Starting phenix.real_space_refine on Sat Aug 23 17:57:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bo2_16138/08_2025/8bo2_16138.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bo2_16138/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8bo2_16138/08_2025/8bo2_16138.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bo2_16138/08_2025/8bo2_16138.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8bo2_16138/08_2025/8bo2_16138.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bo2_16138/08_2025/8bo2_16138.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ASP:plan': 1, 'ARG: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: 3.89, per 1000 atoms: 0.28 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: 1.22 Conformation dependent library (CDL) restraints added in 713.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.46 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: 3.08 Time building geometry restraints manager: 1.67 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: 1.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.740 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.050 ------------------------------------------------------------------------------- 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 : 4.22 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.006 0.001 ARG A 237 TYR 0.245 0.024 TYR P1298 PHE 0.082 0.014 PHE D 144 TRP 0.100 0.021 TRP B 228 HIS 0.017 0.005 HIS B 64 Details of bonding type rmsd covalent geometry : bond 0.01678 (14343) covalent geometry : angle 1.93525 (19474) SS BOND : bond 0.01635 ( 2) SS BOND : angle 2.69747 ( 4) hydrogen bonds : bond 0.12629 ( 696) hydrogen bonds : angle 6.62418 ( 1944) *********************** 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 : 0.600 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: 0.1275 time to fit residues: 44.9036 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 : 0.563 ------------------------------------------------------------------------------- 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 98 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 6.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 207 ASN A 239 ASN ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN A 803 GLN B 62 ASN B 168 ASN ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN D 116 ASN ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 ASN P1064 GLN P1071 HIS P1128 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.147515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.099594 restraints weight = 32321.730| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 4.07 r_work: 0.3511 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14345 Z= 0.155 Angle : 0.616 7.028 19478 Z= 0.330 Chirality : 0.045 0.153 2108 Planarity : 0.004 0.041 2566 Dihedral : 5.403 54.841 1981 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.08 % Favored : 94.81 % Rotamer: Outliers : 1.48 % Allowed : 9.28 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.20), residues: 1791 helix: 0.97 (0.28), residues: 348 sheet: 0.31 (0.20), residues: 646 loop : -1.45 (0.21), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 634 TYR 0.021 0.002 TYR P1060 PHE 0.015 0.001 PHE A 197 TRP 0.016 0.001 TRP A 810 HIS 0.005 0.001 HIS B 324 Details of bonding type rmsd covalent geometry : bond 0.00339 (14343) covalent geometry : angle 0.61565 (19474) SS BOND : bond 0.00104 ( 2) SS BOND : angle 0.22560 ( 4) hydrogen bonds : bond 0.03704 ( 696) hydrogen bonds : angle 5.52815 ( 1944) *********************** 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 209 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 187 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 512 ASP cc_start: 0.8370 (p0) cc_final: 0.8150 (p0) REVERT: A 736 SER cc_start: 0.8789 (p) cc_final: 0.8555 (m) REVERT: B 73 TYR cc_start: 0.7251 (m-80) cc_final: 0.7000 (m-80) REVERT: C 81 ASP cc_start: 