Starting phenix.real_space_refine on Mon Dec 30 05:04:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8odz_16820/12_2024/8odz_16820.cif Found real_map, /net/cci-nas-00/data/ceres_data/8odz_16820/12_2024/8odz_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_16820/12_2024/8odz_16820.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8odz_16820/12_2024/8odz_16820.map" model { file = "/net/cci-nas-00/data/ceres_data/8odz_16820/12_2024/8odz_16820.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8odz_16820/12_2024/8odz_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-5532/modules/chem_data/mon_lib" Total number of atoms: 12100 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1228 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain breaks: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 2336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2336 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 278} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 3854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3854 Classifications: {'peptide': 485} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 33, 'TRANS': 451} Chain breaks: 3 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 4561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 4561 Classifications: {'peptide': 582} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 541} Chain breaks: 3 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 8.93, per 1000 atoms: 0.74 Number of scatterers: 12100 At special positions: 0 Unit cell: (87.58, 135.9, 194.79, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 81 16.00 O 2304 8.00 N 2118 7.00 C 7597 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 Simple disulfide: pdb=" SG CYS A 33 " - pdb=" SG CYS A 106 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 81 " - pdb=" SG CYS A 119 " distance=2.03 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS B 197 " distance=2.03 Simple disulfide: pdb=" SG CYS B 50 " - pdb=" SG CYS B 90 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 139 " distance=2.03 Simple disulfide: pdb=" SG CYS B 167 " - pdb=" SG CYS B 191 " distance=2.04 Simple disulfide: pdb=" SG CYS B 305 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 311 " - pdb=" SG CYS B 328 " distance=2.03 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS C 63 " distance=2.03 Simple disulfide: pdb=" SG CYS C 81 " - pdb=" SG CYS C 95 " distance=2.06 Simple disulfide: pdb=" SG CYS C 194 " - pdb=" SG CYS C 216 " distance=2.03 Simple disulfide: pdb=" SG CYS C 252 " - pdb=" SG CYS C 293 " distance=2.03 Simple disulfide: pdb=" SG CYS C 313 " - pdb=" SG CYS C 390 " distance=2.04 Simple disulfide: pdb=" SG CYS C 315 " - pdb=" SG CYS C 405 " distance=2.03 Simple disulfide: pdb=" SG CYS C 434 " - pdb=" SG CYS C 495 " distance=2.03 Simple disulfide: pdb=" SG CYS D 28 " - pdb=" SG CYS D 127 " distance=2.03 Simple disulfide: pdb=" SG CYS D 51 " - pdb=" SG CYS D 111 " distance=2.03 Simple disulfide: pdb=" SG CYS D 145 " - pdb=" SG CYS D 156 " distance=2.03 Simple disulfide: pdb=" SG CYS D 186 " - pdb=" SG CYS D 194 " distance=2.03 Simple disulfide: pdb=" SG CYS D 432 " - pdb=" SG CYS D 524 " distance=2.03 Simple disulfide: pdb=" SG CYS D 509 " - pdb=" SG CYS D 567 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " NAG-ASN " NAG C 601 " - " ASN C 169 " " NAG C 602 " - " ASN C 144 " " NAG C 603 " - " ASN C 463 " " NAG D 801 " - " ASN D 224 " " NAG D 802 " - " ASN D 48 " " NAG E 1 " - " ASN B 220 " Time building additional restraints: 3.15 Conformation dependent library (CDL) restraints added in 1.6 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: 1.80 Creating SS restraints... Processing helix chain 'A' and resid 32 through 55 removed outlier: 3.698A pdb=" N GLN A 36 " --> pdb=" O ARG A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 81 removed outlier: 3.540A pdb=" N CYS A 81 " --> pdb=" O THR A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 87 removed outlier: 3.536A pdb=" N LEU A 86 " --> pdb=" O PRO A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 112 removed outlier: 3.724A pdb=" N THR A 112 " --> pdb=" O PRO A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 141 removed outlier: 3.778A pdb=" N CYS A 119 " --> pdb=" O MET A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 167 removed outlier: 4.555A pdb=" N LEU A 156 " --> pdb=" O ASP A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 214 removed outlier: 3.672A pdb=" N MET A 189 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N THR A 200 " --> pdb=" O HIS A 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 468 removed outlier: 3.874A pdb=" N ALA C 467 " --> pdb=" O ASN C 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 92 No H-bonds generated for 'chain 'D' and resid 90 through 92' Processing helix chain 'D' and resid 560 through 565 removed outlier: 4.026A pdb=" N GLN D 564 " --> pdb=" O PRO D 560 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ARG D 565 " --> pdb=" O PHE D 561 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 560 through 565' Processing sheet with id=AA1, first strand: chain 'B' and resid 24 through 27 removed outlier: 7.014A pdb=" N VAL B 30 " --> pdb=" O LEU B 26 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N THR B 96 " --> pdb=" O LYS B 92 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LYS B 92 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY B 70 " --> pdb=" O TRP B 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 35 through 36 Processing sheet with id=AA3, first strand: chain 'B' and resid 44 through 49 Processing sheet with id=AA4, first strand: chain 'B' and resid 117 through 118 removed outlier: 4.245A pdb=" N LEU B 142 " --> pdb=" O LYS B 118 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 117 through 118 removed outlier: 4.245A pdb=" N LEU B 142 " --> pdb=" O LYS B 118 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU B 185 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N GLU B 175 " --> pdb=" O LYS B 186 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N SER B 188 " --> pdb=" O SER B 173 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N SER B 173 " --> pdb=" O SER B 188 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N SER B 190 " --> pdb=" O SER B 171 " (cutoff:3.500A) removed outlier: 8.566A pdb=" N SER B 171 " --> pdb=" O SER B 190 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 150 Processing sheet with id=AA7, first strand: chain 'B' and resid 149 through 150 Processing sheet with id=AA8, first strand: chain 'B' and resid 240 through 244 Processing sheet with id=AA9, first strand: chain 'B' and resid 294 through 296 Processing sheet with id=AB1, first strand: chain 'B' and resid 294 through 296 Processing sheet with id=AB2, first strand: chain 'C' and resid 60 through 68 removed outlier: 7.240A pdb=" N ASP C 60 " --> pdb=" O ARG C 55 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ARG C 55 " --> pdb=" O ASP C 60 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N GLU C 62 " --> pdb=" O CYS C 53 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N CYS C 53 " --> pdb=" O GLU C 62 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N SER C 64 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LEU C 51 " --> pdb=" O SER C 64 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N LYS C 147 " --> pdb=" O CYS C 53 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ARG C 55 " --> pdb=" O LYS C 147 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 94 through 99 Processing sheet with id=AB4, first strand: chain 'C' and resid 94 through 99 removed outlier: 3.651A pdb=" N VAL C 120 " --> pdb=" O GLN C 140 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 156 through 160 Processing sheet with id=AB6, first strand: chain 'C' and resid 189 through 193 Processing sheet with id=AB7, first strand: chain 'C' and resid 276 through 279 Processing sheet with id=AB8, first strand: chain 'C' and resid 320 through 324 Processing sheet with id=AB9, first strand: chain 'C' and resid 368 through 372 removed outlier: 3.561A pdb=" N GLY C 372 " --> pdb=" O MET C 375 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET C 375 " --> pdb=" O GLY C 372 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET C 378 " --> pdb=" O HIS C 421 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS C 421 " --> pdb=" O MET C 378 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 404 through 408 removed outlier: 4.495A pdb=" N HIS C 404 " --> pdb=" O TRP C 393 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU C 455 " --> pdb=" O VAL C 439 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ALA C 441 " --> pdb=" O THR C 453 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N THR C 453 " --> pdb=" O ALA C 441 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 471 through 477 removed outlier: 6.294A pdb=" N HIS C 472 " --> pdb=" O THR C 488 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N THR C 488 " --> pdb=" O HIS C 472 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 514 through 519 removed outlier: 3.535A pdb=" N VAL C 503 " --> pdb=" O ARG C 542 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 31 through 36 Processing sheet with id=AC5, first strand: chain 'D' and resid 40 through 41 removed outlier: 3.654A pdb=" N CYS D 127 " --> pdb=" O CYS D 111 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU D 108 " --> pdb=" O PHE D 73 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N LYS D 72 " --> pdb=" O VAL D 79 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N VAL D 79 " --> pdb=" O LYS D 72 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 196 through 198 removed outlier: 4.297A pdb=" N ASN D 159 " --> pdb=" O ASN D 142 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N ASN D 142 " --> pdb=" O ASN D 159 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ILE D 239 " --> pdb=" O CYS D 145 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N GLN D 147 " --> pdb=" O ILE D 239 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 180 through 188 Processing sheet with id=AC8, first strand: chain 'D' and resid 244 through 250 removed outlier: 3.669A pdb=" N ILE D 246 " --> pdb=" O GLN D 261 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N GLN D 261 " --> pdb=" O ILE D 246 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ILE D 248 " --> pdb=" O THR D 259 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N THR D 259 " --> pdb=" O ILE D 248 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 284 through 289 Processing sheet with id=AD1, first strand: chain 'D' and resid 347 through 348 Processing sheet with id=AD2, first strand: chain 'D' and resid 387 through 393 removed outlier: 4.179A pdb=" N THR D 387 " --> pdb=" O GLU D 382 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TRP D 408 " --> pdb=" O ILE D 428 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 443 through 448 removed outlier: 4.419A pdb=" N GLU D 447 " --> pdb=" O ASN D 451 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ASN D 451 " --> pdb=" O GLU D 447 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 487 through 491 removed outlier: 4.117A pdb=" N GLU D 468 " --> pdb=" O LEU D 517 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 544 through 548 Processing sheet with id=AD6, first strand: chain 'D' and resid 585 through 590 458 hydrogen bonds defined for protein. 1185 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.23 Time building geometry restraints manager: 3.63 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: 4.