Starting phenix.real_space_refine on Wed Jul 30 10:43:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8odz_16820/07_2025/8odz_16820.cif Found real_map, /net/cci-nas-00/data/ceres_data/8odz_16820/07_2025/8odz_16820.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8odz_16820/07_2025/8odz_16820.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8odz_16820/07_2025/8odz_16820.map" model { file = "/net/cci-nas-00/data/ceres_data/8odz_16820/07_2025/8odz_16820.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8odz_16820/07_2025/8odz_16820.cif" } resolution = 3.6 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= 0.007 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 81 5.16 5 C 7597 2.51 5 N 2118 2.21 5 O 2304 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12100 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1228 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain breaks: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 2336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2336 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 278} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 3854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3854 Classifications: {'peptide': 485} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 33, 'TRANS': 451} Chain breaks: 3 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 4561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 4561 Classifications: {'peptide': 582} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 541} Chain breaks: 3 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} 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 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" 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: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 8.75, per 1000 atoms: 0.72 Number of scatterers: 12100 At special positions: 0 Unit cell: (87.58, 135.9, 194.79, 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 81 16.00 O 2304 8.00 N 2118 7.00 C 7597 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 Simple disulfide: pdb=" SG CYS A 33 " - pdb=" SG CYS A 106 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 81 " - pdb=" SG CYS A 119 " distance=2.03 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS B 197 " distance=2.03 Simple disulfide: pdb=" SG CYS B 50 " - pdb=" SG CYS B 90 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 139 " distance=2.03 Simple disulfide: pdb=" SG CYS B 167 " - pdb=" SG CYS B 191 " distance=2.04 Simple disulfide: pdb=" SG CYS B 305 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 311 " - pdb=" SG CYS B 328 " distance=2.03 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS C 63 " distance=2.03 Simple disulfide: pdb=" SG CYS C 81 " - pdb=" SG CYS C 95 " distance=2.06 Simple disulfide: pdb=" SG CYS C 194 " - pdb=" SG CYS C 216 " distance=2.03 Simple disulfide: pdb=" SG CYS C 252 " - pdb=" SG CYS C 293 " distance=2.03 Simple disulfide: pdb=" SG CYS C 313 " - pdb=" SG CYS C 390 " distance=2.04 Simple disulfide: pdb=" SG CYS C 315 " - pdb=" SG CYS C 405 " distance=2.03 Simple disulfide: pdb=" SG CYS C 434 " - pdb=" SG CYS C 495 " distance=2.03 Simple disulfide: pdb=" SG CYS D 28 " - pdb=" SG CYS D 127 " distance=2.03 Simple disulfide: pdb=" SG CYS D 51 " - pdb=" SG CYS D 111 " distance=2.03 Simple disulfide: pdb=" SG CYS D 145 " - pdb=" SG CYS D 156 " distance=2.03 Simple disulfide: pdb=" SG CYS D 186 " - pdb=" SG CYS D 194 " distance=2.03 Simple disulfide: pdb=" SG CYS D 432 " - pdb=" SG CYS D 524 " distance=2.03 Simple disulfide: pdb=" SG CYS D 509 " - pdb=" SG CYS D 567 " 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 ALPHA1-3 " BMA E 3 " - " MAN E 4 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " NAG-ASN " NAG C 601 " - " ASN C 169 " " NAG C 602 " - " ASN C 144 " " NAG C 603 " - " ASN C 463 " " NAG D 801 " - " ASN D 224 " " NAG D 802 " - " ASN D 48 " " NAG E 1 " - " ASN B 220 " Time building additional restraints: 3.56 Conformation dependent library (CDL) restraints added in 1.5 seconds 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2870 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 33 sheets defined 8.4% alpha, 36.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.81 Creating SS restraints... Processing helix chain 'A' and resid 32 through 55 removed outlier: 3.698A pdb=" N GLN A 36 " --> pdb=" O ARG A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 81 removed outlier: 3.540A pdb=" N CYS A 81 " --> pdb=" O THR A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 87 removed outlier: 3.536A pdb=" N LEU A 86 " --> pdb=" O PRO A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 112 removed outlier: 3.724A pdb=" N THR A 112 " --> pdb=" O PRO A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 141 removed outlier: 3.778A pdb=" N CYS A 119 " --> pdb=" O MET A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 167 removed outlier: 4.555A pdb=" N LEU A 156 " --> pdb=" O ASP A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 214 removed outlier: 3.672A pdb=" N MET A 189 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N THR A 200 " --> pdb=" O HIS A 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 468 removed outlier: 3.874A pdb=" N ALA C 467 " --> pdb=" O ASN C 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 92 No H-bonds generated for 'chain 'D' and resid 90 through 92' Processing helix chain 'D' and resid 560 through 565 removed outlier: 4.026A pdb=" N GLN D 564 " --> pdb=" O PRO D 560 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ARG D 565 " --> pdb=" O PHE D 561 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 560 through 565' Processing sheet with id=AA1, first strand: chain 'B' and resid 24 through 27 removed outlier: 7.014A pdb=" N VAL B 30 " --> pdb=" O LEU B 26 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N THR B 96 " --> pdb=" O LYS B 92 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LYS B 92 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY B 70 " --> pdb=" O TRP B 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 35 through 36 Processing sheet with id=AA3, first strand: chain 'B' and resid 44 through 49 Processing sheet with id=AA4, first strand: chain 'B' and resid 117 through 118 removed outlier: 4.245A pdb=" N LEU B 142 " --> pdb=" O LYS B 118 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 117 through 118 removed outlier: 4.245A pdb=" N LEU B 142 " --> pdb=" O LYS B 118 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU B 185 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N GLU B 175 " --> pdb=" O LYS B 186 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N SER B 188 " --> pdb=" O SER B 173 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N SER B 173 " --> pdb=" O SER B 188 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N SER B 190 " --> pdb=" O SER B 171 " (cutoff:3.500A) removed outlier: 8.566A pdb=" N SER B 171 " --> pdb=" O SER B 190 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 150 Processing sheet with id=AA7, first strand: chain 'B' and resid 149 through 150 Processing sheet with id=AA8, first strand: chain 'B' and resid 240 through 244 Processing sheet with id=AA9, first strand: chain 'B' and resid 294 through 296 Processing sheet with id=AB1, first strand: chain 'B' and resid 294 through 296 Processing sheet