0.8392 (t0) cc_final: 0.7733 (p0) REVERT: D 207 ASP cc_start: 0.8589 (OUTLIER) cc_final: 0.8185 (m-30) REVERT: P 1029 MET cc_start: 0.8930 (mpp) cc_final: 0.8421 (mpp) REVERT: P 1035 ILE cc_start: 0.9156 (mm) cc_final: 0.8877 (mp) REVERT: P 1046 MET cc_start: 0.7723 (tmm) cc_final: 0.7501 (tpt) REVERT: P 1127 HIS cc_start: 0.7712 (m170) cc_final: 0.6936 (m170) outliers start: 22 outliers final: 13 residues processed: 204 average time/residue: 0.0942 time to fit residues: 29.5578 Evaluate side-chains 173 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 159 time to evaluate : 0.531 ------------------------------------------------------------------------------- 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 430 ILE Chi-restraints excluded: chain A residue 532 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 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 97 optimal weight: 10.0000 chunk 162 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 chunk 4 optimal weight: 40.0000 chunk 159 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 144 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 41 optimal weight: 0.0970 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN B 334 ASN ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.145155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.096472 restraints weight = 32427.598| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 4.11 r_work: 0.3461 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14345 Z= 0.183 Angle : 0.605 8.323 19478 Z= 0.323 Chirality : 0.044 0.167 2108 Planarity : 0.004 0.038 2566 Dihedral : 5.321 57.323 1977 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.36 % Favored : 94.47 % Rotamer: Outliers : 2.35 % Allowed : 11.03 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.20), residues: 1791 helix: 0.88 (0.28), residues: 349 sheet: 0.23 (0.20), residues: 636 loop : -1.48 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 634 TYR 0.026 0.002 TYR A 255 PHE 0.023 0.002 PHE P1082 TRP 0.012 0.001 TRP B 93 HIS 0.005 0.001 HIS B 324 Details of bonding type rmsd covalent geometry : bond 0.00403 (14343) covalent geometry : angle 0.60469 (19474) SS BOND : bond 0.00182 ( 2) SS BOND : angle 0.43360 ( 4) hydrogen bonds : bond 0.03491 ( 696) hydrogen bonds : angle 5.32580 ( 1944) *********************** 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 211 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 176 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 512 ASP cc_start: 0.8467 (p0) cc_final: 0.8226 (p0) REVERT: A 737 PHE cc_start: 0.8427 (t80) cc_final: 0.8216 (t80) REVERT: A 768 MET cc_start: 0.7773 (tmm) cc_final: 0.7370 (tmm) REVERT: B 73 TYR cc_start: 0.7598 (m-80) cc_final: 0.7248 (m-80) REVERT: B 168 ASN cc_start: 0.8441 (t160) cc_final: 0.8016 (t0) REVERT: C 49 GLU cc_start: 0.8755 (tp30) cc_final: 0.8311 (tp30) REVERT: C 56 MET cc_start: 0.8289 (ptm) cc_final: 0.8027 (ptm) REVERT: C 81 ASP cc_start: 0.8518 (OUTLIER) cc_final: 0.7945 (p0) REVERT: D 94 ARG cc_start: 0.8962 (ptm-80) cc_final: 0.8362 (ptt90) REVERT: D 97 ARG cc_start: 0.9149 (ttp80) cc_final: 0.8899 (ptt90) REVERT: D 165 LYS cc_start: 0.9000 (tttp) cc_final: 0.8601 (ttpp) REVERT: D 225 MET cc_start: 0.8557 (mtt) cc_final: 0.8310 (mtt) REVERT: P 1029 MET cc_start: 0.9009 (mpp) cc_final: 0.8533 (mpp) REVERT: P 1035 ILE cc_start: 0.9193 (mm) cc_final: 0.8915 (mp) REVERT: P 1046 MET cc_start: 0.7633 (tmm) cc_final: 0.7354 (tpt) REVERT: P 1082 PHE cc_start: 0.9248 (p90) cc_final: 0.8978 (p90) outliers start: 35 outliers final: 22 residues processed: 198 average time/residue: 0.1163 time to fit residues: 34.7879 Evaluate side-chains 178 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 248 THR 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 430 ILE Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain C residue 81 ASP 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 1268 