Starting phenix.real_space_refine on Tue Apr 7 23:01:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9p1u_71134/04_2026/9p1u_71134.cif Found real_map, /net/cci-nas-00/data/ceres_data/9p1u_71134/04_2026/9p1u_71134.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9p1u_71134/04_2026/9p1u_71134.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9p1u_71134/04_2026/9p1u_71134.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9p1u_71134/04_2026/9p1u_71134.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9p1u_71134/04_2026/9p1u_71134.map" } resolution = 4.1 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= 0.002 sd= 1.021 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: 5 Type Number sf(0) Gaussians S 50 5.16 5 C 9907 2.51 5 N 2762 2.21 5 O 3133 1.98 5 H 14946 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30798 Number of models: 1 Model: "" Number of chains: 7 Chain: "C" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 751 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 7, 'TRANS': 46} Chain: "D" Number of atoms: 3362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 3362 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 9, 'TRANS': 201} Chain: "E" Number of atoms: 1352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 1352 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 5, 'TRANS': 81} Chain: "G" Number of atoms: 2370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 2370 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 8, 'TRANS': 140} Chain: "F" Number of atoms: 7266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 7266 Classifications: {'peptide': 459} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 445} Chain breaks: 4 Chain: "B" Number of atoms: 5102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 5102 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 11, 'TRANS': 331} Chain breaks: 3 Chain: "A" Number of atoms: 10595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 777, 10595 Classifications: {'peptide': 777} Link IDs: {'PTRANS': 29, 'TRANS': 747} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 576 Unresolved non-hydrogen angles: 838 Unresolved non-hydrogen dihedrals: 343 Unresolved non-hydrogen chiralities: 191 Planarities with less than four sites: {'PHE:plan': 7, 'ASP:plan': 13, 'HIS:plan': 1, 'GLU:plan': 9, 'GLN:plan1': 4, 'ARG:plan': 10, 'ASN:plan1': 6, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 257 Time building chain proxies: 4.91, per 1000 atoms: 0.16 Number of scatterers: 30798 At special positions: 0 Unit cell: (145.728, 136.896, 136.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 50 16.00 O 3133 8.00 N 2762 7.00 C 9907 6.00 H 14946 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS F 724 " - pdb=" SG CYS F 725 " distance=2.11 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: 2.68 Conformation dependent library (CDL) restraints added in 789.5 milliseconds 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3552 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 20 sheets defined 23.2% alpha, 34.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'C' and resid 38 through 43 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 47 through 62 Processing helix chain 'D' and resid 66 through 83 removed outlier: 3.795A pdb=" N GLN D 70 " --> pdb=" O PRO D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 99 Processing helix chain 'D' and resid 104 through 120 Processing helix chain 'D' and resid 122 through 129 removed outlier: 3.533A pdb=" N GLY D 126 " --> pdb=" O SER D 122 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE D 127 " --> pdb=" O ALA D 123 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE D 128 " --> pdb=" O LEU D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 135 removed outlier: 3.683A pdb=" N ASP D 134 " --> pdb=" O ASP D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 154 Processing helix chain 'D' and resid 158 through 189 removed outlier: 4.098A pdb=" N ASP D 162 " --> pdb=" O GLN D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 208 through 226 removed outlier: 3.914A 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 243 removed outlier: 4.017A pdb=" N ALA D 231 " --> pdb=" O MET D 227 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N SER D 243 " --> pdb=" O ALA D 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 45 Processing helix chain 'E' and resid 51 through 60 Processing helix chain 'G' and resid 30 through 33 Processing helix chain 'G' and resid 45 through 58 Processing helix chain 'G' and resid 132 through 167 Proline residue: G 160 - end of helix Processing helix chain 'F' and resid 463 through 470 Processing helix chain 'F' and resid 536 through 542 Processing helix chain 'F' and resid 660 through 668 Processing helix chain 'F' and resid 669 through 675 removed outlier: 3.503A pdb=" N THR F 674 " --> pdb=" O LYS F 670 " (cutoff:3.500A) Processing helix chain 'F' and resid 768 through 776 removed outlier: 4.004A pdb=" N ASN F 776 " --> pdb=" O MET F 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 313 No H-bonds generated for 'chain 'B' and resid 311 through 313' Processing helix chain 'A' and resid 37 through 46 removed outlier: 4.212A pdb=" N ALA A 41 " --> pdb=" O VAL A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 69 Processing helix chain 'A' and resid 106 through 118 Processing helix chain 'A' and resid 127 through 144 Processing helix chain 'A' and resid 189 through 196 removed outlier: 3.733A pdb=" N HIS A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 234 Processing helix chain 'A' and resid 280 through 289 Processing helix chain 'A' and resid 297 through 316 Processing helix chain 'A' and resid 361 through 369 removed outlier: 3.992A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU A 368 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET A 369 " --> pdb=" O LEU A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 393 removed outlier: 3.975A pdb=" N GLY A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 Processing helix chain 'A' and resid 542 through 553 Processing helix chain 'A' and resid 647 through 651 Processing helix chain 'A' and resid 726 through 732 Processing sheet with id=AA1, first strand: chain 'E' and resid 32 through 33 removed outlier: 3.777A pdb=" N MET E 64 " --> pdb=" O PHE E 74 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 32 through 33 Processing sheet with id=AA3, first strand: chain 'G' and resid 22 through 23 removed outlier: 3.728A pdb=" N ALA F 427 " --> pdb=" O PHE F 417 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL F 418 " --> pdb=" O ALA F 390 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ALA F 390 " --> pdb=" O VAL F 418 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N TYR F 388 " --> pdb=" O PHE F 377 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N PHE F 377 " --> pdb=" O TYR F 388 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N SER F 373 " --> pdb=" O PRO F 392 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LEU F 394 " --> pdb=" O THR F 371 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N THR F 371 " --> pdb=" O LEU F 394 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N VAL F 396 " --> pdb=" O ASN F 369 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASN F 369 " --> pdb=" O VAL F 396 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 22 through 23 removed outlier: 3.900A pdb=" N PHE F 575 " --> pdb=" O ILE F 566 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N VAL F 607 " --> pdb=" O ILE F 582 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N TYR F 584 " --> pdb=" O SER F 605 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N SER F 605 " --> pdb=" O TYR F 584 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N VAL F 747 " --> pdb=" O ASN F 737 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N TRP F 739 " --> pdb=" O HIS F 745 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N HIS F 745 " --> pdb=" O TRP F 739 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N MET A 768 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE A 791 " --> pdb=" O MET A 768 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 61 through 63 removed outlier: 6.918A pdb=" N MET G 36 " --> pdb=" O LEU G 63 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ASN G 105 " --> pdb=" O GLY G 78 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N VAL G 80 " --> pdb=" O THR G 103 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N THR G 103 " --> pdb=" O VAL G 80 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ILE G 82 " --> pdb=" O ILE G 101 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ILE G 101 " --> pdb=" O ILE G 82 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LYS G 84 " --> pdb=" O GLN G 99 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N GLN G 99 " --> pdb=" O LYS G 84 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N THR G 86 " --> pdb=" O GLU G 97 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N GLU G 97 " --> pdb=" O THR G 86 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 274 through 276 Processing sheet with id=AA7, first strand: chain 'B' and resid 45 through 51 removed outlier: 5.823A pdb=" N THR B 46 " --> pdb=" O THR B 391 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR B 391 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TRP B 48 " --> pdb=" O SER B 389 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 66 through 68 removed outlier: 6.896A pdb=" N VAL B 81 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N SER B 94 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ALA B 83 " --> pdb=" O ILE B 92 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 111 through 118 removed outlier: 6.761A pdb=" N GLY B 114 " --> pdb=" O GLY B 125 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLY B 125 " --> pdb=" O GLY B 114 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLN B 130 " --> pdb=" O SER B 126 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TRP B 143 " --> pdb=" O ALA B 133 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ASN B 135 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL B 141 " --> pdb=" O ASN B 135 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 156 through 158 removed outlier: 3.889A pdb=" N TRP B 183 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ASN B 175 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL B 181 " --> pdb=" O ASN B 175 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 193 through 194 removed outlier: 6.761A pdb=" N SER B 193 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N ILE A 240 " --> pdb=" O THR A 261 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N THR A 261 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N SER A 242 " --> pdb=" O ASN A 259 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASN A 259 " --> pdb=" O SER A 242 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ILE A 254 " --> pdb=" O ILE A 177 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN A 179 " --> pdb=" O ILE A 254 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 201 through 203 removed outlier: 6.777A pdb=" N VAL B 216 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N GLN B 229 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ALA B 218 " --> pdb=" O ILE B 227 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 252 through 254 removed outlier: 6.496A pdb=" N LEU B 267 " --> pdb=" O LYS B 280 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LYS B 280 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA B 269 " --> pdb=" O MET B 278 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 290 through 292 removed outlier: 3.684A pdb=" N TRP B 317 " --> pdb=" O ALA B 307 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N THR B 309 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 6.068A 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 removed outlier: 3.883A pdb=" N ALA B 358 " --> pdb=" O TRP B 348 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ASN B 350 " --> pdb=" O PHE B 356 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N PHE B 356 " --> pdb=" O ASN B 350 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 31 through 32 Processing sheet with id=AB8, first strand: chain 'A' and resid 93 through 100 removed outlier: 7.176A pdb=" N LEU A 165 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ILE A 97 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N LEU A 167 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N PHE A 99 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N PHE A 169 " --> pdb=" O PHE A 99 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 267 through 276 removed outlier: 7.497A pdb=" N LEU A 337 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL A 271 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N VAL A 339 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL A 273 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N VAL A 341 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLY A 275 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 348 through 355 removed outlier: 6.211A pdb=" N TYR A 348 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N VAL A 414 " --> pdb=" O TYR A 348 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N ARG A 350 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 12.750A pdb=" N TYR A 416 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 9.935A pdb=" N ILE A 352 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 12.537A pdb=" N VAL A 418 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 9.738A pdb=" N PHE A 354 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 11.955A pdb=" N GLU A 420 " --> pdb=" O PHE A 354 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N THR A 397 " --> pdb=" O LYS A 419 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 671 through 674 837 hydrogen bonds defined for protein. 2322 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: 7.38 Time building geometry restraints manager: 3.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 14944 1.02 - 1.22: 5 1.22 - 1.42: 7112 1.42 - 1.62: 8981 1.62 - 1.82: 94 Bond restraints: 31136 Sorted by residual: bond pdb=" N SER F 723 " pdb=" H SER F 723 " ideal model delta sigma weight residual 0.860 0.915 -0.055 2.00e-02 2.50e+03 7.48e+00 bond pdb=" N CYS F 725 " pdb=" CA CYS F 725 " ideal model delta sigma weight residual 1.458 1.485 -0.027 1.00e-02 1.00e+04 7.32e+00 bond pdb=" N LEU A 780 " pdb=" H LEU A 780 " ideal model delta sigma weight residual 0.860 0.913 -0.053 2.00e-02 2.50e+03 6.99e+00 bond pdb=" N CYS F 725 " pdb=" H CYS F 725 " ideal model delta sigma weight residual 0.860 0.912 -0.052 2.00e-02 2.50e+03 6.71e+00 bond pdb=" N TYR F 726 " pdb=" H TYR F 726 " ideal model delta sigma weight residual 0.860 0.912 -0.052 2.00e-02 2.50e+03 6.65e+00 ... (remaining 31131 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 55072 2.27 - 4.53: 512 4.53 - 6.80: 32 6.80 - 9.07: 5 9.07 - 11.33: 6 Bond angle restraints: 55627 Sorted by residual: angle pdb=" CA TYR F 726 " pdb=" C TYR F 726 " pdb=" O TYR F 726 " ideal model delta sigma weight residual 121.32 115.84 5.48 1.18e+00 7.18e-01 2.16e+01 angle pdb=" CA MET A 325 " pdb=" CB MET A 325 " pdb=" CG MET A 325 " ideal model delta sigma weight residual 114.10 122.55 -8.45 2.00e+00 2.50e-01 1.79e+01 angle pdb=" CA PRO A 782 " pdb=" C PRO A 782 " pdb=" O PRO A 782 " ideal model delta sigma weight residual 121.86 116.81 5.05 1.22e+00 6.72e-01 1.71e+01 angle pdb=" CA SER F 723 " pdb=" C SER F 723 " pdb=" O SER F 723 " ideal model delta sigma weight residual 121.87 117.07 4.80 1.16e+00 7.43e-01 1.71e+01 angle pdb=" CA TYR F 726 " pdb=" C TYR F 726 " pdb=" N ALA F 727 " ideal model delta sigma weight residual 116.01 121.12 -5.11 1.45e+00 4.76e-01 1.24e+01 ... (remaining 55622 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 13302 17.95 - 35.90: 936 35.90 - 53.84: 298 53.84 - 71.79: 108 71.79 - 89.74: 24 Dihedral angle restraints: 14668 sinusoidal: 7859 harmonic: 6809 Sorted by residual: dihedral pdb=" CB CYS F 724 " pdb=" SG CYS F 724 " pdb=" SG CYS F 725 " pdb=" CB CYS F 725 " ideal model delta sinusoidal sigma weight residual -86.00 -36.22 -49.78 1 1.00e+01 