Starting phenix.real_space_refine on Wed May 14 21:10:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8odz_16820/05_2025/8odz_16820.cif Found real_map, /net/cci-nas-00/data/ceres_data/8odz_16820/05_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_16820/05_2025/8odz_16820.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8odz_16820/05_2025/8odz_16820.map" model { file = "/net/cci-nas-00/data/ceres_data/8odz_16820/05_2025/8odz_16820.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8odz_16820/05_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-5687/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: 7.70, per 1000 atoms: 0.64 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: 2.85 Conformation dependent library (CDL) restraints added in 1.4 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: 1.48 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: 3.70 Time building geometry restraints manager: 3.35 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: 6.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 28.360 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.130 ------------------------------------------------------------------------------- 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 : 1.358 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: 0.2475 time to fit residues: 118.4397 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 : 1.393 ------------------------------------------------------------------------------- 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 = 53)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.109483 restraints weight = 28913.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.113917 restraints weight = 11800.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.116626 restraints weight = 7138.911| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 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 : 1.288 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: 0.4118 (OUTLIER) cc_final: 0.3575 (m-70) REVERT: A 141 LEU cc_start: 0.8683 (mt) cc_final: 0.8432 (mt) REVERT: A 196 HIS cc_start: 0.7714 (t70) cc_final: 0.7417 (t70) REVERT: B 133 TYR cc_start: 0.8483 (m-80) cc_final: 0.8238 (m-80) REVERT: B 147 MET cc_start: 0.7581 (mtt) cc_final: 0.7210 (mtt) REVERT: B 269 LYS cc_start: 0.7372 (ttpt) cc_final: 0.6950 (ptpt) REVERT: B 302 GLU cc_start: 0.7910 (tt0) cc_final: 0.7596 (tt0) REVERT: C 50 ASN cc_start: 0.8365 (m-40) cc_final: 0.7877 (m-40) REVERT: C 60 ASP cc_start: 0.7988 (t0) cc_final: 0.7551 (m-30) REVERT: C 67 TYR cc_start: 0.8185 (t80) cc_final: 0.7724 (t80) REVERT: C 167 ASP cc_start: 0.8518 (m-30) cc_final: 0.7642 (p0) REVERT: C 214 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7336 (mt-10) REVERT: C 343 LYS cc_start: 0.6523 (OUTLIER) cc_final: 0.6102 (ttpt) REVERT: C 431 GLN cc_start: 0.8835 (mt0) cc_final: 0.8213 (mp10) REVERT: C 517 TRP cc_start: 0.8356 (m-90) cc_final: 0.8061 (m-90) REVERT: D 166 LEU cc_start: 0.9336 (tt) cc_final: 0.8951 (pp) REVERT: D 189 ASP cc_start: 0.9176 (p0) cc_final: 0.7763 (p0) REVERT: D 295 TYR cc_start: 0.8881 (t80) cc_final: 0.8335 (t80) REVERT: D 376 TYR cc_start: 0.8865 (m-80) cc_final: 0.8524 (m-80) REVERT: D 449 MET cc_start: 0.8326 (ptt) cc_final: 0.7957 (ppp) REVERT: D 540 PRO cc_start: 0.7393 (Cg_endo) cc_final: 0.6683 (Cg_exo) REVERT: D 613 MET cc_start: 0.8385 (ppp) cc_final: 0.7889 (ppp) outliers start: 30 outliers final: 17 residues processed: 267 average time/residue: 0.2215 time to fit residues: 85.9607 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 : 1.399 ------------------------------------------------------------------------------- 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: 8.9990 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: 0.4980 chunk 111 optimal weight: 0.0980 chunk 85 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 246 ASN ** C 260 GLN ** 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 = 0.4317 r_free = 0.4317 target = 0.162987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.109990 restraints weight = 29338.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.114501 restraints weight = 11946.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.117246 restraints weight = 7187.151| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12416 Z= 0.138 Angle : 0.683 13.636 16906 Z= 0.339 Chirality : 0.045 0.230 1896 Planarity : 0.005 0.070 2147 Dihedral : 6.815 57.640 1813 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.97 % Allowed : 14.23 % Favored : 82.80 % 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: -0.76 (0.22), residues: 1488 helix: 0.93 (0.51), residues: 104 sheet: 0.26 (0.21), residues: 624 loop : -1.38 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 398 HIS 0.003 0.001 HIS C 421 PHE 0.029 0.002 PHE D 234 TYR 0.014 0.001 TYR D 469 ARG 0.006 0.001 ARG C 314 Details of bonding type rmsd link_NAG-ASN : bond 0.00137 ( 6) link_NAG-ASN : angle 2.98945 ( 18) link_BETA1-4 : bond 0.00574 ( 2) link_BETA1-4 : angle 1.79350 ( 6) link_ALPHA1-3 : bond 0.00926 ( 1) link_ALPHA1-3 : angle 2.06984 ( 3) hydrogen bonds : bond 0.03951 ( 437) hydrogen bonds : angle 5.46001 ( 1185) SS BOND : bond 0.00389 ( 22) SS BOND : angle 1.42087 ( 44) covalent geometry : bond 0.00321 (12385) covalent geometry : angle 0.67194 (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 277 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 237 time to evaluate : 1.377 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 58 TYR cc_start: 0.7903 (m-80) cc_final: 0.7549 (m-80) REVERT: A 141 LEU cc_start: 0.8721 (mt) cc_final: 0.8438 (mt) REVERT: B 60 TRP cc_start: 0.7920 (m100) cc_final: 0.7206 (m100) REVERT: B 133 TYR cc_start: 0.8487 (m-80) cc_final: 0.8223 (m-80) REVERT: B 147 MET cc_start: 0.7507 (mtt) cc_final: 0.7138 (mtt) REVERT: B 246 ASN cc_start: 0.8019 (OUTLIER) cc_final: 0.7788 (t0) REVERT: B 269 LYS cc_start: 0.7397 (ttpt) cc_final: 0.6987 (ptpt) REVERT: B 302 GLU cc_start: 0.7881 (tt0) cc_final: 0.7516 (tt0) REVERT: C 50 ASN cc_start: 0.8390 (m-40) cc_final: 0.7898 (m-40) REVERT: C 60 ASP cc_start: 0.7985 (t0) cc_final: 0.7523 (m-30) REVERT: C 67 TYR cc_start: 0.8258 (t80) cc_final: 0.7715 (t80) REVERT: C 167 ASP cc_start: 0.8468 (m-30) cc_final: 0.7563 (p0) REVERT: C 214 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7277 (mt-10) REVERT: C 226 GLU cc_start: 0.6384 (tp30) cc_final: 0.6045 (tp30) REVERT: C 314 ARG cc_start: 0.9237 (ttm-80) cc_final: 0.9015 (ttm-80) REVERT: C 343 LYS cc_start: 0.6429 (OUTLIER) cc_final: 0.6015 (ttpt) REVERT: C 431 GLN cc_start: 0.8791 (mt0) cc_final: 0.8179 (mp10) REVERT: C 548 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8725 (tp) REVERT: D 147 GLN cc_start: 0.7639 (tt0) cc_final: 0.6880 (tp-100) REVERT: D 166 LEU cc_start: 0.9331 (tt) cc_final: 0.8897 (pp) REVERT: D 295 TYR cc_start: 0.8868 (t80) cc_final: 0.8247 (t80) REVERT: D 376 TYR cc_start: 0.8919 (m-80) cc_final: 0.8565 (m-80) REVERT: D 451 ASN cc_start: 0.9482 (t0) cc_final: 0.8966 (p0) REVERT: D 540 PRO cc_start: 0.7632 (Cg_endo) cc_final: 0.6884 (Cg_exo) REVERT: D 613 MET cc_start: 0.8463 (ppp) cc_final: 0.8031 (ppp) outliers start: 40 outliers final: 24 residues processed: 255 average time/residue: 0.2195 time to fit residues: 82.6420 Evaluate side-chains 247 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 220 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 548 LEU 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 589 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 136 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 13 optimal weight: 0.6980 chunk 135 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 0.0980 chunk 66 optimal weight: 0.0570 chunk 9 optimal weight: 0.6980 chunk 131 optimal weight: 5.9990 chunk 126 optimal weight: 8.9990 chunk 105 optimal weight: 10.0000 overall best weight: 1.1100 ------------------------------------------------------------------------------- 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** ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 ASN D 192 GLN D 377 GLN ** D 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.161590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.107554 restraints weight = 29053.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.111934 restraints weight = 11920.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.114628 restraints weight = 7222.633| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.2716 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= 0.158 Angle : 0.677 12.823 16906 Z= 0.338 Chirality : 0.045 0.225 1896 Planarity : 0.005 0.064 2147 Dihedral : 6.469 56.843 1813 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.19 % Allowed : 17.05 % Favored : 79.76 % 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: -0.76 (0.22), residues: 1488 helix: 1.08 (0.52), residues: 104 sheet: 0.19 (0.21), residues: 627 loop : -1.36 (0.21), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 398 HIS 0.011 0.001 HIS D 570 PHE 0.023 0.002 PHE C 108 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 0.00304 ( 6) link_NAG-ASN : angle 3.15229 ( 18) link_BETA1-4 : bond 0.00389 ( 2) link_BETA1-4 : angle 1.61898 ( 6) link_ALPHA1-3 : bond 0.00806 ( 1) link_ALPHA1-3 : angle 2.27111 ( 3) hydrogen bonds : bond 0.03975 ( 437) hydrogen bonds : angle 5.39955 ( 1185) SS BOND : bond 0.00457 ( 22) SS BOND : angle 1.63292 ( 44) covalent geometry : bond 0.00372 (12385) covalent geometry : angle 0.66392 (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 276 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 233 time to evaluate : 1.471 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: 0.8724 (mt) cc_final: 0.8439 (mt) REVERT: A 145 ASN cc_start: 0.7825 (OUTLIER) cc_final: 0.7041 (t0) REVERT: A 153 LYS cc_start: 0.8681 (ttpt) cc_final: 