Starting phenix.real_space_refine on Thu Feb 15 11:40:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8odz_16820/02_2024/8odz_16820.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8odz_16820/02_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8odz_16820/02_2024/8odz_16820.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8odz_16820/02_2024/8odz_16820.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8odz_16820/02_2024/8odz_16820.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8odz_16820/02_2024/8odz_16820.pdb" } 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 Residue "B PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12100 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1228 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain breaks: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 2336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2336 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 278} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 3854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3854 Classifications: {'peptide': 485} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 33, 'TRANS': 451} Chain breaks: 3 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 4561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 4561 Classifications: {'peptide': 582} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 541} Chain breaks: 3 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 7.07, per 1000 atoms: 0.58 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 - 3.50 Amino acid : False - 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: 4.83 Conformation dependent library (CDL) restraints added in 2.4 seconds 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2870 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 33 sheets defined 8.4% alpha, 36.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 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: 5.22 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: 98.38 - 105.61: 341 105.61 - 112.84: 6748 112.84 - 120.07: 4058 120.07 - 127.29: 5498 127.29 - 134.52: 190 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 2.440 nonbonded pdb=" OD2 ASP B 234 " pdb=" OG SER B 258 " model vdw 2.231 2.440 nonbonded pdb=" ND2 ASN B 146 " pdb=" OE2 GLU B 185 " model vdw 2.240 2.520 nonbonded pdb=" O PHE D 73 " pdb=" OG1 THR D 107 " model vdw 2.260 2.440 nonbonded pdb=" OG SER D 443 " pdb=" OG1 THR D 455 " model vdw 2.269 2.440 ... (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 ========== 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: 4.620 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: 19.010 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 36.580 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.820 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 3 poor density : 340 time to evaluate : 1.428 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: 0.2586 time to fit residues: 123.4918 Evaluate side-chains 237 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 1.450 ------------------------------------------------------------------------------- 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: 9.9990 chunk 113 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 38 optimal weight: 0.0970 chunk 76 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 117 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 87 optimal weight: 30.0000 chunk 136 optimal weight: 5.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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 163 GLN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7445 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 12385 Z= 0.307 Angle : 0.698 13.965 16835 Z= 0.354 Chirality : 0.045 0.224 1896 Planarity : 0.005 0.071 2147 Dihedral : 7.699 60.023 1813 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.59 % Allowed : 12.97 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.22), residues: 1488 helix: 1.16 (0.53), residues: 104 sheet: 0.09 (0.21), residues: 623 loop : -1.48 (0.21), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 109 HIS 0.005 0.001 HIS A 196 PHE 0.018 0.002 PHE C 180 TYR 0.027 0.002 TYR D 469 ARG 0.011 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 286 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 251 time to evaluate : 1.512 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 87 HIS cc_start: 0.4286 (OUTLIER) cc_final: 0.3820 (m-70) REVERT: A 141 LEU cc_start: 0.8711 (mt) cc_final: 0.8437 (mt) REVERT: A 196 HIS cc_start: 0.7840 (t70) cc_final: 0.7169 (t-170) REVERT: B 147 MET cc_start: 0.7623 (mtt) cc_final: 0.7202 (mtt) REVERT: B 148 ASP cc_start: 0.7057 (t0) cc_final: 0.6632 (t0) REVERT: B 269 LYS cc_start: 0.7576 (ttpt) cc_final: 0.7171 (ptpt) REVERT: B 302 GLU cc_start: 0.7894 (tt0) cc_final: 0.7628 (tt0) REVERT: C 50 ASN cc_start: 0.8408 (m-40) cc_final: 0.7924 (m-40) REVERT: C 67 TYR cc_start: 0.8269 (t80) cc_final: 0.7769 (t80) REVERT: C 167 ASP cc_start: 0.8393 (m-30) cc_final: 0.7726 (p0) REVERT: C 327 LYS cc_start: 0.7891 (ptmt) cc_final: 0.7520 (ptmm) REVERT: C 