with id=AB2, first strand: chain 'C' and resid 60 through 68 removed outlier: 7.240A pdb=" N ASP C 60 " --> pdb=" O ARG C 55 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ARG C 55 " --> pdb=" O ASP C 60 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N GLU C 62 " --> pdb=" O CYS C 53 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N CYS C 53 " --> pdb=" O GLU C 62 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N SER C 64 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LEU C 51 " --> pdb=" O SER C 64 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N LYS C 147 " --> pdb=" O CYS C 53 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ARG C 55 " --> pdb=" O LYS C 147 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 94 through 99 Processing sheet with id=AB4, first strand: chain 'C' and resid 94 through 99 removed outlier: 3.651A pdb=" N VAL C 120 " --> pdb=" O GLN C 140 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 156 through 160 Processing sheet with id=AB6, first strand: chain 'C' and resid 189 through 193 Processing sheet with id=AB7, first strand: chain 'C' and resid 276 through 279 Processing sheet with id=AB8, first strand: chain 'C' and resid 320 through 324 Processing sheet with id=AB9, first strand: chain 'C' and resid 368 through 372 removed outlier: 3.561A pdb=" N GLY C 372 " --> pdb=" O MET C 375 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET C 375 " --> pdb=" O GLY C 372 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET C 378 " --> pdb=" O HIS C 421 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS C 421 " --> pdb=" O MET C 378 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 404 through 408 removed outlier: 4.495A pdb=" N HIS C 404 " --> pdb=" O TRP C 393 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU C 455 " --> pdb=" O VAL C 439 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ALA C 441 " --> pdb=" O THR C 453 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N THR C 453 " --> pdb=" O ALA C 441 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 471 through 477 removed outlier: 6.294A pdb=" N HIS C 472 " --> pdb=" O THR C 488 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N THR C 488 " --> pdb=" O HIS C 472 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 514 through 519 removed outlier: 3.535A pdb=" N VAL C 503 " --> pdb=" O ARG C 542 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 31 through 36 Processing sheet with id=AC5, first strand: chain 'D' and resid 40 through 41 removed outlier: 3.654A pdb=" N CYS D 127 " --> pdb=" O CYS D 111 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU D 108 " --> pdb=" O PHE D 73 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N LYS D 72 " --> pdb=" O VAL D 79 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N VAL D 79 " --> pdb=" O LYS D 72 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 196 through 198 removed outlier: 4.297A pdb=" N ASN D 159 " --> pdb=" O ASN D 142 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N ASN D 142 " --> pdb=" O ASN D 159 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ILE D 239 " --> pdb=" O CYS D 145 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N GLN D 147 " --> pdb=" O ILE D 239 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 180 through 188 Processing sheet with id=AC8, first strand: chain 'D' and resid 244 through 250 removed outlier: 3.669A pdb=" N ILE D 246 " --> pdb=" O GLN D 261 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N GLN D 261 " --> pdb=" O ILE D 246 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ILE D 248 " --> pdb=" O THR D 259 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N THR D 259 " --> pdb=" O ILE D 248 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 284 through 289 Processing sheet with id=AD1, first strand: chain 'D' and resid 347 through 348 Processing sheet with id=AD2, first strand: chain 'D' and resid 387 through 393 removed outlier: 4.179A pdb=" N THR D 387 " --> pdb=" O GLU D 382 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TRP D 408 " --> pdb=" O ILE D 428 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 443 through 448 removed outlier: 4.419A pdb=" N GLU D 447 " --> pdb=" O ASN D 451 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ASN D 451 " --> pdb=" O GLU D 447 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 487 through 491 removed outlier: 4.117A pdb=" N GLU D 468 " --> pdb=" O LEU D 517 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 544 through 548 Processing sheet with id=AD6, first strand: chain 'D' and resid 585 through 590 458 hydrogen bonds defined for protein. 1185 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: 4.51 Time building geometry restraints manager: 3.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 3954 1.35 - 1.49: 3128 1.49 - 1.62: 5191 1.62 - 1.76: 2 1.76 - 1.90: 110 Bond restraints: 12385 Sorted by residual: bond pdb=" CB PRO B 42 " pdb=" CG PRO B 42 " ideal model delta sigma weight residual 1.492 1.640 -0.148 5.00e-02 4.00e+02 8.73e+00 bond pdb=" N GLN B 248 " pdb=" CA GLN B 248 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.16e-02 7.43e+03 8.66e+00 bond pdb=" CB CYS C 95 " pdb=" SG CYS C 95 " ideal model delta sigma weight residual 1.808 1.898 -0.090 3.30e-02 9.18e+02 7.48e+00 bond pdb=" N ASN A 145 " pdb=" CA ASN A 145 " ideal model delta sigma weight residual 1.456 1.487 -0.032 1.18e-02 7.18e+03 7.14e+00 bond pdb=" N LYS B 245 " pdb=" CA LYS B 245 " ideal model delta sigma weight residual 1.454 1.489 -0.036 1.34e-02 5.57e+03 7.07e+00 ... (remaining 12380 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.02: 16753 4.02 - 8.05: 71 8.05 - 12.07: 10 12.07 - 16.10: 0 16.10 - 20.12: 1 Bond angle restraints: 16835 Sorted by residual: angle pdb=" CA CYS C 81 " pdb=" CB CYS C 81 " pdb=" SG CYS C 81 " ideal model delta sigma weight residual 114.40 134.52 -20.12 2.30e+00 1.89e-01 7.65e+01 angle pdb=" CA PRO B 42 " pdb=" N PRO B 42 " pdb=" CD PRO B 42 " ideal model delta sigma weight residual 112.00 101.54 10.46 1.40e+00 5.10e-01 5.58e+01 angle pdb=" N CYS C 81 " pdb=" CA CYS C 81 " pdb=" C CYS C 81 " ideal model delta sigma weight residual 108.60 116.88 -8.28 1.46e+00 4.69e-01 3.22e+01 angle pdb=" CA GLN B 248 " pdb=" C GLN B 248 " pdb=" O GLN B 248 " ideal model delta sigma weight residual 121.89 115.87 6.02 1.27e+00 6.20e-01 2.25e+01 angle pdb=" C MET B 241 " pdb=" N LYS B 242 " pdb=" CA LYS B 242 " ideal model delta sigma weight residual 120.94 129.67 -8.73 1.90e+00 2.77e-01 2.11e+01 ... (remaining 16830 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.79: 6988 20.79 - 41.57: 521 41.57 - 62.36: 87 62.36 - 83.14: 34 83.14 - 103.93: 11 Dihedral angle restraints: 7641 sinusoidal: 3225 harmonic: 4416 Sorted by residual: dihedral pdb=" CB CYS A 60 " pdb=" SG CYS A 60 " pdb=" SG CYS A 192 " pdb=" CB CYS A 192 " ideal model delta sinusoidal sigma weight residual 93.00 173.49 -80.49 1 1.00e+01 1.00e-02 8.01e+01 dihedral pdb=" CB CYS C 313 " pdb=" SG CYS C 313 " pdb=" SG CYS C 390 " pdb=" CB CYS C 390 " ideal model delta sinusoidal sigma weight residual -86.00 -157.47 71.47 1 1.00e+01 1.00e-02 6.55e+01 dihedral pdb=" CB CYS C 194 " pdb=" SG CYS C 194 " pdb=" SG CYS C 216 " pdb=" CB CYS C 216 " ideal model delta sinusoidal sigma weight residual 93.00 152.22 -59.22 1 1.00e+01 1.00e-02 4.69e+01 ... (remaining 7638 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 1758 0.094 - 0.187: 130 0.187 - 0.281: 5 0.281 - 0.375: 2 0.375 - 0.469: 1 Chirality restraints: 1896 Sorted by residual: chirality pdb=" CB ILE D 559 " pdb=" CA ILE D 559 " pdb=" CG1 ILE D 559 " pdb=" CG2 ILE D 559 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.47 2.00e-01 2.50e+01 5.49e+00 chirality pdb=" CA CYS C 81 " pdb=" N CYS C 81 " pdb=" C CYS C 81 " pdb=" CB CYS C 81 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" CA PRO B 42 " pdb=" N PRO B 42 " pdb=" C PRO B 42 " pdb=" CB PRO B 42 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 1893 not shown) Planarity restraints: 2153 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 109 " 0.025 2.00e-02 2.50e+03 2.62e-02 1.71e+01 pdb=" CG TRP C 109 " -0.070 2.00e-02 2.50e+03 pdb=" CD1 TRP C 109 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TRP C 109 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 109 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP C 109 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 109 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 109 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 109 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP C 109 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 344 " 0.021 2.00e-02 2.50e+03 2.00e-02 1.00e+01 pdb=" CG TRP D 344 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP D 344 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP D 344 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 344 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 344 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP D 344 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 344 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 344 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP D 344 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 41 " -0.046 5.00e-02 4.00e+02 6.43e-02 6.62e+00 pdb=" N PRO B 42 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 42 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 42 " -0.036 5.00e-02 4.00e+02 ... (remaining 2150 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 901 2.74 - 3.28: 11220 3.28 - 3.82: 19404 3.82 - 4.36: 21875 4.36 - 4.90: 37808 Nonbonded interactions: 91208 Sorted by model distance: nonbonded pdb=" OG1 THR D 233 " pdb=" OD1 ASP D 236 " model vdw 2.198 3.040 nonbonded pdb=" OD2 ASP B 234 " pdb=" OG SER B 258 " model vdw 2.231 3.040 nonbonded pdb=" ND2 ASN B 146 " pdb=" OE2 GLU B 185 " model vdw 2.240 3.120 nonbonded pdb=" O PHE D 73 " pdb=" OG1 THR D 107 " model vdw 2.260 3.040 nonbonded pdb=" OG SER D 443 " pdb=" OG1 THR D 455 " model vdw 2.269 3.040 ... (remaining 91203 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 52.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 32.920 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.148 12416 Z= 0.192 Angle : 0.821 20.123 16906 Z= 0.426 Chirality : 0.051 0.469 1896 Planarity : 0.006 0.064 2147 Dihedral : 15.382 103.928 4705 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.22 % Allowed : 0.52 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.22), residues: 1488 helix: 1.14 (0.53), residues: 98 sheet: 0.18 (0.21), residues: 633 loop : -1.50 (0.21), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP C 109 HIS 0.004 0.001 HIS C 421 PHE 0.019 0.002 PHE C 122 TYR 0.015 0.002 TYR A 124 ARG 0.006 0.000 ARG B 182 Details of bonding type rmsd link_NAG-ASN : bond 0.00352 ( 6) link_NAG-ASN : angle 3.01844 ( 18) link_BETA1-4 : bond 0.00896 ( 2) link_BETA1-4 : angle 1.86394 ( 6) link_ALPHA1-3 : bond 0.00343 ( 1) link_ALPHA1-3 : angle 1.87931 ( 3) hydrogen bonds : bond 0.11194 ( 437) hydrogen bonds : angle 6.60803 ( 1185) SS BOND : bond 0.00615 ( 22) SS BOND : angle 2.00813 ( 44) covalent geometry : bond 0.00420 (12385) covalent geometry : angle 0.80866 (16835) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 340 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 THR cc_start: 0.8666 (p) cc_final: 0.8035 (p) REVERT: A 67 HIS cc_start: 0.8174 (t70) cc_final: 0.7790 (t70) REVERT: A 141 LEU cc_start: 0.8713 (mt) cc_final: 0.8371 (mt) REVERT: B 220 ASN cc_start: 0.6992 (m-40) cc_final: 0.6698 (m-40) REVERT: B 246 ASN cc_start: 0.8494 (m-40) cc_final: 0.8243 (t0) REVERT: C 50 ASN cc_start: 0.8264 (m-40) cc_final: 0.7799 (m-40) REVERT: C 60 ASP cc_start: 0.8051 (t0) cc_final: 0.7757 (m-30) REVERT: C 67 TYR cc_start: 0.7909 (t80) cc_final: 0.7583 (t80) REVERT: C 167 ASP cc_start: 0.8449 (m-30) cc_final: 0.7725 (p0) REVERT: C 329 LEU cc_start: 0.8503 (mt) cc_final: 0.8302 (mt) REVERT: C 431 GLN cc_start: 0.8797 (mt0) cc_final: 0.8216 (mp10) REVERT: D 158 TRP cc_start: 0.9018 (p90) cc_final: 0.8616 (p90) REVERT: D 166 LEU cc_start: 0.9384 (tt) cc_final: 0.9092 (pp) REVERT: D 189 ASP cc_start: 0.9319 (p0) cc_final: 0.9042 (p0) REVERT: D 263 GLU cc_start: 0.8611 (tt0) cc_final: 0.8395 (tp30) REVERT: D 295 TYR cc_start: 0.8928 (t80) cc_final: 0.8320 (t80) REVERT: D 376 TYR cc_start: 0.8933 (m-80) cc_final: 0.8621 (m-80) REVERT: D 449 MET cc_start: 0.8397 (ptt) cc_final: 0.8006 (ppp) REVERT: D 540 PRO cc_start: 0.6748 (Cg_endo) cc_final: 0.6450 (Cg_exo) REVERT: D 613 MET cc_start: 0.8280 (ppp) cc_final: 0.7979 (ppp) outliers start: 3 outliers final: 0 residues processed: 343 average time/residue: 0.2725 time to fit residues: 130.3152 Evaluate side-chains 237 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 8.9990 chunk 113 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 38 optimal weight: 0.0170 chunk 76 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 117 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 87 optimal weight: 30.0000 chunk 136 optimal weight: 8.9990 overall best weight: 0.9020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS A 145 ASN B 101 HIS ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.162905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.109482 restraints weight = 28913.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.113916 restraints weight = 11803.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.116652 restraints weight = 7128.338| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12416 Z= 0.155 Angle : 0.709 14.075 16906 Z= 0.355 Chirality : 0.045 0.230 1896 Planarity : 0.005 0.071 2147 Dihedral : 7.663 59.051 1813 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.22 % Allowed : 13.19 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % 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: -0.81 (0.22), residues: 1488 helix: 1.05 (0.51), residues: 104 sheet: 0.17 (0.21), residues: 623 loop : -1.40 (0.21), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 109 HIS 0.004 0.001 HIS A 146 PHE 0.016 0.002 PHE C 265 TYR 0.030 0.002 TYR D 469 ARG 0.010 0.001 ARG D 565 Details of bonding type rmsd link_NAG-ASN : bond 0.00305 ( 6) link_NAG-ASN : angle 3.12184 ( 18) link_BETA1-4 : bond 0.00478 ( 2) link_BETA1-4 : angle 1.59121 ( 6) link_ALPHA1-3 : bond 0.00817 ( 1) link_ALPHA1-3 : angle 1.87882 ( 3) hydrogen bonds : bond 0.04254 ( 437) hydrogen bonds : angle 5.65339 ( 1185) SS BOND : bond 0.00381 ( 22) SS BOND : angle 1.73976 ( 44) covalent geometry : bond 0.00362 (12385) covalent geometry : angle 0.69602 (16835) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 258 time to evaluate : 2.