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 31.680 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.040 ------------------------------------------------------------------------------- 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 12385 Z= 0.279 Angle : 0.809 20.123 16835 Z= 0.423 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 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 340 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 THR cc_start: 0.8666 (p) cc_final: 0.8035 (p) REVERT: A 67 HIS cc_start: 0.8174 (t70) cc_final: 0.7790 (t70) REVERT: A 141 LEU cc_start: 0.8713 (mt) cc_final: 0.8371 (mt) REVERT: B 220 ASN cc_start: 0.6992 (m-40) cc_final: 0.6698 (m-40) REVERT: B 246 ASN cc_start: 0.8494 (m-40) cc_final: 0.8243 (t0) REVERT: C 50 ASN cc_start: 0.8264 (m-40) cc_final: 0.7799 (m-40) REVERT: C 60 ASP cc_start: 0.8051 (t0) cc_final: 0.7757 (m-30) REVERT: C 67 TYR cc_start: 0.7909 (t80) cc_final: 0.7583 (t80) REVERT: C 167 ASP cc_start: 0.8449 (m-30) cc_final: 0.7725 (p0) REVERT: C 329 LEU cc_start: 0.8503 (mt) cc_final: 0.8302 (mt) REVERT: C 431 GLN cc_start: 0.8797 (mt0) cc_final: 0.8216 (mp10) REVERT: D 158 TRP cc_start: 0.9018 (p90) cc_final: 0.8616 (p90) REVERT: D 166 LEU cc_start: 0.9384 (tt) cc_final: 0.9092 (pp) REVERT: D 189 ASP cc_start: 0.9319 (p0) cc_final: 0.9042 (p0) REVERT: D 263 GLU cc_start: 0.8611 (tt0) cc_final: 0.8395 (tp30) REVERT: D 295 TYR cc_start: 0.8928 (t80) cc_final: 0.8320 (t80) REVERT: D 376 TYR cc_start: 0.8933 (m-80) cc_final: 0.8621 (m-80) REVERT: D 449 MET cc_start: 0.8397 (ptt) cc_final: 0.8006 (ppp) REVERT: D 540 PRO cc_start: 0.6748 (Cg_endo) cc_final: 0.6450 (Cg_exo) REVERT: D 613 MET cc_start: 0.8280 (ppp) cc_final: 0.7979 (ppp) outliers start: 3 outliers final: 0 residues processed: 343 average time/residue: 0.2612 time to fit residues: 125.4744 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 : 1.580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 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 12385 Z= 0.233 Angle : 0.696 14.075 16835 Z= 0.352 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 *********************** 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 : 1.452 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: 0.4159 (OUTLIER) cc_final: 0.3616 (m-70) REVERT: A 141 LEU cc_start: 0.8679 (mt) cc_final: 0.8434 (mt) REVERT: A 196 HIS cc_start: 0.7759 (t70) cc_final: 0.7469 (t70) REVERT: B 133 TYR cc_start: 0.8453 (m-80) cc_final: 0.8220 (m-80) REVERT: B 147 MET cc_start: 0.7564 (mtt) cc_final: 0.7204 (mtt) REVERT: B 269 LYS cc_start: 0.7515 (ttpt) cc_final: 0.7110 (ptpt) REVERT: B 302 GLU cc_start: 0.7916 (tt0) cc_final: 0.7603 (tt0) REVERT: C 50 ASN cc_start: 0.8356 (m-40) cc_final: 0.7883 (m-40) REVERT: C 60 ASP cc_start: 0.8033 (t0) cc_final: 0.7614 (m-30) REVERT: C 67 TYR cc_start: 0.8158 (t80) cc_final: 0.7700 (t80) REVERT: C 167 ASP cc_start: 0.8503 (m-30) cc_final: 0.7664 (p0) REVERT: C 214 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7367 (mt-10) REVERT: C 343 LYS cc_start: 0.6594 (OUTLIER) cc_final: 0.6163 (ttpt) REVERT: C 431 GLN cc_start: 0.8830 (mt0) cc_final: 0.8209 (mp10) REVERT: C 517 TRP cc_start: 0.8353 (m-90) cc_final: 0.8055 (m-90) REVERT: D 166 LEU cc_start: 0.9337 (tt) cc_final: 0.8967 (pp) REVERT: D 189 ASP cc_start: 0.9168 (p0) cc_final: 0.7746 (p0) REVERT: D 295 TYR cc_start: 0.8904 (t80) cc_final: 0.8346 (t80) REVERT: D 376 TYR cc_start: 0.8964 (m-80) cc_final: 0.8602 (m-80) REVERT: D 449 MET cc_start: 0.8317 (ptt) cc_final: 0.7969 (ppp) REVERT: D 540 PRO cc_start: 0.7479 (Cg_endo) cc_final: 0.6775 (Cg_exo) REVERT: D 613 MET cc_start: 0.8411 (ppp) cc_final: 0.7914 (ppp) outliers start: 30 outliers final: 17 residues processed: 267 average time/residue: 0.2348 time to fit residues: 91.2310 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 : 1.381 ------------------------------------------------------------------------------- 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 75 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 136 optimal weight: 0.5980 chunk 147 optimal weight: 20.0000 chunk 121 optimal weight: 10.0000 chunk 135 optimal weight: 10.0000 chunk 46 optimal weight: 0.0970 chunk 109 optimal weight: 4.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS A 145 ASN ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 ASN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 ASN D 381 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 12385 Z= 0.294 Angle : 0.695 13.426 16835 Z= 0.350 Chirality : 0.046 0.262 1896 Planarity : 0.005 0.070 2147 Dihedral : 6.830 56.732 1813 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.26 % Allowed : 15.12 % Favored : 81.62 % 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: -0.83 (0.22), residues: 1488 helix: 0.91 (0.51), residues: 104 sheet: 0.17 (0.21), residues: 626 loop : -1.41 (0.21), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 109 HIS 0.006 0.001 HIS A 87 PHE 0.029 0.002 PHE D 234 TYR 0.014 0.001 TYR D 469 ARG 0.007 0.001 ARG D 572 *********************** 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 287 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 243 time to evaluate : 1.505 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 58 TYR cc_start: 0.8003 (m-80) cc_final: 0.7638 (m-80) REVERT: A 141 LEU cc_start: 0.8736 (mt) cc_final: 0.8446 (mt) REVERT: A 196 HIS cc_start: 0.7861 (t70) cc_final: 0.7217 (t-170) REVERT: B 60 TRP cc_start: 0.7910 (m100) cc_final: 0.7133 (m100) REVERT: B 133 TYR cc_start: 0.8553 (m-80) cc_final: 0.8239 (m-80) REVERT: B 147 MET cc_start: 0.7586 (mtt) cc_final: 0.7184 (mtt) REVERT: B 148 ASP cc_start: 0.7236 (t0) cc_final: 0.6740 (t0) REVERT: B 246 ASN cc_start: 0.8087 (OUTLIER) cc_final: 0.7821 (t0) REVERT: B 269 LYS cc_start: 0.7646 (ttpt) cc_final: 0.7265 (ptpt) REVERT: B 302 GLU cc_start: 0.7876 (tt0) cc_final: 0.7556 (tt0) REVERT: C 50 ASN cc_start: 0.8421 (m-40) cc_final: 0.7957 (m-40) REVERT: C 60 ASP cc_start: 0.8092 (t0) cc_final: 0.7730 (m-30) REVERT: C 67 TYR cc_start: 0.8327 (t80) cc_final: 0.7735 (t80) REVERT: C 167 ASP cc_start: 0.8451 (m-30) cc_final: 0.7680 (p0) REVERT: C 214 GLU cc_start: 0.7598 (mt-10) cc_final: 0.7289 (mt-10) REVERT: C 226 GLU cc_start: 0.6548 (tp30) cc_final: 0.6006 (tp30) REVERT: C 343 LYS cc_start: 0.6545 (OUTLIER) cc_final: 0.6111 (ttpt) REVERT: C 431 GLN cc_start: 0.8879 (mt0) cc_final: 0.8275 (mp10) REVERT: C 528 LEU cc_start: 0.8461 (mt) cc_final: 0.8218 (tp) REVERT: C 548 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8725 (tp) REVERT: D 147 GLN cc_start: 0.7745 (tt0) cc_final: 0.6922 (tp-100) REVERT: D 295 TYR cc_start: 0.8939 (t80) cc_final: 0.8329 (t80) REVERT: D 376 TYR cc_start: 0.8956 (m-80) cc_final: 0.8606 (m-80) REVERT: D 451 ASN cc_start: 0.9468 (t0) cc_final: 0.8903 (p0) REVERT: D 540 PRO cc_start: 0.7575 (Cg_endo) cc_final: 0.6813 (Cg_exo) REVERT: D 613 MET cc_start: 0.8472 (ppp) cc_final: 0.8002 (ppp) outliers start: 44 outliers final: 27 residues processed: 261 average time/residue: 0.2311 time to fit residues: 87.8392 Evaluate side-chains 255 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 225 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 87 HIS Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain D residue 427 ASN Chi-restraints excluded: chain D residue 432 CYS Chi-restraints excluded: chain D residue 455 THR Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 589 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 15 optimal weight: 0.7980 chunk 65 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 chunk 136 optimal weight: 0.0270 chunk 144 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 129 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.1442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 ASN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 GLN ** C 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 192 GLN D 377 GLN ** D 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12385 Z= 0.246 Angle : 0.673 12.795 16835 Z= 0.338 Chirality : 0.045 0.222 1896 Planarity : 0.005 0.069 2147 Dihedral : 6.505 54.307 1813 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.93 % Allowed : 16.53 % Favored : 79.54 % 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: -0.82 (0.22), residues: 1488 helix: 1.04 (0.51), residues: 104 sheet: 0.12 (0.21), residues: 631 loop : -1.37 (0.21), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 398 HIS 0.009 0.001 HIS D 570 PHE 0.016 0.002 PHE C 265 TYR 0.013 0.001 TYR D 469 ARG 0.004 0.000 ARG C 309 *********************** 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 284 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 231 time to evaluate : 1.560 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 141 LEU cc_start: 0.8729 (mt) cc_final: 0.8436 (mt) REVERT: A 153 LYS cc_start: 0.8601 (ttpt) cc_final: 0.8036 (ttpp) REVERT: A 196 HIS cc_start: 0.7852 (t70) cc_final: 0.7206 (t-170) REVERT: B 60 TRP cc_start: 0.7920 (m100) cc_final: 0.7115 (m100) REVERT: B 147 MET cc_start: 0.7574 (mtt) cc_final: 0.7238 (mtt) REVERT: B 148 ASP cc_start: 0.7321 (t0) cc_final: 0.6883 (t0) REVERT: B 269 LYS cc_start: 0.7662 (ttpt) cc_final: 0.7344 (ptpt) REVERT: B 302 GLU cc_start: 0.7859 (tt0) cc_final: 0.7528 (tt0) REVERT: C 50 ASN cc_start: 0.8389 (m-40) cc_final: 0.7930 (m-40) REVERT: C 60 ASP cc_start: 0.8072 (t0) cc_final: 0.7739 (m-30) REVERT: C 67 TYR cc_start: 0.8279 (t80) cc_final: 0.7778 (t80) REVERT: C 167 ASP cc_start: 0.8407 (m-30) cc_final: 0.7686 (p0) REVERT: C 214 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7256 (mt-10) REVERT: C 226 GLU cc_start: 0.6457 (tp30) cc_final: 0.6100 (tp30) REVERT: C 343 LYS cc_start: 0.6471 (OUTLIER) cc_final: 0.6037 (ttpt) REVERT: C 431 GLN cc_start: 0.8846 (mt0) cc_final: 0.8243 (mp10) REVERT: C 517 TRP cc_start: 0.8728 (m-90) cc_final: 0.8184 (m-90) REVERT: C 548 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8518 (tp) REVERT: D 147 GLN cc_start: 0.7630 (tt0) cc_final: 0.6769 (tp-100) REVERT: D 166 LEU cc_start: 0.9205 (tt) cc_final: 0.8687 (pp) REVERT: D 260 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.8835 (mt) REVERT: D 295 TYR cc_start: 0.8992 (t80) cc_final: 0.8456 (t80) REVERT: D 376 TYR cc_start: 0.8914 (m-80) cc_final: 0.8561 (m-80) REVERT: D 451 ASN cc_start: 0.9438 (t0) cc_final: 0.8891 (p0) REVERT: D 540 PRO cc_start: 0.7440 (Cg_endo) cc_final: 0.6710 (Cg_exo) REVERT: D 613 MET cc_start: 0.8451 (ppp) cc_final: 0.8033 (ppp) outliers start: 53 outliers final: 34 residues processed: 255 average time/residue: 0.2325 time to fit residues: 86.9669 Evaluate side-chains 258 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 221 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 87 HIS Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain 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 146 VAL Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 427 ASN Chi-restraints excluded: chain D residue 432 CYS Chi-restraints excluded: chain D residue 455 THR Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 589 ILE Chi-restraints excluded: chain D residue 611 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 chunk 107 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 chunk 123 optimal weight: 10.0000 chunk 100 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 130 optimal weight: 0.0060 chunk 36 optimal weight: 3.9990 overall best weight: 2.5802 ------------------------------------------------------------------------------- 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 163 GLN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 304 HIS C 398 GLN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 12385 Z= 0.428 Angle : 0.747 11.704 16835 Z= 0.380 Chirality : 0.047 0.269 1896 Planarity : 0.005 0.066 2147 Dihedral : 6.544 53.886 1813 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 4.60 % Allowed : 17.94 % 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: -0.99 (0.22), residues: 1488 helix: 1.09 (0.52), residues: 98 sheet: -0.02 (0.21), residues: 642 loop : -1.49 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 109 HIS 0.019 0.001 HIS A 87 PHE 0.027 0.002 PHE C 180 TYR 0.015 0.002 TYR C 61 ARG 0.008 0.001 ARG C 233 *********************** 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 296 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 234 time to evaluate : 1.570 