Starting phenix.real_space_refine on Tue Mar 3 23:43:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fim_31603/03_2026/7fim_31603.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fim_31603/03_2026/7fim_31603.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7fim_31603/03_2026/7fim_31603.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fim_31603/03_2026/7fim_31603.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7fim_31603/03_2026/7fim_31603.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fim_31603/03_2026/7fim_31603.map" } resolution = 3.4 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= 0.063 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 5877 2.51 5 N 1595 2.21 5 O 1687 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9213 Number of models: 1 Model: "" Number of chains: 6 Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "B" Number of atoms: 2588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2588 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 1884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1884 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 6, 'TRANS': 219} Chain breaks: 3 Chain: "R" Number of atoms: 3115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3115 Classifications: {'peptide': 382} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 13, 'TRANS': 368} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 2, 'GLN:plan1': 1, 'PHE:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "P" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'AIB:plan-1': 2} Unresolved non-hydrogen planarities: 2 Time building chain proxies: 2.08, per 1000 atoms: 0.23 Number of scatterers: 9213 At special positions: 0 Unit cell: (79.254, 99.603, 174.573, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 1687 8.00 N 1595 7.00 C 5877 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS N 24 " - pdb=" SG CYS N 98 " distance=2.03 Simple disulfide: pdb=" SG CYS N 101 " - pdb=" SG CYS N 109 " distance=2.03 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.04 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.58 Conformation dependent library (CDL) restraints added in 346.8 milliseconds 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2176 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 11 sheets defined 41.3% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'N' and resid 63 through 67 removed outlier: 3.961A pdb=" N LYS N 67 " --> pdb=" O GLY N 64 " (cutoff:3.500A) Processing helix chain 'N' and resid 89 through 93 removed outlier: 3.950A pdb=" N THR N 93 " --> pdb=" O PRO N 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 30 removed outlier: 3.910A pdb=" N GLN B 14 " --> pdb=" O ASP B 10 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU B 15 " --> pdb=" O GLN B 11 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N CYS B 30 " --> pdb=" O ALA B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 39 Processing helix chain 'B' and resid 133 through 137 removed outlier: 3.693A pdb=" N GLY B 136 " --> pdb=" O THR B 133 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN B 137 " --> pdb=" O ARG B 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 133 through 137' Processing helix chain 'A' and resid 13 through 38 removed outlier: 3.746A pdb=" N ALA A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU A 21 " --> pdb=" O LYS A 17 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LYS A 24 " --> pdb=" O ARG A 20 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LYS A 25 " --> pdb=" O GLU A 21 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 64 removed outlier: 3.752A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 237 removed outlier: 3.831A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 removed outlier: 3.796A pdb=" N LEU A 272 " --> pdb=" O ALA A 268 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE A 273 " --> pdb=" O ALA A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.872A pdb=" N ALA A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 removed outlier: 4.039A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 4.143A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N PHE A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 391 removed outlier: 3.641A pdb=" N ASP A 378 " --> pdb=" O ARG A 374 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASP A 