1.00e-02 3.40e+01 dihedral pdb=" CA PHE A 791 " pdb=" C PHE A 791 " pdb=" N LYS A 792 " pdb=" CA LYS A 792 " ideal model delta harmonic sigma weight residual 180.00 151.30 28.70 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CB CYS A 690 " pdb=" SG CYS A 690 " pdb=" SG CYS A 700 " pdb=" CB CYS A 700 " ideal model delta sinusoidal sigma weight residual -86.00 -134.45 48.45 1 1.00e+01 1.00e-02 3.23e+01 ... (remaining 14665 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1432 0.036 - 0.071: 559 0.071 - 0.107: 199 0.107 - 0.142: 81 0.142 - 0.178: 12 Chirality restraints: 2283 Sorted by residual: chirality pdb=" CG LEU F 773 " pdb=" CB LEU F 773 " pdb=" CD1 LEU F 773 " pdb=" CD2 LEU F 773 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.92e-01 chirality pdb=" CA VAL G 35 " pdb=" N VAL G 35 " pdb=" C VAL G 35 " pdb=" CB VAL G 35 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.17 2.00e-01 2.50e+01 7.64e-01 chirality pdb=" CA ILE F 752 " pdb=" N ILE F 752 " pdb=" C ILE F 752 " pdb=" CB ILE F 752 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.59e-01 ... (remaining 2280 not shown) Planarity restraints: 4918 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 661 " 0.043 9.50e-02 1.11e+02 7.14e-02 1.10e+02 pdb=" NE ARG A 661 " 0.039 2.00e-02 2.50e+03 pdb=" CZ ARG A 661 " -0.033 2.00e-02 2.50e+03 pdb=" NH1 ARG A 661 " -0.129 2.00e-02 2.50e+03 pdb=" NH2 ARG A 661 " 0.056 2.00e-02 2.50e+03 pdb="HH11 ARG A 661 " -0.014 2.00e-02 2.50e+03 pdb="HH12 ARG A 661 " 0.135 2.00e-02 2.50e+03 pdb="HH21 ARG A 661 " 0.002 2.00e-02 2.50e+03 pdb="HH22 ARG A 661 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 217 " 0.045 2.00e-02 2.50e+03 5.45e-02 4.46e+01 pdb=" CD GLN A 217 " -0.041 2.00e-02 2.50e+03 pdb=" OE1 GLN A 217 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 GLN A 217 " -0.085 2.00e-02 2.50e+03 pdb="HE21 GLN A 217 " -0.003 2.00e-02 2.50e+03 pdb="HE22 GLN A 217 " 0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN F 720 " -0.034 2.00e-02 2.50e+03 3.74e-02 2.10e+01 pdb=" CD GLN F 720 " 0.047 2.00e-02 2.50e+03 pdb=" OE1 GLN F 720 " -0.008 2.00e-02 2.50e+03 pdb=" NE2 GLN F 720 " 0.047 2.00e-02 2.50e+03 pdb="HE21 GLN F 720 " -0.000 2.00e-02 2.50e+03 pdb="HE22 GLN F 720 " -0.052 2.00e-02 2.50e+03 ... (remaining 4915 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.05: 597 2.05 - 2.68: 46812 2.68 - 3.32: 87078 3.32 - 3.96: 111728 3.96 - 4.60: 170562 Nonbonded interactions: 416777 Sorted by model distance: nonbonded pdb=" HG SER A 360 " pdb=" OE2 GLU A 420 " model vdw 1.407 2.450 nonbonded pdb=" OD2 ASP G 137 " pdb=" HZ3 LYS F 358 " model vdw 1.452 2.450 nonbonded pdb=" OE1 GLU A 435 " pdb=" HG SER A 436 " model vdw 1.472 2.450 nonbonded pdb=" OD1 ASP F 647 " pdb=" H ARG F 650 " model vdw 1.486 2.450 nonbonded pdb=" OG1 THR B 369 " pdb="HE21 GLN B 381 " model vdw 1.513 2.450 ... (remaining 416772 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.990 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: 0.200 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 28.010 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 16192 Z= 0.184 Angle : 0.760 30.313 21936 Z= 0.414 Chirality : 0.046 0.178 2283 Planarity : 0.006 0.123 2935 Dihedral : 13.638 89.739 5798 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.20 % Favored : 95.61 % Rotamer: Outliers : 0.25 % Allowed : 0.37 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % 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 are not related in a simple way. whole: -0.16 (0.18), residues: 2050 helix: 1.24 (0.24), residues: 420 sheet: 0.33 (0.18), residues: 707 loop : -1.07 (0.20), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.002 ARG F 774 TYR 0.025 0.002 TYR F 537 PHE 0.047 0.002 PHE D 128 TRP 0.029 0.002 TRP F 597 HIS 0.011 0.002 HIS F 431 Details of bonding type rmsd covalent geometry : bond 0.00373 (16190) covalent geometry : angle 0.72220 (21932) SS BOND : bond 0.05745 ( 2) SS BOND : angle 17.64525 ( 4) hydrogen bonds : bond 0.11653 ( 829) hydrogen bonds : angle 6.83717 ( 2322) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue VAL 37 is missing expected H atoms. Skipping. Residue ALA 38 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue ALA 41 is missing expected H atoms. Skipping. Residue ALA 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 46 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue THR 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue ALA 68 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue VAL 77 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue ALA 95 is missing expected H atoms. Skipping. Residue SER 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue SER 104 is missing expected H atoms. Skipping. Residue VAL 105 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue MET 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue ALA 116 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 119 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue TYR 147 is missing expected H atoms. Skipping. Residue SER 148 is missing expected H atoms. Skipping. Residue ALA 149 is missing expected H atoms. Skipping. Residue SER 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue ALA 153 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue VAL 168 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Evaluate side-chains 319 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 315 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 82 ASN cc_start: 0.8782 (t0) cc_final: 0.8442 (t0) REVERT: G 68 THR cc_start: 0.9450 (m) cc_final: 0.9145 (m) REVERT: G 69 ARG cc_start: 0.8383 (tpm170) cc_final: 0.8128 (mtt180) REVERT: F 771 GLU cc_start: 0.9257 (mp0) cc_final: 0.8976 (mp0) outliers start: 4 outliers final: 2 residues processed: 317 average time/residue: 0.2973 time to fit residues: 136.4850 Evaluate side-chains 257 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 255 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 40.0000 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.6980 chunk 200 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 534 GLN F 776 ASN F 782 ASN B 144 GLN B 350 ASN A 542 GLN A 666 ASN ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.086456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.064678 restraints weight = 184188.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.067806 restraints weight = 74961.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.069818 restraints weight = 42721.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.071099 restraints weight = 29793.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.071936 restraints weight = 23673.916| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 16192 Z= 0.212 Angle : 0.640 8.306 21936 Z= 0.359 Chirality : 0.044 0.166 2283 Planarity : 0.005 0.079 2935 Dihedral : 6.321 67.539 2283 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.63 % Favored : 95.22 % Rotamer: Outliers : 0.18 % Allowed : 2.76 % Favored : 97.