343 LYS cc_start: 0.6624 (OUTLIER) cc_final: 0.6196 (ttpt) REVERT: C 431 GLN cc_start: 0.8869 (mt0) cc_final: 0.8267 (mp10) REVERT: C 517 TRP cc_start: 0.8435 (m-90) cc_final: 0.8083 (m-90) REVERT: D 166 LEU cc_start: 0.9349 (tt) cc_final: 0.8930 (pp) REVERT: D 189 ASP cc_start: 0.9173 (p0) cc_final: 0.8902 (p0) REVERT: D 295 TYR cc_start: 0.8973 (t80) cc_final: 0.8416 (t80) REVERT: D 376 TYR cc_start: 0.8991 (m-80) cc_final: 0.8623 (m-80) REVERT: D 449 MET cc_start: 0.8394 (ptt) cc_final: 0.8008 (ppp) REVERT: D 540 PRO cc_start: 0.7512 (Cg_endo) cc_final: 0.6778 (Cg_exo) REVERT: D 613 MET cc_start: 0.8447 (ppp) cc_final: 0.7930 (ppp) outliers start: 35 outliers final: 24 residues processed: 263 average time/residue: 0.2251 time to fit residues: 86.9072 Evaluate side-chains 247 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 221 time to evaluate : 1.500 ------------------------------------------------------------------------------- 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 123 ILE Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain C residue 105 THR 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 301 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 290 ASN 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: 10.0000 chunk 42 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 92 optimal weight: 0.0770 chunk 37 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 147 optimal weight: 10.0000 chunk 121 optimal weight: 2.9990 chunk 135 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 overall best weight: 1.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 246 ASN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 GLN C 398 GLN ** C 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 381 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: 0.7497 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 12385 Z= 0.331 Angle : 0.697 13.357 16835 Z= 0.353 Chirality : 0.045 0.293 1896 Planarity : 0.005 0.071 2147 Dihedral : 6.771 54.541 1813 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 3.71 % Allowed : 16.09 % Favored : 80.21 % 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: -0.98 (0.22), residues: 1488 helix: 1.32 (0.54), residues: 98 sheet: 0.02 (0.21), residues: 632 loop : -1.53 (0.21), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 109 HIS 0.012 0.001 HIS A 87 PHE 0.026 0.002 PHE C 108 TYR 0.015 0.002 TYR A 58 ARG 0.007 0.001 ARG C 314 *********************** 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 292 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 242 time to evaluate : 1.499 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 87 HIS cc_start: 0.4616 (OUTLIER) cc_final: 0.4064 (m170) REVERT: A 196 HIS cc_start: 0.7875 (t70) cc_final: 0.7273 (t-170) REVERT: B 60 TRP cc_start: 0.7893 (m100) cc_final: 0.7055 (m100) REVERT: B 147 MET cc_start: 0.7748 (mtt) cc_final: 0.7505 (mtt) REVERT: B 148 ASP cc_start: 0.7465 (t0) cc_final: 0.7070 (t0) REVERT: B 181 GLN cc_start: 0.8591 (mp10) cc_final: 0.8334 (pp30) REVERT: B 246 ASN cc_start: 0.8195 (OUTLIER) cc_final: 0.7919 (t0) REVERT: B 269 LYS cc_start: 0.7709 (ttpt) cc_final: 0.7299 (ptpt) REVERT: B 302 GLU cc_start: 0.7870 (tt0) cc_final: 0.7564 (tt0) REVERT: C 50 ASN cc_start: 0.8439 (m-40) cc_final: 0.7962 (m-40) REVERT: C 67 TYR cc_start: 0.8397 (t80) cc_final: 0.7807 (t80) REVERT: C 167 ASP cc_start: 0.8348 (m-30) cc_final: 0.7769 (p0) REVERT: C 226 GLU cc_start: 0.6639 (tp30) cc_final: 0.6285 (tp30) REVERT: C 311 LEU cc_start: 0.9399 (pt) cc_final: 0.9078 (pp) REVERT: C 314 ARG cc_start: 0.9251 (ttm-80) cc_final: 0.9021 (ttm-80) REVERT: C 343 LYS cc_start: 0.6612 (OUTLIER) cc_final: 0.6178 (ttpt) REVERT: C 431 GLN cc_start: 0.8905 (mt0) cc_final: 0.8317 (mp10) REVERT: C 449 MET cc_start: 0.7973 (ppp) cc_final: 0.7738 (ppp) REVERT: D 295 TYR cc_start: 0.9041 (t80) cc_final: 0.8525 (t80) REVERT: D 376 TYR cc_start: 0.8967 (m-80) cc_final: 0.8609 (m-80) REVERT: D 449 MET cc_start: 0.8332 (ptt) cc_final: 0.7941 (ppp) REVERT: D 540 PRO cc_start: 0.7590 (Cg_endo) cc_final: 0.6866 (Cg_exo) REVERT: D 613 MET cc_start: 0.8481 (ppp) cc_final: 0.7966 (ppp) outliers start: 50 outliers final: 33 residues processed: 258 average time/residue: 0.2220 time to fit residues: 84.0438 Evaluate side-chains 246 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 210 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 87 HIS Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 63 ASP 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 105 THR 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 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 519 VAL 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 233 THR Chi-restraints excluded: chain D residue 290 ASN Chi-restraints excluded: chain D residue 427 ASN 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: 7.9990 chunk 102 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 136 optimal weight: 6.9990 chunk 144 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 129 optimal weight: 8.9990 chunk 39 optimal weight: 0.7980 overall best weight: 3.5186 ------------------------------------------------------------------------------- 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 105 HIS ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 304 HIS ** C 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 ASN ** 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: 0.7609 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.124 12385 Z= 0.572 Angle : 0.850 12.157 16835 Z= 0.437 Chirality : 0.050 0.315 1896 Planarity : 0.006 0.069 2147 Dihedral : 6.988 54.217 1813 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 26.