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 171 optimal weight: 40.0000 chunk 39 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 96 optimal weight: 9.9990 chunk 133 optimal weight: 0.6980 chunk 78 optimal weight: 6.9990 chunk 129 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 664 GLN ** D 50 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.142813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.094089 restraints weight = 32636.260| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 4.02 r_work: 0.3404 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 14345 Z= 0.233 Angle : 0.626 7.287 19478 Z= 0.336 Chirality : 0.045 0.173 2108 Planarity : 0.004 0.045 2566 Dihedral : 5.338 51.536 1977 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.25 % Favored : 93.58 % Rotamer: Outliers : 2.49 % Allowed : 13.25 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.19), residues: 1791 helix: 0.81 (0.28), residues: 349 sheet: 0.03 (0.20), residues: 623 loop : -1.54 (0.21), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 47 TYR 0.032 0.002 TYR B 333 PHE 0.022 0.002 PHE P1296 TRP 0.013 0.001 TRP B 93 HIS 0.005 0.001 HIS B 324 Details of bonding type rmsd covalent geometry : bond 0.00513 (14343) covalent geometry : angle 0.62561 (19474) SS BOND : bond 0.00122 ( 2) SS BOND : angle 0.31033 ( 4) hydrogen bonds : bond 0.03556 ( 696) hydrogen bonds : angle 5.31438 ( 1944) *********************** 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 211 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 174 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 ASP cc_start: 0.8980 (m-30) cc_final: 0.8650 (p0) REVERT: A 248 THR cc_start: 0.8245 (OUTLIER) cc_final: 0.8034 (p) REVERT: A 464 ASP cc_start: 0.8136 (p0) cc_final: 0.7899 (p0) REVERT: A 512 ASP cc_start: 0.8463 (p0) cc_final: 0.8194 (p0) REVERT: A 737 PHE cc_start: 0.8374 (t80) cc_final: 0.8121 (t80) REVERT: A 768 MET cc_start: 0.8011 (tmm) cc_final: 0.7202 (tmm) REVERT: B 73 TYR cc_start: 0.7855 (m-80) cc_final: 0.7526 (m-10) REVERT: B 168 ASN cc_start: 0.8505 (t160) cc_final: 0.8009 (t0) REVERT: C 81 ASP cc_start: 0.8540 (OUTLIER) cc_final: 0.8058 (p0) REVERT: D 97 ARG cc_start: 0.9144 (ttp80) cc_final: 0.8908 (ptt90) REVERT: D 165 LYS cc_start: 0.9074 (tttp) cc_final: 0.8768 (tttp) REVERT: P 1029 MET cc_start: 0.9060 (mpp) cc_final: 0.8553 (mpp) REVERT: P 1035 ILE cc_start: 0.9204 (mm) cc_final: 0.8933 (mp) REVERT: P 1046 MET cc_start: 0.7527 (tmm) cc_final: 0.7211 (tpt) REVERT: P 1230 GLN cc_start: 0.9420 (pm20) cc_final: 0.9087 (tp-100) outliers start: 37 outliers final: 25 residues processed: 198 average time/residue: 0.1064 time to fit residues: 32.5026 Evaluate side-chains 182 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 0.544 ------------------------------------------------------------------------------- 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 245 VAL Chi-restraints excluded: chain A residue 248 THR 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 430 ILE Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 599 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 87 ASP Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 314 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 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 1268 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 122 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 176 optimal weight: 6.9990 chunk 147 optimal weight: 0.9990 chunk 149 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 135 optimal weight: 0.5980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 GLN B 276 GLN ** D 50 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** P1071 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.145442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.097523 restraints weight = 32362.402| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 4.07 r_work: 0.3470 