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 HIS cc_start: 0.4121 (OUTLIER) cc_final: 0.3579 (m-70) REVERT: A 141 LEU cc_start: 0.8684 (mt) cc_final: 0.8432 (mt) REVERT: A 196 HIS cc_start: 0.7713 (t70) cc_final: 0.7417 (t70) REVERT: B 133 TYR cc_start: 0.8484 (m-80) cc_final: 0.8237 (m-80) REVERT: B 147 MET cc_start: 0.7580 (mtt) cc_final: 0.7211 (mtt) REVERT: B 269 LYS cc_start: 0.7370 (ttpt) cc_final: 0.6948 (ptpt) REVERT: B 302 GLU cc_start: 0.7912 (tt0) cc_final: 0.7598 (tt0) REVERT: C 50 ASN cc_start: 0.8365 (m-40) cc_final: 0.7876 (m-40) REVERT: C 60 ASP cc_start: 0.7989 (t0) cc_final: 0.7553 (m-30) REVERT: C 67 TYR cc_start: 0.8183 (t80) cc_final: 0.7725 (t80) REVERT: C 167 ASP cc_start: 0.8519 (m-30) cc_final: 0.7641 (p0) REVERT: C 214 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7332 (mt-10) REVERT: C 343 LYS cc_start: 0.6527 (OUTLIER) cc_final: 0.6106 (ttpt) REVERT: C 431 GLN cc_start: 0.8835 (mt0) cc_final: 0.8213 (mp10) REVERT: C 517 TRP cc_start: 0.8359 (m-90) cc_final: 0.8066 (m-90) REVERT: D 166 LEU cc_start: 0.9334 (tt) cc_final: 0.8952 (pp) REVERT: D 189 ASP cc_start: 0.9175 (p0) cc_final: 0.7763 (p0) REVERT: D 295 TYR cc_start: 0.8879 (t80) cc_final: 0.8334 (t80) REVERT: D 376 TYR cc_start: 0.8862 (m-80) cc_final: 0.8521 (m-80) REVERT: D 449 MET cc_start: 0.8326 (ptt) cc_final: 0.7958 (ppp) REVERT: D 540 PRO cc_start: 0.7386 (Cg_endo) cc_final: 0.6674 (Cg_exo) REVERT: D 613 MET cc_start: 0.8382 (ppp) cc_final: 0.7884 (ppp) outliers start: 30 outliers final: 17 residues processed: 267 average time/residue: 0.3112 time to fit residues: 122.5116 Evaluate side-chains 248 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 229 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 HIS Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 427 ASN Chi-restraints excluded: chain D residue 432 CYS Chi-restraints excluded: chain D residue 455 THR Chi-restraints excluded: chain D residue 589 ILE Chi-restraints excluded: chain D residue 611 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 60 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 11 optimal weight: 0.4980 chunk 30 optimal weight: 0.7980 chunk 111 optimal weight: 6.9990 chunk 85 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 41 optimal weight: 9.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS A 145 ASN ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 ASN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 ASN D 381 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.162320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.108924 restraints weight = 29386.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.113341 restraints weight = 12040.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.116079 restraints weight = 7281.447| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12416 Z= 0.154 Angle : 0.689 13.629 16906 Z= 0.343 Chirality : 0.045 0.233 1896 Planarity : 0.005 0.070 2147 Dihedral : 6.841 57.379 1813 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.04 % Allowed : 14.46 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % 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: -0.77 (0.22), residues: 1488 helix: 0.98 (0.51), residues: 104 sheet: 0.23 (0.21), residues: 624 loop : -1.39 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 109 HIS 0.003 0.001 HIS C 421 PHE 0.029 0.002 PHE D 234 TYR 0.015 0.001 TYR D 469 ARG 0.006 0.001 ARG D 572 Details of bonding type rmsd link_NAG-ASN : bond 0.00188 ( 6) link_NAG-ASN : angle 3.13900 ( 18) link_BETA1-4 : bond 0.00446 ( 2) link_BETA1-4 : angle 1.82109 ( 6) link_ALPHA1-3 : bond 0.00793 ( 1) link_ALPHA1-3 : angle 2.08015 ( 3) hydrogen bonds : bond 0.04031 ( 437) hydrogen bonds : angle 5.48607 ( 1185) SS BOND : bond 0.00398 ( 22) SS BOND : angle 1.43338 ( 44) covalent geometry : bond 0.00360 (12385) covalent geometry : angle 0.67727 (16835) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 235 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 TYR cc_start: 0.7911 (m-80) cc_final: 0.7574 (m-80) REVERT: A 141 LEU cc_start: 0.8707 (mt) cc_final: 0.8428 (mt) REVERT: B 60 TRP cc_start: 0.7915 (m100) cc_final: 0.7184 (m100) REVERT: B 133 TYR cc_start: 0.8515 (m-80) cc_final: 0.8218 (m-80) REVERT: B 147 MET cc_start: 0.7518 (mtt) cc_final: 0.7128 (mtt) REVERT: B 246 ASN cc_start: 0.8036 (OUTLIER) cc_final: 0.7796 (t0) REVERT: B 269 LYS cc_start: 0.7429 (ttpt) cc_final: 0.7014 (ptpt) REVERT: B 302 GLU cc_start: 0.7891 (tt0) cc_final: 0.7547 (tt0) REVERT: C 50 ASN cc_start: 0.8372 (m-40) cc_final: 0.7889 (m-40) REVERT: C 60 ASP cc_start: 0.7963 (t0) cc_final: 0.7536 (m-30) REVERT: C 67 TYR cc_start: 0.8281 (t80) cc_final: 0.7703 (t80) REVERT: C 167 ASP cc_start: 0.8467 (m-30) cc_final: 0.7623 (p0) REVERT: C 214 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7267 (mt-10) REVERT: C 226 GLU cc_start: 0.6410 (tp30) cc_final: 0.5898 (tp30) REVERT: C 314 ARG cc_start: 0.9246 (ttm-80) cc_final: 0.9025 (ttm-80) REVERT: C 343 LYS cc_start: 0.6445 (OUTLIER) cc_final: 0.6028 (ttpt) REVERT: C 431 GLN cc_start: 0.8811 (mt0) cc_final: 0.8199 (mp10) REVERT: C 548 LEU cc_start: 0.9251 (mt) cc_final: 0.8737 (tp) REVERT: D 147 GLN cc_start: 0.7666 (tt0) cc_final: 0.6896 (tp-100) REVERT: D 166 LEU cc_start: 0.9340 (tt) cc_final: 0.8900 (pp) REVERT: D 295 TYR cc_start: 0.8887 (t80) cc_final: 0.8309 (t80) REVERT: D 376 TYR cc_start: 0.8929 (m-80) cc_final: 0.8577 (m-80) REVERT: D 451 ASN cc_start: 0.9488 (t0) cc_final: 0.8894 (p0) REVERT: D 540 PRO cc_start: 0.7646 (Cg_endo) cc_final: 0.6900 (Cg_exo) REVERT: D 613 MET cc_start: 0.8488 (ppp) cc_final: 0.8060 (ppp) outliers start: 41 outliers final: 27 residues processed: 252 average time/residue: 0.3033 time to fit residues: 113.9881 Evaluate side-chains 250 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 221 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 87 HIS Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain D residue 427 ASN Chi-restraints excluded: chain D residue 432 CYS Chi-restraints excluded: chain D residue 455 THR Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 589 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 136 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 135 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 131 optimal weight: 7.9990 chunk 126 optimal weight: 9.9990 chunk 105 optimal weight: 6.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 192 GLN D 377 GLN ** D 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.160831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.106693 restraints weight = 29029.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.111022 restraints weight = 11979.