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: A 153 LYS cc_start: 0.8695 (ttpt) cc_final: 0.8142 (ttpp) REVERT: A 186 ARG cc_start: 0.7509 (mmt90) cc_final: 0.7279 (mmt90) REVERT: A 196 HIS cc_start: 0.7941 (t70) cc_final: 0.7405 (t-170) REVERT: A 212 LEU cc_start: 0.9120 (tp) cc_final: 0.8888 (tp) REVERT: B 60 TRP cc_start: 0.7914 (m100) cc_final: 0.6920 (m100) REVERT: B 147 MET cc_start: 0.7752 (mtt) cc_final: 0.7399 (mtt) REVERT: B 148 ASP cc_start: 0.7740 (t0) cc_final: 0.7358 (t0) REVERT: B 201 GLU cc_start: 0.8182 (tp30) cc_final: 0.7539 (tp30) REVERT: C 50 ASN cc_start: 0.8466 (m-40) cc_final: 0.7996 (m-40) REVERT: C 60 ASP cc_start: 0.8127 (t0) cc_final: 0.7777 (m-30) REVERT: C 67 TYR cc_start: 0.8488 (t80) cc_final: 0.7905 (t80) REVERT: C 114 ILE cc_start: 0.8159 (OUTLIER) cc_final: 0.7841 (tp) REVERT: C 128 LEU cc_start: 0.8852 (pt) cc_final: 0.8641 (mm) REVERT: C 167 ASP cc_start: 0.8298 (m-30) cc_final: 0.7701 (p0) REVERT: C 214 GLU cc_start: 0.7493 (mt-10) cc_final: 0.7182 (mt-10) REVERT: C 311 LEU cc_start: 0.9399 (pt) cc_final: 0.9188 (pp) REVERT: C 343 LYS cc_start: 0.6599 (OUTLIER) cc_final: 0.6150 (ttpt) REVERT: C 431 GLN cc_start: 0.8940 (mt0) cc_final: 0.8335 (mp10) REVERT: C 449 MET cc_start: 0.7924 (ppp) cc_final: 0.7714 (ppp) REVERT: C 517 TRP cc_start: 0.8849 (m-90) cc_final: 0.8455 (m-90) REVERT: C 548 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8555 (tp) REVERT: D 147 GLN cc_start: 0.7862 (tt0) cc_final: 0.6914 (tp-100) REVERT: D 260 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8993 (mt) REVERT: D 295 TYR cc_start: 0.9169 (t80) cc_final: 0.8597 (t80) REVERT: D 376 TYR cc_start: 0.8944 (m-80) cc_final: 0.8602 (m-80) REVERT: D 540 PRO cc_start: 0.7556 (Cg_endo) cc_final: 0.6778 (Cg_exo) REVERT: D 546 THR cc_start: 0.9053 (OUTLIER) cc_final: 0.8816 (t) REVERT: D 549 LYS cc_start: 0.8676 (mmtm) cc_final: 0.8385 (tptp) REVERT: D 551 ARG cc_start: 0.9065 (mmp80) cc_final: 0.8854 (mmp-170) REVERT: D 613 MET cc_start: 0.8627 (ppp) cc_final: 0.8174 (ppp) REVERT: D 621 GLU cc_start: 0.8911 (tt0) cc_final: 0.8318 (mp0) outliers start: 62 outliers final: 40 residues processed: 264 average time/residue: 0.2329 time to fit residues: 89.8952 Evaluate side-chains 264 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 219 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 87 HIS Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 206 ILE 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 124 VAL Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain 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 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 233 THR Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 290 ASN Chi-restraints excluded: chain D residue 427 ASN 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 611 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 0.9990 chunk 130 optimal weight: 0.0670 chunk 28 optimal weight: 0.8980 chunk 85 optimal weight: 10.0000 chunk 35 optimal weight: 0.5980 chunk 145 optimal weight: 5.9990 chunk 120 optimal weight: 9.9990 chunk 67 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 76 optimal weight: 0.0570 chunk 139 optimal weight: 7.9990 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 ASN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 12385 Z= 0.188 Angle : 0.666 13.544 16835 Z= 0.331 Chirality : 0.044 0.223 1896 Planarity : 0.005 0.065 2147 Dihedral : 6.112 54.929 1813 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.41 % Allowed : 20.61 % 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: -0.72 (0.22), residues: 1488 helix: 1.36 (0.52), residues: 98 sheet: 0.24 (0.21), residues: 619 loop : -1.35 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D 398 HIS 0.004 0.001 HIS A 87 PHE 0.041 0.002 PHE D 234 TYR 0.014 0.001 TYR D 275 ARG 0.009 0.001 ARG C 314 *********************** 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 276 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 230 time to evaluate : 1.578 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 54 LYS cc_start: 0.8818 (mmtp) cc_final: 0.8311 (mmmt) REVERT: A 87 HIS cc_start: 0.4695 (OUTLIER) cc_final: 0.4329 (m-70) REVERT: A 141 LEU cc_start: 0.8724 (mt) cc_final: 0.8444 (mt) REVERT: A 153 LYS cc_start: 0.8550 (ttpt) cc_final: 0.8032 (ttpp) REVERT: B 60 TRP cc_start: 0.7828 (m100) cc_final: 0.7131 (m100) REVERT: B 147 MET cc_start: 0.7582 (mtt) cc_final: 0.7218 (mtt) REVERT: B 148 ASP cc_start: 0.7395 (t0) cc_final: 0.7009 (t0) REVERT: B 206 ILE cc_start: 0.8454 (mt) cc_final: 0.8160 (tt) REVERT: B 208 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8416 (mm) REVERT: C 50 ASN cc_start: 0.8389 (m-40) cc_final: 0.7943 (m-40) REVERT: C 60 ASP cc_start: 0.8001 (t0) cc_final: 0.7632 (m-30) REVERT: C 67 TYR cc_start: 0.8339 (t80) cc_final: 0.7804 (t80) REVERT: C 114 ILE cc_start: 0.8087 (OUTLIER) cc_final: 0.7850 (tp) REVERT: C 214 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7209 (mt-10) REVERT: C 226 GLU cc_start: 0.6277 (tp30) cc_final: 0.5993 (tp30) REVERT: C 311 LEU cc_start: 0.9341 (pt) cc_final: 0.9139 (pp) REVERT: C 343 LYS cc_start: 0.6429 (OUTLIER) cc_final: 0.5998 (ttpt) REVERT: C 431 GLN cc_start: 0.8802 (mt0) cc_final: 0.8158 (mp10) REVERT: C 517 TRP cc_start: 0.8870 (m-90) cc_final: 0.8373 (m-90) REVERT: C 548 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8504 (tp) REVERT: D 147 GLN cc_start: 0.7657 (tt0) cc_final: 0.6770 (tp-100) REVERT: D 166 LEU cc_start: 0.9244 (tt) cc_final: 0.8727 (pp) REVERT: D 260 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8915 (mt) REVERT: D 295 TYR cc_start: 0.9095 (t80) cc_final: 0.8483 (t80) REVERT: D 376 TYR cc_start: 0.8901 (m-80) cc_final: 0.8551 (m-80) REVERT: D 540 PRO cc_start: 0.7374 (Cg_endo) cc_final: 0.6661 (Cg_exo) REVERT: D 546 THR cc_start: 0.9067 (OUTLIER) cc_final: 0.8834 (t) REVERT: D 613 MET cc_start: 0.8476 (ppp) cc_final: 0.8067 (ppp) outliers start: 46 outliers final: 27 residues processed: 255 average time/residue: 0.2356 