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 14345 Z= 0.128 Angle : 0.568 7.310 19478 Z= 0.301 Chirality : 0.044 0.155 2108 Planarity : 0.003 0.035 2566 Dihedral : 5.061 53.931 1977 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.03 % Favored : 94.81 % Rotamer: Outliers : 1.95 % Allowed : 14.19 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.20), residues: 1791 helix: 0.97 (0.28), residues: 349 sheet: 0.15 (0.20), residues: 627 loop : -1.45 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 47 TYR 0.021 0.001 TYR A 255 PHE 0.018 0.001 PHE A 426 TRP 0.013 0.001 TRP B 93 HIS 0.004 0.001 HIS B 324 Details of bonding type rmsd covalent geometry : bond 0.00280 (14343) covalent geometry : angle 0.56813 (19474) SS BOND : bond 0.00147 ( 2) SS BOND : angle 0.16653 ( 4) hydrogen bonds : bond 0.03143 ( 696) hydrogen bonds : angle 5.07457 ( 1944) *********************** 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 210 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 181 time to evaluate : 0.599 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: 0.8656 (p0) REVERT: A 464 ASP cc_start: 0.8204 (p0) cc_final: 0.7982 (p0) REVERT: A 512 ASP cc_start: 0.8424 (p0) cc_final: 0.8200 (p0) REVERT: A 768 MET cc_start: 0.8063 (tmm) cc_final: 0.7613 (tmm) REVERT: B 73 TYR cc_start: 0.7762 (m-80) cc_final: 0.7524 (m-80) REVERT: B 168 ASN cc_start: 0.8348 (t160) cc_final: 0.7844 (t0) REVERT: C 81 ASP cc_start: 0.8571 (OUTLIER) cc_final: 0.7958 (p0) REVERT: D 94 ARG cc_start: 0.8905 (ptm-80) cc_final: 0.8384 (ptt90) REVERT: D 97 ARG cc_start: 0.9194 (ttp80) cc_final: 0.8967 (ptt90) REVERT: D 165 LYS cc_start: 0.9022 (tttp) cc_final: 0.8626 (tttp) REVERT: D 237 ILE cc_start: 0.8917 (mm) cc_final: 0.8642 (mt) REVERT: P 1029 MET cc_start: 0.8977 (mpp) cc_final: 0.8637 (mpp) REVERT: P 1035 ILE cc_start: 0.9178 (mm) cc_final: 0.8911 (mp) REVERT: P 1046 MET cc_start: 0.7583 (tmm) cc_final: 0.7232 (tpt) REVERT: P 1230 GLN cc_start: 0.9321 (pm20) cc_final: 0.9090 (tp-100) outliers start: 29 outliers final: 17 residues processed: 196 average time/residue: 0.1188 time to fit residues: 35.0220 Evaluate side-chains 180 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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 741 MET Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain P residue 1065 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 112 optimal weight: 6.9990 chunk 160 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 94 optimal weight: 8.9990 chunk 28 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 120 optimal weight: 0.0070 chunk 32 optimal weight: 3.9990 overall best weight: 3.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 803 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.141755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.091923 restraints weight = 32365.762| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 4.12 r_work: 0.3370 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 14345 Z= 0.240 Angle : 0.632 8.809 19478 Z= 0.336 Chirality : 0.045 0.197 2108 Planarity : 0.004 0.046 2566 Dihedral : 5.214 51.103 1977 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.37 % Favored : 93.47 % Rotamer: Outliers : 2.42 % Allowed : 15.00 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.19), residues: 1791 helix: 0.79 (0.27), residues: 356 sheet: 0.03 (0.20), residues: 626 loop : -1.51 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 47 TYR 0.024 0.002 TYR A 255 PHE 0.033 0.002 PHE A 804 TRP 0.014 0.001 TRP B 93 HIS 0.005 0.001 HIS B 324 Details of bonding type rmsd covalent geometry : bond 0.00528 (14343) covalent geometry : angle 0.63182 (19474) SS BOND : bond 0.00096 ( 2) SS BOND : angle 0.28657 ( 4) hydrogen bonds : bond 0.03522 ( 696) hydrogen bonds : angle 5.22354 ( 1944) *********************** 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 204 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 168 