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.113688 restraints weight = 7292.943| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12416 Z= 0.169 Angle : 0.681 12.779 16906 Z= 0.341 Chirality : 0.045 0.223 1896 Planarity : 0.005 0.065 2147 Dihedral : 6.522 55.894 1813 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.56 % Allowed : 16.46 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % 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: -0.78 (0.22), residues: 1488 helix: 1.08 (0.52), residues: 104 sheet: 0.16 (0.21), residues: 629 loop : -1.37 (0.21), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 398 HIS 0.010 0.001 HIS D 570 PHE 0.015 0.002 PHE C 180 TYR 0.013 0.001 TYR D 469 ARG 0.004 0.000 ARG C 314 Details of bonding type rmsd link_NAG-ASN : bond 0.00360 ( 6) link_NAG-ASN : angle 3.29971 ( 18) link_BETA1-4 : bond 0.00381 ( 2) link_BETA1-4 : angle 1.51247 ( 6) link_ALPHA1-3 : bond 0.00770 ( 1) link_ALPHA1-3 : angle 2.43029 ( 3) hydrogen bonds : bond 0.04034 ( 437) hydrogen bonds : angle 5.42821 ( 1185) SS BOND : bond 0.00582 ( 22) SS BOND : angle 1.60467 ( 44) covalent geometry : bond 0.00395 (12385) covalent geometry : angle 0.66699 (16835) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 232 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 LEU cc_start: 0.8722 (mt) cc_final: 0.8429 (mt) REVERT: A 153 LYS cc_start: 0.8650 (ttpt) cc_final: 0.8067 (ttpp) REVERT: A 196 HIS cc_start: 0.7808 (t70) cc_final: 0.7530 (t70) REVERT: B 60 TRP cc_start: 0.7880 (m100) cc_final: 0.7158 (m100) REVERT: B 147 MET cc_start: 0.7588 (mtt) cc_final: 0.7278 (mtt) REVERT: B 148 ASP cc_start: 0.7199 (t0) cc_final: 0.6697 (t0) REVERT: B 246 ASN cc_start: 0.7989 (t0) cc_final: 0.7781 (t0) REVERT: B 269 LYS cc_start: 0.7551 (ttpt) cc_final: 0.7213 (ptpt) REVERT: B 302 GLU cc_start: 0.7857 (tt0) cc_final: 0.7528 (tt0) REVERT: C 50 ASN cc_start: 0.8408 (m-40) cc_final: 0.7936 (m-40) REVERT: C 60 ASP cc_start: 0.8058 (t0) cc_final: 0.7705 (m-30) REVERT: C 67 TYR cc_start: 0.8294 (t80) cc_final: 0.7785 (t80) REVERT: C 167 ASP cc_start: 0.8408 (m-30) cc_final: 0.7649 (p0) REVERT: C 214 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7226 (mt-10) REVERT: C 343 LYS cc_start: 0.6413 (OUTLIER) cc_final: 0.5985 (ttpt) REVERT: C 431 GLN cc_start: 0.8822 (mt0) cc_final: 0.8213 (mp10) REVERT: C 517 TRP cc_start: 0.8788 (m-90) cc_final: 0.8206 (m-90) REVERT: C 548 LEU cc_start: 0.9233 (mt) cc_final: 0.8711 (tp) REVERT: D 147 GLN cc_start: 0.7576 (tt0) cc_final: 0.6747 (tp-100) REVERT: D 260 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.8810 (mt) REVERT: D 295 TYR cc_start: 0.8950 (t80) cc_final: 0.8463 (t80) REVERT: D 376 TYR cc_start: 0.8818 (m-80) cc_final: 0.8487 (m-80) REVERT: D 451 ASN cc_start: 0.9413 (t0) cc_final: 0.8875 (p0) REVERT: D 540 PRO cc_start: 0.7496 (Cg_endo) cc_final: 0.6763 (Cg_exo) REVERT: D 613 MET cc_start: 0.8454 (ppp) cc_final: 0.8058 (ppp) outliers start: 48 outliers final: 33 residues processed: 253 average time/residue: 0.2195 time to fit residues: 81.2046 Evaluate side-chains 258 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 223 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 87 HIS Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 427 ASN Chi-restraints excluded: chain D residue 432 CYS Chi-restraints excluded: chain D residue 455 THR Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 589 ILE Chi-restraints excluded: chain D residue 611 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 88 optimal weight: 0.3980 chunk 21 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 145 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 29 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 377 GLN ** D 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.161270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.107072 restraints weight = 29242.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.111386 restraints weight = 12138.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.114035 restraints weight = 7397.728| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12416 Z= 0.140 Angle : 0.662 11.891 16906 Z= 0.327 Chirality : 0.044 0.223 1896 Planarity : 0.005 0.063 2147 Dihedral : 6.203 54.534 1813 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.41 % Allowed : 18.68 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % 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: -0.62 (0.22), residues: 1488 helix: 1.17 (0.52), residues: 104 sheet: 0.34 (0.21), residues: 629 loop : -1.32 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 109 HIS 0.004 0.001 HIS D 570 PHE 0.012 0.001 PHE C 180 TYR 0.011 0.001 TYR D 574 ARG 0.007 0.000 ARG C 314 Details of bonding type rmsd link_NAG-ASN : bond 0.00274 ( 6) link_NAG-ASN : angle 3.12105 ( 18) link_BETA1-4 : bond 0.00405 ( 2) link_BETA1-4 : angle 1.47381 ( 6) link_ALPHA1-3 : bond 0.00799 ( 1) link_ALPHA1-3 : angle 2.22448 ( 3) hydrogen bonds : bond 0.03768 ( 437) hydrogen bonds : angle 5.27776 ( 1185) SS BOND : bond 0.00392 ( 22) SS BOND : angle 1.38919 ( 44) covalent geometry : bond 0.00330 (12385) covalent geometry : angle 0.65032 (16835) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 237 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 LEU cc_start: 0.8731 (mt) cc_final: 0.8439 (mt) REVERT: B 60 TRP cc_start: 0.7835 (m100) cc_final: 0.7069 (m100) REVERT: B 147 MET cc_start: 0.7566 (mtt) cc_final: 0.7151 (mtt) REVERT: B 148 ASP cc_start: 0.7213 (t0) cc_final: 0.6724 (t0) REVERT: B 246 ASN cc_start: 0.8167 (t0) cc_final: 0.7932 (t0) REVERT: B 269 LYS cc_start: 0.7570 (ttpt) cc_final: 0.7294 (ptpt) REVERT: B 302 GLU cc_start: 0.7819 (tt0) cc_final: 0.7437 (tt0) REVERT: C 50 ASN cc_start: 0.8410 (m-40) cc_final: 0.7942 (m-40) REVERT: C 60 ASP cc_start: 0.8022 (t0) cc_final: 0.7607 (m-30) REVERT: C 67 TYR cc_start: 0.8340 (t80) cc_final: 0.7745 (t80) REVERT: C 114 ILE cc_start: 0.8024 (OUTLIER) cc_final: 0.7807 (tp) REVERT: C 128 LEU cc_start: 0.8736 (pt) cc_final: 0.8519 (mm) REVERT: C 167 ASP cc_start: 0.8367 (m-30) cc_final: 0.7500 (p0) REVERT: C 214 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7235 (mt-10) REVERT: C 343 LYS cc_start: 0.6430 (OUTLIER) cc_final: 0.5998 (ttpt) REVERT: C 431 GLN cc_start: 0.8793 (mt0) cc_final: 0.8193 (mp10) REVERT: C 517 TRP cc_start: 0.8863 (m-90) cc_final: 0.8259 (m-90) REVERT: C 548 LEU cc_start: 0.9248 (mt) cc_final: 0.8532 (tp) REVERT: D 106 MET cc_start: 0.8895 (ptp) cc_final: 0.8671 (ptm) REVERT: D 147 GLN cc_start: 0.7611 (tt0) cc_final: 0.6762 (tp-100) REVERT: D 166 LEU cc_start: 0.9193 (tt) cc_final: 0.8671 (pp) REVERT: D 260 LEU cc_start: 0.9153 (mt) cc_final: 0.8848 (mt) REVERT: D 295 TYR cc_start: 0.8999 (t80) cc_final: 0.8488 (t80) REVERT: D 376 TYR cc_start: 0.8794 (m-80) cc_final: 0.8464 (m-80) REVERT: D 451 ASN cc_start: 0.9455 (t0) cc_final: 0.8898 (p0) REVERT: D 540 PRO cc_start: 0.7473 (Cg_endo) cc_final: 0.6736 (Cg_exo) REVERT: D 613 MET cc_start: 0.8465 (ppp) cc_final: 0.8082 (ppp) outliers start: 46 outliers final: 33 residues processed: 260 average time/residue: 0.2407 time to fit residues: 93.4613 Evaluate side-chains 252 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 217 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 87 HIS Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 427 ASN Chi-restraints excluded: chain D residue 432 CYS Chi-restraints excluded: chain D residue 455 THR Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 589 ILE Chi-restraints excluded: chain D residue 611 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 56 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 40 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 144 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 chunk 91 optimal weight: 0.0020 chunk 67 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 49 optimal weight: 0.3980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 GLN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.162293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.108001 restraints weight = 29388.