Starting phenix.real_space_refine on Thu Jun 12 09:18:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bo2_16138/06_2025/8bo2_16138.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bo2_16138/06_2025/8bo2_16138.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bo2_16138/06_2025/8bo2_16138.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bo2_16138/06_2025/8bo2_16138.map" model { file = "/net/cci-nas-00/data/ceres_data/8bo2_16138/06_2025/8bo2_16138.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bo2_16138/06_2025/8bo2_16138.cif" } resolution = 3.1 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= 0.016 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 41 5.16 5 C 8835 2.51 5 N 2399 2.21 5 O 2762 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14037 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 787, 6229 Classifications: {'peptide': 787} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 757} Chain: "B" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2750 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 11, 'TRANS': 355} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 356 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 6, 'TRANS': 44} Chain: "D" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1722 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 10, 'TRANS': 202} Chain: "E" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 645 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "P" Number of atoms: 2335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2335 Classifications: {'peptide': 302} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 299} Time building chain proxies: 8.14, per 1000 atoms: 0.58 Number of scatterers: 14037 At special positions: 0 Unit cell: (104.16, 138.57, 140.43, 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 41 16.00 O 2762 8.00 N 2399 7.00 C 8835 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 425 " - pdb=" SG CYS P1299 " distance=2.01 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 700 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.22 Conformation dependent library (CDL) restraints added in 1.9 seconds 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3276 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 18 sheets defined 21.0% alpha, 34.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 38 through 46 removed outlier: 3.620A pdb=" N ALA A 42 " --> pdb=" O ALA A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 69 Processing helix chain 'A' and resid 106 through 117 removed outlier: 3.811A pdb=" N LEU A 110 " --> pdb=" O LYS A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 145 removed outlier: 3.605A pdb=" N ILE A 130 " --> pdb=" O ASP A 126 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA A 131 " --> pdb=" O ARG A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 197 removed outlier: 3.906A pdb=" N LEU A 193 " --> pdb=" O THR A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 234 removed outlier: 3.528A pdb=" N LEU A 219 " --> pdb=" O GLN A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 286 removed outlier: 3.600A pdb=" N GLN A 286 " --> pdb=" O ALA A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 315 removed outlier: 3.791A pdb=" N TYR A 315 " --> pdb=" O LEU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 368 removed outlier: 4.224A pdb=" N GLU A 368 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 393 removed outlier: 4.011A pdb=" N GLY A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 removed outlier: 3.577A pdb=" N GLY A 451 " --> pdb=" O ASN A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 552 Processing helix chain 'A' and resid 647 through 651 removed outlier: 3.751A pdb=" N ASN A 651 " --> pdb=" O PHE A 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 45 removed outlier: 3.822A pdb=" N ASP D 45 " --> pdb=" O GLN D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 62 Processing helix chain 'D' and resid 68 through 82 Processing helix chain 'D' and resid 84 through 99 removed outlier: 3.758A pdb=" N ARG D 97 " --> pdb=" O ASP D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 120 Processing helix chain 'D' and resid 130 through 134 removed outlier: 3.928A pdb=" N SER D 133 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 154 Processing helix chain 'D' and resid 159 through 189 removed outlier: 3.550A pdb=" N VAL D 168 " --> pdb=" O THR D 164 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE D 169 " --> pdb=" O LYS D 165 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU D 178 " --> pdb=" O LEU D 174 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR D 186 " --> pdb=" O ALA D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 208 through 224 removed outlier: 3.700A pdb=" N ARG D 212 " --> pdb=" O THR D 208 " (cutoff:3.500A) Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 227 through 239 removed outlier: 3.907A pdb=" N ILE D 237 " --> pdb=" O LYS D 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 45 removed outlier: 3.530A pdb=" N VAL E 43 " --> pdb=" O THR E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 60 Processing helix chain 'P' and resid 1000 through 1024 removed outlier: 4.002A pdb=" N ASP P1014 " --> pdb=" O LEU P1010 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N TYR P1015 " --> pdb=" O PHE P1011 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN P1024 " --> pdb=" O ASN P1020 " (cutoff:3.500A) Processing helix chain 'P' and resid 1025 through 1035 removed outlier: 3.682A pdb=" N ASP P1031 " --> pdb=" O LYS P1027 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU P1032 " --> pdb=" O ARG P1028 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 7.235A pdb=" N HIS A 30 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N VAL A 88 " --> pdb=" O HIS A 30 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N GLU A 32 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N GLU A 90 " --> pdb=" O GLU A 32 