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 ASP cc_start: 0.9096 (m-30) cc_final: 0.8688 (p0) REVERT: A 464 ASP cc_start: 0.8234 (p0) cc_final: 0.7979 (p0) REVERT: A 512 ASP cc_start: 0.8466 (p0) cc_final: 0.8216 (p0) REVERT: A 768 MET cc_start: 0.8256 (tmm) cc_final: 0.7366 (tmm) REVERT: A 805 ASN cc_start: 0.8346 (t0) cc_final: 0.8025 (t0) REVERT: B 168 ASN cc_start: 0.8499 (t160) cc_final: 0.8042 (t0) REVERT: B 189 MET cc_start: 0.6974 (mmm) cc_final: 0.6566 (mmm) REVERT: C 81 ASP cc_start: 0.8616 (OUTLIER) cc_final: 0.7863 (p0) REVERT: D 94 ARG cc_start: 0.9001 (ptm-80) cc_final: 0.8397 (ptt90) REVERT: D 165 LYS cc_start: 0.9042 (tttp) cc_final: 0.8702 (tttp) REVERT: D 237 ILE cc_start: 0.8930 (mm) cc_final: 0.8692 (mt) REVERT: E 64 MET cc_start: 0.8550 (mmm) cc_final: 0.8332 (mtt) REVERT: P 1035 ILE cc_start: 0.9227 (mm) cc_final: 0.8969 (mp) outliers start: 36 outliers final: 29 residues processed: 187 average time/residue: 0.1142 time to fit residues: 32.4035 Evaluate side-chains 188 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 158 time to evaluate : 0.531 ------------------------------------------------------------------------------- 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 430 ILE 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 63 LEU 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 314 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 53 THR Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 48 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 6 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 80 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 9 optimal weight: 10.0000 chunk 99 optimal weight: 20.0000 chunk 46 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 803 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** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.142619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.093652 restraints weight = 32210.743| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 4.03 r_work: 0.3397 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14345 Z= 0.172 Angle : 0.611 9.258 19478 Z= 0.322 Chirality : 0.044 0.186 2108 Planarity : 0.004 0.081 2566 Dihedral : 5.155 53.140 1977 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.75 % Favored : 94.08 % Rotamer: Outliers : 2.35 % Allowed : 15.94 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.20), residues: 1791 helix: 0.81 (0.28), residues: 357 sheet: -0.02 (0.20), residues: 634 loop : -1.46 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 97 TYR 0.023 0.001 TYR A 255 PHE 0.023 0.001 PHE A 804 TRP 0.011 0.001 TRP B 93 HIS 0.004 0.001 HIS B 324 Details of bonding type rmsd covalent geometry : bond 0.00377 (14343) covalent geometry : angle 0.61144 (19474) SS BOND : bond 0.00120 ( 2) SS BOND : angle 0.16632 ( 4) hydrogen bonds : bond 0.03282 ( 696) hydrogen bonds : angle 5.14800 ( 1944) *********************** 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 201 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 166 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 ASP cc_start: 0.9072 (m-30) cc_final: 0.8663 (p0) REVERT: A 464 ASP cc_start: 0.8173 (p0) cc_final: 0.7924 (p0) REVERT: A 512 ASP cc_start: 0.8437 (p0) cc_final: 0.8191 (p0) REVERT: A 768 MET cc_start: 0.8220 (tmm) cc_final: 0.7874 (tmm) REVERT: B 168 ASN cc_start: 0.8427 (t160) cc_final: 0.7976 (t0) REVERT: C 81 ASP cc_start: 0.8578 (OUTLIER) cc_final: 0.7855 (p0) REVERT: D 94 ARG cc_start: 0.8978 (ptm-80) cc_final: 0.8423 (ptt90) REVERT: D 165 LYS cc_start: 0.9004 (tttp) cc_final: 0.8702 (tttp) REVERT: D 237 ILE cc_start: 0.8919 (mm) cc_final: 0.8663 (mt) REVERT: E 64 MET cc_start: 0.8520 (mmm) cc_final: 0.8263 (mtt) REVERT: P 1029 MET cc_start: 0.9106 (mmm) cc_final: 0.8383 (mpp) REVERT: P 1035 ILE cc_start: 0.9221 (mm) cc_final: 0.8974 (mp) REVERT: P 1046 MET cc_start: 0.7796 (tpt) cc_final: 0.7400 (tpt) REVERT: P 1259 LEU cc_start: 0.9183 (mt) cc_final: 0.8912 (mt) outliers start: 35 outliers final: 27 residues processed: 183 average time/residue: 0.0988 time to fit residues: 27.6477 Evaluate side-chains 184 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 0.520 ------------------------------------------------------------------------------- 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 461 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 615 THR 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 314 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 150 LEU Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain P residue 1045 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 104 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 112 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 3 optimal weight: 20.0000 chunk 170 optimal weight: 8.9990 chunk 0 optimal weight: 40.0000 chunk 142 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN A 803 GLN ** 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** P1191 HIS ** P1230 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 = 0.4403 r_free = 0.4403 target = 0.141989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.093488 restraints weight = 32334.956| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 4.00 r_work: 0.3412 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 14345 Z= 0.160 Angle : 0.610 10.710 19478 Z= 0.317 Chirality : 0.044 0.187 2108 Planarity : 0.004 0.037 2566 Dihedral : 5.036 53.507 1977 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.92 % Favored : 93.91 % Rotamer: Outliers : 2.22 % Allowed : 16.41 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.20), residues: 1791 helix: 0.92 (0.28), residues: 357 sheet: -0.01 (0.20), residues: 635 loop : -1.44 (0.21), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 97 TYR 0.022 0.001 TYR A 255 PHE 0.019 0.001 PHE A 804 TRP 0.011 0.001 TRP A 810 HIS 0.004 0.001 HIS B 324 Details of bonding type rmsd covalent geometry : bond 0.00352 (14343) covalent geometry : angle 0.60970 (19474) SS BOND : bond 0.00097 ( 2) SS BOND : angle 0.15058 ( 4) hydrogen bonds : bond 0.03198 ( 696) hydrogen bonds : angle 5.04690 ( 1944) *********************** 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 205 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 172 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 ASP cc_start: 0.9058 (m-30) cc_final: 0.8664 (p0) REVERT: A 464 ASP cc_start: 0.8222 (p0) cc_final: 0.8010 (p0) REVERT: A 512 ASP cc_start: 0.8414 (p0) cc_final: 0.8172 (p0) REVERT: A 545 MET cc_start: 0.9166 (ptm) cc_final: 0.8859 (ptp) REVERT: A 768 MET cc_start: 0.8275 (tmm) cc_final: 0.7931 (tmm) REVERT: B 168 ASN cc_start: 0.8412 (t160) cc_final: 0.7909 (t0) REVERT: C 81 ASP cc_start: 0.8574 (OUTLIER) cc_final: 0.7945 (p0) REVERT: D 94 ARG cc_start: 0.8957 (ptm-80) cc_final: 0.8315 (ptt90) REVERT: D 97 ARG cc_start: 0.9079 (ttp80) cc_final: 0.8826 (ptt90) REVERT: D 165 LYS cc_start: 0.9012 (tttp) cc_final: 0.8752 (ttmm) REVERT: E 64 MET cc_start: 0.8526 (mmm) cc_final: 0.8284 (mtt) REVERT: P 1046 MET cc_start: 0.7695 (tpt) cc_final: 0.7330 (tmm) REVERT: P 1082 PHE cc_start: 0.9259 (p90) cc_final: 0.8912 (p90) outliers start: 33 outliers final: 24 residues processed: 192 average time/residue: 0.1114 time to fit residues: 32.2540 Evaluate side-chains 183 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 0.482 ------------------------------------------------------------------------------- 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 461 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 615 THR 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 314 VAL Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 48 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 16 optimal weight: 7.9990 chunk 127 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 123 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 