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.112300 restraints weight = 12262.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.114920 restraints weight = 7488.700| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 12416 Z= 0.123 Angle : 0.661 13.494 16906 Z= 0.327 Chirality : 0.044 0.227 1896 Planarity : 0.005 0.063 2147 Dihedral : 5.985 54.769 1813 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.19 % Allowed : 18.90 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % 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: -0.56 (0.22), residues: 1488 helix: 1.06 (0.51), residues: 104 sheet: 0.47 (0.21), residues: 624 loop : -1.34 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP D 398 HIS 0.004 0.001 HIS D 570 PHE 0.041 0.002 PHE D 234 TYR 0.011 0.001 TYR D 574 ARG 0.010 0.000 ARG C 233 Details of bonding type rmsd link_NAG-ASN : bond 0.00175 ( 6) link_NAG-ASN : angle 2.85834 ( 18) link_BETA1-4 : bond 0.00507 ( 2) link_BETA1-4 : angle 1.35374 ( 6) link_ALPHA1-3 : bond 0.00842 ( 1) link_ALPHA1-3 : angle 2.00232 ( 3) hydrogen bonds : bond 0.03656 ( 437) hydrogen bonds : angle 5.21919 ( 1185) SS BOND : bond 0.00474 ( 22) SS BOND : angle 1.49708 ( 44) covalent geometry : bond 0.00291 (12385) covalent geometry : angle 0.65070 (16835) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 229 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 TYR cc_start: 0.7895 (m-80) cc_final: 0.7544 (m-80) REVERT: A 141 LEU cc_start: 0.8721 (mt) cc_final: 0.8435 (mt) REVERT: A 186 ARG cc_start: 0.7337 (mmt90) cc_final: 0.7019 (mmt90) REVERT: B 60 TRP cc_start: 0.7835 (m100) cc_final: 0.7116 (m100) REVERT: B 147 MET cc_start: 0.7464 (mtt) cc_final: 0.7092 (mtt) REVERT: B 148 ASP cc_start: 0.7126 (t0) cc_final: 0.6638 (t0) REVERT: B 246 ASN cc_start: 0.8211 (t0) cc_final: 0.7970 (t0) REVERT: B 302 GLU cc_start: 0.7811 (tt0) cc_final: 0.7407 (tt0) REVERT: C 50 ASN cc_start: 0.8402 (m-40) cc_final: 0.7945 (m-40) REVERT: C 60 ASP cc_start: 0.7996 (t0) cc_final: 0.7560 (m-30) REVERT: C 67 TYR cc_start: 0.8316 (t80) cc_final: 0.7781 (t80) REVERT: C 167 ASP cc_start: 0.8315 (m-30) cc_final: 0.7463 (p0) REVERT: C 184 MET cc_start: 0.6462 (tpp) cc_final: 0.6200 (tpt) REVERT: C 214 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7180 (mt-10) REVERT: C 343 LYS cc_start: 0.6416 (OUTLIER) cc_final: 0.5995 (ttpt) REVERT: C 431 GLN cc_start: 0.8695 (mt0) cc_final: 0.8048 (mp10) REVERT: C 517 TRP cc_start: 0.8841 (m-90) cc_final: 0.8222 (m-90) REVERT: C 548 LEU cc_start: 0.9147 (mt) cc_final: 0.8525 (tp) REVERT: D 147 GLN cc_start: 0.7518 (tt0) cc_final: 0.6677 (tp-100) REVERT: D 166 LEU cc_start: 0.9228 (tt) cc_final: 0.8708 (pp) REVERT: D 260 LEU cc_start: 0.9169 (mt) cc_final: 0.8862 (mt) REVERT: D 295 TYR cc_start: 0.9003 (t80) cc_final: 0.8461 (t80) REVERT: D 376 TYR cc_start: 0.8817 (m-80) cc_final: 0.8484 (m-80) REVERT: D 540 PRO cc_start: 0.7410 (Cg_endo) cc_final: 0.6670 (Cg_exo) REVERT: D 613 MET cc_start: 0.8417 (ppp) cc_final: 0.8059 (ppp) outliers start: 43 outliers final: 26 residues processed: 252 average time/residue: 0.2377 time to fit residues: 90.2080 Evaluate side-chains 244 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 217 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 87 HIS Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 427 ASN Chi-restraints excluded: chain D residue 455 THR Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 589 ILE Chi-restraints excluded: chain D residue 611 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 106 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 141 optimal weight: 20.0000 chunk 147 optimal weight: 20.0000 chunk 77 optimal weight: 0.0000 chunk 114 optimal weight: 7.9990 chunk 27 optimal weight: 0.9990 chunk 148 optimal weight: 5.9990 chunk 96 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 GLN ** C 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.160765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.107007 restraints weight = 29056.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.111354 restraints weight = 11993.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.113935 restraints weight = 7265.447| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12416 Z= 0.157 Angle : 0.683 12.239 16906 Z= 0.337 Chirality : 0.044 0.225 1896 Planarity : 0.005 0.063 2147 Dihedral : 5.907 54.466 1813 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.89 % Allowed : 20.24 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % 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: -0.61 (0.22), residues: 1488 helix: 1.07 (0.51), residues: 104 sheet: 0.36 (0.21), residues: 631 loop : -1.31 (0.22), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP D 398 HIS 0.004 0.001 HIS A 87 PHE 0.027 0.002 PHE D 234 TYR 0.014 0.001 TYR B 265 ARG 0.009 0.000 ARG C 314 Details of bonding type rmsd link_NAG-ASN : bond 0.00324 ( 6) link_NAG-ASN : angle 3.11843 ( 18) link_BETA1-4 : bond 0.00435 ( 2) link_BETA1-4 : angle 1.38454 ( 6) link_ALPHA1-3 : bond 0.00675 ( 1) link_ALPHA1-3 : angle 2.03771 ( 3) hydrogen bonds : bond 0.03785 ( 437) hydrogen bonds : angle 5.22285 ( 1185) SS BOND : bond 0.00324 ( 22) SS BOND : angle 1.26340 ( 44) covalent geometry : bond 0.00369 (12385) covalent geometry : angle 0.67221 (16835) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 220 time to evaluate : 1.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ASP cc_start: 0.9397 (m-30) cc_final: 0.9153 (m-30) REVERT: A 54 LYS cc_start: 0.8826 (mmtp) cc_final: 0.8333 (mmmt) REVERT: A 58 TYR cc_start: 0.7953 (m-80) cc_final: 0.7603 (m-80) REVERT: A 153 LYS cc_start: 0.8603 (ttpt) cc_final: 0.8048 (ttpp) REVERT: A 212 LEU cc_start: 0.9000 (tp) cc_final: 0.8796 (tp) REVERT: B 60 TRP cc_start: 0.7800 (m100) cc_final: 0.7006 (m100) REVERT: B 147 MET cc_start: 0.7526 (mtt) cc_final: 0.7130 (mtt) REVERT: B 148 ASP cc_start: 0.7233 (t0) cc_final: 0.6803 (t0) REVERT: B 208 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8330 (mm) REVERT: B 246 ASN cc_start: 0.8231 (t0) cc_final: 0.7988 (t0) REVERT: C 50 ASN cc_start: 0.8418 (m-40) cc_final: 0.7964 (m-40) REVERT: C 60 ASP cc_start: 0.8017 (t0) cc_final: 0.7598 (m-30) REVERT: C 67 TYR cc_start: 0.8362 (t80) cc_final: 0.7766 (t80) REVERT: C 167 ASP cc_start: 0.8320 (m-30) cc_final: 0.7503 (p0) REVERT: C 184 MET cc_start: 0.6615 (tpp) cc_final: 0.6406 (tpt) REVERT: C 214 GLU cc_start: 0.7522 (mt-10) cc_final: 0.7184 (mt-10) REVERT: C 343 LYS cc_start: 0.6450 (OUTLIER) cc_final: 0.6013 (ttpt) REVERT: C 431 GLN cc_start: 0.8712 (mt0) cc_final: 0.8079 (mp10) REVERT: C 517 TRP cc_start: 0.8870 (m-90) cc_final: 0.8253 (m-90) REVERT: C 548 LEU cc_start: 0.9134 (mt) cc_final: 0.8506 (tp) REVERT: D 147 GLN cc_start: 0.7517 (tt0) cc_final: 0.6676 (tp-100) REVERT: D 166 LEU cc_start: 0.9260 (tt) cc_final: 0.8755 (pp) REVERT: D 260 LEU cc_start: 0.9197 (mt) cc_final: 0.8889 (mt) REVERT: D 295 TYR cc_start: 0.9029 (t80) cc_final: 0.8517 (t80) REVERT: D 376 TYR cc_start: 0.8776 (m-80) cc_final: 0.8460 (m-80) REVERT: D 540 PRO cc_start: 0.7349 (Cg_endo) cc_final: 0.6616 (Cg_exo) REVERT: D 613 MET cc_start: 0.8437 (ppp) cc_final: 0.8091 (ppp) outliers start: 39 outliers final: 29 residues processed: 237 average time/residue: 0.2608 time to fit residues: 92.2028 Evaluate side-chains 244 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 213 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 398 TRP Chi-restraints excluded: chain D residue 455 THR Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 570 HIS Chi-restraints excluded: chain D residue 589 ILE Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 611 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 66 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 118 optimal weight: 0.0470 chunk 37 optimal weight: 0.9990 chunk 144 optimal weight: 4.9990 chunk 142 optimal weight: 5.9990 chunk 139 optimal weight: 6.9990 chunk 28 optimal weight: 0.0170 chunk 25 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 GLN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.162145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.108829 restraints weight = 29318.