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % 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 are not related in a simple way. whole: -0.12 (0.18), residues: 2050 helix: 1.47 (0.24), residues: 432 sheet: 0.22 (0.18), residues: 693 loop : -1.04 (0.21), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 774 TYR 0.021 0.002 TYR B 73 PHE 0.025 0.002 PHE F 327 TRP 0.016 0.001 TRP F 597 HIS 0.008 0.002 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00437 (16190) covalent geometry : angle 0.63757 (21932) SS BOND : bond 0.00641 ( 2) SS BOND : angle 3.75241 ( 4) hydrogen bonds : bond 0.04664 ( 829) hydrogen bonds : angle 5.71619 ( 2322) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue VAL 37 is missing expected H atoms. Skipping. Residue ALA 38 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue ALA 41 is missing expected H atoms. Skipping. Residue ALA 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 46 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue THR 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue ALA 68 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue VAL 77 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue ALA 95 is missing expected H atoms. Skipping. Residue SER 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue SER 104 is missing expected H atoms. Skipping. Residue VAL 105 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue MET 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue ALA 116 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 119 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue TYR 147 is missing expected H atoms. Skipping. Residue SER 148 is missing expected H atoms. Skipping. Residue ALA 149 is missing expected H atoms. Skipping. Residue SER 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue ALA 153 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue VAL 168 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Evaluate side-chains 303 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 300 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 GLU cc_start: 0.9139 (mp0) cc_final: 0.8710 (mp0) REVERT: D 82 ASN cc_start: 0.8845 (t0) cc_final: 0.8250 (t0) REVERT: D 84 ASP cc_start: 0.8640 (m-30) cc_final: 0.7955 (m-30) REVERT: D 207 ASP cc_start: 0.8843 (m-30) cc_final: 0.8099 (m-30) REVERT: G 90 PHE cc_start: 0.9438 (m-80) cc_final: 0.9226 (m-80) REVERT: G 123 PHE cc_start: 0.8047 (m-80) cc_final: 0.7846 (m-80) REVERT: F 524 ASP cc_start: 0.8323 (m-30) cc_final: 0.8066 (p0) REVERT: F 716 MET cc_start: 0.8861 (ppp) cc_final: 0.8455 (ppp) REVERT: B 64 HIS cc_start: 0.7656 (p90) cc_final: 0.7153 (p90) REVERT: A 305 GLU cc_start: 0.8981 (tt0) cc_final: 0.8776 (tt0) REVERT: A 531 TYR cc_start: 0.8317 (t80) cc_final: 0.8111 (t80) outliers start: 3 outliers final: 2 residues processed: 303 average time/residue: 0.2758 time to fit residues: 122.1622 Evaluate side-chains 256 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 254 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 72 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 chunk 164 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 70 optimal weight: 9.9990 chunk 150 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 177 optimal weight: 5.9990 chunk 110 optimal weight: 9.9990 chunk 190 optimal weight: 7.9990 chunk 155 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 52 GLN ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 460 GLN ** F 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 ASN ** A 693 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 = 0.3702 r_free = 0.3702 target = 0.084196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.062434 restraints weight = 186957.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.065465 restraints weight = 77236.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.067413 restraints weight = 44239.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.068643 restraints weight = 31028.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.069425 restraints weight = 24834.967| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 16192 Z= 0.284 Angle : 0.648 6.235 21936 Z= 0.367 Chirality : 0.043 0.192 2283 Planarity : 0.005 0.061 2935 Dihedral : 6.226 68.182 2283 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.15 % Favored : 93.76 % Rotamer: Outliers : 0.06 % Allowed : 3.55 % Favored : 96.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % 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 are not related in a simple way. whole: -0.51 (0.18), residues: 2050 helix: 1.20 (0.24), residues: 434 sheet: -0.12 (0.18), residues: 711 loop : -1.25 (0.21), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 91 TYR 0.026 0.002 TYR F 537 PHE 0.021 0.002 PHE F 327 TRP 0.020 0.002 TRP F 597 HIS 0.010 0.002 HIS F 457 Details of bonding type rmsd covalent geometry : bond 0.00580 (16190) covalent geometry : angle 0.64796 (21932) SS BOND : bond 0.01767 ( 2) SS BOND : angle 1.74574 ( 4) hydrogen bonds : bond 0.04784 ( 829) hydrogen bonds : angle 5.84188 ( 2322) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue VAL 37 is missing expected H atoms. Skipping. Residue ALA 38 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue ALA 41 is missing expected H atoms. Skipping. Residue ALA 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 46 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue THR 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue ALA 68 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue VAL 77 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue ALA 95 is missing expected H atoms. Skipping. Residue SER 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue SER 104 is missing expected H atoms. Skipping. Residue VAL 105 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue MET 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue ALA 116 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 119 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue TYR 147 is missing expected H atoms. Skipping. Residue SER 148 is missing expected H atoms. Skipping. Residue ALA 149 is missing expected H atoms. Skipping. Residue SER 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue ALA 153 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue VAL 168 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Evaluate side-chains 283 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 282 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 GLU cc_start: 0.9029 (mp0) cc_final: 0.8758 (mp0) REVERT: D 82 ASN cc_start: 0.8825 (t0) cc_final: 0.8201 (t0) REVERT: D 84 ASP cc_start: 0.8706 (m-30) cc_final: 0.8013 (m-30) REVERT: D 117 MET cc_start: 0.9216 (tpp) cc_final: 0.8748 (tpp) REVERT: G 90 PHE cc_start: 0.9483 (m-80) cc_final: 0.9275 (m-80) REVERT: F 627 GLN cc_start: 0.8205 (tm-30) cc_final: 0.7896 (tm-30) REVERT: F 716 MET cc_start: 0.8825 (ppp) cc_final: 0.8314 (ppp) REVERT: A 369 MET cc_start: 0.9104 (mmp) cc_final: 0.8555 (mmp) REVERT: A 531 TYR cc_start: 0.8352 (t80) cc_final: 0.8143 (t80) REVERT: A 630 LEU cc_start: 0.8687 (tp) cc_final: 0.8325 (tt) outliers start: 1 outliers final: 0 residues processed: 283 average time/residue: 0.2958 time to fit residues: 121.0719 Evaluate side-chains 236 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 177 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 170 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 chunk 195 optimal weight: 1.9990 chunk 38 optimal weight: 0.0470 chunk 96 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 178 optimal weight: 4.9990 chunk 152 optimal weight: 0.7980 overall best weight: 1.1684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 69 GLN D 99 ASN F 460 GLN B 301 GLN A 693 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.086918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.065170 restraints weight = 179236.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.068368 restraints weight = 73034.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.070432 restraints weight = 41367.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.071759 restraints weight = 28658.