381 " --> pdb=" O ASN A 377 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 53 removed outlier: 4.300A pdb=" N ASP R 53 " --> pdb=" O SER R 49 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 169 removed outlier: 3.580A pdb=" N ILE R 147 " --> pdb=" O PHE R 143 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL R 150 " --> pdb=" O ILE R 146 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE R 161 " --> pdb=" O SER R 157 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU R 166 " --> pdb=" O ALA R 162 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE R 169 " --> pdb=" O ILE R 165 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 205 removed outlier: 3.752A pdb=" N SER R 193 " --> pdb=" O LEU R 189 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LYS R 202 " --> pdb=" O ASP R 198 " (cutoff:3.500A) Processing helix chain 'R' and resid 206 through 215 removed outlier: 3.632A pdb=" N HIS R 212 " --> pdb=" O ALA R 208 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN R 213 " --> pdb=" O ALA R 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 223 through 239 removed outlier: 3.684A pdb=" N ARG R 227 " --> pdb=" O SER R 223 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE R 230 " --> pdb=" O CYS R 226 " (cutoff:3.500A) Processing helix chain 'R' and resid 242 through 256 removed outlier: 3.581A pdb=" N GLU R 247 " --> pdb=" O TRP R 243 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 275 removed outlier: 3.564A pdb=" N SER R 271 " --> pdb=" O ARG R 267 " (cutoff:3.500A) Processing helix chain 'R' and resid 276 through 279 Processing helix chain 'R' and resid 281 through 291 Processing helix chain 'R' and resid 294 through 298 removed outlier: 3.634A pdb=" N TRP R 297 " --> pdb=" O GLU R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 306 through 336 Proline residue: R 312 - end of helix removed outlier: 3.637A pdb=" N ILE R 317 " --> pdb=" O ILE R 313 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE R 323 " --> pdb=" O VAL R 319 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE R 324 " --> pdb=" O ASN R 320 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL R 327 " --> pdb=" O ILE R 323 " (cutoff:3.500A) Processing helix chain 'R' and resid 346 through 361 Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 362 through 368 removed outlier: 4.015A pdb=" N ILE R 366 " --> pdb=" O HIS R 363 " (cutoff:3.500A) Processing helix chain 'R' and resid 377 through 387 removed outlier: 3.729A pdb=" N GLU R 387 " --> pdb=" O LYS R 383 " (cutoff:3.500A) Processing helix chain 'R' and resid 393 through 404 removed outlier: 4.076A pdb=" N TYR R 402 " --> pdb=" O VAL R 398 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 422 removed outlier: 3.571A pdb=" N GLU R 412 " --> pdb=" O GLU R 408 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 23 removed outlier: 3.577A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.810A pdb=" N ASP G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N CYS G 41 " --> pdb=" O LEU G 37 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU G 42 " --> pdb=" O MET G 38 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 29 removed outlier: 3.707A pdb=" N ILE P 17 " --> pdb=" O AIB P 13 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'N' and resid 5 through 8 removed outlier: 3.881A pdb=" N THR N 80 " --> pdb=" O ASP N 75 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASP N 75 " --> pdb=" O THR N 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 47 through 53 removed outlier: 6.626A pdb=" N TRP N 38 " --> pdb=" O VAL N 50 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ASP N 52 " --> pdb=" O MET N 36 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N MET N 36 " --> pdb=" O ASP N 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 52 through 57 removed outlier: 3.844A pdb=" N ARG B 54 " --> pdb=" O ILE B 343 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N PHE B 340 " --> pdb=" O SER B 336 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER B 336 " --> pdb=" O PHE B 340 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LYS B 342 " --> pdb=" O THR B 334 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 63 through 68 removed outlier: 4.059A pdb=" N ALA B 65 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA B 78 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU B 75 " --> pdb=" O TRP B 87 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N HIS B 96 " --> pdb=" O ILE B 86 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ASP B 88 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LYS B 94 " --> pdb=" O ASP B 88 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 107 through 108 removed outlier: 4.246A pdb=" N GLY B 120 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG B 142 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ASN B 130 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL B 140 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 151 through 156 removed outlier: 4.152A pdb=" N THR B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 192 through 197 removed outlier: 3.788A pdb=" N SER B 194 " --> pdb=" O GLY B 207 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS B 214 " --> pdb=" O SER B 206 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLN B 225 " --> pdb=" O LEU B 215 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 234 through 239 removed outlier: 3.543A pdb=" N ARG B 256 " --> pdb=" O THR B 248 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N SER B 250 " --> pdb=" O THR B 254 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N THR B 254 " --> pdb=" O SER B 250 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N MET B 267 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ASP B 259 " --> pdb=" O GLU B 265 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLU B 265 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 281 through 283 removed outlier: 3.644A pdb=" N LEU B 313 " --> pdb=" O CYS B 299 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 213 through 214 removed outlier: 3.897A pdb=" N PHE A 222 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 9.672A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR A 360 " --> pdb=" O VAL A 287 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 82 through 84 399 hydrogen bonds defined for protein. 1137 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: 1.40 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1492 1.31 - 1.44: 2686 1.44 - 1.57: 5168 1.57 - 1.69: 1 1.69 - 1.82: 73 Bond restraints: 9420 Sorted by residual: bond pdb=" C GLU P 3 " pdb=" N GLY P 4 " ideal model delta sigma weight residual 1.333 1.392 -0.059 1.43e-02 4.89e+03 1.68e+01 bond pdb=" C AIB P 2 " pdb=" N GLU P 3 " ideal model delta sigma weight residual 1.329 1.279 0.050 1.40e-02 5.10e+03 1.28e+01 bond pdb=" CA LEU R 172 " pdb=" CB LEU R 172 " ideal model delta sigma weight residual 1.527 1.586 -0.059 1.75e-02 3.27e+03 1.13e+01 bond pdb=" N LEU A 266 " pdb=" CA LEU A 266 " ideal model delta sigma weight residual 1.459 1.487 -0.027 1.19e-02 7.06e+03 5.30e+00 bond pdb=" N SER A 250 " pdb=" CA SER A 250 " ideal model delta sigma weight residual 1.457 1.486 -0.030 1.31e-02 5.83e+03 5.18e+00 ... (remaining 9415 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 12337 1.96 - 3.93: 350 3.93 - 5.89: 51 5.89 - 7.85: 24 7.85 - 9.82: 8 Bond angle restraints: 12770 Sorted by residual: angle pdb=" N ARG A 265 " pdb=" CA ARG A 265 " pdb=" C ARG A 265 " ideal model delta sigma weight residual 114.31 104.68 9.63 1.29e+00 6.01e-01 5.58e+01 angle pdb=" N LEU R 411 " pdb=" CA LEU R 411 " pdb=" C LEU R 411 " ideal model delta sigma weight residual 111.28 106.76 4.52 1.09e+00 8.42e-01 1.72e+01 angle pdb=" CB LYS P 16 " pdb=" CG LYS P 16 " pdb=" CD LYS P 16 " ideal model delta sigma weight residual 111.30 120.47 -9.17 2.30e+00 1.89e-01 1.59e+01 angle pdb=" C ILE R 147 " pdb=" N TYR R 148 " pdb=" CA TYR R 148 " ideal model delta sigma weight residual 121.58 114.32 7.26 1.95e+00 2.63e-01 1.39e+01 angle pdb=" CA AIB P 2 " pdb=" C AIB P 2 " pdb=" N GLU P 3 " ideal model delta sigma weight residual 116.20 123.36 -7.16 2.00e+00 2.50e-01 1.28e+01 ... (remaining 12765 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 5015 17.46 - 34.91: 456 34.91 - 52.37: 74 52.37 - 69.83: 10 69.83 - 87.28: 11 Dihedral angle restraints: 5566 sinusoidal: 2199 harmonic: 3367 Sorted by residual: dihedral pdb=" CB CYS R 85 " pdb=" SG CYS R 85 " pdb=" SG CYS R 126 " pdb=" CB CYS R 126 " ideal model delta sinusoidal sigma weight residual 93.00 164.38 -71.38 1 1.00e+01 1.00e-02 6.53e+01 dihedral pdb=" CA PRO R 55 " pdb=" C PRO R 55 " pdb=" N PRO R 56 " pdb=" CA PRO R 56 " ideal