT: D 500 PRO cc_start: 0.7993 (Cg_exo) cc_final: 0.7740 (Cg_endo) REVERT: D 503 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7924 (tt) REVERT: D 534 LYS cc_start: 0.7871 (mtpt) cc_final: 0.7505 (mmmm) REVERT: D 557 MET cc_start: 0.8169 (tmm) cc_final: 0.7891 (tmm) REVERT: D 574 VAL cc_start: 0.8620 (t) cc_final: 0.8306 (p) REVERT: D 577 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7849 (mtpt) outliers start: 56 outliers final: 46 residues processed: 291 average time/residue: 0.2494 time to fit residues: 96.0697 Evaluate side-chains 311 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 255 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 101 GLN Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 271 TRP Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 300 GLN Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 460 ARG Chi-restraints excluded: chain D residue 477 TRP Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 577 LYS Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 608 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 57 optimal weight: 0.2980 chunk 42 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 89 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 9 optimal weight: 0.0570 chunk 39 optimal weight: 0.0060 chunk 37 optimal weight: 0.6980 overall best weight: 0.3314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN D 101 GLN D 250 ASN ** D 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.127499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.108652 restraints weight = 14985.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.112282 restraints weight = 6926.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.114696 restraints weight = 4208.915| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9956 Z= 0.166 Angle : 0.648 10.253 13580 Z= 0.321 Chirality : 0.047 0.258 1505 Planarity : 0.005 0.054 1718 Dihedral : 6.065 52.091 1720 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 5.44 % Allowed : 17.09 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.25), residues: 1156 helix: 0.79 (0.27), residues: 402 sheet: -0.75 (0.38), residues: 183 loop : -1.51 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 610 HIS 0.004 0.001 HIS C 207 PHE 0.037 0.002 PHE D 285 TYR 0.031 0.002 TYR A 473 ARG 0.006 0.001 ARG D 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00240 ( 15) link_NAG-ASN : angle 1.51906 ( 45) link_BETA1-4 : bond 0.00255 ( 6) link_BETA1-4 : angle 1.51662 ( 18) hydrogen bonds : bond 0.03884 ( 362) hydrogen bonds : angle 4.72837 ( 1041) SS BOND : bond 0.00209 ( 11) SS BOND : angle 0.73121 ( 22) covalent geometry : bond 0.00383 ( 9924) covalent geometry : angle 0.64075 (13495) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 255 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 GLN cc_start: 0.7049 (OUTLIER) cc_final: 0.6663 (pp30) REVERT: A 324 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.6886 (tp30) REVERT: A 326 ILE cc_start: 0.7855 (pt) cc_final: 0.7624 (pt) REVERT: A 328 ARG cc_start: 0.8495 (mtt-85) cc_final: 0.8264 (mtp180) REVERT: A 345 THR cc_start: 0.8229 (p) cc_final: 0.8008 (m) REVERT: A 362 VAL cc_start: 0.7758 (OUTLIER) cc_final: 0.7245 (p) REVERT: A 370 ASN cc_start: 0.7574 (t0) cc_final: 0.7244 (t0) REVERT: A 378 LYS cc_start: 0.7237 (mtpp) cc_final: 0.6700 (mtpp) REVERT: A 394 ASN cc_start: 0.7677 (OUTLIER) cc_final: 0.7327 (m110) REVERT: A 403 ARG cc_start: 0.8134 (ttp-170) cc_final: 0.7676 (ttp-170) REVERT: A 408 ARG cc_start: 0.8026 (ptm-80) cc_final: 0.7768 (ptt90) REVERT: A 414 GLN cc_start: 0.8418 (mm-40) cc_final: 0.8124 (mm-40) REVERT: A 442 ASP cc_start: 0.7469 (t0) cc_final: 0.7050 (t0) REVERT: A 450 ASN cc_start: 0.7965 (m-40) cc_final: 0.7385 (m-40) REVERT: A 536 ASN cc_start: 0.8063 (t0) cc_final: 0.7087 (p0) REVERT: A 542 ASN cc_start: 0.7226 (t0) cc_final: 0.7001 (t0) REVERT: C 41 LYS cc_start: 0.8060 (mttp) cc_final: 0.7817 (mttp) REVERT: C 116 SER cc_start: 0.7970 (m) cc_final: 0.7409 (t) REVERT: C 133 PHE cc_start: 0.7666 (m-80) cc_final: 0.7255 (m-80) REVERT: C 182 LYS cc_start: 0.8114 (mmmt) cc_final: 0.7740 (mmmt) REVERT: C 