0.8080 (ttpp) REVERT: B 60 TRP cc_start: 0.7911 (m100) cc_final: 0.7181 (m100) REVERT: B 147 MET cc_start: 0.7563 (mtt) cc_final: 0.7256 (mtt) REVERT: B 148 ASP cc_start: 0.7086 (t0) cc_final: 0.6545 (t0) REVERT: B 246 ASN cc_start: 0.7997 (t0) cc_final: 0.7770 (t0) REVERT: B 265 TYR cc_start: 0.7043 (t80) cc_final: 0.6828 (t80) REVERT: B 269 LYS cc_start: 0.7439 (ttpt) cc_final: 0.7100 (ptpt) REVERT: B 302 GLU cc_start: 0.7896 (tt0) cc_final: 0.7574 (tt0) REVERT: C 50 ASN cc_start: 0.8403 (m-40) cc_final: 0.7919 (m-40) REVERT: C 60 ASP cc_start: 0.8012 (t0) cc_final: 0.7580 (m-30) REVERT: C 67 TYR cc_start: 0.8279 (t80) cc_final: 0.7778 (t80) REVERT: C 108 PHE cc_start: 0.8987 (p90) cc_final: 0.8760 (p90) REVERT: C 167 ASP cc_start: 0.8404 (m-30) cc_final: 0.7633 (p0) REVERT: C 214 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7200 (mt-10) REVERT: C 343 LYS cc_start: 0.6360 (OUTLIER) cc_final: 0.5945 (ttpt) REVERT: C 431 GLN cc_start: 0.8806 (mt0) cc_final: 0.8198 (mp10) REVERT: C 517 TRP cc_start: 0.8773 (m-90) cc_final: 0.8189 (m-90) REVERT: C 548 LEU cc_start: 0.9234 (mt) cc_final: 0.8524 (tp) REVERT: D 147 GLN cc_start: 0.7586 (tt0) cc_final: 0.6755 (tp-100) REVERT: D 260 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.8815 (mt) REVERT: D 295 TYR cc_start: 0.8922 (t80) cc_final: 0.8396 (t80) REVERT: D 376 TYR cc_start: 0.8832 (m-80) cc_final: 0.8496 (m-80) REVERT: D 451 ASN cc_start: 0.9414 (t0) cc_final: 0.8863 (p0) REVERT: D 540 PRO cc_start: 0.7533 (Cg_endo) cc_final: 0.6782 (Cg_exo) REVERT: D 613 MET cc_start: 0.8446 (ppp) cc_final: 0.8059 (ppp) outliers start: 43 outliers final: 27 residues processed: 253 average time/residue: 0.2377 time to fit residues: 87.8941 Evaluate side-chains 249 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 219 time to evaluate : 1.326 ------------------------------------------------------------------------------- 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 A residue 145 ASN 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 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 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: 0.0980 chunk 21 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 9 optimal weight: 0.5980 chunk 145 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4317 r_free = 0.4317 target = 0.162509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.109185 restraints weight = 28884.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.113618 restraints weight = 11881.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.116277 restraints weight = 7184.374| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.2866 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= 0.125 Angle : 0.658 11.947 16906 Z= 0.325 Chirality : 0.044 0.226 1896 Planarity : 0.005 0.064 2147 Dihedral : 6.200 55.463 1813 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.11 % Allowed : 18.46 % Favored : 78.43 % 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: -0.58 (0.22), residues: 1488 helix: 1.23 (0.52), residues: 103 sheet: 0.40 (0.22), residues: 618 loop : -1.31 (0.21), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 109 HIS 0.004 0.001 HIS D 570 PHE 0.017 0.001 PHE C 108 TYR 0.011 0.001 TYR D 574 ARG 0.004 0.000 ARG C 309 Details of bonding type rmsd link_NAG-ASN : bond 0.00192 ( 6) link_NAG-ASN : angle 2.87524 ( 18) link_BETA1-4 : bond 0.00529 ( 2) link_BETA1-4 : angle 1.39034 ( 6) link_ALPHA1-3 : bond 0.00963 ( 1) link_ALPHA1-3 : angle 2.28920 ( 3) hydrogen bonds : bond 0.03674 ( 437) hydrogen bonds : angle 5.24210 ( 1185) SS BOND : bond 0.00378 ( 22) SS BOND : angle 1.40807 ( 44) covalent geometry : bond 0.00291 (12385) covalent geometry : angle 0.64743 (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 278 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 236 time to evaluate : 1.383 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: A 186 ARG cc_start: 0.7324 (mmt90) cc_final: 0.7062 (mmt90) REVERT: B 60 TRP cc_start: 0.7835 (m100) cc_final: 0.7144 (m100) REVERT: B 147 MET cc_start: 0.7524 (mtt) cc_final: 0.7213 (mtt) REVERT: B 246 ASN cc_start: 0.8154 (t0) cc_final: 0.7916 (t0) REVERT: B 269 LYS cc_start: 0.7514 (ttpt) cc_final: 0.7206 (ptpt) REVERT: B 302 GLU cc_start: 0.7843 (tt0) cc_final: 0.7478 (tt0) REVERT: C 50 ASN cc_start: 0.8409 (m-40) cc_final: 0.7946 (m-40) REVERT: C 60 ASP cc_start: 0.8020 (t0) cc_final: 0.7593 (m-30) REVERT: C 67 TYR cc_start: 0.8306 (t80) cc_final: 0.7751 (t80) REVERT: C 128 LEU cc_start: 0.8743 (pt) cc_final: 0.8520 (mm) REVERT: C 167 ASP cc_start: 0.8379 (m-30) cc_final: 0.7598 (p0) REVERT: C 214 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7212 (mt-10) REVERT: C 343 LYS cc_start: 0.6410 (OUTLIER) cc_final: 0.5984 (ttpt) REVERT: C 431 GLN cc_start: 0.8765 (mt0) cc_final: 0.8171 (mp10) REVERT: C 517 TRP cc_start: 0.8831 (m-90) cc_final: 0.8229 (m-90) REVERT: C 548 LEU cc_start: 0.9109 (mt) cc_final: 0.8466 (tp) REVERT: D 147 GLN cc_start: 0.7577 (tt0) cc_final: 0.6755 (tp-100) REVERT: D 166 LEU cc_start: 0.9252 (tt) cc_final: 0.8766 (pp) REVERT: D 260 LEU cc_start: 0.9129 (mt) cc_final: 0.8821 (mt) REVERT: D 295 TYR cc_start: 0.8953 (t80) cc_final: 0.8406 (t80) REVERT: D 376 TYR cc_start: 0.8758 (m-80) cc_final: 0.8436 (m-80) REVERT: D 451 ASN cc_start: 0.9459 (t0) cc_final: 0.8907 (p0) REVERT: D 540 PRO cc_start: 0.7415 (Cg_endo) cc_final: 0.6682 (Cg_exo) REVERT: D 613 MET cc_start: 0.8403 (ppp) cc_final: 0.8042 (ppp) outliers start: 42 outliers final: 29 residues processed: 257 average time/residue: 0.2159 time to fit residues: 81.7564 Evaluate side-chains 252 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 222 time to evaluate : 1.302 ------------------------------------------------------------------------------- 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 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 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 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: 4.9990 chunk 123 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 144 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 69 optimal weight: 8.9990 chunk 91 optimal weight: 0.7980 chunk 67 optimal weight: 0.0370 chunk 50 optimal weight: 2.9990 chunk 49 optimal weight: 0.0970 overall best weight: 0.9860 ------------------------------------------------------------------------------- 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 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.161425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.108485 restraints weight = 29324.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.112793 restraints weight = 12135.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.115425 restraints weight = 7340.217| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 12416 Z= 0.147 Angle : 0.662 13.335 16906 Z= 0.330 Chirality : 0.044 0.225 1896 Planarity : 0.005 0.064 2147 Dihedral : 6.014 54.505 1813 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.34 % Allowed : 19.20 % Favored : 77.46 % 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: 1.12 (0.51), residues: 101 sheet: 0.49 (0.21), residues: 624 loop : -1.34 (0.21), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 109 HIS 0.004 0.001 HIS C 402 PHE 0.038 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 0.00281 ( 6) link_NAG-ASN : angle 3.05257 ( 18) link_BETA1-4 : bond 0.00388 ( 2) link_BETA1-4 : angle 1.37758 ( 6) link_ALPHA1-3 : bond 0.00767 ( 1) link_ALPHA1-3 : angle 2.19632 ( 3) hydrogen bonds : bond 0.03682 ( 437) hydrogen bonds : angle 5.27078 ( 1185) SS BOND : bond 0.00412 ( 22) SS BOND : angle 1.53521 ( 44) covalent geometry : bond 0.00349 (12385) covalent geometry : angle 0.64948 (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 268 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 223 time to evaluate : 1.272 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: 0.7888 (m-80) cc_final: 0.7545 (m-80) REVERT: B 60 TRP cc_start: 0.7846 (m100) cc_final: 0.7058 (m100) REVERT: B 147 MET cc_start: 0.7555 (mtt) cc_final: 0.7101 (mtt) REVERT: B 148 ASP cc_start: 0.7214 (t0) cc_final: 0.6685 (t0) REVERT: B 246 ASN cc_start: 0.8195 (t0) cc_final: 0.7960 (t0) REVERT: B 302 GLU cc_start: 0.7809 (tt0) cc_final: 0.7415 (tt0) REVERT: C 50 ASN cc_start: 0.8411 (m-40) cc_final: 0.7960 (m-40) REVERT: C 60 ASP cc_start: 0.8020 (t0) cc_final: 0.7576 (m-30) REVERT: C 67 TYR cc_start: 0.8344 (t80) cc_final: 0.7764 (t80) REVERT: C 114 ILE cc_start: 0.8091 (OUTLIER) cc_final: 0.7856 (tp) REVERT: C 167 ASP cc_start: 0.8344 (m-30) cc_final: 0.7484 (p0) REVERT: C 184 MET cc_start: 0.6498 (tpp) cc_final: 0.6235 (tpt) REVERT: C 214 GLU cc_start: 0.7513 (mt-10) cc_final: 0.7182 (mt-10) REVERT: C 343 LYS cc_start: 0.6415 (OUTLIER) cc_final: 0.5990 (ttpt) REVERT: C 431 GLN cc_start: 0.8738 (mt0) cc_final: 0.8123 (mp10) REVERT: C 517 TRP cc_start: 0.8837 (m-90) cc_final: 0.8222 (m-90) REVERT: C 548 LEU cc_start: 0.9121 (mt) cc_final: 0.8470 (tp) REVERT: D 147 GLN cc_start: 0.7554 (tt0) cc_final: 0.6712 (tp-100) REVERT: D 166 LEU cc_start: 0.9264 (tt) cc_final: 0.8742 (pp) REVERT: D 260 LEU cc_start: 0.9186 (mt) cc_final: 0.8886 (mt) REVERT: D 295 TYR cc_start: 0.9000 (t80) cc_final: 0.8481 (t80) REVERT: D 376 TYR cc_start: 0.8824 (m-80) cc_final: 0.8499 (m-80) REVERT: D 451 ASN cc_start: 0.9462 (t0) cc_final: 0.8930 (p0) REVERT: D 540 PRO cc_start: 0.7431 (Cg_endo) cc_final: 0.6697 (Cg_exo) REVERT: D 546 THR cc_start: 0.8901 (OUTLIER) cc_final: 0.8615 (t) REVERT: D 613 MET cc_start: 0.8456 (ppp) cc_final: 0.8098 (ppp) outliers start: 45 outliers final: 32 residues processed: 245 average time/residue: 0.1987 time to fit residues: 73.0967 Evaluate side-chains 251 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 216 time to evaluate : 1.254 ------------------------------------------------------------------------------- 