model delta harmonic sigma weight residual -180.00 -152.01 -27.99 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA THR B 70 " pdb=" C THR B 70 " pdb=" N ASP B 71 " pdb=" CA ASP B 71 " ideal model delta harmonic sigma weight residual 180.00 159.98 20.02 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 5563 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1064 0.052 - 0.104: 290 0.104 - 0.155: 49 0.155 - 0.207: 4 0.207 - 0.259: 3 Chirality restraints: 1410 Sorted by residual: chirality pdb=" CA LEU R 411 " pdb=" N LEU R 411 " pdb=" C LEU R 411 " pdb=" CB LEU R 411 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CB ILE R 357 " pdb=" CA ILE R 357 " pdb=" CG1 ILE R 357 " pdb=" CG2 ILE R 357 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CB VAL R 319 " pdb=" CA VAL R 319 " pdb=" CG1 VAL R 319 " pdb=" CG2 VAL R 319 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 1407 not shown) Planarity restraints: 1620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 311 " 0.053 5.00e-02 4.00e+02 7.98e-02 1.02e+01 pdb=" N PRO R 312 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO R 312 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO R 312 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO R 55 " 0.053 5.00e-02 4.00e+02 7.92e-02 1.00e+01 pdb=" N PRO R 56 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO R 56 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO R 56 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 54 " -0.029 5.00e-02 4.00e+02 4.47e-02 3.19e+00 pdb=" N PRO G 55 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO G 55 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO G 55 " -0.025 5.00e-02 4.00e+02 ... (remaining 1617 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1404 2.76 - 3.30: 8974 3.30 - 3.83: 15382 3.83 - 4.37: 17808 4.37 - 4.90: 29983 Nonbonded interactions: 73551 Sorted by model distance: nonbonded pdb=" OD1 ASP N 52 " pdb=" OG SER N 61 " model vdw 2.226 3.040 nonbonded pdb=" O PHE R 367 " pdb=" NZ LYS R 383 " model vdw 2.244 3.120 nonbonded pdb=" O SER N 54 " pdb=" NH1 ARG N 74 " model vdw 2.249 3.120 nonbonded pdb=" OG SER B 152 " pdb=" O VAL B 192 " model vdw 2.251 3.040 nonbonded pdb=" OG1 THR R 105 " pdb=" O LEU R 109 " model vdw 2.256 3.040 ... (remaining 73546 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.100 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6203 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 0.059 9426 Z= 0.189 Angle : 0.835 9.816 12782 Z= 0.458 Chirality : 0.047 0.259 1410 Planarity : 0.005 0.080 1620 Dihedral : 13.919 87.284 3372 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.41 % Allowed : 0.31 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.72 (0.23), residues: 1130 helix: -1.95 (0.21), residues: 438 sheet: -1.54 (0.35), residues: 222 loop : -1.56 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG G 13 TYR 0.015 0.001 TYR P 10 PHE 0.017 0.001 PHE N 110 TRP 0.018 0.001 TRP R 72 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 9420) covalent geometry : angle 0.83455 (12770) SS BOND : bond 0.00344 ( 6) SS BOND : angle 1.33496 ( 12) hydrogen bonds : bond 0.21641 ( 399) hydrogen bonds : angle 7.68338 ( 1137) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 315 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU R 127 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 34 TYR cc_start: 0.6825 (m-10) cc_final: 0.6121 (m-80) REVERT: N 48 GLU cc_start: 0.8312 (pp20) cc_final: 0.7946 (pp20) REVERT: N 111 ASP cc_start: 0.7222 (m-30) cc_final: 0.6950 (t0) REVERT: N 114 SER cc_start: 0.8261 (t) cc_final: 0.7461 (m) REVERT: N 115 THR cc_start: 0.8470 (p) cc_final: 0.8207 (p) REVERT: B 17 GLU cc_start: 0.8702 (tm-30) cc_final: 0.8413 (tm-30) REVERT: B 49 GLN cc_start: 0.6725 (pp30) cc_final: 0.6380 (pp30) REVERT: B 63 ILE cc_start: 0.6849 (mt) cc_final: 0.6600 (mm) REVERT: B 194 SER cc_start: 0.8287 (t) cc_final: 0.8079 (p) REVERT: B 248 THR cc_start: 0.7754 (p) cc_final: 0.7540 (p) REVERT: B 251 ASP cc_start: 0.7170 (t0) cc_final: 0.6789 (m-30) REVERT: B 264 GLN cc_start: 0.7312 (pt0) cc_final: 0.6704 (tm-30) REVERT: B 285 LYS cc_start: 0.6623 (pptt) cc_final: 0.5466 (mmpt) REVERT: A 265 ARG cc_start: 0.7110 (OUTLIER) cc_final: 0.6787 (tpt170) REVERT: A 343 ASP cc_start: 0.8150 (m-30) cc_final: 0.7592 (m-30) REVERT: A 356 ARG cc_start: 0.6894 (mtm-85) cc_final: 0.6532 (mtm180) REVERT: A 377 ASN cc_start: 0.6999 (m-40) cc_final: 0.6494 (m110) REVERT: R 44 ARG cc_start: 0.9093 (ttp-110) cc_final: 0.8760 (ttp80) REVERT: R 74 ASP cc_start: 0.7590 (t0) cc_final: 0.7258 (t0) REVERT: R 170 ARG cc_start: 0.7599 (tpp80) cc_final: 0.7141 (mmm-85) REVERT: R 336 LYS cc_start: 0.7984 (mmtt) cc_final: 0.7188 (mtmt) REVERT: R 397 MET cc_start: 0.6642 (mmp) cc_final: 0.5785 (mtt) REVERT: G 9 ILE cc_start: 0.8573 (mt) cc_final: 0.8284 (mm) REVERT: G 14 LYS cc_start: 0.8839 (ptpp) cc_final: 0.8627 (pttt) REVERT: G 17 GLU cc_start: 0.9169 (pp20) cc_final: 0.8939 (pp20) REVERT: P 25 TRP cc_start: 0.6556 (t60) cc_final: 0.6266 (t60) outliers start: 4 outliers final: 2 residues processed: 319 average time/residue: 0.1131 time to fit residues: 47.1578 Evaluate side-chains 194 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 191 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain R residue 320 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.0060 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 106 optimal weight: 0.7980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN R 177 ASN R 210 GLN R 212 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.164322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.129361 restraints weight = 13119.901| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.49 r_work: 0.3456 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9426 Z= 0.144 Angle : 0.634 10.869 12782 Z= 0.330 Chirality : 0.044 0.177 1410 Planarity : 0.005 0.066 1620 Dihedral : 5.234 54.970 1273 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.75 % Allowed : 11.10 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.24), residues: 1130 helix: -0.61 (0.24), residues: 437 sheet: -1.31 (0.33), residues: 236 loop : -1.24 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 40 TYR 0.019 0.001 TYR R 145 PHE 0.014 0.001 PHE N 110 TRP 0.013 0.001 TRP N 49 HIS 0.010 0.001 HIS R 212 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 9420) covalent geometry : angle 0.63371 (12770) SS BOND : bond 0.00449 ( 6) SS BOND : angle 0.81122 ( 12) hydrogen bonds : bond 0.04319 ( 399) hydrogen bonds : angle 5.07197 ( 1137) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 215 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU R 127 " (corrupted residue). Skipping it. REVERT: N 48 GLU cc_start: 0.8242 (pp20) cc_final: 0.7406 (pt0) REVERT: N 114 SER cc_start: 0.8228 (t) cc_final: 0.7662 (t) REVERT: B 285 LYS cc_start: 0.7482 (pptt) cc_final: 0.6531 (mmpt) REVERT: A 343 ASP cc_start: 0.8576 (m-30) cc_final: 0.7964 (m-30) REVERT: R 74 ASP cc_start: 0.6890 (t0) cc_final: 0.6435 (t0) REVERT: R 99 HIS cc_start: 0.8079 (m90) cc_final: 0.7827 (t-90) REVERT: R 182 ASN cc_start: 0.8637 (t0) cc_final: 0.8414 (t0) REVERT: R 215 ASP cc_start: 0.7694 (m-30) cc_final: 0.7113 (p0) REVERT: R 304 ASN cc_start: 0.7830 (m-40) cc_final: 0.6822 (t0) REVERT: R 336 LYS cc_start: 0.7427 (mmtt) cc_final: 0.7062 (mtmm) REVERT: R 397 MET cc_start: 0.7750 (mmp) cc_final: 0.7202 (mtm) REVERT: G 14 LYS cc_start: 0.8842 (ptpp) cc_final: 0.8419 (pttt) REVERT: P 19 GLN cc_start: 0.8344 (mm-40) cc_final: 0.8058 (mm-40) outliers start: 27 outliers final: 16 residues processed: 233 average time/residue: 0.1061 time to fit residues: 32.8030 Evaluate side-chains 197 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 181 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain R residue 72 TRP Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 320 ASN Chi-restraints excluded: chain R residue 389 SER Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain P residue 27 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 79 optimal weight: 0.9990 chunk 20 optimal weight: 0.3980 chunk 78 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 105 optimal weight: 8.9990 chunk 46 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 GLN A 220 HIS ** R 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.161955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.126139 restraints weight = 13025.053| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.48 r_work: 0.3413 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9426 Z= 0.138 Angle : 0.588 7.693 12782 Z= 0.308 Chirality : 0.043 0.169 1410 Planarity : 0.004 0.065 1620 Dihedral : 4.700 45.346 1269 