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR A 83 " --> pdb=" O ASP A 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 8.286A pdb=" N LEU A 165 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ILE A 97 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N LEU A 167 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N PHE A 99 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N PHE A 169 " --> pdb=" O PHE A 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 181 removed outlier: 4.805A pdb=" N ILE A 177 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N VAL A 256 " --> pdb=" O ILE A 177 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N GLN A 179 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N VAL A 258 " --> pdb=" O GLN A 179 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ASN A 181 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ILE A 260 " --> pdb=" O ASN A 181 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N THR A 261 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ILE A 240 " --> pdb=" O THR A 261 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 267 through 276 removed outlier: 5.936A pdb=" N VAL A 335 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLY A 270 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU A 337 " --> pdb=" O GLY A 270 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER A 274 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 348 through 355 removed outlier: 4.258A pdb=" N VAL A 349 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N VAL A 414 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LYS A 351 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N TYR A 416 " --> pdb=" O LYS A 351 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ARG A 353 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N VAL A 418 " --> pdb=" O ARG A 353 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N GLU A 355 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLU A 420 " --> pdb=" O GLU A 355 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N GLN A 411 " --> pdb=" O ARG A 404 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N ARG A 404 " --> pdb=" O GLN A 411 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ASP A 413 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N THR A 402 " --> pdb=" O ASP A 413 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL A 415 " --> pdb=" O THR A 400 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N THR A 400 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LYS A 417 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL A 398 " --> pdb=" O LYS A 417 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LYS A 419 " --> pdb=" O GLU A 396 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 426 through 427 removed outlier: 3.903A pdb=" N ASN A 506 " --> pdb=" O PHE A 494 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N MET A 768 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE A 791 " --> pdb=" O MET A 768 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY A 437 " --> pdb=" O GLY A 433 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 671 through 674 removed outlier: 4.131A pdb=" N ALA A 672 " --> pdb=" O SER A 702 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 49 through 51 removed outlier: 3.529A pdb=" N THR B 50 " --> pdb=" O VAL B 387 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 66 through 68 Processing sheet with id=AB1, first strand: chain 'B' and resid 115 through 118 Processing sheet with id=AB2, first strand: chain 'B' and resid 156 through 158 Processing sheet with id=AB3, first strand: chain 'B' and resid 201 through 203 removed outlier: 4.102A pdb=" N ALA B 218 " --> pdb=" O TRP B 228 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N TRP B 228 " --> pdb=" O ALA B 218 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 253 through 254 removed outlier: 3.969A pdb=" N TRP B 279 " --> pdb=" O ALA B 269 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 290 through 292 removed outlier: 3.606A pdb=" N VAL B 305 " --> pdb=" O GLN B 319 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TRP B 317 " --> pdb=" O ALA B 307 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N THR B 309 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N THR B 315 " --> pdb=" O THR B 309 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 331 through 333 Processing sheet with id=AB7, first strand: chain 'E' and resid 32 through 35 Processing sheet with id=AB8, first strand: chain 'P' and resid 1159 through 1162 removed outlier: 4.545A pdb=" N VAL P1161 " --> pdb=" O ALA P1165 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N ALA P1165 " --> pdb=" O VAL P1161 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N MET P1258 " --> pdb=" O ALA P1282 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA P1282 " --> pdb=" O MET P1258 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET P1260 " --> pdb=" O LYS P1280 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS P1280 " --> pdb=" O MET P1260 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL P1262 " --> pdb=" O PHE P1278 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL P1272 " --> pdb=" O ILE P1268 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ARG P1273 " --> pdb=" O ARG P1297 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ARG P1297 " --> pdb=" O ARG P1273 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY P1275 " --> pdb=" O ASN P1295 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU P1277 " --> pdb=" O ASN P1293 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA P1291 " --> pdb=" O GLU P1279 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N SER P1281 " --> pdb=" O ASP P1289 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ASP P1289 " --> pdb=" O SER P1281 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N VAL P1288 " --> pdb=" O SER P1051 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N SER P1051 " --> pdb=" O VAL P1288 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU P1078 " --> pdb=" O HIS P1071 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'P' and resid 1182 through 1187 696 hydrogen bonds defined for protein. 