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.072609 restraints weight = 22640.639| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16192 Z= 0.117 Angle : 0.536 5.838 21936 Z= 0.297 Chirality : 0.044 0.176 2283 Planarity : 0.005 0.080 2935 Dihedral : 5.635 63.187 2283 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.59 % Favored : 95.32 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % 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 are not related in a simple way. whole: -0.06 (0.19), residues: 2050 helix: 1.99 (0.25), residues: 435 sheet: -0.05 (0.18), residues: 715 loop : -1.02 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 367 TYR 0.016 0.001 TYR D 184 PHE 0.014 0.001 PHE F 327 TRP 0.021 0.001 TRP F 597 HIS 0.006 0.001 HIS F 431 Details of bonding type rmsd covalent geometry : bond 0.00244 (16190) covalent geometry : angle 0.53577 (21932) SS BOND : bond 0.00843 ( 2) SS BOND : angle 1.94713 ( 4) hydrogen bonds : bond 0.04004 ( 829) hydrogen bonds : angle 5.25020 ( 2322) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue VAL 37 is missing expected H atoms. Skipping. Residue ALA 38 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue ALA 41 is missing expected H atoms. Skipping. Residue ALA 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 46 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue THR 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue ALA 68 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue VAL 77 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue ALA 95 is missing expected H atoms. Skipping. Residue SER 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue SER 104 is missing expected H atoms. Skipping. Residue VAL 105 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue MET 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue ALA 116 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 119 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue TYR 147 is missing expected H atoms. Skipping. Residue SER 148 is missing expected H atoms. Skipping. Residue ALA 149 is missing expected H atoms. Skipping. Residue SER 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue ALA 153 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue VAL 168 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Evaluate side-chains 309 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 309 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 38 ASP cc_start: 0.8194 (p0) cc_final: 0.7975 (p0) REVERT: C 39 GLU cc_start: 0.9086 (mp0) cc_final: 0.8789 (mp0) REVERT: D 82 ASN cc_start: 0.8905 (t0) cc_final: 0.8287 (t0) REVERT: D 84 ASP cc_start: 0.8668 (m-30) cc_final: 0.8031 (m-30) REVERT: D 117 MET cc_start: 0.9179 (tpp) cc_final: 0.8772 (tpp) REVERT: D 204 ASP cc_start: 0.8861 (m-30) cc_final: 0.8287 (p0) REVERT: D 207 ASP cc_start: 0.8598 (m-30) cc_final: 0.8088 (m-30) REVERT: D 232 GLU cc_start: 0.9132 (mm-30) cc_final: 0.8930 (tp30) REVERT: G 134 LEU cc_start: 0.9014 (pt) cc_final: 0.8666 (pt) REVERT: F 524 ASP cc_start: 0.8301 (m-30) cc_final: 0.8089 (m-30) REVERT: F 716 MET cc_start: 0.8774 (ppp) cc_final: 0.8311 (ppp) REVERT: B 144 GLN cc_start: 0.9149 (pp30) cc_final: 0.8901 (tm-30) REVERT: A 307 ASP cc_start: 0.9106 (m-30) cc_final: 0.8803 (m-30) REVERT: A 332 ASP cc_start: 0.8917 (t70) cc_final: 0.8692 (t0) REVERT: A 369 MET cc_start: 0.9101 (mmp) cc_final: 0.8510 (mmt) REVERT: A 447 ASP cc_start: 0.9366 (m-30) cc_final: 0.9155 (p0) REVERT: A 589 ASP cc_start: 0.8607 (t70) cc_final: 0.8185 (m-30) REVERT: A 768 MET cc_start: 0.7369 (mmm) cc_final: 0.7130 (mmm) outliers start: 0 outliers final: 0 residues processed: 309 average time/residue: 0.2962 time to fit residues: 132.5926 Evaluate side-chains 249 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 56 optimal weight: 0.0270 chunk 67 optimal weight: 8.9990 chunk 188 optimal weight: 2.9990 chunk 112 optimal weight: 10.0000 chunk 195 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 100 optimal weight: 9.9990 chunk 169 optimal weight: 2.9990 chunk 198 optimal weight: 0.6980 chunk 197 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 overall best weight: 1.7444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 69 GLN D 99 ASN A 459 ASN A 678 GLN A 693 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.087367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.065739 restraints weight = 182701.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.068903 restraints weight = 74282.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.070954 restraints weight = 42221.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.072259 restraints weight = 29321.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.073085 restraints weight = 23243.934| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16192 Z= 0.137 Angle : 0.524 6.650 21936 Z= 0.291 Chirality : 0.042 0.174 2283 Planarity : 0.004 0.083 2935 Dihedral : 5.450 66.526 2283 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.17 % Favored : 94.73 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % 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 are not related in a simple way. whole: -0.08 (0.19), residues: 2050 helix: 2.09 (0.25), residues: 435 sheet: -0.10 (0.18), residues: 740 loop : -1.07 (0.22), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 231 TYR 0.017 0.001 TYR D 205 PHE 0.013 0.001 PHE G 90 TRP 0.020 0.001 TRP F 597 HIS 0.005 0.001 HIS F 431 Details of bonding type rmsd covalent geometry : bond 0.00281 (16190) covalent geometry : angle 0.52409 (21932) SS BOND : bond 0.02256 ( 2) SS BOND : angle 1.42049 ( 4) hydrogen bonds : bond 0.03828 ( 829) hydrogen bonds : angle 5.11078 ( 2322) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue VAL 37 is missing expected H atoms. Skipping. Residue ALA 38 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue ALA 41 is missing expected H atoms. Skipping. Residue ALA 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 46 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue THR 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue ALA 68 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue VAL 77 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue ALA 95 is missing expected H atoms. Skipping. Residue SER 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue SER 104 is missing expected H atoms. Skipping. Residue VAL 105 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue MET 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue ALA 116 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 119 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue TYR 147 is missing expected H atoms. Skipping. Residue SER 148 is missing expected H atoms. Skipping. Residue ALA 149 is missing expected H atoms. Skipping. Residue SER 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue ALA 153 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue VAL 168 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Evaluate side-chains 295 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 38 ASP cc_start: 0.8165 (p0) cc_final: 0.7894 (p0) REVERT: C 39 GLU cc_start: 0.9066 (mp0) cc_final: 0.8769 (mp0) REVERT: D 82 ASN cc_start: 0.8919 (t0) cc_final: 0.8285 (t0) REVERT: D 84 ASP cc_start: 0.8699 (m-30) cc_final: 0.8029 (m-30) REVERT: D 117 MET cc_start: 0.9197 (tpp) cc_final: 0.8809 (tpp) REVERT: D 204 ASP cc_start: 0.8954 (m-30) cc_final: 0.8367 (p0) REVERT: D 207 ASP cc_start: 0.8609 (m-30) cc_final: 0.8144 (m-30) REVERT: D 227 MET cc_start: 0.8921 (mmm) cc_final: 0.8693 (mmm) REVERT: G 134 LEU cc_start: 0.9052 (pt) cc_final: 0.8719 (pt) REVERT: F 627 GLN cc_start: 0.8183 (tm-30) cc_final: 0.7755 (tm-30) REVERT: F 716 MET cc_start: 0.8765 (ppp) cc_final: 0.8363 (ppp) REVERT: B 64 HIS cc_start: 0.7571 (p90) cc_final: 0.7070 (p90) REVERT: B 144 GLN cc_start: 0.9146 (pp30) cc_final: 0.8872 (tm-30) REVERT: A 307 ASP cc_start: 0.9071 (m-30) cc_final: 0.8781 (m-30) REVERT: A 332 ASP cc_start: 0.8914 (t70) cc_final: 0.8670 (t0) REVERT: A 369 MET cc_start: 0.9162 (mmp) cc_final: 0.8592 (mmp) outliers start: 0 outliers final: 0 residues processed: 295 average time/residue: 0.2910 time to fit residues: 124.7155 Evaluate side-chains 249 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 166 optimal weight: 0.9990 chunk 56 optimal weight: 0.0010 chunk 39 optimal weight: 7.9990 chunk 176 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 190 optimal weight: 0.0670 chunk 147 optimal weight: 5.9990 chunk 48 optimal weight: 20.0000 overall best weight: 1.0130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 ASN A 693 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.088160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.066842 restraints weight = 179674.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.070038 restraints weight = 73017.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.072114 restraints weight = 41185.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.073413 restraints weight = 28457.