235 ILE cc_start: 0.8618 (mm) cc_final: 0.8316 (mt) REVERT: D 44 SER cc_start: 0.8528 (m) cc_final: 0.8188 (t) REVERT: D 70 SER cc_start: 0.8376 (m) cc_final: 0.8015 (t) REVERT: D 76 GLN cc_start: 0.7785 (mm-40) cc_final: 0.7013 (mm-40) REVERT: D 98 GLN cc_start: 0.8028 (tt0) cc_final: 0.7632 (tt0) REVERT: D 148 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.6943 (mt) REVERT: D 151 ILE cc_start: 0.8396 (OUTLIER) cc_final: 0.7929 (tp) REVERT: D 152 MET cc_start: 0.8068 (tpp) cc_final: 0.7196 (mmp) REVERT: D 203 TRP cc_start: 0.8434 (OUTLIER) cc_final: 0.8052 (m-10) REVERT: D 208 GLU cc_start: 0.7400 (tt0) cc_final: 0.6877 (mt-10) REVERT: D 231 GLU cc_start: 0.6490 (mm-30) cc_final: 0.6220 (mm-30) REVERT: D 341 LYS cc_start: 0.7624 (mmmt) cc_final: 0.7287 (mmmt) REVERT: D 349 TRP cc_start: 0.8607 (m100) cc_final: 0.8321 (m100) REVERT: D 376 MET cc_start: 0.7477 (ttm) cc_final: 0.7122 (mtt) REVERT: D 393 ARG cc_start: 0.8132 (mtm-85) cc_final: 0.7897 (mtt180) REVERT: D 435 GLU cc_start: 0.5454 (mp0) cc_final: 0.4991 (mp0) REVERT: D 455 MET cc_start: 0.6408 (tmm) cc_final: 0.6093 (ttp) REVERT: D 460 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.6701 (mtt90) REVERT: D 470 LYS cc_start: 0.7810 (tppt) cc_final: 0.7222 (tppt) REVERT: D 479 GLU cc_start: 0.6314 (tm-30) cc_final: 0.5898 (tp30) REVERT: D 500 PRO cc_start: 0.8002 (Cg_exo) cc_final: 0.7768 (Cg_endo) REVERT: D 503 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7875 (tt) REVERT: D 534 LYS cc_start: 0.7874 (mtpt) cc_final: 0.7461 (mmmm) REVERT: D 557 MET cc_start: 0.8269 (tmm) cc_final: 0.7961 (tmm) REVERT: D 571 GLU cc_start: 0.7147 (mm-30) cc_final: 0.6924 (mm-30) outliers start: 56 outliers final: 46 residues processed: 284 average time/residue: 0.2449 time to fit residues: 92.0810 Evaluate side-chains 308 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 253 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 101 GLN Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 271 TRP Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 300 GLN Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 460 ARG Chi-restraints excluded: chain D residue 477 TRP Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 608 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 61 optimal weight: 0.2980 chunk 45 optimal weight: 0.2980 chunk 6 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 79 optimal weight: 0.5980 chunk 106 optimal weight: 0.0770 chunk 93 optimal weight: 0.1980 chunk 52 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 41 optimal weight: 0.0770 chunk 88 optimal weight: 0.5980 overall best weight: 0.1896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN D 81 GLN D 101 GLN D 250 ASN ** D 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.127732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.109399 restraints weight = 14955.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.112809 restraints weight = 7210.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.115094 restraints weight = 4497.533| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9956 Z= 0.131 Angle : 0.627 9.818 13580 Z= 0.311 Chirality : 0.045 0.253 1505 Planarity : 0.005 0.047 1718 Dihedral : 5.842 51.918 1720 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 5.24 % Allowed : 17.48 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.25), residues: 1156 helix: 0.89 (0.27), residues: 402 sheet: -0.73 (0.39), residues: 182 loop : -1.44 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP D 610 HIS 0.004 0.001 HIS C 69 PHE 0.034 0.002 PHE D 285 TYR 0.030 0.001 TYR A 473 ARG 0.005 0.001 ARG D 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00252 ( 15) link_NAG-ASN : angle 1.43793 ( 45) link_BETA1-4 : bond 0.00306 ( 6) link_BETA1-4 : angle 1.45838 ( 18) hydrogen bonds : bond 0.03656 ( 362) hydrogen bonds : angle 4.68575 ( 1041) SS BOND : bond 0.00278 ( 11) SS BOND : angle 0.54710 ( 22) covalent geometry : bond 0.00298 ( 9924) covalent geometry : angle 0.62103 (13495) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3906.27 seconds wall clock time: 68 minutes 53.26 seconds (4133.26 seconds total)