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 5.41 % Allowed : 17.87 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.21), residues: 1488 helix: 0.65 (0.53), residues: 94 sheet: -0.36 (0.21), residues: 644 loop : -1.71 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP C 109 HIS 0.007 0.001 HIS A 87 PHE 0.045 0.003 PHE C 108 TYR 0.018 0.003 TYR C 61 ARG 0.008 0.001 ARG C 466 *********************** 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 287 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 214 time to evaluate : 1.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 HIS cc_start: 0.5217 (OUTLIER) cc_final: 0.4941 (m-70) REVERT: A 153 LYS cc_start: 0.8767 (ttpt) cc_final: 0.8199 (ttpp) REVERT: A 186 ARG cc_start: 0.7518 (mmt90) cc_final: 0.7270 (mmt90) REVERT: A 196 HIS cc_start: 0.7977 (t70) cc_final: 0.7742 (t70) REVERT: B 80 LYS cc_start: 0.8748 (pttp) cc_final: 0.8023 (mttt) REVERT: B 148 ASP cc_start: 0.8062 (t0) cc_final: 0.7798 (t0) REVERT: B 201 GLU cc_start: 0.8257 (tp30) cc_final: 0.6811 (tp30) REVERT: B 246 ASN cc_start: 0.8098 (t0) cc_final: 0.7799 (t0) REVERT: B 269 LYS cc_start: 0.7758 (ttpt) cc_final: 0.7340 (ptpt) REVERT: B 302 GLU cc_start: 0.7665 (tt0) cc_final: 0.7355 (tt0) REVERT: C 50 ASN cc_start: 0.8498 (m-40) cc_final: 0.7993 (m-40) REVERT: C 67 TYR cc_start: 0.8528 (t80) cc_final: 0.7959 (t80) REVERT: C 167 ASP cc_start: 0.8205 (m-30) cc_final: 0.7797 (p0) REVERT: C 226 GLU cc_start: 0.6622 (tp30) cc_final: 0.6023 (tp30) REVERT: C 343 LYS cc_start: 0.6676 (OUTLIER) cc_final: 0.6223 (ttpt) REVERT: C 431 GLN cc_start: 0.8995 (mt0) cc_final: 0.8370 (mp10) REVERT: C 517 TRP cc_start: 0.9037 (m-90) cc_final: 0.8285 (m-90) REVERT: C 518 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8992 (mm) REVERT: D 147 GLN cc_start: 0.7878 (tt0) cc_final: 0.7080 (tp-100) REVERT: D 306 TYR cc_start: 0.9173 (OUTLIER) cc_final: 0.8880 (t80) REVERT: D 308 PHE cc_start: 0.8991 (m-80) cc_final: 0.8542 (m-80) REVERT: D 376 TYR cc_start: 0.9041 (m-80) cc_final: 0.8704 (m-80) REVERT: D 540 PRO cc_start: 0.7617 (Cg_endo) cc_final: 0.6878 (Cg_exo) REVERT: D 613 MET cc_start: 0.8716 (ppp) cc_final: 0.8178 (ppp) REVERT: D 628 ARG cc_start: 0.9542 (tpm170) cc_final: 0.9338 (tpp-160) outliers start: 73 outliers final: 58 residues processed: 256 average time/residue: 0.2256 time to fit residues: 84.3766 Evaluate side-chains 267 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 205 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 87 HIS Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 91 HIS Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain C residue 80 CYS Chi-restraints excluded: chain C residue 105 THR 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 343 LYS Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 547 ARG 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 50 SER Chi-restraints excluded: chain D residue 102 LEU 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 169 ASN 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 290 ASN Chi-restraints excluded: chain D residue 306 TYR Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 393 THR 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 500 ILE Chi-restraints excluded: chain D residue 554 ILE 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: 10.0000 chunk 82 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 107 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 chunk 123 optimal weight: 0.2980 chunk 100 optimal weight: 2.9990 chunk 0 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- 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** ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 12385 Z= 0.325 Angle : 0.704 11.305 16835 Z= 0.356 Chirality : 0.045 0.252 1896 Planarity : 0.005 0.069 2147 Dihedral : 6.582 54.824 1813 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 20.