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.85 % Allowed : 14.56 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.25), residues: 1130 helix: 0.01 (0.25), residues: 431 sheet: -1.06 (0.35), residues: 219 loop : -1.28 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 333 TYR 0.013 0.001 TYR N 97 PHE 0.015 0.001 PHE A 376 TRP 0.018 0.001 TRP P 25 HIS 0.003 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 9420) covalent geometry : angle 0.58825 (12770) SS BOND : bond 0.00366 ( 6) SS BOND : angle 0.72017 ( 12) hydrogen bonds : bond 0.03851 ( 399) hydrogen bonds : angle 4.64628 ( 1137) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 192 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU R 127 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: B 231 GLU cc_start: 0.7953 (pt0) cc_final: 0.7682 (pt0) REVERT: B 285 LYS cc_start: 0.7581 (pptt) cc_final: 0.6638 (mmpt) REVERT: A 30 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8689 (tp) REVERT: A 343 ASP cc_start: 0.8456 (m-30) cc_final: 0.7870 (m-30) REVERT: R 74 ASP cc_start: 0.6844 (t0) cc_final: 0.6390 (t0) REVERT: R 189 LEU cc_start: 0.8500 (tp) cc_final: 0.8246 (tt) REVERT: R 215 ASP cc_start: 0.7651 (m-30) cc_final: 0.7114 (p0) REVERT: R 293 ASP cc_start: 0.5941 (t0) cc_final: 0.5720 (t0) REVERT: R 336 LYS cc_start: 0.7618 (mmtt) cc_final: 0.7206 (mtmt) REVERT: R 397 MET cc_start: 0.7846 (mmp) cc_final: 0.7218 (mtm) REVERT: G 14 LYS cc_start: 0.8891 (ptpp) cc_final: 0.8602 (ptmt) REVERT: P 3 GLU cc_start: 0.6868 (OUTLIER) cc_final: 0.6169 (mp0) REVERT: P 19 GLN cc_start: 0.8303 (mm-40) cc_final: 0.8064 (mm-40) outliers start: 28 outliers final: 21 residues processed: 206 average time/residue: 0.1065 time to fit residues: 29.0334 Evaluate side-chains 189 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 166 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 264 GLN Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain R residue 72 TRP Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 161 ILE Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 320 ASN Chi-restraints excluded: chain R residue 389 SER Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain P residue 3 GLU Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain P residue 27 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 98 optimal weight: 0.6980 chunk 12 optimal weight: 0.0270 chunk 13 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 GLN R 320 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.160865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.125763 restraints weight = 13174.071| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.80 r_work: 0.3376 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9426 Z= 0.134 Angle : 0.573 7.540 12782 Z= 0.298 Chirality : 0.042 0.157 1410 Planarity : 0.004 0.065 1620 Dihedral : 4.672 46.277 1269 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.26 % Allowed : 15.78 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.25), residues: 1130 helix: 0.22 (0.26), residues: 433 sheet: -1.00 (0.34), residues: 226 loop : -1.14 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 317 TYR 0.019 0.001 TYR R 145 PHE 0.011 0.001 PHE N 110 TRP 0.012 0.001 TRP N 49 HIS 0.002 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 9420) covalent geometry : angle 0.57200 (12770) SS BOND : bond 0.00336 ( 6) SS BOND : angle 0.99720 ( 12) hydrogen bonds : bond 0.03518 ( 399) hydrogen bonds : angle 4.45522 ( 1137) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 175 time to evaluate : 0.353 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLU R 127 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: B 193 MET cc_start: 0.8490 (mmm) cc_final: 0.8250 (mmt) REVERT: B 231 GLU cc_start: 0.7951 (pt0) cc_final: 0.7599 (pt0) REVERT: B 285 LYS cc_start: 0.7712 (pptt) cc_final: 0.6797 (mmmt) REVERT: A 343 ASP cc_start: 0.8414 (m-30) cc_final: 0.7892 (m-30) REVERT: R 74 ASP cc_start: 0.6885 (t0) cc_final: 0.6453 (t0) REVERT: R 293 ASP cc_start: 0.6060 (t0) cc_final: 0.5818 (t0) REVERT: R 336 LYS cc_start: 0.7517 (mmtt) cc_final: 0.6979 (mtmm) REVERT: R 397 MET cc_start: 0.7851 (mmp) cc_final: 0.7154 (mtt) REVERT: G 14 LYS cc_start: 0.8897 (ptpp) cc_final: 0.8616 (ptmt) REVERT: P 3 GLU cc_start: 0.6925 (OUTLIER) cc_final: 0.6208 (mp0) REVERT: P 19 GLN cc_start: 0.8424 (mm-40) cc_final: 0.8210 (mm-40) outliers