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 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 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 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 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 546 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 106 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 6 optimal weight: 0.0370 chunk 141 optimal weight: 5.9990 chunk 147 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 114 optimal weight: 7.9990 chunk 27 optimal weight: 0.2980 chunk 148 optimal weight: 9.9990 chunk 96 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 overall best weight: 0.6058 ------------------------------------------------------------------------------- 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 = 0.4314 r_free = 0.4314 target = 0.162303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.108341 restraints weight = 28930.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.112632 restraints weight = 12164.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.115203 restraints weight = 7431.602| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.3196 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= 0.123 Angle : 0.655 12.536 16906 Z= 0.324 Chirality : 0.044 0.228 1896 Planarity : 0.005 0.063 2147 Dihedral : 5.859 54.847 1813 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.26 % Allowed : 19.72 % Favored : 77.02 % 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: -0.51 (0.22), residues: 1488 helix: 1.08 (0.51), residues: 101 sheet: 0.48 (0.21), residues: 632 loop : -1.27 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 398 HIS 0.004 0.001 HIS C 402 PHE 0.028 0.001 PHE D 234 TYR 0.012 0.001 TYR B 265 ARG 0.009 0.000 ARG C 233 Details of bonding type rmsd link_NAG-ASN : bond 0.00192 ( 6) link_NAG-ASN : angle 2.82395 ( 18) link_BETA1-4 : bond 0.00520 ( 2) link_BETA1-4 : angle 1.30347 ( 6) link_ALPHA1-3 : bond 0.00823 ( 1) link_ALPHA1-3 : angle 1.99118 ( 3) hydrogen bonds : bond 0.03581 ( 437) hydrogen bonds : angle 5.12322 ( 1185) SS BOND : bond 0.00366 ( 22) SS BOND : angle 1.21282 ( 44) covalent geometry : bond 0.00285 (12385) covalent geometry : angle 0.64572 (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 275 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 231 time to evaluate : 1.299 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: 0.9368 (m-30) cc_final: 0.9138 (m-30) REVERT: A 58 TYR cc_start: 0.7884 (m-80) cc_final: 0.7563 (m-80) REVERT: A 186 ARG cc_start: 0.7384 (mmt90) cc_final: 0.7096 (mmt90) REVERT: B 60 TRP cc_start: 0.7778 (m100) cc_final: 0.7084 (m100) REVERT: B 147 MET cc_start: 0.7446 (mtt) cc_final: 0.7075 (mtt) REVERT: B 148 ASP cc_start: 0.7134 (t0) cc_final: 0.6644 (t0) REVERT: B 206 ILE cc_start: 0.8447 (mt) cc_final: 0.8146 (tt) REVERT: B 246 ASN cc_start: 0.8209 (t0) cc_final: 0.7968 (t0) REVERT: B 302 GLU cc_start: 0.7765 (tt0) cc_final: 0.7326 (tt0) REVERT: C 50 ASN cc_start: 0.8388 (m-40) cc_final: 0.7942 (m-40) REVERT: C 60 ASP cc_start: 0.7996 (t0) cc_final: 0.7568 (m-30) REVERT: C 67 TYR cc_start: 0.8310 (t80) cc_final: 0.7773 (t80) REVERT: C 114 ILE cc_start: 0.7939 (OUTLIER) cc_final: 0.7734 (tp) REVERT: C 167 ASP cc_start: 0.8290 (m-30) cc_final: 0.7449 (p0) REVERT: C 214 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7157 (mt-10) REVERT: C 343 LYS cc_start: 0.6409 (OUTLIER) cc_final: 0.5986 (ttpt) REVERT: C 431 GLN cc_start: 0.8661 (mt0) cc_final: 0.8025 (mp10) REVERT: C 517 TRP cc_start: 0.8839 (m-90) cc_final: 0.8229 (m-90) REVERT: C 548 LEU cc_start: 0.9106 (mt) cc_final: 0.8468 (tp) REVERT: D 147 GLN cc_start: 0.7472 (tt0) cc_final: 0.6644 (tp-100) REVERT: D 166 LEU cc_start: 0.9253 (tt) cc_final: 0.8765 (pp) REVERT: D 260 LEU cc_start: 0.9177 (mt) cc_final: 0.8872 (mt) REVERT: D 271 ASN cc_start: 0.9326 (t0) cc_final: 0.8855 (m-40) REVERT: D 295 TYR cc_start: 0.8985 (t80) cc_final: 0.8450 (t80) REVERT: D 376 TYR cc_start: 0.8771 (m-80) cc_final: 0.8457 (m-80) REVERT: D 398 TRP cc_start: 0.7474 (t-100) cc_final: 0.7261 (t60) REVERT: D 540 PRO cc_start: 0.7283 (Cg_endo) cc_final: 0.6563 (Cg_exo) REVERT: D 613 MET cc_start: 0.8365 (ppp) cc_final: 0.8061 (ppp) outliers start: 44 outliers final: 27 residues processed: 253 average time/residue: 0.2114 time to fit residues: 78.5085 Evaluate side-chains 242 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 213 time to evaluate : 1.260 ------------------------------------------------------------------------------- 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 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 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 174 LEU Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain D residue 248 ILE 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: 1.9990 chunk 49 optimal weight: 0.4980 chunk 108 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 37 optimal weight: 0.4980 chunk 144 optimal weight: 7.9990 chunk 142 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 28 optimal weight: 0.0980 chunk 25 optimal weight: 0.2980 chunk 87 optimal weight: 4.