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 5.49 % Allowed : 20.76 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.22), residues: 1488 helix: 1.20 (0.53), residues: 95 sheet: -0.11 (0.21), residues: 632 loop : -1.64 (0.21), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 398 HIS 0.006 0.001 HIS A 87 PHE 0.023 0.002 PHE C 108 TYR 0.013 0.002 TYR D 574 ARG 0.008 0.001 ARG C 314 *********************** 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 297 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 223 time to evaluate : 1.439 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: 0.8868 (ttmt) cc_final: 0.8448 (mmmt) REVERT: A 145 ASN cc_start: 0.8111 (p0) cc_final: 0.7830 (p0) REVERT: A 153 LYS cc_start: 0.8679 (ttpt) cc_final: 0.8125 (ttpp) REVERT: A 186 ARG cc_start: 0.7483 (mmt90) cc_final: 0.7118 (mmt90) REVERT: A 189 MET cc_start: 0.7752 (mmt) cc_final: 0.7201 (mmt) REVERT: A 212 LEU cc_start: 0.9130 (tp) cc_final: 0.8901 (tp) REVERT: B 60 TRP cc_start: 0.7853 (m100) cc_final: 0.7063 (m100) REVERT: B 148 ASP cc_start: 0.7868 (t0) cc_final: 0.7592 (t0) REVERT: B 201 GLU cc_start: 0.8299 (tp30) cc_final: 0.7734 (tp30) REVERT: B 208 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8414 (mm) REVERT: B 246 ASN cc_start: 0.8413 (t0) cc_final: 0.8139 (t0) REVERT: B 302 GLU cc_start: 0.7609 (tt0) cc_final: 0.7275 (tt0) REVERT: C 50 ASN cc_start: 0.8467 (m-40) cc_final: 0.7979 (m-40) REVERT: C 67 TYR cc_start: 0.8524 (t80) cc_final: 0.7930 (t80) REVERT: C 167 ASP cc_start: 0.8178 (m-30) cc_final: 0.7739 (p0) REVERT: C 311 LEU cc_start: 0.9414 (pt) cc_final: 0.9110 (pp) REVERT: C 343 LYS cc_start: 0.6577 (OUTLIER) cc_final: 0.6132 (ttpt) REVERT: C 431 GLN cc_start: 0.8940 (mt0) cc_final: 0.8276 (mp10) REVERT: C 449 MET cc_start: 0.7973 (ppp) cc_final: 0.7769 (ppp) REVERT: C 517 TRP cc_start: 0.9036 (m-90) cc_final: 0.8332 (m-90) REVERT: C 518 LEU cc_start: 0.9256 (mm) cc_final: 0.8983 (mm) REVERT: D 147 GLN cc_start: 0.7846 (tt0) cc_final: 0.6994 (tp-100) REVERT: D 295 TYR cc_start: 0.9225 (t80) cc_final: 0.8556 (t80) REVERT: D 376 TYR cc_start: 0.8982 (m-80) cc_final: 0.8624 (m-80) REVERT: D 449 MET cc_start: 0.8162 (ptt) cc_final: 0.7688 (ppp) REVERT: D 540 PRO cc_start: 0.7578 (Cg_endo) cc_final: 0.6864 (Cg_exo) REVERT: D 546 THR cc_start: 0.9076 (OUTLIER) cc_final: 0.8855 (t) REVERT: D 564 GLN cc_start: 0.8391 (mp-120) cc_final: 0.7912 (mp10) REVERT: D 613 MET cc_start: 0.8588 (ppp) cc_final: 0.8073 (ppp) REVERT: D 621 GLU cc_start: 0.9032 (tt0) cc_final: 0.8382 (mp0) outliers start: 74 outliers final: 52 residues processed: 262 average time/residue: 0.2245 time to fit residues: 86.7632 Evaluate side-chains 269 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 214 time to evaluate : 1.443 ------------------------------------------------------------------------------- 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 120 LEU Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 91 HIS Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain C residue 80 CYS Chi-restraints excluded: chain C residue 105 THR 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 135 SER Chi-restraints excluded: chain C residue 171 SER 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 519 VAL 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 102 LEU 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 166 LEU 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 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 500 ILE Chi-restraints excluded: chain D residue 546 THR Chi-restraints excluded: chain D residue 554 ILE Chi-restraints excluded: chain D residue 556 TRP Chi-restraints excluded: chain D residue 571 TYR 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: 4.9990 chunk 130 optimal weight: 5.9990 chunk 28 optimal weight: 0.0070 chunk 85 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 145 optimal weight: 30.0000 chunk 120 optimal weight: 7.9990 chunk 67 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 139 optimal weight: 7.9990 overall best weight: 1.9804 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 12385 Z= 0.350 Angle : 0.718 13.568 16835 Z= 0.360 Chirality : 0.046 0.262 1896 Planarity : 0.005 0.066 2147 Dihedral : 6.423 55.005 1813 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 21.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 6.23 % Allowed : 21.28 % Favored : 72.50 % 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: -1.20 (0.22), residues: 1488 helix: 1.12 (0.52), residues: 95 sheet: -0.14 (0.21), residues: 631 loop : -1.64 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 344 HIS 0.014 0.001 HIS A 196 PHE 0.037 0.002 PHE D 234 TYR 0.013 0.002 TYR D 574 ARG 0.010 0.001 ARG D 572 *********************** 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 301 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 217 time to evaluate : 1.437 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 54 LYS cc_start: 0.8900 (ttmt) cc_final: 0.8485 (mmmt) REVERT: A 68 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8164 (mp0) REVERT: A 153 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8136 (ttpp) REVERT: A 186 ARG cc_start: 0.7504 (mmt90) cc_final: 0.7056 (mmt90) REVERT: B 60 TRP cc_start: 0.7821 (m100) cc_final: 0.7022 (m100) REVERT: B 115 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.7881 (mt-10) REVERT: B 148 ASP cc_start: 0.7973 (t0) cc_final: 0.7724 (t0) REVERT: B 201 GLU cc_start: 0.8285 (tp30) cc_final: 0.6885 (tp30) REVERT: B 208 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8397 (mm) REVERT: B 246 ASN cc_start: 0.8446 (t0) cc_final: 0.8194 (t0) REVERT: B 269 LYS cc_start: 0.7823 (pttt) cc_final: 0.6918 (ptpp) REVERT: C 50 ASN cc_start: 0.8506 (m-40) cc_final: 0.8031 (m-40) REVERT: C 67 TYR cc_start: 0.8522 (t80) cc_final: 