1944 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: 5.71 Time building geometry restraints manager: 3.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3004 1.33 - 1.46: 5120 1.46 - 1.58: 6139 1.58 - 1.71: 2 1.71 - 1.83: 78 Bond restraints: 14343 Sorted by residual: bond pdb=" CA ARG B 195 " pdb=" C ARG B 195 " ideal model delta sigma weight residual 1.532 1.493 0.039 9.60e-03 1.09e+04 1.69e+01 bond pdb=" ND1 HIS B 324 " pdb=" CE1 HIS B 324 " ideal model delta sigma weight residual 1.321 1.362 -0.041 1.00e-02 1.00e+04 1.68e+01 bond pdb=" ND1 HIS C 51 " pdb=" CE1 HIS C 51 " ideal model delta sigma weight residual 1.321 1.362 -0.041 1.00e-02 1.00e+04 1.66e+01 bond pdb=" ND1 HIS E 83 " pdb=" CE1 HIS E 83 " ideal model delta sigma weight residual 1.321 1.361 -0.040 1.00e-02 1.00e+04 1.59e+01 bond pdb=" CD ARG B 195 " pdb=" NE ARG B 195 " ideal model delta sigma weight residual 1.458 1.514 -0.056 1.40e-02 5.10e+03 1.59e+01 ... (remaining 14338 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 15300 2.45 - 4.90: 3956 4.90 - 7.34: 200 7.34 - 9.79: 16 9.79 - 12.24: 2 Bond angle restraints: 19474 Sorted by residual: angle pdb=" CA ASP A 683 " pdb=" CB ASP A 683 " pdb=" CG ASP A 683 " ideal model delta sigma weight residual 112.60 104.35 8.25 1.00e+00 1.00e+00 6.81e+01 angle pdb=" CA ASP D 146 " pdb=" CB ASP D 146 " pdb=" CG ASP D 146 " ideal model delta sigma weight residual 112.60 104.81 7.79 1.00e+00 1.00e+00 6.06e+01 angle pdb=" CA ASP D 131 " pdb=" CB ASP D 131 " pdb=" CG ASP D 131 " ideal model delta sigma weight residual 112.60 105.02 7.58 1.00e+00 1.00e+00 5.74e+01 angle pdb=" CA ASP A 762 " pdb=" CB ASP A 762 " pdb=" CG ASP A 762 " ideal model delta sigma weight residual 112.60 118.76 -6.16 1.00e+00 1.00e+00 3.80e+01 angle pdb=" CA ASP A 694 " pdb=" CB ASP A 694 " pdb=" CG ASP A 694 " ideal model delta sigma weight residual 112.60 118.70 -6.10 1.00e+00 1.00e+00 3.72e+01 ... (remaining 19469 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 7722 17.59 - 35.18: 555 35.18 - 52.77: 95 52.77 - 70.37: 45 70.37 - 87.96: 21 Dihedral angle restraints: 8438 sinusoidal: 3274 harmonic: 5164 Sorted by residual: dihedral pdb=" CA VAL A 543 " pdb=" C VAL A 543 " pdb=" N ALA A 544 " pdb=" CA ALA A 544 " ideal model delta harmonic sigma weight residual 180.00 152.11 27.89 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" C ASP A 795 " pdb=" N ASP A 795 " pdb=" CA ASP A 795 " pdb=" CB ASP A 795 " ideal model delta harmonic sigma weight residual -122.60 -135.79 13.19 0 2.50e+00 1.60e-01 2.78e+01 dihedral pdb=" CA PRO A 326 " pdb=" C PRO A 326 " pdb=" N GLU A 327 " pdb=" CA GLU A 327 " ideal model delta harmonic sigma weight residual 180.00 154.52 25.48 0 5.00e+00 4.00e-02 2.60e+01 ... (remaining 8435 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1413 0.097 - 0.195: 550 0.195 - 0.292: 113 0.292 - 0.389: 24 0.389 - 0.487: 8 Chirality restraints: 2108 Sorted by residual: chirality pdb=" CA ASP A 795 " pdb=" N ASP A 795 " pdb=" C ASP A 795 " pdb=" CB ASP A 795 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.92e+00 chirality pdb=" CA ASP B 159 " pdb=" N ASP B 159 " pdb=" C ASP B 159 " pdb=" CB ASP B 159 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.43 2.00e-01 2.50e+01 4.52e+00 chirality pdb=" CA THR E 94 " pdb=" N THR E 94 " pdb=" C THR E 94 " pdb=" CB THR E 94 " both_signs ideal model delta sigma weight residual False 2.53 2.12 0.41 2.00e-01 2.50e+01 4.21e+00 ... (remaining 2105 not shown) Planarity restraints: 2566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR P1298 " 0.245 2.00e-02 2.50e+03 1.44e-01 4.16e+02 pdb=" CG TYR P1298 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR P1298 " -0.157 2.00e-02 2.50e+03 pdb=" CD2 TYR P1298 " -0.106 2.00e-02 2.50e+03 pdb=" CE1 TYR P1298 " -0.083 2.00e-02 2.50e+03 pdb=" CE2 TYR P1298 " -0.131 2.00e-02 2.50e+03 pdb=" CZ TYR P1298 " 0.042 2.00e-02 2.50e+03 pdb=" OH TYR P1298 " 0.210 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 230 " 0.144 2.00e-02 2.50e+03 1.10e-01 2.40e+02 pdb=" CG TYR A 230 " -0.004 2.00e-02 2.50e+03 pdb=" CD1 TYR A 230 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR A 230 " -0.060 2.00e-02 2.50e+03 pdb=" CE1 TYR A 230 " -0.113 2.00e-02 2.50e+03 pdb=" CE2 TYR A 230 " -0.083 2.00e-02 2.50e+03 pdb=" CZ TYR A 230 " -0.072 2.00e-02 2.50e+03 pdb=" OH TYR A 230 " 0.215 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 222 " 0.130 2.00e-02 2.50e+03 7.55e-02 1.14e+02 pdb=" CG TYR D 222 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR D 222 " -0.056 2.00e-02 2.50e+03 pdb=" CD2 TYR D 222 " -0.052 2.00e-02 2.50e+03 pdb=" CE1 TYR D 222 " -0.048 2.00e-02 2.50e+03 pdb=" CE2 TYR D 222 " -0.048 2.00e-02 2.50e+03 pdb=" CZ TYR D 222 " -0.025 2.00e-02 2.50e+03 pdb=" OH TYR D 222 " 0.129 2.00e-02 2.50e+03 ... (remaining 2563 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 6880 2.98 - 3.46: 14041 3.46 - 3.94: 23547 3.94 - 4.42: 26197 4.42 - 4.90: 43793 Nonbonded interactions: 114458 Sorted by model distance: nonbonded pdb=" OD2 ASP P1232 " pdb=" NZ LYS P1254 " model vdw 2.505 3.120 nonbonded pdb=" OH TYR P1118 " pdb=" OE1 GLU P1154 " model vdw 2.507 3.040 nonbonded pdb=" OH TYR A 468 " pdb=" OE1 GLU A 470 " model vdw 2.534 3.040 nonbonded pdb=" O LEU B 110 " pdb=" N GLU B 127 " model vdw 2.535 3.120 nonbonded pdb=" NZ LYS A 106 " pdb=" OE1 GLU P1072 " model vdw 2.541 3.120 ... (remaining 114453 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 34.590 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.070 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5137 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 : 0.017 0.057 14345 Z= 1.069 Angle : 1.935 12.238 19478 Z= 1.344 Chirality : 0.108 0.487 2108 Planarity : 0.015 0.157 2566 Dihedral : 14.135 87.956 5156 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.70 % Favored : 93.24 % Rotamer: Outliers : 0.47 % Allowed : 4.37 % Favored : 95.16 % Cbeta Deviations : 0.61 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.19), residues: 1791 helix: 0.84 (0.28), residues: 343 sheet: 0.35 (0.20), residues: 641 loop : -1.72 (0.20), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.100 0.021 TRP B 228 HIS 0.017 0.005 HIS B 64 PHE 0.082 0.014 PHE D 144 TYR 0.245 0.024 TYR P1298 ARG 0.006 0.001 ARG A 237 Details of bonding type rmsd hydrogen bonds : bond 0.12629 ( 696) hydrogen bonds : angle 6.62418 ( 1944) SS BOND : bond 0.01635 ( 2) SS BOND : angle 2.69747 ( 4) covalent geometry : bond 0.01678 (14343) covalent geometry : angle 1.93525 (19474) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 232 time to evaluate : 1.