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.113262 restraints weight = 12014.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.115953 restraints weight = 7226.154| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 12416 Z= 0.119 Angle : 0.671 14.161 16906 Z= 0.325 Chirality : 0.044 0.230 1896 Planarity : 0.005 0.063 2147 Dihedral : 5.684 55.015 1813 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.74 % Allowed : 20.53 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % 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: -0.46 (0.22), residues: 1488 helix: 1.14 (0.51), residues: 104 sheet: 0.57 (0.21), residues: 623 loop : -1.30 (0.22), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 344 HIS 0.004 0.001 HIS C 402 PHE 0.026 0.001 PHE D 234 TYR 0.011 0.001 TYR D 574 ARG 0.008 0.001 ARG C 233 Details of bonding type rmsd link_NAG-ASN : bond 0.00187 ( 6) link_NAG-ASN : angle 2.71008 ( 18) link_BETA1-4 : bond 0.00532 ( 2) link_BETA1-4 : angle 1.20003 ( 6) link_ALPHA1-3 : bond 0.00767 ( 1) link_ALPHA1-3 : angle 1.71227 ( 3) hydrogen bonds : bond 0.03570 ( 437) hydrogen bonds : angle 5.16245 ( 1185) SS BOND : bond 0.00430 ( 22) SS BOND : angle 1.24981 ( 44) covalent geometry : bond 0.00279 (12385) covalent geometry : angle 0.66219 (16835) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 227 time to evaluate : 1.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ASP cc_start: 0.9326 (m-30) cc_final: 0.8971 (m-30) REVERT: A 54 LYS cc_start: 0.8824 (mmtp) cc_final: 0.8317 (mmmt) REVERT: A 58 TYR cc_start: 0.7990 (m-80) cc_final: 0.7725 (m-80) REVERT: B 60 TRP cc_start: 0.7738 (m100) cc_final: 0.7029 (m100) REVERT: B 147 MET cc_start: 0.7504 (mtt) cc_final: 0.7170 (mtt) REVERT: B 148 ASP cc_start: 0.7106 (t0) cc_final: 0.6677 (t0) REVERT: B 206 ILE cc_start: 0.8427 (mt) cc_final: 0.8147 (tt) REVERT: B 246 ASN cc_start: 0.8246 (t0) cc_final: 0.8008 (t0) REVERT: C 50 ASN cc_start: 0.8371 (m-40) cc_final: 0.7945 (m-40) REVERT: C 60 ASP cc_start: 0.7971 (t0) cc_final: 0.7568 (m-30) REVERT: C 67 TYR cc_start: 0.8300 (t80) cc_final: 0.7761 (t80) REVERT: C 128 LEU cc_start: 0.8791 (pt) cc_final: 0.8551 (tt) REVERT: C 167 ASP cc_start: 0.8291 (m-30) cc_final: 0.7445 (p0) REVERT: C 214 GLU cc_start: 0.7541 (mt-10) cc_final: 0.7197 (mt-10) REVERT: C 343 LYS cc_start: 0.6433 (OUTLIER) cc_final: 0.6013 (ttpt) REVERT: C 431 GLN cc_start: 0.8641 (mt0) cc_final: 0.7994 (mp10) REVERT: C 517 TRP cc_start: 0.8863 (m-90) cc_final: 0.8283 (m-90) REVERT: C 548 LEU cc_start: 0.9098 (mt) cc_final: 0.8477 (tp) REVERT: D 41 ILE cc_start: 0.9188 (tp) cc_final: 0.8899 (mm) REVERT: D 147 GLN cc_start: 0.7563 (tt0) cc_final: 0.6686 (tp-100) REVERT: D 166 LEU cc_start: 0.9274 (tt) cc_final: 0.8782 (pp) REVERT: D 260 LEU cc_start: 0.9174 (mt) cc_final: 0.8860 (mt) REVERT: D 271 ASN cc_start: 0.9268 (t0) cc_final: 0.8820 (m-40) REVERT: D 295 TYR cc_start: 0.9009 (t80) cc_final: 0.8470 (t80) REVERT: D 376 TYR cc_start: 0.8720 (m-80) cc_final: 0.8410 (m-80) REVERT: D 451 ASN cc_start: 0.9463 (t0) cc_final: 0.8936 (p0) REVERT: D 540 PRO cc_start: 0.7258 (Cg_endo) cc_final: 0.6533 (Cg_exo) REVERT: D 613 MET cc_start: 0.8383 (ppp) cc_final: 0.8038 (ppp) outliers start: 37 outliers final: 25 residues processed: 246 average time/residue: 0.2277 time to fit residues: 83.7869 Evaluate side-chains 239 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 213 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 87 HIS Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 455 THR Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 570 HIS Chi-restraints excluded: chain D residue 589 ILE Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 611 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 85 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 76 optimal weight: 7.9990 chunk 139 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 147 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 chunk 68 optimal weight: 0.8980 chunk 137 optimal weight: 3.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 GLN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 ASN ** D 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.158736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.104761 restraints weight = 29104.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.108925 restraints weight = 12169.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.111467 restraints weight = 7422.096| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 12416 Z= 0.214 Angle : 0.738 12.368 16906 Z= 0.363 Chirality : 0.045 0.269 1896 Planarity : 0.005 0.064 2147 Dihedral : 5.728 53.988 1813 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.89 % Allowed : 20.53 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % 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: -0.66 (0.22), residues: 1488 helix: 1.41 (0.52), residues: 98 sheet: 0.32 (0.21), residues: 624 loop : -1.37 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP D 398 HIS 0.006 0.001 HIS A 196 PHE 0.020 0.002 PHE C 180 TYR 0.015 0.002 TYR B 265 ARG 0.014 0.001 ARG C 233 Details of bonding type rmsd link_NAG-ASN : bond 0.00549 ( 6) link_NAG-ASN : angle 3.55264 ( 18) link_BETA1-4 : bond 0.00263 ( 2) link_BETA1-4 : angle 1.45400 ( 6) link_ALPHA1-3 : bond 0.00745 ( 1) link_ALPHA1-3 : angle 2.32337 ( 3) hydrogen bonds : bond 0.04102 ( 437) hydrogen bonds : angle 5.35631 ( 1185) SS BOND : bond 0.00352 ( 22) SS BOND : angle 2.19305 ( 44) covalent geometry : bond 0.00494 (12385) covalent geometry : angle 0.72014 (16835) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 221 time to evaluate : 1.