0.7932 (t80) REVERT: C 223 MET cc_start: 0.6725 (OUTLIER) cc_final: 0.6398 (pmm) REVERT: C 226 GLU cc_start: 0.6573 (tp30) cc_final: 0.6182 (tp30) REVERT: C 311 LEU cc_start: 0.9408 (pt) cc_final: 0.9196 (pp) REVERT: C 343 LYS cc_start: 0.6571 (OUTLIER) cc_final: 0.6121 (ttpt) REVERT: C 431 GLN cc_start: 0.8946 (mt0) cc_final: 0.8284 (mp10) REVERT: C 449 MET cc_start: 0.8037 (ppp) cc_final: 0.7825 (ppp) REVERT: C 517 TRP cc_start: 0.9020 (m-90) cc_final: 0.8302 (m-90) REVERT: C 518 LEU cc_start: 0.9256 (mm) cc_final: 0.8989 (mm) REVERT: C 548 LEU cc_start: 0.9194 (mt) cc_final: 0.8545 (tp) REVERT: D 106 MET cc_start: 0.8894 (ptp) cc_final: 0.8651 (ptm) REVERT: D 147 GLN cc_start: 0.7846 (tt0) cc_final: 0.6951 (tp-100) REVERT: D 295 TYR cc_start: 0.9256 (t80) cc_final: 0.8623 (t80) REVERT: D 376 TYR cc_start: 0.8986 (m-80) cc_final: 0.8634 (m-80) REVERT: D 449 MET cc_start: 0.8139 (ptt) cc_final: 0.7672 (ppp) REVERT: D 540 PRO cc_start: 0.7557 (Cg_endo) cc_final: 0.6831 (Cg_exo) REVERT: D 546 THR cc_start: 0.9075 (OUTLIER) cc_final: 0.8845 (t) REVERT: D 613 MET cc_start: 0.8632 (ppp) cc_final: 0.8160 (ppp) REVERT: D 621 GLU cc_start: 0.9057 (tt0) cc_final: 0.8468 (mp0) outliers start: 84 outliers final: 62 residues processed: 268 average time/residue: 0.2358 time to fit residues: 94.7548 Evaluate side-chains 279 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 210 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 84 LEU 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 A residue 153 LYS Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 91 HIS Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain C residue 80 CYS Chi-restraints excluded: chain C residue 105 THR 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 135 SER Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 180 PHE Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 524 THR Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 50 SER 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 166 LEU Chi-restraints excluded: chain D residue 169 ASN 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 290 ASN 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 471 VAL Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 546 THR Chi-restraints excluded: chain D residue 554 ILE 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: 0.7980 chunk 82 optimal weight: 3.9990 chunk 105 optimal weight: 7.9990 chunk 122 optimal weight: 0.6980 chunk 81 optimal weight: 9.9990 chunk 144 optimal weight: 6.9990 chunk 90 optimal weight: 7.9990 chunk 88 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 overall best weight: 1.4982 ------------------------------------------------------------------------------- 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 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 556 GLN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 12385 Z= 0.278 Angle : 0.675 12.980 16835 Z= 0.338 Chirality : 0.045 0.241 1896 Planarity : 0.005 0.064 2147 Dihedral : 6.151 54.982 1813 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 18.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 6.15 % Allowed : 21.87 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.22), residues: 1488 helix: 1.24 (0.53), residues: 95 sheet: -0.10 (0.21), residues: 631 loop : -1.55 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 344 HIS 0.003 0.001 HIS D 558 PHE 0.024 0.002 PHE D 234 TYR 0.017 0.001 TYR D 469 ARG 0.011 0.001 ARG C 314 *********************** 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 306 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 223 time to evaluate : 1.468 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 54 LYS cc_start: 0.8884 (ttmt) cc_final: 0.8456 (mmmt) REVERT: A 58 TYR cc_start: 0.7723 (m-80) cc_final: 0.7355 (m-80) REVERT: A 68 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8149 (mp0) REVERT: A 153 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8095 (ttpp) REVERT: A 212 LEU cc_start: 0.9103 (tp) cc_final: 0.8901 (tp) REVERT: B 60 TRP cc_start: 0.7808 (m100) cc_final: 0.7049 (m100) REVERT: B 80 LYS cc_start: 0.8760 (pttp) cc_final: 0.7909 (mttt) REVERT: B 148 ASP cc_start: 0.7959 (t0) cc_final: 0.7701 (t0) REVERT: B 208 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8376 (mm) REVERT: B 246 ASN cc_start: 0.8474 (t0) cc_final: 0.8222 (t0) REVERT: B 269 LYS cc_start: 0.7791 (pttt) cc_final: 0.6949 (ptpp) REVERT: C 50 ASN cc_start: 0.8507 (m-40) cc_final: 0.8035 (m-40) REVERT: C 67 TYR cc_start: 0.8502 (t80) cc_final: 0.7842 (t80) REVERT: C 226 GLU cc_start: 0.6517 (tp30) cc_final: 0.6147 (tp30) REVERT: C 311 LEU cc_start: 0.9369 (pt) cc_final: 0.9169 (pp) REVERT: C 343 LYS cc_start: 0.6529 (OUTLIER) cc_final: 0.6085 (ttpt) REVERT: C 431 GLN cc_start: 0.8906 (mt0) cc_final: 0.8241 (mp10) REVERT: C 449 MET cc_start: 0.8022 (ppp) cc_final: 0.7802 (ppp) REVERT: C 517 TRP cc_start: 0.9028 (m-90) cc_final: 0.8281 (m-90) REVERT: C 518 LEU cc_start: 0.9259 (mm) cc_final: 0.8983 (mm) REVERT: D 147 GLN cc_start: 0.7836 (tt0) cc_final: 0.6942 (tp-100) REVERT: D 295 TYR cc_start: 0.9256 (t80) cc_final: 0.8602 (t80) REVERT: D 376 TYR cc_start: 0.8980 (m-80) cc_final: 0.8621 (m-80) REVERT: D 449 MET cc_start: 0.8158 (ptt) cc_final: 0.7691 (ppp) REVERT: D 540 PRO cc_start: 0.7535 (Cg_endo) cc_final: 0.6793 (Cg_exo) REVERT: D 613 MET cc_start: 0.8638 (ppp) cc_final: 0.8157 (ppp) REVERT: D 621 GLU cc_start: 0.9067 (tt0) cc_final: 0.8477 (mp0) outliers start: 83 outliers final: 68 residues processed: 275 average time/residue: 0.2170 time to fit residues: 88.0437 Evaluate side-chains 285 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 213 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 76 SER 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 A residue 153 LYS Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 91 HIS Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain C residue 80 CYS Chi-restraints excluded: chain C residue 105 THR 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 135 SER Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 223 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 393 TRP Chi-restraints excluded: chain C residue 405 CYS 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 50 SER Chi-restraints excluded: chain D residue 100 THR 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 166 LEU Chi-restraints excluded: chain D residue 169 ASN 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 290 ASN 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 471 VAL Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain D residue 556 TRP 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: 3.9990 chunk 43 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 chunk 71 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 131 optimal weight: 0.0770 chunk 138 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 overall best weight: 1.1140 ------------------------------------------------------------------------------- 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 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 556 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 12385 Z= 0.241 Angle : 0.688 13.654 16835 Z= 0.340 Chirality : 0.045 0.227 1896 Planarity : 0.005 0.063 2147 Dihedral : 6.043 55.080 1813 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 18.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 5.71 % Allowed : 22.68 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.22), residues: 1488 helix: 1.26 (0.52), residues: 95 sheet: -0.04 (0.21), residues: 632 loop : -1.51 (0.22), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 344 HIS 0.017 0.001 HIS A 87 PHE 0.019 0.002 PHE D 234 TYR 0.010 0.001 TYR D 574 ARG 0.009 0.000 ARG C 314 *********************** 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 295 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 218 time to evaluate : 1.569 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: 0.8855 (ttmt) cc_final: 0.8445 (mmmt) REVERT: A 58 TYR cc_start: 0.7748 (m-80) cc_final: 0.7230 (m-80) REVERT: A 68 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8149 (mp0) REVERT: A 153 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8097 (ttpp) REVERT: A 186 ARG cc_start: 0.7389 (mmt90) cc_final: 0.7109 (mmt90) REVERT: B 60 TRP cc_start: 0.7769 (m100) cc_final: 0.7048 (m100) REVERT: B 80 LYS cc_start: 0.8766 (pttp) cc_final: 0.7905 (mttt) REVERT: B 148 ASP cc_start: 0.7919 (t0) cc_final: 0.7675 (t0) REVERT: B 208 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8400 (mm) REVERT: B 211 GLU cc_start: 0.8367 (mt-10) cc_final: 0.7843 (mm-30) REVERT: B 246 ASN cc_start: 0.8474 (t0) cc_final: 0.8218 (t0) REVERT: B 269 LYS cc_start: 0.7790 (pttt) cc_final: 0.7063 (ptpp) REVERT: C 50 ASN cc_start: 0.8488 (m-40) cc_final: 0.8023 (m-40) REVERT: C 67 TYR cc_start: 0.8397 (t80) cc_final: 0.7891 (t80) REVERT: C 226 GLU cc_start: 0.6432 (OUTLIER) cc_final: 0.6069 (tp30) REVERT: C 311 LEU cc_start: 0.9367 (pt) cc_final: 0.9153 (pp) REVERT: C 343 LYS cc_start: 0.6530 (OUTLIER) cc_final: 0.6084 (ttpt) REVERT: C 431 GLN cc_start: 0.8884 (mt0) cc_final: 0.8231 (mp10) REVERT: C 449 MET cc_start: 0.8009 (ppp) cc_final: 0.7787 (ppp) REVERT: C 517 TRP cc_start: 0.9049 (m-90) cc_final: 0.8302 (m-90) REVERT: C 518 LEU cc_start: 0.9252 (mm) cc_final: 0.8977 (mm) REVERT: D 147 GLN cc_start: 0.7847 (tt0) cc_final: 0.6872 (tp-100) REVERT: D 295 TYR cc_start: 0.9266 (t80) cc_final: 0.8606 (t80) REVERT: D 376 TYR cc_start: 0.8977 (m-80) cc_final: 0.8614 (m-80) REVERT: D 449 MET cc_start: 0.8149 (ptt) cc_final: 0.7684 (ppp) REVERT: D 540 PRO cc_start: 0.7475 (Cg_endo) cc_final: 0.6724 (Cg_exo) REVERT: D 613 MET cc_start: 0.8627 (ppp) cc_final: 0.8164 (ppp) REVERT: D 621 GLU cc_start: 0.9071 (tt0) cc_final: 0.8479 (mp0) outliers start: 77 outliers final: 59 residues processed: 261 average time/residue: 0.2130 time to fit residues: 82.8540 Evaluate side-chains 276 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 212 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 84 LEU 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 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 33 VAL Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 91 