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 278 MET cc_start: 0.4842 (mmm) cc_final: 0.4214 (mmp) REVERT: D 109 MET cc_start: 0.4884 (mtp) cc_final: 0.4522 (mtp) outliers start: 7 outliers final: 3 residues processed: 238 average time/residue: 0.2575 time to fit residues: 89.8638 Evaluate side-chains 168 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 165 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain P residue 1045 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 5.9990 chunk 134 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 53 optimal weight: 8.9990 chunk 84 optimal weight: 7.9990 chunk 103 optimal weight: 7.9990 chunk 161 optimal weight: 8.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN A 185 ASN A 239 ASN ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN B 168 ASN ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN D 104 ASN D 116 ASN ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 ASN P1064 GLN P1071 HIS P1128 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.145253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.096788 restraints weight = 32290.975| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 4.00 r_work: 0.3463 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 14345 Z= 0.198 Angle : 0.636 6.893 19478 Z= 0.342 Chirality : 0.046 0.154 2108 Planarity : 0.004 0.046 2566 Dihedral : 5.568 52.963 1981 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.36 % Favored : 94.47 % Rotamer: Outliers : 1.41 % Allowed : 9.75 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.19), residues: 1791 helix: 0.87 (0.28), residues: 348 sheet: 0.27 (0.20), residues: 648 loop : -1.50 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 810 HIS 0.006 0.001 HIS B 324 PHE 0.017 0.002 PHE A 197 TYR 0.021 0.002 TYR P1060 ARG 0.007 0.001 ARG A 634 Details of bonding type rmsd hydrogen bonds : bond 0.03783 ( 696) hydrogen bonds : angle 5.58736 ( 1944) SS BOND : bond 0.00104 ( 2) SS BOND : angle 0.22624 ( 4) covalent geometry : bond 0.00439 (14343) covalent geometry : angle 0.63645 (19474) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 185 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 512 ASP cc_start: 0.8424 (p0) cc_final: 0.8193 (p0) REVERT: B 73 TYR cc_start: 0.7400 (m-80) cc_final: 0.7119 (m-80) REVERT: C 81 ASP cc_start: 0.8518 (t0) cc_final: 0.7788 (p0) REVERT: D 207 ASP cc_start: 0.8632 (OUTLIER) cc_final: 0.8296 (m-30) REVERT: E 47 ARG cc_start: 0.6864 (pmt-80) cc_final: 0.6417 (ptm-80) REVERT: E 48 VAL cc_start: 0.7836 (t) cc_final: 0.7328 (p) REVERT: P 1029 MET cc_start: 0.8978 (mpp) cc_final: 0.8479 (mpp) REVERT: P 1035 ILE cc_start: 0.9165 (mm) cc_final: 0.8886 (mp) REVERT: P 1046 MET cc_start: 0.7678 (tmm) cc_final: 0.7475 (tpt) REVERT: P 1082 PHE cc_start: 0.9218 (p90) cc_final: 0.8949 (p90) REVERT: P 1127 HIS cc_start: 0.7765 (m170) cc_final: 0.6956 (m170) outliers start: 21 outliers final: 13 residues processed: 202 average time/residue: 0.2432 time to fit residues: 75.5808 Evaluate side-chains 177 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 163 time to evaluate : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain P residue 1058 ASP Chi-restraints excluded: chain P residue 1065 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 102 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 17 optimal weight: 0.0270 chunk 111 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 chunk 100 optimal weight: 0.0970 chunk 107 optimal weight: 20.0000 chunk 27 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 13 optimal weight: 0.0770 overall best weight: 2.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN B 334 ASN ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1071 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.143592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.095427 restraints weight = 32407.283| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 3.99 r_work: 0.3435 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 14345 Z= 0.213 Angle : 0.623 8.780 19478 Z= 0.334 Chirality : 0.045 0.159 2108 Planarity : 0.004 0.039 2566 Dihedral : 5.426 59.424 1977 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.75 % Favored : 94.08 % Rotamer: Outliers : 2.02 % Allowed : 11.70 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.19), residues: 1791 helix: 0.76 (0.28), residues: 347 sheet: 0.16 (0.20), residues: 638 loop : -1.53 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 810 HIS 0.006 0.001 HIS B 324 PHE 0.019 0.002 PHE A 197 TYR 0.035 0.002 TYR A 255 ARG 0.004 0.001 ARG A 367 Details of bonding type rmsd hydrogen bonds : bond 0.03601 ( 696) hydrogen bonds : angle 5.40600 ( 1944) SS BOND : bond 0.00167 ( 2) SS BOND : angle 0.44826 ( 4) covalent geometry : bond 0.00470 (14343) covalent geometry : angle 0.62326 (19474) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 179 time to evaluate : 1.