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ASP cc_start: 0.9342 (m-30) cc_final: 0.8976 (m-30) REVERT: A 54 LYS cc_start: 0.8848 (mmtp) cc_final: 0.8352 (mmmt) REVERT: A 212 LEU cc_start: 0.9033 (tp) cc_final: 0.8801 (tp) REVERT: B 60 TRP cc_start: 0.7855 (m100) cc_final: 0.6960 (m100) REVERT: B 148 ASP cc_start: 0.7472 (t0) cc_final: 0.7083 (t0) REVERT: B 201 GLU cc_start: 0.7947 (tp30) cc_final: 0.7358 (tp30) REVERT: B 208 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8345 (mm) REVERT: B 246 ASN cc_start: 0.8309 (t0) cc_final: 0.8053 (t0) REVERT: C 50 ASN cc_start: 0.8397 (m-40) cc_final: 0.7961 (m-40) REVERT: C 60 ASP cc_start: 0.8031 (t0) cc_final: 0.7749 (m-30) REVERT: C 67 TYR cc_start: 0.8462 (t80) cc_final: 0.7856 (t80) REVERT: C 128 LEU cc_start: 0.8787 (pt) cc_final: 0.8551 (tt) REVERT: C 214 GLU cc_start: 0.7510 (mt-10) cc_final: 0.7055 (mt-10) REVERT: C 343 LYS cc_start: 0.6443 (OUTLIER) cc_final: 0.6026 (ttpt) REVERT: C 431 GLN cc_start: 0.8729 (mt0) cc_final: 0.8081 (mp10) REVERT: C 517 TRP cc_start: 0.8942 (m-90) cc_final: 0.8347 (m-90) REVERT: C 537 TYR cc_start: 0.8734 (m-10) cc_final: 0.7993 (m-80) REVERT: C 548 LEU cc_start: 0.9127 (mt) cc_final: 0.8503 (tp) REVERT: D 147 GLN cc_start: 0.7634 (tt0) cc_final: 0.6764 (tp-100) REVERT: D 166 LEU cc_start: 0.9274 (tt) cc_final: 0.8815 (pp) REVERT: D 260 LEU cc_start: 0.9233 (mt) cc_final: 0.8927 (mt) REVERT: D 295 TYR cc_start: 0.9096 (t80) cc_final: 0.8536 (t80) REVERT: D 376 TYR cc_start: 0.8807 (m-80) cc_final: 0.8496 (m-80) REVERT: D 540 PRO cc_start: 0.7333 (Cg_endo) cc_final: 0.6630 (Cg_exo) REVERT: D 613 MET cc_start: 0.8527 (ppp) cc_final: 0.8181 (ppp) outliers start: 39 outliers final: 31 residues processed: 245 average time/residue: 0.2286 time to fit residues: 83.0193 Evaluate side-chains 245 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 212 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 432 CYS Chi-restraints excluded: chain D residue 455 THR Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 570 HIS Chi-restraints excluded: chain D residue 589 ILE Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 611 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 4 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 121 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 chunk 83 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 chunk 112 optimal weight: 10.0000 chunk 118 optimal weight: 0.0170 overall best weight: 1.0024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 GLN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.160385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.106161 restraints weight = 29007.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.110252 restraints weight = 12311.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.112735 restraints weight = 7572.848| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 12416 Z= 0.152 Angle : 0.715 12.656 16906 Z= 0.350 Chirality : 0.045 0.295 1896 Planarity : 0.005 0.062 2147 Dihedral : 5.681 54.491 1813 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.37 % Allowed : 21.50 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % 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: -0.63 (0.22), residues: 1488 helix: 1.22 (0.51), residues: 98 sheet: 0.44 (0.22), residues: 608 loop : -1.38 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP D 398 HIS 0.004 0.001 HIS D 515 PHE 0.018 0.001 PHE D 234 TYR 0.016 0.001 TYR C 143 ARG 0.012 0.001 ARG C 233 Details of bonding type rmsd link_NAG-ASN : bond 0.00125 ( 6) link_NAG-ASN : angle 3.02669 ( 18) link_BETA1-4 : bond 0.00469 ( 2) link_BETA1-4 : angle 1.24267 ( 6) link_ALPHA1-3 : bond 0.00539 ( 1) link_ALPHA1-3 : angle 1.75285 ( 3) hydrogen bonds : bond 0.03863 ( 437) hydrogen bonds : angle 5.29484 ( 1185) SS BOND : bond 0.00469 ( 22) SS BOND : angle 1.87102 ( 44) covalent geometry : bond 0.00360 (12385) covalent geometry : angle 0.70217 (16835) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 223 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ASP cc_start: 0.9287 (m-30) cc_final: 0.8903 (m-30) REVERT: A 54 LYS cc_start: 0.8830 (mmtp) cc_final: 0.8332 (mmmt) REVERT: A 58 TYR cc_start: 0.7942 (m-80) cc_final: 0.7634 (m-80) REVERT: A 74 GLN cc_start: 0.8756 (tp-100) cc_final: 0.8504 (tp-100) REVERT: A 212 LEU cc_start: 0.9016 (tp) cc_final: 0.8810 (tp) REVERT: B 60 TRP cc_start: 0.7778 (m100) cc_final: 0.6989 (m100) REVERT: B 147 MET cc_start: 0.7566 (mtt) cc_final: 0.7257 (mtt) REVERT: B 148 ASP cc_start: 0.7390 (t0) cc_final: 0.6993 (t0) REVERT: B 201 GLU cc_start: 0.7882 (tp30) cc_final: 0.7302 (tp30) REVERT: B 246 ASN cc_start: 0.8302 (t0) cc_final: 0.8057 (t0) REVERT: B 269 LYS cc_start: 0.7438 (pttt) cc_final: 0.6499 (ptpp) REVERT: C 50 ASN cc_start: 0.8352 (m-40) cc_final: 0.7910 (m-40) REVERT: C 60 ASP cc_start: 0.7966 (t0) cc_final: 0.7610 (m-30) REVERT: C 67 TYR cc_start: 0.8396 (t80) cc_final: 0.7829 (t80) REVERT: C 128 LEU cc_start: 0.8808 (pt) cc_final: 0.8575 (tt) REVERT: C 167 ASP cc_start: 0.8533 (m-30) cc_final: 0.7380 (p0) REVERT: C 214 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7195 (mt-10) REVERT: C 343 LYS cc_start: 0.6442 (OUTLIER) cc_final: 0.6006 (ttpt) REVERT: C 431 GLN cc_start: 0.8691 (mt0) cc_final: 0.8049 (mp10) REVERT: C 517 TRP cc_start: 0.8906 (m-90) cc_final: 0.8263 (m-90) REVERT: C 548 LEU cc_start: 0.9118 (mt) cc_final: 0.8461 (tp) REVERT: D 147 GLN cc_start: 0.7675 (tt0) cc_final: 0.6797 (tp-100) REVERT: D 166 LEU cc_start: 0.9311 (tt) cc_final: 0.8834 (pp) REVERT: D 260 LEU cc_start: 0.9221 (mt) cc_final: 0.8909 (mt) REVERT: D 271 ASN cc_start: 0.9316 (t0) cc_final: 0.8823 (m-40) REVERT: D 295 TYR cc_start: 0.9084 (t80) cc_final: 0.8517 (t80) REVERT: D 376 TYR cc_start: 0.8791 (m-80) cc_final: 0.8476 (m-80) REVERT: D 540 PRO cc_start: 0.7292 (Cg_endo) cc_final: 0.6576 (Cg_exo) REVERT: D 613 MET cc_start: 0.8484 (ppp) cc_final: 0.8120 (ppp) outliers start: 32 outliers final: 27 residues processed: 240 average time/residue: 0.2253 time to fit residues: 80.5382 Evaluate side-chains 244 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 216 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 405 CYS Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 432 CYS Chi-restraints excluded: chain D residue 455 THR Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 571 TYR Chi-restraints excluded: chain D residue 589 ILE Chi-restraints excluded: chain D residue 610 VAL Chi-restraints excluded: chain D residue 611 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 14 optimal weight: 0.7980 chunk 109 optimal weight: 0.5980 chunk 116 optimal weight: 10.0000 chunk 72 optimal weight: 0.1980 chunk 42 optimal weight: 0.7980 chunk 64 optimal weight: 8.9990 chunk 136 optimal weight: 0.0050 chunk 95 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.161933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.107825 restraints weight = 28999.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.112011 restraints weight = 12280.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.114574 restraints weight = 7523.380| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 12416 Z= 0.126 Angle : 0.713 12.521 16906 Z= 0.347 Chirality : 0.046 0.308 1896 Planarity : 0.005 0.065 2147 Dihedral : 5.562 54.883 1813 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.15 % Allowed : 21.94 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % 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: -0.55 (0.22), residues: 1488 helix: 1.27 (0.52), residues: 98 sheet: 0.52 (0.22), residues: 612 loop : -1.36 (0.22), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP D 398 HIS 0.006 0.001 HIS C 404 PHE 0.019 0.001 PHE D 234 TYR 0.011 0.001 TYR D 574 ARG 0.012 0.001 ARG C 233 Details of bonding type rmsd link_NAG-ASN : bond 0.00163 ( 6) link_NAG-ASN : angle 2.63451 ( 18) link_BETA1-4 : bond 0.00613 ( 2) link_BETA1-4 : angle 1.18149 ( 6) link_ALPHA1-3 : bond 0.00656 ( 1) link_ALPHA1-3 : angle 1.58026 ( 3) hydrogen bonds : bond 0.03654 ( 437) hydrogen bonds : angle 5.25688 ( 1185) SS BOND : bond 0.00450 ( 22) SS BOND : angle 1.75769 ( 44) covalent geometry : bond 0.00299 (12385) covalent geometry : angle 0.70271 (16835) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6510.56 seconds wall clock time: 117 minutes 18.59 seconds (7038.59 seconds total)