HIS Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain C residue 80 CYS Chi-restraints excluded: chain C residue 105 THR 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 171 SER Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 405 CYS 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 50 SER Chi-restraints excluded: chain D residue 100 THR 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 166 LEU Chi-restraints excluded: chain D residue 169 ASN Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 290 ASN Chi-restraints excluded: chain D residue 432 CYS Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 500 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 9.9990 chunk 138 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 105 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 121 optimal weight: 0.2980 chunk 127 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 GLN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 556 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 12385 Z= 0.304 Angle : 0.705 13.512 16835 Z= 0.351 Chirality : 0.045 0.222 1896 Planarity : 0.005 0.061 2147 Dihedral : 6.080 54.894 1813 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 20.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 5.11 % Allowed : 23.57 % Favored : 71.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.22), residues: 1488 helix: 1.19 (0.52), residues: 95 sheet: -0.03 (0.21), residues: 630 loop : -1.58 (0.22), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 393 HIS 0.009 0.001 HIS C 404 PHE 0.018 0.002 PHE C 180 TYR 0.010 0.001 TYR B 255 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 287 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 218 time to evaluate : 1.539 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: 0.8849 (ttmt) cc_final: 0.8595 (mmmt) REVERT: A 68 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8097 (mp0) REVERT: A 153 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8090 (ttpp) REVERT: A 186 ARG cc_start: 0.7443 (mmt90) cc_final: 0.7140 (mmt90) REVERT: B 60 TRP cc_start: 0.7788 (m100) cc_final: 0.7061 (m100) REVERT: B 80 LYS cc_start: 0.8762 (pttp) cc_final: 0.7910 (mttt) REVERT: B 148 ASP cc_start: 0.7976 (t0) cc_final: 0.7744 (t0) REVERT: B 208 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8378 (mm) REVERT: B 246 ASN cc_start: 0.8478 (t0) cc_final: 0.8222 (t0) REVERT: B 269 LYS cc_start: 0.7806 (pttt) cc_final: 0.7091 (ptpp) REVERT: C 50 ASN cc_start: 0.8502 (m-40) cc_final: 0.8035 (m-40) REVERT: C 67 TYR cc_start: 0.8502 (t80) cc_final: 0.7913 (t80) REVERT: C 226 GLU cc_start: 0.6486 (OUTLIER) cc_final: 0.6108 (tp30) REVERT: C 309 ARG cc_start: 0.9237 (tpp80) cc_final: 0.9023 (tpp80) REVERT: C 311 LEU cc_start: 0.9380 (pt) cc_final: 0.9172 (pp) REVERT: C 343 LYS cc_start: 0.6542 (OUTLIER) cc_final: 0.6088 (ttpt) REVERT: C 431 GLN cc_start: 0.8902 (mt0) cc_final: 0.8254 (mp10) REVERT: C 449 MET cc_start: 0.8014 (ppp) cc_final: 0.7792 (ppp) REVERT: C 517 TRP cc_start: 0.9068 (m-90) cc_final: 0.8368 (m-90) REVERT: C 518 LEU cc_start: 0.9263 (mm) cc_final: 0.8981 (mm) REVERT: C 548 LEU cc_start: 0.9100 (mt) cc_final: 0.8523 (tp) REVERT: D 147 GLN cc_start: 0.7882 (tt0) cc_final: 0.6902 (tp-100) REVERT: D 295 TYR cc_start: 0.9284 (t80) cc_final: 0.8618 (t80) REVERT: D 376 TYR cc_start: 0.9017 (m-80) cc_final: 0.8662 (m-80) REVERT: D 449 MET cc_start: 0.8196 (ptt) cc_final: 0.7728 (ppp) REVERT: D 540 PRO cc_start: 0.7486 (Cg_endo) cc_final: 0.6736 (Cg_exo) REVERT: D 613 MET cc_start: 0.8698 (ppp) cc_final: 0.8238 (ppp) REVERT: D 621 GLU cc_start: 0.9091 (tt0) cc_final: 0.8515 (mp0) outliers start: 69 outliers final: 60 residues processed: 260 average time/residue: 0.2264 time to fit residues: 87.3014 Evaluate side-chains 277 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 212 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 84 LEU 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 A residue 153 LYS Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 91 HIS Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain C residue 80 CYS Chi-restraints excluded: chain C residue 105 THR 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 171 SER Chi-restraints excluded: chain C residue 180 PHE Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain C residue 226 GLU 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 408 ILE Chi-restraints excluded: chain C residue 524 THR 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 50 SER Chi-restraints excluded: chain D residue 100 THR 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 166 LEU Chi-restraints excluded: chain D residue 169 ASN 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 290 ASN Chi-restraints excluded: chain D residue 432 CYS Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain D residue 556 TRP 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: 0.3980 chunk 99 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 chunk 137 optimal weight: 7.9990 chunk 118 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 12385 Z= 0.276 Angle : 0.698 13.024 16835 Z= 0.346 Chirality : 0.045 0.224 1896 Planarity : 0.005 0.062 2147 Dihedral : 6.060 54.917 1813 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 19.