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.4310 r_free = 0.4310 target = 0.161922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.108709 restraints weight = 29118.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.113094 restraints weight = 11951.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.115730 restraints weight = 7215.111| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.3346 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= 0.128 Angle : 0.678 13.015 16906 Z= 0.331 Chirality : 0.044 0.230 1896 Planarity : 0.005 0.062 2147 Dihedral : 5.738 54.782 1813 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.89 % Allowed : 20.90 % Favored : 76.20 % 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: -0.45 (0.22), residues: 1488 helix: 1.22 (0.51), residues: 101 sheet: 0.54 (0.21), residues: 628 loop : -1.27 (0.22), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 398 HIS 0.004 0.001 HIS C 402 PHE 0.024 0.001 PHE D 234 TYR 0.010 0.001 TYR D 574 ARG 0.012 0.000 ARG C 233 Details of bonding type rmsd link_NAG-ASN : bond 0.00203 ( 6) link_NAG-ASN : angle 2.80211 ( 18) link_BETA1-4 : bond 0.00505 ( 2) link_BETA1-4 : angle 1.28821 ( 6) link_ALPHA1-3 : bond 0.00625 ( 1) link_ALPHA1-3 : angle 1.77125 ( 3) hydrogen bonds : bond 0.03592 ( 437) hydrogen bonds : angle 5.16078 ( 1185) SS BOND : bond 0.00471 ( 22) SS BOND : angle 2.03984 ( 44) covalent geometry : bond 0.00304 (12385) covalent geometry : angle 0.66437 (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 261 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 222 time to evaluate : 1.479 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 45 ASP cc_start: 0.9345 (m-30) cc_final: 0.9028 (m-30) REVERT: A 54 LYS cc_start: 0.8820 (mmtp) cc_final: 0.8291 (mmmt) REVERT: A 58 TYR cc_start: 0.7912 (m-80) cc_final: 0.7605 (m-80) REVERT: A 186 ARG cc_start: 0.7448 (mmt90) cc_final: 0.7142 (mmt90) REVERT: B 60 TRP cc_start: 0.7762 (m100) cc_final: 0.7079 (m100) REVERT: B 147 MET cc_start: 0.7495 (mtt) cc_final: 0.7113 (mtt) REVERT: B 148 ASP cc_start: 0.7142 (t0) cc_final: 0.6662 (t0) REVERT: B 206 ILE cc_start: 0.8432 (mt) cc_final: 0.8110 (tt) REVERT: B 246 ASN cc_start: 0.8243 (t0) cc_final: 0.8002 (t0) REVERT: C 50 ASN cc_start: 0.8368 (m-40) cc_final: 0.7941 (m-40) REVERT: C 60 ASP cc_start: 0.7997 (t0) cc_final: 0.7565 (m-30) REVERT: C 67 TYR cc_start: 0.8323 (t80) cc_final: 0.7760 (t80) REVERT: C 128 LEU cc_start: 0.8786 (pt) cc_final: 0.8468 (tt) REVERT: C 167 ASP cc_start: 0.8308 (m-30) cc_final: 0.7476 (p0) REVERT: C 214 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7179 (mt-10) REVERT: C 280 MET cc_start: 0.8516 (tpt) cc_final: 0.7764 (tpp) REVERT: C 343 LYS cc_start: 0.6399 (OUTLIER) cc_final: 0.5965 (ttpt) REVERT: C 431 GLN cc_start: 0.8650 (mt0) cc_final: 0.8026 (mp10) REVERT: C 517 TRP cc_start: 0.8853 (m-90) cc_final: 0.8249 (m-90) REVERT: C 548 LEU cc_start: 0.9078 (mt) cc_final: 0.8440 (tp) REVERT: D 147 GLN cc_start: 0.7515 (tt0) cc_final: 0.7145 (mm-40) REVERT: D 166 LEU cc_start: 0.9262 (tt) cc_final: 0.8786 (pp) REVERT: D 260 LEU cc_start: 0.9184 (mt) cc_final: 0.8869 (mt) REVERT: D 271 ASN cc_start: 0.9304 (t0) cc_final: 0.8835 (m-40) REVERT: D 295 TYR cc_start: 0.8985 (t80) cc_final: 0.8482 (t80) REVERT: D 376 TYR cc_start: 0.8717 (m-80) cc_final: 0.8417 (m-80) REVERT: D 398 TRP cc_start: 0.7512 (t-100) cc_final: 0.7272 (t60) REVERT: D 451 ASN cc_start: 0.9442 (t0) cc_final: 0.8847 (p0) REVERT: D 540 PRO cc_start: 0.7187 (Cg_endo) cc_final: 0.6487 (Cg_exo) REVERT: D 613 MET cc_start: 0.8387 (ppp) cc_final: 0.8043 (ppp) outliers start: 39 outliers final: 29 residues processed: 242 average time/residue: 0.2078 time to fit residues: 75.9537 Evaluate side-chains 242 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 212 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 38 THR 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 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 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 432 CYS 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: 5.9990 chunk 139 optimal weight: 8.9990 chunk 42 optimal weight: 0.7980 chunk 84 optimal weight: 8.9990 chunk 147 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 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 = 0.4281 r_free = 0.4281 target = 0.159219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.104654 restraints weight = 29039.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.108781 restraints weight = 12295.