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.074264 restraints weight = 22492.566| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16192 Z= 0.105 Angle : 0.501 7.229 21936 Z= 0.275 Chirality : 0.043 0.168 2283 Planarity : 0.004 0.069 2935 Dihedral : 5.178 65.232 2283 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.44 % Favored : 95.46 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % 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 are not related in a simple way. whole: 0.11 (0.19), residues: 2050 helix: 2.40 (0.25), residues: 435 sheet: -0.01 (0.18), residues: 718 loop : -1.00 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 421 TYR 0.016 0.001 TYR D 184 PHE 0.014 0.001 PHE A 586 TRP 0.019 0.001 TRP F 597 HIS 0.005 0.001 HIS F 431 Details of bonding type rmsd covalent geometry : bond 0.00219 (16190) covalent geometry : angle 0.50029 (21932) SS BOND : bond 0.01750 ( 2) SS BOND : angle 1.36349 ( 4) hydrogen bonds : bond 0.03569 ( 829) hydrogen bonds : angle 4.87977 ( 2322) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue VAL 37 is missing expected H atoms. Skipping. Residue ALA 38 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue ALA 41 is missing expected H atoms. Skipping. Residue ALA 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 46 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue THR 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue ALA 68 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue VAL 77 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue ALA 95 is missing expected H atoms. Skipping. Residue SER 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue SER 104 is missing expected H atoms. Skipping. Residue VAL 105 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue MET 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue ALA 116 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 119 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue TYR 147 is missing expected H atoms. Skipping. Residue SER 148 is missing expected H atoms. Skipping. Residue ALA 149 is missing expected H atoms. Skipping. Residue SER 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue ALA 153 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue VAL 168 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Evaluate side-chains 295 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 38 ASP cc_start: 0.8191 (p0) cc_final: 0.7954 (p0) REVERT: C 39 GLU cc_start: 0.9057 (mp0) cc_final: 0.8712 (mp0) REVERT: D 82 ASN cc_start: 0.8945 (t0) cc_final: 0.8328 (t0) REVERT: D 84 ASP cc_start: 0.8709 (m-30) cc_final: 0.8038 (m-30) REVERT: D 204 ASP cc_start: 0.8941 (m-30) cc_final: 0.8271 (p0) REVERT: D 207 ASP cc_start: 0.8549 (m-30) cc_final: 0.8090 (m-30) REVERT: G 134 LEU cc_start: 0.9023 (pt) cc_final: 0.8682 (pt) REVERT: F 716 MET cc_start: 0.8769 (ppp) cc_final: 0.8447 (ppp) REVERT: B 64 HIS cc_start: 0.7584 (p90) cc_final: 0.7142 (p90) REVERT: B 144 GLN cc_start: 0.9142 (pp30) cc_final: 0.8856 (tm-30) REVERT: B 165 HIS cc_start: 0.7826 (t-90) cc_final: 0.7013 (t-90) REVERT: A 307 ASP cc_start: 0.9074 (m-30) cc_final: 0.8783 (m-30) REVERT: A 332 ASP cc_start: 0.8934 (t70) cc_final: 0.8684 (t0) REVERT: A 369 MET cc_start: 0.9186 (mmp) cc_final: 0.8519 (mmt) REVERT: A 775 GLN cc_start: 0.9532 (mt0) cc_final: 0.9206 (mp10) outliers start: 0 outliers final: 0 residues processed: 295 average time/residue: 0.2844 time to fit residues: 122.7276 Evaluate side-chains 248 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 161 optimal weight: 2.9990 chunk 193 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 184 optimal weight: 5.9990 chunk 82 optimal weight: 0.7980 chunk 3 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 160 optimal weight: 0.9980 chunk 6 optimal weight: 9.9990 chunk 154 optimal weight: 6.9990 chunk 153 optimal weight: 5.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 69 GLN D 99 ASN F 443 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.086702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.064893 restraints weight = 186219.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.068018 restraints weight = 76421.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.070022 restraints weight = 43681.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.071276 restraints weight = 30668.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.072100 restraints weight = 24557.255| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16192 Z= 0.182 Angle : 0.539 8.747 21936 Z= 0.299 Chirality : 0.042 0.163 2283 Planarity : 0.004 0.059 2935 Dihedral : 5.306 68.875 2283 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.56 % Favored : 94.39 % Rotamer: Outliers : 0.06 % Allowed : 1.23 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % 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 are not related in a simple way. whole: -0.11 (0.19), residues: 2050 helix: 2.12 (0.25), residues: 435 sheet: -0.16 (0.18), residues: 744 loop : -1.09 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 47 TYR 0.015 0.001 TYR D 205 PHE 0.013 0.001 PHE A 572 TRP 0.020 0.001 TRP A 635 HIS 0.010 0.002 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00375 (16190) covalent geometry : angle 0.53894 (21932) SS BOND : bond 0.01331 ( 2) SS BOND : angle 1.44387 ( 4) hydrogen bonds : bond 0.03812 ( 829) hydrogen bonds : angle 5.07811 ( 2322) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue VAL 37 is missing expected H atoms. Skipping. Residue ALA 38 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue ALA 41 is missing expected H atoms. Skipping. Residue ALA 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 46 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue THR 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue ALA 68 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue VAL 77 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue ALA 95 is missing expected H atoms. Skipping. Residue SER 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue SER 104 is missing expected H atoms. Skipping. Residue VAL 105 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue MET 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue ALA 116 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 119 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue TYR 147 is missing expected H atoms. Skipping. Residue SER 148 is missing expected H atoms. Skipping. Residue ALA 149 is missing expected H atoms. Skipping. Residue SER 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue ALA 153 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue VAL 168 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Evaluate side-chains 283 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 282 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 38 ASP cc_start: 0.8195 (p0) cc_final: 0.7961 (p0) REVERT: C 39 GLU cc_start: 0.9052 (mp0) cc_final: 0.8725 (mp0) REVERT: D 82 ASN cc_start: 0.8946 (t0) cc_final: 0.8310 (t0) REVERT: D 84 ASP cc_start: 0.8759 (m-30) cc_final: 0.7991 (m-30) REVERT: D 117 MET cc_start: 0.9227 (tpp) cc_final: 0.8855 (tpp) REVERT: G 28 GLN cc_start: 0.8673 (pm20) cc_final: 0.8433 (pm20) REVERT: G 134 LEU cc_start: 0.9095 (pt) cc_final: 0.8765 (pt) REVERT: G 142 MET cc_start: 0.8269 (tmm) cc_final: 0.7435 (tmm) REVERT: G 146 GLU cc_start: 0.9141 (mt-10) cc_final: 0.8518 (mt-10) REVERT: F 287 MET cc_start: 0.8046 (mtt) cc_final: 0.7505 (mtt) REVERT: F 443 ASN cc_start: 0.7304 (OUTLIER) cc_final: 0.7063 (t0) REVERT: F 716 MET cc_start: 0.8794 (ppp) cc_final: 0.8424 (ppp) REVERT: B 64 HIS cc_start: 0.7530 (p90) cc_final: 0.7064 (p90) REVERT: A 332 ASP cc_start: 0.8949 (t70) cc_final: 0.8693 (t0) REVERT: A 369 MET cc_start: 0.9198 (mmp) cc_final: 0.8638 (mmp) REVERT: A 775 GLN cc_start: 0.9525 (mt0) cc_final: 0.9221 (mp10) outliers start: 1 outliers final: 0 residues processed: 283 average time/residue: 0.2778 time to fit residues: 115.7432 Evaluate side-chains 242 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 241 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 112 optimal weight: 10.0000 chunk 69 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 189 optimal weight: 7.9990 chunk 74 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 chunk 98 optimal weight: 7.9990 chunk 103 optimal weight: 7.9990 chunk 180 optimal weight: 3.