time to fit residues: 87.7242 Evaluate side-chains 256 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 222 time to evaluate : 1.408 ------------------------------------------------------------------------------- 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 146 HIS Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain C residue 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 548 LEU Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 455 THR Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 546 THR Chi-restraints excluded: chain D residue 556 TRP Chi-restraints excluded: chain D residue 589 ILE Chi-restraints excluded: chain D residue 611 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 0.5980 chunk 82 optimal weight: 4.9990 chunk 105 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 144 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 88 optimal weight: 0.0870 chunk 66 optimal weight: 0.7980 chunk 89 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 overall best weight: 1.0960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 ASN ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 GLN B 214 GLN B 246 ASN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 ASN ** D 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12385 Z= 0.240 Angle : 0.684 12.717 16835 Z= 0.342 Chirality : 0.045 0.225 1896 Planarity : 0.005 0.063 2147 Dihedral : 5.982 54.684 1813 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.71 % Allowed : 21.57 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.22), residues: 1488 helix: 1.37 (0.53), residues: 98 sheet: 0.23 (0.21), residues: 620 loop : -1.34 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 398 HIS 0.003 0.001 HIS C 402 PHE 0.025 0.002 PHE D 234 TYR 0.009 0.001 TYR D 574 ARG 0.011 0.001 ARG C 233 *********************** 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 273 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 223 time to evaluate : 1.535 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 54 LYS cc_start: 0.8839 (mmtp) cc_final: 0.8335 (mmmt) REVERT: A 58 TYR cc_start: 0.7893 (m-80) cc_final: 0.7542 (m-80) REVERT: A 145 ASN cc_start: 0.7771 (OUTLIER) cc_final: 0.6903 (t0) REVERT: A 153 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8081 (ttpp) REVERT: A 186 ARG cc_start: 0.7486 (mmt90) cc_final: 0.7190 (mmt90) REVERT: A 212 LEU cc_start: 0.9009 (tp) cc_final: 0.8808 (tp) REVERT: B 60 TRP cc_start: 0.7857 (m100) cc_final: 0.7070 (m100) REVERT: B 148 ASP cc_start: 0.7508 (t0) cc_final: 0.7128 (t0) REVERT: B 208 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8348 (mm) REVERT: B 269 LYS cc_start: 0.7534 (pttt) cc_final: 0.6551 (ptpp) REVERT: C 50 ASN cc_start: 0.8404 (m-40) cc_final: 0.7977 (m-40) REVERT: C 60 ASP cc_start: 0.8033 (t0) cc_final: 0.7709 (m-30) REVERT: C 67 TYR cc_start: 0.8386 (t80) cc_final: 0.7809 (t80) REVERT: C 114 ILE cc_start: 0.8062 (OUTLIER) cc_final: 0.7779 (tp) REVERT: C 128 LEU cc_start: 0.8843 (pt) cc_final: 0.8610 (tt) REVERT: C 167 ASP cc_start: 0.8532 (m-30) cc_final: 0.7489 (p0) REVERT: C 214 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7247 (mt-10) REVERT: C 226 GLU cc_start: 0.6376 (tp30) cc_final: 0.6058 (tp30) REVERT: C 343 LYS cc_start: 0.6527 (OUTLIER) cc_final: 0.6089 (ttpt) REVERT: C 431 GLN cc_start: 0.8804 (mt0) cc_final: 0.8162 (mp10) REVERT: C 517 TRP cc_start: 0.8907 (m-90) cc_final: 0.8380 (m-90) REVERT: C 548 LEU cc_start: 0.9112 (mt) cc_final: 0.8519 (tp) REVERT: D 41 ILE cc_start: 0.9180 (tp) cc_final: 0.8898 (mm) REVERT: D 147 GLN cc_start: 0.7716 (tt0) cc_final: 0.6805 (tp-100) REVERT: D 166 LEU cc_start: 0.9270 (tt) cc_final: 0.8806 (pp) REVERT: D 260 LEU cc_start: 0.9279 (mt) cc_final: 0.8964 (mt) REVERT: D 295 TYR cc_start: 0.9127 (t80) cc_final: 0.8516 (t80) REVERT: D 376 TYR cc_start: 0.8896 (m-80) cc_final: 0.8549 (m-80) REVERT: D 540 PRO cc_start: 0.7395 (Cg_endo) cc_final: 0.6686 (Cg_exo) REVERT: D 546 THR cc_start: 0.9033 (OUTLIER) cc_final: 0.8787 (t) REVERT: D 613 MET cc_start: 0.8515 (ppp) cc_final: 0.8114 (ppp) outliers start: 50 outliers final: 35 residues processed: 252 average time/residue: 0.2260 time to fit residues: 85.2824 Evaluate side-chains 256 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 215 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 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 35 VAL 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 160 SER Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 398 TRP Chi-restraints excluded: chain D residue 455 THR Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 0.4980 chunk 43 optimal weight: 0.1980 chunk 28 optimal weight: 0.7980 chunk 91 optimal weight: 0.0000 chunk 98 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 113 optimal weight: 0.0870 chunk 131 optimal weight: 0.8980 chunk 138 optimal weight: 5.9990 chunk 126 optimal weight: 10.0000 overall best weight: 0.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 ASN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 12385 Z= 0.177 Angle : 0.687 13.058 16835 Z= 0.338 Chirality : 0.045 0.231 1896 Planarity : 0.005 0.065 2147 Dihedral : 5.796 55.061 1813 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.41 % Allowed : 22.09 % Favored : 74.50 % 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: -0.60 (0.22), residues: 1488 helix: 1.08 (0.52), residues: 104 sheet: 0.43 (0.21), residues: 613 loop : -1.32 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 344 HIS 0.006 0.001 HIS D 515 PHE 0.024 0.001 PHE D 234 TYR 0.010 0.001 TYR B 31 ARG 0.010 0.001 ARG C 233 *********************** 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 267 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 221 time to evaluate : 1.370 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 54 LYS cc_start: 0.8818 (mmtp) cc_final: 0.8322 (mmmt) REVERT: A 58 TYR cc_start: 0.7906 (m-80) cc_final: 0.7590 (m-80) REVERT: A 74 GLN cc_start: 0.8710 (tp-100) cc_final: 0.8438 (tp-100) REVERT: A 141 LEU cc_start: 0.8761 (mt) cc_final: 0.8490 (mt) REVERT: A 186 ARG cc_start: 0.7496 (mmt90) cc_final: 0.7165 (mmt90) REVERT: B 60 TRP cc_start: 0.7781 (m100) cc_final: 0.7100 (m100) REVERT: B 147 MET cc_start: 0.7547 (mtt) cc_final: 0.7256 (mtt) REVERT: B 148 ASP cc_start: 0.7419 (t0) cc_final: 0.7011 (t0) REVERT: B 206 ILE cc_start: 0.8373 (mt) cc_final: 0.8115 (tt) REVERT: B 208 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8354 (mm) REVERT: B 211 GLU cc_start: 0.8341 (mt-10) cc_final: 0.7744 (tp30) REVERT: C 50 ASN cc_start: 0.8358 (m-40) cc_final: 0.7936 (m-40) REVERT: C 60 ASP cc_start: 0.7972 (t0) cc_final: 0.7581 (m-30) REVERT: C 67 TYR cc_start: 0.8316 (t80) cc_final: 0.7724 (t80) REVERT: C 78 LEU cc_start: 0.8028 (tp) cc_final: 0.7474 (pp) REVERT: C 114 ILE cc_start: 0.8053 (OUTLIER) cc_final: 0.7829 (tp) REVERT: C 128 LEU cc_start: 0.8827 (pt) cc_final: 0.8539 (mp) REVERT: C 167 ASP cc_start: 0.8550 (m-30) cc_final: 0.7310 (p0) REVERT: C 184 MET cc_start: 0.6555 (tpp) cc_final: 0.6326 (tpt) REVERT: C 214 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7288 (mt-10) REVERT: C 226 GLU cc_start: 0.6241 (tp30) cc_final: 0.5977 (tp30) REVERT: C 343 LYS cc_start: 0.6500 (OUTLIER) cc_final: 0.6067 (ttpt) REVERT: C 431 GLN cc_start: 0.8700 (mt0) cc_final: 0.8053 (mp10) REVERT: C 517 TRP cc_start: 0.8865 (m-90) cc_final: 0.8317 (m-90) REVERT: C 548 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8459 (tp) REVERT: D 41 ILE cc_start: 0.9178 (tp) cc_final: 0.8918 (mm) REVERT: D 147 GLN cc_start: 0.7578 (tt0) cc_final: 0.6711 (tp-100) REVERT: D 166 LEU cc_start: 0.9306 (tt) cc_final: 0.8846 (pp) REVERT: D 260 LEU cc_start: 0.9255 (mt) cc_final: 0.8933 (mt) REVERT: D 295 TYR cc_start: 0.9084 (t80) cc_final: 0.8487 (t80) REVERT: D 376 TYR cc_start: 0.8878 (m-80) cc_final: 0.8530 (m-80) REVERT: D 540 PRO cc_start: 0.7287 (Cg_endo) cc_final: 0.6575 (Cg_exo) REVERT: D 546 THR cc_start: 0.9055 (OUTLIER) cc_final: 0.8664 (t) REVERT: D 613 MET cc_start: 0.8382 (ppp) cc_final: 0.8009 (ppp) outliers start: 46 outliers final: 34 residues processed: 247 average time/residue: 0.2174 time to fit residues: 80.8470 Evaluate side-chains 249 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 210 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 246 ASN 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 124 VAL Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 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 548 LEU Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 146 VAL 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 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 134 optimal weight: 10.0000 chunk 138 optimal weight: 7.9990 chunk 81 optimal weight: 0.7980 chunk 58 optimal weight: 0.0060 chunk 105 optimal weight: 7.9990 chunk 41 optimal weight: 10.0000 chunk 121 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 88 optimal weight: 0.0980 chunk 142 optimal weight: 8.9990 chunk 86 optimal weight: 0.6980 overall best weight: 0.7198 ------------------------------------------------------------------------------- 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 A 147 GLN ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 ASN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 ASN ** D 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12385 Z= 0.207 Angle : 0.690 13.122 16835 Z= 0.344 Chirality : 0.044 0.231 1896 Planarity : 0.005 0.066 2147 Dihedral : 5.660 54.789 1813 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.93 % Allowed : 21.94 % Favored : 74.13 % 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: -0.56 (0.22), residues: 1488 helix: 1.48 (0.53), residues: 98 sheet: 0.44 (0.21), residues: 619 loop : -1.35 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.001 TRP D 398 HIS 0.004 0.001 HIS C 402 PHE 0.019 0.001 PHE D 234 TYR 0.016 0.001 TYR A 185 ARG 0.009 0.001 ARG C 314 *********************** 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 275 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 222 time to evaluate : 1.493 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 58 TYR cc_start: 0.7925 (m-80) cc_final: 0.7633 (m-80) REVERT: A 145 ASN cc_start: 0.8030 (OUTLIER) cc_final: 0.6629 (t0) REVERT: B 60 TRP cc_start: 0.7755 (m100) cc_final: 0.7026 (m100) REVERT: B 147 MET cc_start: 0.7546 (mtt) cc_final: 0.7227 (mtt) REVERT: B 148 ASP cc_start: 0.7466 (t0) cc_final: 0.7099 (t0) REVERT: B 208 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8354 (mm) REVERT: B 269 LYS cc_start: 0.7565 (pttt) cc_final: 0.6818 (ptpp) REVERT: C 50 ASN cc_start: 0.8359 (m-40) cc_final: 0.7949 (m-40) REVERT: C 60 ASP cc_start: 0.7959 (t0) cc_final: 0.7578 (m-30) REVERT: C 67 TYR cc_start: 0.8361 (t80) cc_final: 0.7812 (t80) REVERT: C 114 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7747 (tp) REVERT: C 128 LEU cc_start: 0.8832 (pt) cc_final: 0.8592 (tt) REVERT: C 131 ARG cc_start: 0.8423 (tpp80) cc_final: 0.8217 (tpp80) REVERT: C 167 ASP cc_start: 0.8554 (m-30) cc_final: 0.7331 (p0) REVERT: C 214 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7268 (mt-10) REVERT: C 226 GLU cc_start: 0.6291 (tp30) cc_final: 0.6002 (tp30) REVERT: C 280 MET cc_start: 0.8635 (tpt) cc_final: 0.7899 (tpp) REVERT: C 343 LYS cc_start: 0.6486 (OUTLIER) cc_final: 0.6045 (ttpt) REVERT: C 431 GLN cc_start: 0.8673 (mt0) cc_final: 0.8028 (mp10) REVERT: C 517 TRP cc_start: 0.8876 (m-90) cc_final: 0.8326 (m-90) REVERT: C 548 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8441 (tp) REVERT: D 41 ILE cc_start: 0.9195 (tp) cc_final: 0.8941 (mm) REVERT: D 147 GLN cc_start: 0.7644 (tt0) cc_final: 0.6791 (mm-40) REVERT: D 166 LEU cc_start: 0.9333 (tt) cc_final: 0.8841 (pp) REVERT: D 260 LEU cc_start: 0.9267 (mt) cc_final: 0.8954 (mt) REVERT: D 295 TYR cc_start: 0.9102 (t80) cc_final: 0.8514 (t80) REVERT: D 376 TYR cc_start: 0.8883 (m-80) cc_final: 0.8533 (m-80) REVERT: D 540 PRO cc_start: 0.7258 (Cg_endo) cc_final: 0.6536 (Cg_exo) REVERT: D 546 THR cc_start: 0.8943 (OUTLIER) cc_final: 0.8699 (t) REVERT: D 613 MET cc_start: 0.8406 (ppp) cc_final: 0.8027 (ppp) outliers start: 53 outliers final: 37 residues processed: 251 average time/residue: 0.2232 time to fit residues: 83.9956 Evaluate side-chains 251 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 208 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 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 548 LEU Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 306 TYR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 432 CYS Chi-restraints excluded: chain D residue 455 THR Chi-restraints excluded: chain D residue 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 67 optimal weight: 6.9990 chunk 99 optimal weight: 0.0370 chunk 149 optimal weight: 7.9990 chunk 137 optimal weight: 0.7980 chunk 118 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 91 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 chunk 94 optimal weight: 9.9990 chunk 126 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 overall best weight: 1.2260 ------------------------------------------------------------------------------- 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 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 12385 Z= 0.255 Angle : 0.705 12.804 16835 Z= 0.354 Chirality : 0.045 0.225 1896 Planarity : 0.005 0.066 2147 Dihedral : 5.682 54.486 1813 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.56 % Allowed : 22.31 % Favored : 74.13 % 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: -0.61 (0.22), residues: 1488 helix: 1.51 (0.53), residues: 98 sheet: 0.38 (0.21), residues: 622 loop : -1.37 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP D 398 HIS 0.009 0.001 HIS A 144 PHE 0.016 0.001 PHE D 234 TYR 0.017 0.001 TYR A 185 ARG 0.009 0.001 ARG C 314 ********************** 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 265 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 217 time to evaluate : 1.420 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: A 54 LYS cc_start: 0.8913 (mmtp) cc_final: 0.8428 (mmmt) REVERT: A 58 TYR cc_start: 0.7985 (m-80) cc_final: 0.7699 (m-80) REVERT: A 74 GLN cc_start: 0.8750 (tp-100) cc_final: 0.8498 (tp-100) REVERT: A 145 ASN cc_start: 0.6926 (OUTLIER) cc_final: 0.6705 (t0) REVERT: B 60 TRP cc_start: 0.7805 (m100) cc_final: 0.6998 (m100) REVERT: B 147 MET cc_start: 0.7508 (mtt) cc_final: 0.7159 (mtt) REVERT: B 148 ASP cc_start: 0.7504 (t0) cc_final: 0.7170 (t0) REVERT: B 208 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8329 (mm) REVERT: B 269 LYS cc_start: 0.7591 (pttt) cc_final: 0.6839 (ptpp) REVERT: C 50 ASN cc_start: 0.8372 (m-40) cc_final: 0.7956 (m-40) REVERT: C 60 ASP cc_start: 0.8005 (t0) cc_final: 0.7695 (m-30) REVERT: C 67 TYR cc_start: 0.8395 (t80) cc_final: 0.7804 (t80) REVERT: C 114 ILE cc_start: 0.8119 (OUTLIER) cc_final: 0.7862 (tp) REVERT: C 128 LEU cc_start: 0.8855 (pt) cc_final: 0.8618 (tt) REVERT: C 167 ASP cc_start: 0.8544 (m-30) cc_final: 0.7304 (p0) REVERT: C 214 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7210 (mt-10) REVERT: C 226 GLU cc_start: 0.6288 (tp30) cc_final: 0.5977 (tp30) REVERT: C 280 MET cc_start: 0.8650 (tpt) cc_final: 0.7965 (tpp) REVERT: C 343 LYS cc_start: 0.6474 (OUTLIER) cc_final: 0.6033 (ttpt) REVERT: C 431 GLN cc_start: 0.8704 (mt0) cc_final: 0.8064 (mp10) REVERT: C 517 TRP cc_start: 0.8937 (m-90) cc_final: 0.8381 (m-90) REVERT: C 548 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8440 (tp) REVERT: D 41 ILE cc_start: 0.9198 (tp) cc_final: 0.8942 (mm) REVERT: D 147 GLN cc_start: 0.7763 (tt0) cc_final: 0.6817 (tp-100) REVERT: D 166 LEU cc_start: 0.9380 (tt) cc_final: 0.8989 (pp) REVERT: D 260 LEU cc_start: 0.9257 (mt) cc_final: 0.8947 (mt) REVERT: D 295 TYR cc_start: 0.9123 (t80) cc_final: 0.8528 (t80) REVERT: D 376 TYR cc_start: 0.8906 (m-80) cc_final: 0.8559 (m-80) REVERT: D 540 PRO cc_start: 0.7203 (Cg_endo) cc_final: 0.6473 (Cg_exo) REVERT: D 613 MET cc_start: 0.8439 (ppp) cc_final: 0.8053 (ppp) outliers start: 48 outliers final: 38 residues processed: 245 average time/residue: 0.2120 time to fit residues: 78.0172 Evaluate side-chains 256 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 213 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE 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 38 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 405 CYS Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 127 CYS Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 306 TYR 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 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 109 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 119 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 chunk 15 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 86 optimal weight: 10.0000 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS A 145 ASN A 147 GLN ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 GLN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.160127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.106094 restraints weight = 28926.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.110218 restraints weight = 12280.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.112701 restraints weight = 7534.727| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 12385 Z= 0.240 Angle : 0.704 12.491 16835 Z= 0.353 Chirality : 0.045 0.226 1896 Planarity : 0.005 0.067 2147 Dihedral : 5.670 54.578 1813 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.63 % Allowed : 22.31 % Favored : 74.05 % 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: -0.60 (0.22), residues: 1488 helix: 1.47 (0.53), residues: 98 sheet: 0.45 (0.21), residues: 614 loop : -1.39 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP D 398 HIS 0.013 0.001 HIS A 146 PHE 0.018 0.001 PHE D 234 TYR 0.020 0.001 TYR C 143 ARG 0.010 0.001 ARG C 314 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3089.02 seconds wall clock time: 57 minutes 3.92 seconds (3423.92 seconds total)