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.111272 restraints weight = 7549.637| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 12416 Z= 0.197 Angle : 0.716 14.219 16906 Z= 0.354 Chirality : 0.045 0.235 1896 Planarity : 0.005 0.063 2147 Dihedral : 5.762 54.115 1813 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.74 % Allowed : 21.13 % 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: -0.59 (0.22), residues: 1488 helix: 1.45 (0.52), residues: 95 sheet: 0.34 (0.21), residues: 633 loop : -1.30 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 109 HIS 0.004 0.001 HIS A 146 PHE 0.019 0.002 PHE C 180 TYR 0.013 0.001 TYR B 265 ARG 0.012 0.001 ARG C 233 Details of bonding type rmsd link_NAG-ASN : bond 0.00477 ( 6) link_NAG-ASN : angle 3.49566 ( 18) link_BETA1-4 : bond 0.00364 ( 2) link_BETA1-4 : angle 1.52702 ( 6) link_ALPHA1-3 : bond 0.00401 ( 1) link_ALPHA1-3 : angle 2.12047 ( 3) hydrogen bonds : bond 0.03943 ( 437) hydrogen bonds : angle 5.34962 ( 1185) SS BOND : bond 0.00500 ( 22) SS BOND : angle 1.81037 ( 44) covalent geometry : bond 0.00460 (12385) covalent geometry : angle 0.70089 (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 257 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 220 time to evaluate : 1.273 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: 0.9324 (m-30) cc_final: 0.8949 (m-30) REVERT: A 54 LYS cc_start: 0.8838 (mmtp) cc_final: 0.8342 (mmmt) REVERT: A 58 TYR cc_start: 0.8028 (m-80) cc_final: 0.7775 (m-80) REVERT: A 196 HIS cc_start: 0.7874 (t70) cc_final: 0.7615 (t70) REVERT: A 212 LEU cc_start: 0.9040 (tp) cc_final: 0.8799 (tp) REVERT: B 60 TRP cc_start: 0.7857 (m100) cc_final: 0.7034 (m100) REVERT: B 147 MET cc_start: 0.7571 (mtt) cc_final: 0.7262 (mtt) REVERT: B 148 ASP cc_start: 0.7463 (t0) cc_final: 0.7066 (t0) REVERT: B 246 ASN cc_start: 0.8290 (t0) cc_final: 0.8047 (t0) REVERT: C 50 ASN cc_start: 0.8389 (m-40) cc_final: 0.7953 (m-40) REVERT: C 60 ASP cc_start: 0.8010 (t0) cc_final: 0.7737 (m-30) REVERT: C 67 TYR cc_start: 0.8420 (t80) cc_final: 0.7839 (t80) REVERT: C 128 LEU cc_start: 0.8758 (pt) cc_final: 0.8515 (tt) REVERT: C 214 GLU cc_start: 0.7498 (mt-10) cc_final: 0.7037 (mt-10) REVERT: C 343 LYS cc_start: 0.6457 (OUTLIER) cc_final: 0.6001 (ttpt) REVERT: C 431 GLN cc_start: 0.8723 (mt0) cc_final: 0.8076 (mp10) REVERT: C 449 MET cc_start: 0.7864 (ppp) cc_final: 0.7616 (ppp) REVERT: C 548 LEU cc_start: 0.9111 (mt) cc_final: 0.8488 (tp) REVERT: D 147 GLN cc_start: 0.7578 (tt0) cc_final: 0.6768 (tp-100) REVERT: D 166 LEU cc_start: 0.9258 (tt) cc_final: 0.8786 (pp) REVERT: D 295 TYR cc_start: 0.9080 (t80) cc_final: 0.8545 (t80) REVERT: D 376 TYR cc_start: 0.8771 (m-80) cc_final: 0.8473 (m-80) REVERT: D 540 PRO cc_start: 0.7285 (Cg_endo) cc_final: 0.6580 (Cg_exo) REVERT: D 613 MET cc_start: 0.8540 (ppp) cc_final: 0.8190 (ppp) outliers start: 37 outliers final: 29 residues processed: 242 average time/residue: 0.2203 time to fit residues: 78.3908 Evaluate side-chains 243 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 213 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain B residue 32 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 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 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 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 314 LEU Chi-restraints excluded: chain D residue 432 CYS 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 546 THR 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: 4.9990 chunk 10 optimal weight: 4.9990 chunk 121 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 109 optimal weight: 0.0570 chunk 105 optimal weight: 9.9990 chunk 112 optimal weight: 6.9990 chunk 118 optimal weight: 0.5980 overall best weight: 2.7304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 GLN ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 GLN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 304 HIS ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 556 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.155796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.102029 restraints weight = 29386.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.106025 restraints weight = 12484.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.108463 restraints weight = 7673.828| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 12416 Z= 0.304 Angle : 0.833 14.307 16906 Z= 0.414 Chirality : 0.049 0.330 1896 Planarity : 0.006 0.065 2147 Dihedral : 6.250 54.093 1813 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 19.