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 69 GLN D 99 ASN ** D 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 138 ASN ** F 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN A 371 GLN A 561 GLN A 606 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.083144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.061676 restraints weight = 190400.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.064566 restraints weight = 79635.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.066425 restraints weight = 46448.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.067583 restraints weight = 33025.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.068325 restraints weight = 26707.685| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 16192 Z= 0.341 Angle : 0.691 7.146 21936 Z= 0.389 Chirality : 0.044 0.164 2283 Planarity : 0.006 0.056 2935 Dihedral : 6.027 71.528 2283 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.46 % Favored : 92.49 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % 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 are not related in a simple way. whole: -0.91 (0.18), residues: 2050 helix: 1.09 (0.25), residues: 431 sheet: -0.44 (0.18), residues: 757 loop : -1.60 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 346 TYR 0.021 0.002 TYR F 644 PHE 0.026 0.002 PHE A 572 TRP 0.025 0.002 TRP F 597 HIS 0.017 0.003 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00696 (16190) covalent geometry : angle 0.69099 (21932) SS BOND : bond 0.02892 ( 2) SS BOND : angle 1.20254 ( 4) hydrogen bonds : bond 0.04578 ( 829) hydrogen bonds : angle 5.81400 ( 2322) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue VAL 37 is missing expected H atoms. Skipping. Residue ALA 38 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue ALA 41 is missing expected H atoms. Skipping. Residue ALA 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 46 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue THR 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue ALA 68 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue VAL 77 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue ALA 95 is missing expected H atoms. Skipping. Residue SER 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue SER 104 is missing expected H atoms. Skipping. Residue VAL 105 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue MET 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue ALA 116 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 119 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue TYR 147 is missing expected H atoms. Skipping. Residue SER 148 is missing expected H atoms. Skipping. Residue ALA 149 is missing expected H atoms. Skipping. Residue SER 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue ALA 153 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue VAL 168 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Evaluate side-chains 253 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 38 ASP cc_start: 0.8229 (p0) cc_final: 0.7987 (p0) REVERT: C 39 GLU cc_start: 0.9022 (mp0) cc_final: 0.8693 (mp0) REVERT: C 80 LEU cc_start: 0.7998 (tp) cc_final: 0.7794 (tp) REVERT: D 82 ASN cc_start: 0.8969 (t0) cc_final: 0.8331 (t0) REVERT: D 84 ASP cc_start: 0.8823 (m-30) cc_final: 0.8125 (m-30) REVERT: D 117 MET cc_start: 0.9290 (tpp) cc_final: 0.8804 (tpp) REVERT: D 183 GLU cc_start: 0.9042 (tm-30) cc_final: 0.8789 (tm-30) REVERT: G 134 LEU cc_start: 0.9207 (pt) cc_final: 0.8815 (pt) REVERT: G 142 MET cc_start: 0.8257 (tmm) cc_final: 0.7323 (tmm) REVERT: G 146 GLU cc_start: 0.9143 (mt-10) cc_final: 0.8560 (mt-10) REVERT: F 627 GLN cc_start: 0.7795 (tm-30) cc_final: 0.7504 (tm-30) REVERT: F 716 MET cc_start: 0.8832 (ppp) cc_final: 0.8295 (ppp) REVERT: B 231 ARG cc_start: 0.9261 (ttt-90) cc_final: 0.8983 (ttp80) REVERT: A 332 ASP cc_start: 0.8970 (t70) cc_final: 0.8723 (t0) REVERT: A 765 ASN cc_start: 0.9165 (m110) cc_final: 0.8754 (p0) REVERT: A 775 GLN cc_start: 0.9541 (mt0) cc_final: 0.9222 (mp10) outliers start: 0 outliers final: 0 residues processed: 253 average time/residue: 0.2821 time to fit residues: 104.7493 Evaluate side-chains 202 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 100 optimal weight: 7.9990 chunk 137 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 134 optimal weight: 20.0000 chunk 171 optimal weight: 0.0170 chunk 20 optimal weight: 0.9990 chunk 68 optimal weight: 7.9990 chunk 130 optimal weight: 40.0000 chunk 80 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.1824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 367 ASN A 446 GLN A 561 GLN A 693 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.086250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.064648 restraints weight = 182692.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.067748 restraints weight = 74999.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.069747 restraints weight = 43014.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.071024 restraints weight = 30157.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.071846 restraints weight = 24027.553| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 16192 Z= 0.116 Angle : 0.539 10.311 21936 Z= 0.295 Chirality : 0.044 0.209 2283 Planarity : 0.005 0.052 2935 Dihedral : 5.394 65.555 2283 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.20 % Favored : 95.71 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 1.22 % 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 are not related in a simple way. whole: -0.31 (0.19), residues: 2050 helix: 1.99 (0.25), residues: 434 sheet: -0.25 (0.18), residues: 728 loop : -1.26 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 231 TYR 0.016 0.001 TYR F 537 PHE 0.017 0.001 PHE G 123 TRP 0.040 0.001 TRP B 348 HIS 0.007 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00242 (16190) covalent geometry : angle 0.53860 (21932) SS BOND : bond 0.02292 ( 2) SS BOND : angle 2.16701 ( 4) hydrogen bonds : bond 0.03711 ( 829) hydrogen bonds : angle 5.13020 ( 2322) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue VAL 37 is missing expected H atoms. Skipping. Residue ALA 38 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue ALA 41 is missing expected H atoms. Skipping. Residue ALA 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 46 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue THR 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue ALA 68 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue VAL 77 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue ALA 95 is missing expected H atoms. Skipping. Residue SER 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue SER 104 is missing expected H atoms. Skipping. Residue VAL 105 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue MET 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue ALA 116 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 119 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue TYR 147 is missing expected H atoms. Skipping. Residue SER 148 is missing expected H atoms. Skipping. Residue ALA 149 is missing expected H atoms. Skipping. Residue SER 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue ALA 153 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue VAL 168 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Evaluate side-chains 280 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 38 ASP cc_start: 0.8170 (p0) cc_final: 0.7916 (p0) REVERT: C 39 GLU cc_start: 0.9057 (mp0) cc_final: 0.8725 (mp0) REVERT: D 82 ASN cc_start: 0.9004 (t0) cc_final: 0.8386 (t0) REVERT: D 84 ASP cc_start: 0.8725 (m-30) cc_final: 0.8075 (m-30) REVERT: D 117 MET cc_start: 0.9262 (tpp) cc_final: 0.8806 (tpp) REVERT: D 219 GLU cc_start: 0.8943 (tp30) cc_final: 0.8418 (tm-30) REVERT: G 114 ASP cc_start: 0.7970 (t70) cc_final: 0.7620 (t70) REVERT: G 134 LEU cc_start: 0.9069 (pt) cc_final: 0.8814 (pt) REVERT: G 142 MET cc_start: 0.8272 (tmm) cc_final: 0.7707 (tmm) REVERT: G 143 ILE cc_start: 0.9480 (pt) cc_final: 0.9178 (pt) REVERT: G 146 GLU cc_start: 0.9137 (mt-10) cc_final: 0.8850 (mt-10) REVERT: F 716 MET cc_start: 0.8766 (ppp) cc_final: 0.8335 (ppp) REVERT: B 231 ARG cc_start: 0.9225 (ttt-90) cc_final: 0.8954 (ttp80) REVERT: A 369 MET cc_start: 0.9213 (mmp) cc_final: 0.8648 (mmp) REVERT: A 765 ASN cc_start: 0.9068 (m110) cc_final: 0.8713 (p0) REVERT: A 775 GLN cc_start: 0.9546 (mt0) cc_final: 0.9255 (mp10) outliers start: 0 outliers final: 0 residues processed: 280 average time/residue: 0.2749 time to fit residues: 113.2858 Evaluate side-chains 226 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 154 optimal weight: 6.9990 chunk 126 optimal weight: 10.0000 chunk 97 optimal weight: 7.9990 chunk 131 optimal weight: 40.0000 chunk 19 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 chunk 48 optimal weight: 20.0000 chunk 102 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 446 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.085282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.063536 restraints weight = 189836.