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 ASP cc_start: 0.9002 (m-30) cc_final: 0.8646 (p0) REVERT: A 512 ASP cc_start: 0.8466 (p0) cc_final: 0.8207 (p0) REVERT: A 768 MET cc_start: 0.7766 (tmm) cc_final: 0.7364 (tmm) REVERT: B 73 TYR cc_start: 0.7669 (m-80) cc_final: 0.7300 (m-80) REVERT: C 49 GLU cc_start: 0.8692 (tp30) cc_final: 0.8094 (tp30) REVERT: C 81 ASP cc_start: 0.8660 (t0) cc_final: 0.7986 (p0) REVERT: D 94 ARG cc_start: 0.8968 (ptm-80) cc_final: 0.8496 (ptt90) REVERT: D 97 ARG cc_start: 0.9143 (ttp80) cc_final: 0.8925 (ptt90) REVERT: D 165 LYS cc_start: 0.9023 (tttp) cc_final: 0.8714 (tttp) REVERT: D 207 ASP cc_start: 0.8453 (OUTLIER) cc_final: 0.8225 (m-30) REVERT: E 48 VAL cc_start: 0.8112 (t) cc_final: 0.7668 (p) REVERT: P 1029 MET cc_start: 0.9061 (mpp) cc_final: 0.8580 (mpp) REVERT: P 1035 ILE cc_start: 0.9213 (mm) cc_final: 0.8939 (mp) REVERT: P 1046 MET cc_start: 0.7645 (tmm) cc_final: 0.7358 (tpt) outliers start: 30 outliers final: 19 residues processed: 199 average time/residue: 0.2461 time to fit residues: 74.1299 Evaluate side-chains 179 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain P residue 1058 ASP Chi-restraints excluded: chain P residue 1065 VAL Chi-restraints excluded: chain P residue 1173 LEU Chi-restraints excluded: chain P residue 1268 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 70 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 97 optimal weight: 6.9990 chunk 149 optimal weight: 7.9990 chunk 151 optimal weight: 8.9990 chunk 109 optimal weight: 9.9990 chunk 157 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 18 optimal weight: 30.0000 chunk 117 optimal weight: 4.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN A 664 GLN ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.139897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.090222 restraints weight = 32255.930| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 4.10 r_work: 0.3336 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 14345 Z= 0.318 Angle : 0.695 7.049 19478 Z= 0.374 Chirality : 0.047 0.274 2108 Planarity : 0.005 0.057 2566 Dihedral : 5.654 49.051 1977 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.81 % Favored : 93.02 % Rotamer: Outliers : 2.62 % Allowed : 14.19 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.19), residues: 1791 helix: 0.54 (0.27), residues: 345 sheet: -0.07 (0.21), residues: 613 loop : -1.62 (0.20), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 93 HIS 0.006 0.001 HIS B 324 PHE 0.019 0.002 PHE A 197 TYR 0.033 0.002 TYR B 333 ARG 0.007 0.001 ARG E 47 Details of bonding type rmsd hydrogen bonds : bond 0.03890 ( 696) hydrogen bonds : angle 5.62431 ( 1944) SS BOND : bond 0.00112 ( 2) SS BOND : angle 0.37779 ( 4) covalent geometry : bond 0.00698 (14343) covalent geometry : angle 0.69498 (19474) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 176 time to evaluate : 1.457 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 ASP cc_start: 0.9091 (m-30) cc_final: 0.8750 (p0) REVERT: A 512 ASP cc_start: 0.8513 (p0) cc_final: 0.8247 (p0) REVERT: A 545 MET cc_start: 0.9233 (ptm) cc_final: 0.8904 (ptp) REVERT: A 737 PHE cc_start: 0.8472 (t80) cc_final: 0.8182 (t80) REVERT: A 768 MET cc_start: 0.8189 (tmm) cc_final: 0.7758 (tmm) REVERT: B 73 TYR cc_start: 0.8050 (m-80) cc_final: 0.7836 (m-80) REVERT: B 189 MET cc_start: 0.7232 (mmm) cc_final: 0.6949 (mpp) REVERT: C 49 GLU cc_start: 0.8697 (tp30) cc_final: 0.8271 (tp30) REVERT: C 81 ASP cc_start: 0.8666 (OUTLIER) cc_final: 0.7856 (p0) REVERT: D 97 ARG cc_start: 0.9184 (ttp80) cc_final: 0.8916 (ptt90) REVERT: D 165 LYS cc_start: 0.9084 (tttp) cc_final: 0.8871 (tttp) REVERT: P 1029 MET cc_start: 0.9120 (mpp) cc_final: 0.8622 (mpp) REVERT: P 1035 ILE cc_start: 0.9237 (mm) cc_final: 0.8974 (mp) REVERT: P 1230 GLN cc_start: 0.9454 (pm20) cc_final: 0.9084 (tp-100) REVERT: P 1277 GLU cc_start: 0.8721 (tp30) cc_final: 0.8410 (tp30) outliers start: 39 outliers final: 30 residues processed: 203 average time/residue: 0.2345 time to fit residues: 72.9003 Evaluate side-chains 177 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain P residue 1058 ASP Chi-restraints excluded: chain P residue 1065 VAL Chi-restraints excluded: chain P residue 1173 LEU Chi-restraints excluded: chain P residue 1174 VAL Chi-restraints excluded: chain P residue 1268 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 4 optimal weight: 40.0000 chunk 24 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 130 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 174 optimal weight: 7.9990 chunk 119 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 151 optimal weight: 20.0000 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 GLN B 276 GLN ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1071 HIS P1271 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.138620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.089151 restraints weight = 32393.410| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 4.03 r_work: 0.3318 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 14345 Z= 0.307 Angle : 0.685 7.668 19478 Z= 0.367 Chirality : 0.047 0.273 2108 Planarity : 0.004 0.048 2566 Dihedral : 5.665 51.508 1977 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.76 % Favored : 93.08 % Rotamer: Outliers : 2.82 % Allowed : 15.60 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.19), residues: 1791 helix: 0.41 (0.27), residues: 354 sheet: -0.16 (0.21), residues: 630 loop : -1.67 (0.21), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 93 HIS 0.006 0.001 HIS B 324 PHE 0.037 0.002 PHE P1296 TYR 0.025 0.002 TYR A 255 ARG 0.008 0.001 ARG A 421 Details of bonding type rmsd hydrogen bonds : bond 0.03747 ( 696) hydrogen bonds : angle 5.55685 ( 1944) SS BOND : bond 0.00151 ( 2) SS BOND : angle 0.30530 ( 4) covalent geometry : bond 0.00675 (14343) covalent geometry : angle 0.68526 (19474) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 166 time to evaluate : 1.