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 2.37 % Allowed : 21.65 % Favored : 75.98 % 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: -1.00 (0.22), residues: 1488 helix: 0.97 (0.53), residues: 95 sheet: -0.03 (0.21), residues: 626 loop : -1.43 (0.22), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP C 109 HIS 0.008 0.001 HIS D 570 PHE 0.031 0.002 PHE C 180 TYR 0.020 0.002 TYR B 218 ARG 0.009 0.001 ARG C 233 Details of bonding type rmsd link_NAG-ASN : bond 0.00958 ( 6) link_NAG-ASN : angle 4.40828 ( 18) link_BETA1-4 : bond 0.00547 ( 2) link_BETA1-4 : angle 1.71654 ( 6) link_ALPHA1-3 : bond 0.00147 ( 1) link_ALPHA1-3 : angle 2.34943 ( 3) hydrogen bonds : bond 0.04749 ( 437) hydrogen bonds : angle 5.83264 ( 1185) SS BOND : bond 0.00491 ( 22) SS BOND : angle 1.87560 ( 44) covalent geometry : bond 0.00702 (12385) covalent geometry : angle 0.81517 (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 251 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 219 time to evaluate : 1.291 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 45 ASP cc_start: 0.9312 (m-30) cc_final: 0.8936 (m-30) REVERT: A 54 LYS cc_start: 0.8871 (mmtp) cc_final: 0.8428 (mmmt) REVERT: A 58 TYR cc_start: 0.8181 (m-80) cc_final: 0.7964 (m-80) REVERT: A 186 ARG cc_start: 0.7661 (mmt90) cc_final: 0.7437 (mmt90) REVERT: A 196 HIS cc_start: 0.7885 (t70) cc_final: 0.7303 (t-170) REVERT: A 212 LEU cc_start: 0.9106 (tp) cc_final: 0.8866 (tp) REVERT: B 60 TRP cc_start: 0.7826 (m100) cc_final: 0.6899 (m100) REVERT: B 148 ASP cc_start: 0.7734 (t0) cc_final: 0.7378 (t0) REVERT: B 211 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8271 (tt0) REVERT: B 246 ASN cc_start: 0.8370 (t0) cc_final: 0.8127 (t0) REVERT: B 269 LYS cc_start: 0.7726 (pttt) cc_final: 0.7417 (pttm) REVERT: B 295 LEU cc_start: 0.9124 (pt) cc_final: 0.8910 (pp) REVERT: C 50 ASN cc_start: 0.8431 (m-40) cc_final: 0.7968 (m-40) REVERT: C 60 ASP cc_start: 0.8108 (t0) cc_final: 0.7877 (m-30) REVERT: C 67 TYR cc_start: 0.8550 (t80) cc_final: 0.7946 (t80) REVERT: C 128 LEU cc_start: 0.8770 (pt) cc_final: 0.8550 (tt) REVERT: C 214 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7247 (mt-10) REVERT: C 343 LYS cc_start: 0.6589 (OUTLIER) cc_final: 0.6157 (ttpt) REVERT: C 431 GLN cc_start: 0.8862 (mt0) cc_final: 0.8212 (mp10) REVERT: C 517 TRP cc_start: 0.8943 (m-90) cc_final: 0.7987 (m-90) REVERT: C 518 LEU cc_start: 0.9232 (mm) cc_final: 0.8980 (mm) REVERT: C 548 LEU cc_start: 0.9166 (mt) cc_final: 0.8541 (tp) REVERT: D 147 GLN cc_start: 0.7790 (tt0) cc_final: 0.6829 (tp-100) REVERT: D 308 PHE cc_start: 0.8924 (m-80) cc_final: 0.8145 (m-80) REVERT: D 376 TYR cc_start: 0.8867 (m-80) cc_final: 0.8575 (m-80) REVERT: D 540 PRO cc_start: 0.7425 (Cg_endo) cc_final: 0.6740 (Cg_exo) REVERT: D 551 ARG cc_start: 0.9031 (mmp-170) cc_final: 0.8608 (mmm160) REVERT: D 613 MET cc_start: 0.8672 (ppp) cc_final: 0.8283 (ppp) REVERT: D 621 GLU cc_start: 0.8943 (tt0) cc_final: 0.8278 (mp0) outliers start: 32 outliers final: 28 residues processed: 237 average time/residue: 0.2168 time to fit residues: 75.3307 Evaluate side-chains 241 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 212 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain B residue 32 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 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 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 102 LEU 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 260 LEU 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 466 VAL Chi-restraints excluded: chain D residue 546 THR 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: 0.5980 chunk 109 optimal weight: 1.9990 chunk 116 optimal weight: 10.0000 chunk 72 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 64 optimal weight: 8.9990 chunk 136 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 87 GLN ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.159264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.105005 restraints weight = 29238.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.109223 restraints weight = 12107.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.111808 restraints weight = 7352.602| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 12416 Z= 0.144 Angle : 0.734 13.005 16906 Z= 0.359 Chirality : 0.046 0.300 1896 Planarity : 0.005 0.063 2147 Dihedral : 5.913 54.769 1813 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.37 % Allowed : 22.46 % Favored : 75.17 % 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: -0.80 (0.22), residues: 1488 helix: 1.31 (0.51), residues: 95 sheet: 0.20 (0.21), residues: 618 loop : -1.41 (0.22), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 393 HIS 0.008 0.001 HIS D 570 PHE 0.018 0.001 PHE D 234 TYR 0.012 0.001 TYR D 574 ARG 0.010 0.001 ARG C 314 Details of bonding type rmsd link_NAG-ASN : bond 0.00338 ( 6) link_NAG-ASN : angle 3.09097 ( 18) link_BETA1-4 : bond 0.00536 ( 2) link_BETA1-4 : angle 1.26439 ( 6) link_ALPHA1-3 : bond 0.00502 ( 1) link_ALPHA1-3 : angle 1.84575 ( 3) hydrogen bonds : bond 0.03866 ( 437) hydrogen bonds : angle 5.43533 ( 1185) SS BOND : bond 0.00467 ( 22) SS BOND : angle 1.67111 ( 44) covalent geometry : bond 0.00337 (12385) covalent geometry : angle 0.72317 (16835) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5639.98 seconds wall clock time: 99 minutes 8.03 seconds (5948.03 seconds total)