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.066540 restraints weight = 78854.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.068460 restraints weight = 45928.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.069658 restraints weight = 32590.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.070423 restraints weight = 26345.787| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.4589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16192 Z= 0.206 Angle : 0.575 9.913 21936 Z= 0.318 Chirality : 0.042 0.178 2283 Planarity : 0.005 0.057 2935 Dihedral : 5.478 67.184 2283 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.95 % Favored : 93.95 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 1.22 % 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 are not related in a simple way. whole: -0.53 (0.19), residues: 2050 helix: 1.80 (0.25), residues: 433 sheet: -0.34 (0.18), residues: 733 loop : -1.43 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 623 TYR 0.020 0.002 TYR E 28 PHE 0.017 0.002 PHE G 123 TRP 0.027 0.002 TRP B 348 HIS 0.011 0.002 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00422 (16190) covalent geometry : angle 0.57436 (21932) SS BOND : bond 0.02796 ( 2) SS BOND : angle 1.50483 ( 4) hydrogen bonds : bond 0.03910 ( 829) hydrogen bonds : angle 5.30400 ( 2322) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4100 Ramachandran restraints generated. 2050 Oldfield, 0 Emsley, 2050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 25 is missing expected H atoms. Skipping. Residue VAL 26 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LEU 34 is missing expected H atoms. Skipping. Residue VAL 37 is missing expected H atoms. Skipping. Residue ALA 38 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue ALA 41 is missing expected H atoms. Skipping. Residue ALA 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue MET 46 is missing expected H atoms. Skipping. Residue VAL 48 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue THR 53 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue SER 60 is missing expected H atoms. Skipping. Residue THR 62 is missing expected H atoms. Skipping. Residue ILE 63 is missing expected H atoms. Skipping. Residue ALA 65 is missing expected H atoms. Skipping. Residue LEU 66 is missing expected H atoms. Skipping. Residue ALA 68 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue VAL 75 is missing expected H atoms. Skipping. Residue VAL 77 is missing expected H atoms. Skipping. Residue LEU 78 is missing expected H atoms. Skipping. Residue THR 83 is missing expected H atoms. Skipping. Residue LEU 84 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue VAL 88 is missing expected H atoms. Skipping. Residue LYS 89 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue ILE 94 is missing expected H atoms. Skipping. Residue ALA 95 is missing expected H atoms. Skipping. Residue SER 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LYS 103 is missing expected H atoms. Skipping. Residue SER 104 is missing expected H atoms. Skipping. Residue VAL 105 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue MET 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue ALA 116 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 119 is missing expected H atoms. Skipping. Residue VAL 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue ILE 130 is missing expected H atoms. Skipping. Residue ALA 131 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue LYS 135 is missing expected H atoms. Skipping. Residue LEU 137 is missing expected H atoms. Skipping. Residue TYR 141 is missing expected H atoms. Skipping. Residue TYR 142 is missing expected H atoms. Skipping. Residue SER 143 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue TYR 147 is missing expected H atoms. Skipping. Residue SER 148 is missing expected H atoms. Skipping. Residue ALA 149 is missing expected H atoms. Skipping. Residue SER 150 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue ALA 153 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue THR 156 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue VAL 163 is missing expected H atoms. Skipping. Residue LEU 165 is missing expected H atoms. Skipping. Residue LYS 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue VAL 168 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Evaluate side-chains 265 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 38 ASP cc_start: 0.8231 (p0) cc_final: 0.7957 (p0) REVERT: C 39 GLU cc_start: 0.9078 (mp0) cc_final: 0.8750 (mp0) REVERT: D 82 ASN cc_start: 0.9008 (t0) cc_final: 0.8365 (t0) REVERT: D 84 ASP cc_start: 0.8787 (m-30) cc_final: 0.8123 (m-30) REVERT: D 117 MET cc_start: 0.9265 (tpp) cc_final: 0.8823 (tpp) REVERT: G 134 LEU cc_start: 0.9164 (pt) cc_final: 0.8813 (pt) REVERT: G 142 MET cc_start: 0.8255 (tmm) cc_final: 0.7331 (tmm) REVERT: G 146 GLU cc_start: 0.9181 (mt-10) cc_final: 0.8583 (mt-10) REVERT: F 716 MET cc_start: 0.8818 (ppp) cc_final: 0.8357 (ppp) REVERT: B 231 ARG cc_start: 0.9252 (ttt-90) cc_final: 0.8992 (ttp80) REVERT: A 765 ASN cc_start: 0.9100 (m110) cc_final: 0.8718 (p0) REVERT: A 775 GLN cc_start: 0.9558 (mt0) cc_final: 0.9233 (mp10) outliers start: 0 outliers final: 0 residues processed: 265 average time/residue: 0.2611 time to fit residues: 102.2549 Evaluate side-chains 212 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 186 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 48 optimal weight: 20.0000 chunk 78 optimal weight: 4.9990 chunk 123 optimal weight: 10.0000 chunk 143 optimal weight: 6.9990 chunk 151 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 446 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.084332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.062572 restraints weight = 193534.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.065516 restraints weight = 80943.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.067372 restraints weight = 47424.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.068559 restraints weight = 33919.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.069214 restraints weight = 27494.558| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.4848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16192 Z= 0.249 Angle : 0.604 9.276 21936 Z= 0.336 Chirality : 0.043 0.173 2283 Planarity : 0.005 0.053 2935 Dihedral : 5.662 70.738 2283 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.88 % Favored : 93.02 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 1.22 % 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 are not related in a simple way. whole: -0.81 (0.19), residues: 2050 helix: 1.48 (0.25), residues: 434 sheet: -0.53 (0.18), residues: 722 loop : -1.54 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 623 TYR 0.020 0.002 TYR E 28 PHE 0.016 0.002 PHE A 572 TRP 0.027 0.002 TRP B 348 HIS 0.008 0.002 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00505 (16190) covalent geometry : angle 0.60365 (21932) SS BOND : bond 0.02565 ( 2) SS BOND : angle 1.17286 ( 4) hydrogen bonds : bond 0.04057 ( 829) hydrogen bonds : angle 5.48121 ( 2322) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5217.90 seconds wall clock time: 89 minutes 28.61 seconds (5368.61 seconds total)