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8343 (m-80) cc_final: 0.8124 (m-80) REVERT: A 191 ASP cc_start: 0.9136 (m-30) cc_final: 0.8778 (p0) REVERT: A 512 ASP cc_start: 0.8512 (p0) cc_final: 0.8254 (p0) REVERT: A 768 MET cc_start: 0.8311 (tmm) cc_final: 0.7515 (tmm) REVERT: B 192 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7954 (tt) REVERT: C 49 GLU cc_start: 0.8600 (tp30) cc_final: 0.8388 (tp30) REVERT: C 56 MET cc_start: 0.8841 (ptm) cc_final: 0.8550 (ptm) REVERT: D 94 ARG cc_start: 0.9028 (ptm-80) cc_final: 0.8339 (ptt90) REVERT: D 165 LYS cc_start: 0.9081 (tttp) cc_final: 0.8869 (ttmm) REVERT: P 1029 MET cc_start: 0.9148 (mpp) cc_final: 0.8805 (mpp) REVERT: P 1035 ILE cc_start: 0.9250 (mm) cc_final: 0.8995 (mp) REVERT: P 1046 MET cc_start: 0.7611 (tpt) cc_final: 0.7249 (tpt) REVERT: P 1082 PHE cc_start: 0.9252 (p90) cc_final: 0.9009 (p90) REVERT: P 1230 GLN cc_start: 0.9451 (pm20) cc_final: 0.9145 (tp-100) REVERT: P 1277 GLU cc_start: 0.8802 (tp30) cc_final: 0.8399 (tp30) outliers start: 42 outliers final: 31 residues processed: 196 average time/residue: 0.2446 time to fit residues: 72.9799 Evaluate side-chains 179 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 147 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain P residue 1065 VAL Chi-restraints excluded: chain P residue 1173 LEU Chi-restraints excluded: chain P residue 1268 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 42 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 169 optimal weight: 40.0000 chunk 71 optimal weight: 8.9990 chunk 61 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 102 optimal weight: 8.9990 chunk 15 optimal weight: 0.9990 chunk 70 optimal weight: 0.2980 overall best weight: 1.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 GLN ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1236 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.142305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.093548 restraints weight = 32456.017| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 4.09 r_work: 0.3404 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 14345 Z= 0.135 Angle : 0.604 7.738 19478 Z= 0.319 Chirality : 0.045 0.181 2108 Planarity : 0.004 0.036 2566 Dihedral : 5.265 53.796 1977 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.53 % Favored : 94.30 % Rotamer: Outliers : 2.15 % Allowed : 16.54 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.20), residues: 1791 helix: 0.82 (0.28), residues: 356 sheet: -0.05 (0.21), residues: 628 loop : -1.57 (0.21), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 810 HIS 0.004 0.001 HIS B 324 PHE 0.022 0.001 PHE A 426 TYR 0.022 0.001 TYR A 255 ARG 0.006 0.000 ARG D 97 Details of bonding type rmsd hydrogen bonds : bond 0.03224 ( 696) hydrogen bonds : angle 5.20448 ( 1944) SS BOND : bond 0.00134 ( 2) SS BOND : angle 0.10096 ( 4) covalent geometry : bond 0.00293 (14343) covalent geometry : angle 0.60424 (19474) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 176 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 ASP cc_start: 0.9105 (m-30) cc_final: 0.8722 (p0) REVERT: A 465 TYR cc_start: 0.8390 (p90) cc_final: 0.8186 (p90) REVERT: A 512 ASP cc_start: 0.8416 (p0) cc_final: 0.8180 (p0) REVERT: A 634 ARG cc_start: 0.8491 (mtp-110) cc_final: 0.8083 (mtp-110) REVERT: A 768 MET cc_start: 0.8295 (tmm) cc_final: 0.7458 (tmm) REVERT: C 56 MET cc_start: 0.8860 (ptm) cc_final: 0.8550 (ptm) REVERT: D 94 ARG cc_start: 0.8962 (ptm-80) cc_final: 0.8377 (ptt90) REVERT: D 165 LYS cc_start: 0.9055 (tttp) cc_final: 0.8818 (ttmm) REVERT: E 79 GLN cc_start: 0.9114 (OUTLIER) cc_final: 0.8679 (mp10) REVERT: P 1035 ILE cc_start: 0.9221 (mm) cc_final: 0.8958 (mp) REVERT: P 1046 MET cc_start: 0.7715 (tpt) cc_final: 0.7460 (tpt) REVERT: P 1082 PHE cc_start: 0.9272 (p90) cc_final: 0.9009 (p90) REVERT: P 1230 GLN cc_start: 0.9396 (pm20) cc_final: 0.9131 (tp-100) REVERT: P 1277 GLU cc_start: 0.8708 (tp30) cc_final: 0.8257 (tp30) outliers start: 32 outliers final: 19 residues processed: 199 average time/residue: 0.2586 time to fit residues: 78.1754 Evaluate side-chains 175 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain P residue 1065 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 5 optimal weight: 30.0000 chunk 145 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 164 optimal weight: 30.0000 chunk 38 optimal weight: 0.8980 chunk 67 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 160 optimal weight: 30.0000 chunk 108 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 125 optimal weight: 0.8980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1191 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.142369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.094362 restraints weight = 32194.169| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 3.94 r_work: 0.3429 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14345 Z= 0.127 Angle : 0.602 8.451 19478 Z= 0.313 Chirality : 0.044 0.210 2108 Planarity : 0.004 0.042 2566 Dihedral : 5.063 53.610 1977 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.19 % Favored : 94.64 % Rotamer: Outliers : 1.82 % Allowed : 17.75 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.20), residues: 1791 helix: 0.93 (0.28), residues: 357 sheet: 0.01 (0.21), residues: 632 loop : -1.48 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 93 HIS 0.004 0.001 HIS B 324 PHE 0.020 0.001 PHE A 426 TYR 0.021 0.001 TYR B 333 ARG 0.005 0.000 ARG E 47 Details of bonding type rmsd hydrogen bonds : bond 0.03118 ( 696) hydrogen bonds : angle 5.05816 ( 1944) SS BOND : bond 0.00149 ( 2) SS BOND : angle 0.17727 ( 4) covalent geometry : bond 0.00280 (14343) covalent geometry : angle 0.60214 (19474) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 ASP cc_start: 0.9048 (m-30) cc_final: 0.8703 (p0) REVERT: A 410 ASP cc_start: 0.7906 (OUTLIER) cc_final: 0.7685 (t0) REVERT: A 512 ASP cc_start: 0.8424 (p0) cc_final: 0.8195 (p0) REVERT: A 634 ARG cc_start: 0.8507 (mtp-110) cc_final: 0.8096 (mtp-110) REVERT: A 768 MET cc_start: 0.8296 (tmm) cc_final: 0.7961 (tmm) REVERT: C 56 MET cc_start: 0.8861 (ptm) cc_final: 0.8550 (ptm) REVERT: D 33 ASN cc_start: 0.9121 (m-40) cc_final: 0.8883 (p0) REVERT: D 94 ARG cc_start: 0.8925 (ptm-80) cc_final: 0.8366 (ptt90) REVERT: D 97 ARG cc_start: 0.9089 (ttp80) cc_final: 0.8883 (ptt90) REVERT: D 165 LYS cc_start: 0.9049 (tttp) cc_final: 0.8777 (ttmm) REVERT: E 57 TYR cc_start: 0.9128 (t80) cc_final: 0.8882 (t80) REVERT: E 79 GLN cc_start: 0.9119 (OUTLIER) cc_final: 0.8700 (mp10) REVERT: P 1029 MET cc_start: 0.9116 (mmm) cc_final: 0.8429 (mpp) REVERT: P 1035 ILE cc_start: 0.9213 (mm) cc_final: 0.8955 (mp) REVERT: P 1046 MET cc_start: 0.7734 (tpt) cc_final: 0.7511 (tpt) REVERT: P 1082 PHE cc_start: 0.9267 (p90) cc_final: 0.8993 (p90) REVERT: P 1277 GLU cc_start: 0.8661 (tp30) cc_final: 0.8428 (tp30) outliers start: 27 outliers final: 20 residues processed: 186 average time/residue: 0.2436 time to fit residues: 68.8294 Evaluate side-chains 177 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 59 LEU Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain P residue 1065 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 89 optimal weight: 3.9990 chunk 22 optimal weight: 0.2980 chunk 10 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 153 optimal weight: 50.0000 chunk 145 optimal weight: 2.9990 chunk 118 optimal weight: 7.9990 chunk 173 optimal weight: 0.7980 chunk 18 optimal weight: 0.0020 chunk 16 optimal weight: 7.9990 chunk 164 optimal weight: 30.0000 overall best weight: 1.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 GLN ** 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 = 0.4395 r_free = 0.4395 target = 0.141577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.092932 restraints weight = 32141.716| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 4.04 r_work: 0.3391 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14345 Z= 0.156 Angle : 0.623 10.567 19478 Z= 0.322 Chirality : 0.045 0.171 2108 Planarity : 0.004 0.037 2566 Dihedral : 5.044 53.144 1977 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.14 % Favored : 93.69 % Rotamer: Outliers : 2.08 % Allowed : 17.89 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.20), residues: 1791 helix: 0.93 (0.28), residues: 357 sheet: -0.05 (0.20), residues: 636 loop : -1.49 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 810 HIS 0.004 0.001 HIS B 324 PHE 0.019 0.001 PHE A 426 TYR 0.020 0.001 TYR B 333 ARG 0.004 0.000 ARG D 173 Details of bonding type rmsd hydrogen bonds : bond 0.03200 ( 696) hydrogen bonds : angle 5.00857 ( 1944) SS BOND : bond 0.00136 ( 2) SS BOND : angle 0.17051 ( 4) covalent geometry : bond 0.00343 (14343) covalent geometry : angle 0.62303 (19474) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 159 time to evaluate : 1.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 TYR cc_start: 0.7672 (m-80) cc_final: 0.7456 (m-10) REVERT: A 191 ASP cc_start: 0.9105 (m-30) cc_final: 0.8733 (p0) REVERT: A 362 ASP cc_start: 0.9000 (OUTLIER) cc_final: 0.8609 (t70) REVERT: A 512 ASP cc_start: 0.8465 (p0) cc_final: 0.8235 (p0) REVERT: A 634 ARG cc_start: 0.8567 (mtp-110) cc_final: 0.8128 (mtp-110) REVERT: A 768 MET cc_start: 0.8421 (tmm) cc_final: 0.8052 (tmm) REVERT: B 197 GLU cc_start: 0.7369 (mt-10) cc_final: 0.6877 (mt-10) REVERT: C 56 MET cc_start: 0.8888 (ptm) cc_final: 0.8620 (ptm) REVERT: D 33 ASN cc_start: 0.9103 (m-40) cc_final: 0.8863 (p0) REVERT: D 94 ARG cc_start: 0.8983 (ptm-80) cc_final: 0.8440 (ptt90) REVERT: D 165 LYS cc_start: 0.9053 (tttp) cc_final: 0.8771 (ttmm) REVERT: E 79 GLN cc_start: 0.9162 (OUTLIER) cc_final: 0.8721 (mp10) REVERT: P 1046 MET cc_start: 0.7754 (tpt) cc_final: 0.7504 (tpt) REVERT: P 1082 PHE cc_start: 0.9267 (p90) cc_final: 0.8997 (p90) REVERT: P 1166 TRP cc_start: 0.7851 (p-90) cc_final: 0.7510 (p-90) REVERT: P 1230 GLN cc_start: 0.9364 (pm20) cc_final: 0.9130 (tp-100) REVERT: P 1277 GLU cc_start: 0.8725 (tp30) cc_final: 0.8505 (tp30) outliers start: 31 outliers final: 18 residues processed: 182 average time/residue: 0.2466 time to fit residues: 68.4537 Evaluate side-chains 171 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 151 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain P residue 1058 ASP Chi-restraints excluded: chain P residue 1065 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 133 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 59 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 72 optimal weight: 7.9990 chunk 156 optimal weight: 20.0000 chunk 15 optimal weight: 4.9990 chunk 134 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 chunk 140 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 GLN ** 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 = 0.4414 r_free = 0.4414 target = 0.142759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.094067 restraints weight = 32068.711| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 4.08 r_work: 0.3414 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14345 Z= 0.131 Angle : 0.625 11.637 19478 Z= 0.318 Chirality : 0.045 0.281 2108 Planarity : 0.003 0.040 2566 Dihedral : 4.949 54.096 1977 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.53 % Favored : 94.30 % Rotamer: Outliers : 1.68 % Allowed : 18.49 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.20), residues: 1791 helix: 0.99 (0.28), residues: 356 sheet: -0.03 (0.20), residues: 633 loop : -1.46 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP P1166 HIS 0.003 0.001 HIS B 324 PHE 0.018 0.001 PHE A 426 TYR 0.020 0.001 TYR B 333 ARG 0.010 0.000 ARG D 97 Details of bonding type rmsd hydrogen bonds : bond 0.03073 ( 696) hydrogen bonds : angle 4.92140 ( 1944) SS BOND : bond 0.00118 ( 2) SS BOND : angle 0.16456 ( 4) covalent geometry : bond 0.00288 (14343) covalent geometry : angle 0.62472 (19474) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 163 time to evaluate : 1.