99 optimal weight: 20.0000 chunk 107 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 135 optimal weight: 0.6980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 241 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.142678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.094389 restraints weight = 32354.825| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 3.99 r_work: 0.3423 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 14345 Z= 0.142 Angle : 0.613 11.013 19478 Z= 0.317 Chirality : 0.044 0.181 2108 Planarity : 0.003 0.039 2566 Dihedral : 4.970 53.669 1977 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.19 % Favored : 94.64 % Rotamer: Outliers : 1.61 % Allowed : 17.08 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.20), residues: 1791 helix: 0.94 (0.28), residues: 357 sheet: 0.03 (0.20), residues: 636 loop : -1.44 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 173 TYR 0.023 0.001 TYR B 73 PHE 0.016 0.001 PHE A 804 TRP 0.011 0.001 TRP A 810 HIS 0.003 0.001 HIS B 324 Details of bonding type rmsd covalent geometry : bond 0.00313 (14343) covalent geometry : angle 0.61297 (19474) SS BOND : bond 0.00098 ( 2) SS BOND : angle 0.14833 ( 4) hydrogen bonds : bond 0.03122 ( 696) hydrogen bonds : angle 4.99549 ( 1944) *********************** 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 196 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 172 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 ASP cc_start: 0.9035 (m-30) cc_final: 0.8657 (p0) REVERT: A 512 ASP cc_start: 0.8415 (p0) cc_final: 0.8179 (p0) REVERT: A 545 MET cc_start: 0.9215 (ptm) cc_final: 0.8873 (ptp) REVERT: A 768 MET cc_start: 0.8262 (tmm) cc_final: 0.7904 (tmm) REVERT: B 168 ASN cc_start: 0.8365 (t160) cc_final: 0.7874 (t0) REVERT: B 197 GLU cc_start: 0.7385 (mt-10) cc_final: 0.7106 (mt-10) REVERT: B 388 TYR cc_start: 0.4901 (t80) cc_final: 0.4334 (t80) REVERT: C 81 ASP cc_start: 0.8573 (t0) cc_final: 0.7933 (p0) REVERT: D 94 ARG cc_start: 0.8942 (ptm-80) cc_final: 0.8403 (ptt90) REVERT: D 97 ARG cc_start: 0.9033 (ttp80) cc_final: 0.8800 (ptt90) REVERT: D 165 LYS cc_start: 0.8987 (tttp) cc_final: 0.8718 (ttmm) REVERT: E 64 MET cc_start: 0.8427 (mmm) cc_final: 0.8206 (mtt) REVERT: P 1035 ILE cc_start: 0.9230 (mm) cc_final: 0.8991 (mp) REVERT: P 1046 MET cc_start: 0.7696 (tpt) cc_final: 0.7355 (tmm) REVERT: P 1082 PHE cc_start: 0.9270 (p90) cc_final: 0.8942 (p90) outliers start: 24 outliers final: 21 residues processed: 187 average time/residue: 0.0899 time to fit residues: 25.9845 Evaluate side-chains 185 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 164 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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 461 THR Chi-restraints excluded: chain A residue 615 THR 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 314 VAL Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain E residue 48 VAL 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 72 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 136 optimal weight: 0.5980 chunk 14 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 99 optimal weight: 20.0000 chunk 95 optimal weight: 0.3980 chunk 173 optimal weight: 7.9990 chunk 118 optimal weight: 8.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 241 ASN ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 GLN P1236 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.141224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.092042 restraints weight = 32337.392| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 4.06 r_work: 0.3369 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 14345 Z= 0.191 Angle : 0.646 11.226 19478 Z= 0.338 Chirality : 0.045 0.195 2108 Planarity : 0.004 0.043 2566 Dihedral : 5.102 52.891 1977 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.31 % Favored : 93.52 % Rotamer: Outliers : 1.68 % Allowed : 16.95 