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 4.97 % Allowed : 24.09 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.22), residues: 1488 helix: 1.07 (0.52), residues: 96 sheet: 0.05 (0.21), residues: 627 loop : -1.55 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 393 HIS 0.007 0.001 HIS C 404 PHE 0.017 0.002 PHE D 234 TYR 0.010 0.001 TYR D 574 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 285 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 218 time to evaluate : 1.569 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: 0.8835 (ttmt) cc_final: 0.8592 (mmmt) REVERT: A 68 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8092 (mp0) REVERT: A 116 MET cc_start: 0.8208 (mmm) cc_final: 0.7973 (mmp) REVERT: A 153 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8087 (ttpp) REVERT: A 186 ARG cc_start: 0.7484 (mmt90) cc_final: 0.7179 (mmt90) REVERT: B 60 TRP cc_start: 0.7752 (m100) cc_final: 0.7032 (m100) REVERT: B 80 LYS cc_start: 0.8762 (pttp) cc_final: 0.7921 (mttt) REVERT: B 148 ASP cc_start: 0.7979 (t0) cc_final: 0.7754 (t0) REVERT: B 208 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8377 (mm) REVERT: B 211 GLU cc_start: 0.8372 (mt-10) cc_final: 0.7886 (mm-30) REVERT: B 246 ASN cc_start: 0.8430 (t0) cc_final: 0.8177 (t0) REVERT: B 269 LYS cc_start: 0.7831 (pttt) cc_final: 0.7141 (ptpp) REVERT: C 50 ASN cc_start: 0.8493 (m-40) cc_final: 0.8034 (m-40) REVERT: C 67 TYR cc_start: 0.8474 (t80) cc_final: 0.7941 (t80) REVERT: C 226 GLU cc_start: 0.6463 (OUTLIER) cc_final: 0.6093 (tp30) REVERT: C 311 LEU cc_start: 0.9375 (pt) cc_final: 0.9143 (pp) REVERT: C 343 LYS cc_start: 0.6543 (OUTLIER) cc_final: 0.6083 (ttpt) REVERT: C 356 LEU cc_start: 0.8778 (tp) cc_final: 0.8518 (tt) REVERT: C 431 GLN cc_start: 0.8882 (mt0) cc_final: 0.8240 (mp10) REVERT: C 517 TRP cc_start: 0.9071 (m-90) cc_final: 0.8371 (m-90) REVERT: C 518 LEU cc_start: 0.9251 (mm) cc_final: 0.8975 (mm) REVERT: D 147 GLN cc_start: 0.7893 (tt0) cc_final: 0.6892 (tp-100) REVERT: D 189 ASP cc_start: 0.9128 (p0) cc_final: 0.8794 (p0) REVERT: D 295 TYR cc_start: 0.9299 (t80) cc_final: 0.8631 (t80) REVERT: D 376 TYR cc_start: 0.9004 (m-80) cc_final: 0.8642 (m-80) REVERT: D 398 TRP cc_start: 0.7586 (t-100) cc_final: 0.7307 (t-100) REVERT: D 449 MET cc_start: 0.8202 (ptt) cc_final: 0.7734 (ppp) REVERT: D 540 PRO cc_start: 0.7451 (Cg_endo) cc_final: 0.6689 (Cg_exo) REVERT: D 613 MET cc_start: 0.8690 (ppp) cc_final: 0.8245 (ppp) REVERT: D 621 GLU cc_start: 0.9111 (tt0) cc_final: 0.8559 (mp0) outliers start: 67 outliers final: 61 residues processed: 258 average time/residue: 0.2192 time to fit residues: 83.7764 Evaluate side-chains 278 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 212 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 76 SER 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 A residue 153 LYS Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 91 HIS Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain C residue 80 CYS Chi-restraints excluded: chain C residue 105 THR 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 171 SER Chi-restraints excluded: chain C residue 180 PHE Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 253 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 524 THR 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 50 SER Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 100 THR 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 166 LEU Chi-restraints excluded: chain D residue 169 ASN 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 290 ASN Chi-restraints excluded: chain D residue 432 CYS Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 556 TRP 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: 3.9990 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 49 optimal weight: 0.2980 chunk 122 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 86 optimal weight: 0.6980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.157453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.103630 restraints weight = 29258.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.107619 restraints weight = 12512.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.110100 restraints weight = 7721.133| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 12385 Z= 0.242 Angle : 0.692 12.846 16835 Z= 0.340 Chirality : 0.045 0.227 1896 Planarity : 0.005 0.061 2147 Dihedral : 5.977 54.970 1813 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 18.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 4.74 % Allowed : 24.68 % Favored : 70.57 % 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: -0.96 (0.22), residues: 1488 helix: 1.12 (0.53), residues: 96 sheet: 0.09 (0.21), residues: 625 loop : -1.53 (0.22), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 393 HIS 0.005 0.001 HIS C 404 PHE 0.019 0.002 PHE C 265 TYR 0.010 0.001 TYR D 574 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: 3050.43 seconds wall clock time: 56 minutes 23.43 seconds (3383.43 seconds total)