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 ASP cc_start: 0.9100 (m-30) cc_final: 0.8721 (p0) REVERT: A 362 ASP cc_start: 0.8957 (OUTLIER) cc_final: 0.8598 (t70) REVERT: A 410 ASP cc_start: 0.7855 (OUTLIER) cc_final: 0.7583 (t0) REVERT: A 512 ASP cc_start: 0.8443 (p0) cc_final: 0.8228 (p0) REVERT: A 634 ARG cc_start: 0.8566 (mtp-110) cc_final: 0.8164 (mtp-110) REVERT: A 768 MET cc_start: 0.8349 (tmm) cc_final: 0.7979 (tmm) REVERT: B 197 GLU cc_start: 0.7367 (mt-10) cc_final: 0.6915 (mt-10) REVERT: C 56 MET cc_start: 0.8873 (ptm) cc_final: 0.8618 (ptm) REVERT: D 33 ASN cc_start: 0.9110 (m-40) cc_final: 0.8892 (p0) REVERT: D 94 ARG cc_start: 0.8982 (ptm-80) cc_final: 0.8337 (ptt90) REVERT: D 165 LYS cc_start: 0.9027 (tttp) cc_final: 0.8734 (ttmm) REVERT: E 79 GLN cc_start: 0.9146 (OUTLIER) cc_final: 0.8830 (mp10) REVERT: P 1046 MET cc_start: 0.7756 (tpt) cc_final: 0.7510 (tpt) REVERT: P 1082 PHE cc_start: 0.9227 (p90) cc_final: 0.8919 (p90) REVERT: P 1230 GLN cc_start: 0.9386 (pm20) cc_final: 0.9107 (tp-100) REVERT: P 1258 MET cc_start: 0.8510 (ppp) cc_final: 0.7887 (tmm) REVERT: P 1259 LEU cc_start: 0.9285 (mt) cc_final: 0.8632 (mt) REVERT: P 1277 GLU cc_start: 0.8703 (tp30) cc_final: 0.8475 (tp30) outliers start: 25 outliers final: 19 residues processed: 182 average time/residue: 0.2872 time to fit residues: 82.1195 Evaluate side-chains 180 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 158 time to evaluate : 1.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain P residue 1065 VAL Chi-restraints excluded: chain P residue 1268 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 91 optimal weight: 0.9980 chunk 113 optimal weight: 20.0000 chunk 73 optimal weight: 8.9990 chunk 151 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 139 optimal weight: 0.0570 chunk 51 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 chunk 52 optimal weight: 0.9990 overall best weight: 1.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 GLN ** 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 = 0.4398 r_free = 0.4398 target = 0.141631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.093060 restraints weight = 32194.843| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 4.04 r_work: 0.3413 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14345 Z= 0.145 Angle : 0.638 11.901 19478 Z= 0.326 Chirality : 0.045 0.281 2108 Planarity : 0.004 0.038 2566 Dihedral : 4.949 53.638 1977 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.86 % Favored : 93.97 % Rotamer: Outliers : 1.68 % Allowed : 18.49 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.20), residues: 1791 helix: 0.96 (0.28), residues: 357 sheet: -0.01 (0.20), residues: 625 loop : -1.49 (0.22), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 143 HIS 0.003 0.001 HIS B 324 PHE 0.018 0.001 PHE A 426 TYR 0.020 0.001 TYR B 333 ARG 0.011 0.000 ARG D 97 Details of bonding type rmsd hydrogen bonds : bond 0.03162 ( 696) hydrogen bonds : angle 4.96438 ( 1944) SS BOND : bond 0.00120 ( 2) SS BOND : angle 0.12520 ( 4) covalent geometry : bond 0.00321 (14343) covalent geometry : angle 0.63822 (19474) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 1.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 ASP cc_start: 0.9030 (m-30) cc_final: 0.8684 (p0) REVERT: A 362 ASP cc_start: 0.8941 (OUTLIER) cc_final: 0.8536 (t70) REVERT: A 512 ASP cc_start: 0.8446 (p0) cc_final: 0.8220 (p0) REVERT: A 634 ARG cc_start: 0.8545 (mtp-110) cc_final: 0.8138 (mtp-110) REVERT: A 768 MET cc_start: 0.8382 (tmm) cc_final: 0.8014 (tmm) REVERT: D 33 ASN cc_start: 0.9126 (m-40) cc_final: 0.8904 (p0) REVERT: D 74 ASP cc_start: 0.9012 (m-30) cc_final: 0.8699 (m-30) REVERT: D 94 ARG cc_start: 0.8904 (ptm-80) cc_final: 0.8303 (ptt90) REVERT: D 152 ARG cc_start: 0.8377 (ptp90) cc_final: 0.8103 (ptp90) REVERT: D 165 LYS cc_start: 0.9044 (tttp) cc_final: 0.8762 (ttmm) REVERT: E 79 GLN cc_start: 0.9117 (OUTLIER) cc_final: 0.8728 (mp10) REVERT: P 1046 MET cc_start: 0.7709 (tpt) cc_final: 0.7475 (tpt) REVERT: P 1082 PHE cc_start: 0.9276 (p90) cc_final: 0.8959 (p90) REVERT: P 1230 GLN cc_start: 0.9363 (pm20) cc_final: 0.9069 (tp-100) REVERT: P 1259 LEU cc_start: 0.9294 (mt) cc_final: 0.8509 (mt) REVERT: P 1277 GLU cc_start: 0.8649 (tp30) cc_final: 0.8445 (tp30) outliers start: 25 outliers final: 21 residues processed: 177 average time/residue: 0.2560 time to fit residues: 68.9240 Evaluate side-chains 180 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 157 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain P residue 1065 VAL Chi-restraints excluded: chain P residue 1174 VAL Chi-restraints excluded: chain P residue 1268 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 163 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 96 optimal weight: 8.9990 chunk 123 optimal weight: 2.9990 chunk 119 optimal weight: 9.9990 chunk 73 optimal weight: 5.9990 chunk 114 optimal weight: 0.2980 chunk 151 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 153 optimal weight: 50.0000 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 GLN ** 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 = 0.4373 r_free = 0.4373 target = 0.139641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.090065 restraints weight = 32394.216| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 4.07 r_work: 0.3339 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 14345 Z= 0.207 Angle : 0.668 11.931 19478 Z= 0.344 Chirality : 0.046 0.262 2108 Planarity : 0.004 0.039 2566 Dihedral : 5.171 53.024 1977 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.53 % Favored : 93.30 % Rotamer: Outliers : 1.82 % Allowed : 18.36 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.20), residues: 1791 helix: 0.80 (0.28), residues: 356 sheet: -0.06 (0.20), residues: 628 loop : -1.56 (0.21), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 93 HIS 0.004 0.001 HIS B 347 PHE 0.018 0.002 PHE P1018 TYR 0.021 0.002 TYR B 333 ARG 0.005 0.001 ARG E 47 Details of bonding type rmsd hydrogen bonds : bond 0.03383 ( 696) hydrogen bonds : angle 5.12332 ( 1944) SS BOND : bond 0.00132 ( 2) SS BOND : angle 0.17346 ( 4) covalent geometry : bond 0.00456 (14343) covalent geometry : angle 0.66764 (19474) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11238.00 seconds wall clock time: 196 minutes 32.76 seconds (11792.76 seconds total)