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.20), residues: 1791 helix: 0.85 (0.28), residues: 356 sheet: -0.09 (0.20), residues: 637 loop : -1.48 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 195 TYR 0.023 0.002 TYR A 255 PHE 0.021 0.002 PHE A 197 TRP 0.017 0.001 TRP A 206 HIS 0.004 0.001 HIS B 324 Details of bonding type rmsd covalent geometry : bond 0.00424 (14343) covalent geometry : angle 0.64640 (19474) SS BOND : bond 0.00100 ( 2) SS BOND : angle 0.21816 ( 4) hydrogen bonds : bond 0.03349 ( 696) hydrogen bonds : angle 5.08357 ( 1944) ********************** 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 191 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 166 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 ASP cc_start: 0.9048 (m-30) cc_final: 0.8713 (p0) REVERT: A 512 ASP cc_start: 0.8439 (p0) cc_final: 0.8187 (p0) REVERT: A 768 MET cc_start: 0.8361 (tmm) cc_final: 0.7995 (tmm) REVERT: B 168 ASN cc_start: 0.8414 (t160) cc_final: 0.7906 (t0) REVERT: B 388 TYR cc_start: 0.4970 (t80) cc_final: 0.4147 (t80) REVERT: C 81 ASP cc_start: 0.8575 (t0) cc_final: 0.7956 (p0) REVERT: D 94 ARG cc_start: 0.8961 (ptm-80) cc_final: 0.8469 (ptt90) REVERT: D 165 LYS cc_start: 0.9008 (tttp) cc_final: 0.8762 (ttmm) REVERT: E 46 ILE cc_start: 0.8924 (mm) cc_final: 0.8723 (mm) REVERT: E 54 GLN cc_start: 0.9175 (OUTLIER) cc_final: 0.8944 (pm20) REVERT: P 1035 ILE cc_start: 0.9297 (mm) cc_final: 0.9071 (mp) REVERT: P 1046 MET cc_start: 0.7736 (tpt) cc_final: 0.7383 (tmm) REVERT: P 1082 PHE cc_start: 0.9241 (p90) cc_final: 0.8918 (p90) REVERT: P 1230 GLN cc_start: 0.9415 (pm20) cc_final: 0.9049 (tp-100) outliers start: 25 outliers final: 21 residues processed: 183 average time/residue: 0.1068 time to fit residues: 29.4269 Evaluate side-chains 182 residues out of total 1491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 0.477 ------------------------------------------------------------------------------- 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 461 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 615 THR 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 314 VAL Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 241 ASN Chi-restraints excluded: chain E residue 54 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 59 optimal weight: 10.0000 chunk 121 optimal weight: 0.6980 chunk 153 optimal weight: 50.0000 chunk 148 optimal weight: 50.0000 chunk 11 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 chunk 76 optimal weight: 4.9990 chunk 80 optimal weight: 8.9990 chunk 172 optimal weight: 10.0000 chunk 86 optimal weight: 6.9990 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 803 GLN ** 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** D 241 ASN ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.136933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.085766 restraints weight = 32510.360| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 4.20 r_work: 0.3247 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.090 14345 Z= 0.379 Angle : 0.791 11.684 19478 Z= 0.417 Chirality : 0.049 0.282 2108 Planarity : 0.005 0.065 2566 Dihedral : 5.685 50.826 1977 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.43 % Favored : 92.41 % Rotamer: Outliers : 1.82 % Allowed : 17.55 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.19), residues: 1791 helix: 0.33 (0.27), residues: 355 sheet: -0.31 (0.20), residues: 616 loop : -1.75 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 97 TYR 0.032 0.002 TYR A 255 PHE 0.021 0.002 PHE A 197 TRP 0.022 0.002 TRP P1042 HIS 0.007 0.002 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00837 (14343) covalent geometry : angle 0.79059 (19474) SS BOND : bond 0.00135 ( 2) SS BOND : angle 0.57138 ( 4) hydrogen bonds : bond 0.04058 ( 696) hydrogen bonds : angle 5.56902 ( 1944) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4760.32 seconds wall clock time: 82 minutes 5.50 seconds (4925.50 seconds total)