start: 32 outliers final: 20 residues processed: 196 average time/residue: 0.0920 time to fit residues: 25.0402 Evaluate side-chains 191 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 170 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 111 ASP Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain R residue 72 TRP Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 161 ILE Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 389 SER Chi-restraints excluded: chain R residue 400 ILE Chi-restraints excluded: chain P residue 3 GLU Chi-restraints excluded: chain P residue 23 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 105 optimal weight: 3.9990 chunk 92 optimal weight: 0.1980 chunk 60 optimal weight: 0.0980 chunk 87 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 56 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 21 ASN B 264 GLN A 29 GLN A 59 GLN A 220 HIS ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.158523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.122795 restraints weight = 13107.003| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.81 r_work: 0.3335 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9426 Z= 0.160 Angle : 0.587 8.981 12782 Z= 0.305 Chirality : 0.044 0.198 1410 Planarity : 0.004 0.065 1620 Dihedral : 4.556 49.394 1267 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.46 % Allowed : 18.23 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.25), residues: 1130 helix: 0.44 (0.26), residues: 431 sheet: -1.24 (0.33), residues: 239 loop : -1.13 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 317 TYR 0.019 0.001 TYR R 145 PHE 0.022 0.001 PHE A 376 TRP 0.014 0.001 TRP N 49 HIS 0.003 0.001 HIS B 188 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 9420) covalent geometry : angle 0.58716 (12770) SS BOND : bond 0.00477 ( 6) SS BOND : angle 0.73924 ( 12) hydrogen bonds : bond 0.03568 ( 399) hydrogen bonds : angle 4.47797 ( 1137) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 181 time to evaluate : 0.522 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLU R 127 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: N 89 LYS cc_start: 0.8918 (mmmt) cc_final: 0.8151 (mtpt) REVERT: N 122 GLN cc_start: 0.8317 (pt0) cc_final: 0.7945 (pm20) REVERT: B 231 GLU cc_start: 0.7940 (pt0) cc_final: 0.7561 (pt0) REVERT: B 285 LYS cc_start: 0.7892 (pptt) cc_final: 0.7098 (mmpt) REVERT: A 286 SER cc_start: 0.8874 (OUTLIER) cc_final: 0.8554 (m) REVERT: A 343 ASP cc_start: 0.8478 (m-30) cc_final: 0.7960 (m-30) REVERT: R 74 ASP cc_start: 0.6991 (t0) cc_final: 0.6550 (t0) REVERT: R 215 ASP cc_start: 0.7696 (m-30) cc_final: 0.6976 (p0) REVERT: R 293 ASP cc_start: 0.6261 (t0) cc_final: 0.5973 (t0) REVERT: R 336 LYS cc_start: 0.7490 (mmtt) cc_final: 0.7027 (mtmt) REVERT: R 397 MET cc_start: 0.7950 (mmp) cc_final: 0.7210 (mtt) REVERT: G 14 LYS cc_start: 0.8922 (ptpp) cc_final: 0.8638 (ptmt) REVERT: P 3 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.6135 (mp0) outliers start: 34 outliers final: 23 residues processed: 200 average time/residue: 0.0909 time to fit residues: 25.1024 Evaluate side-chains 196 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 171 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 111 ASP Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain R residue 72 TRP Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 161 ILE Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 182 ASN Chi-restraints excluded: chain R residue 328 ILE Chi-restraints excluded: chain R residue 330 ILE Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain P residue 3 GLU Chi-restraints excluded: chain P residue 23 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 17 optimal weight: 3.9990 chunk 106 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 60 optimal weight: 0.0970 chunk 25 optimal weight: 4.9990 chunk 35 optimal weight: 0.5980 chunk 75 optimal weight: 10.0000 chunk 49 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.156938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.121495 restraints weight = 13120.561| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.77 r_work: 0.3318 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.4304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9426 Z= 0.172 Angle : 0.611 10.928 12782 Z= 0.315 Chirality : 0.044 0.219 1410 Planarity : 0.004 0.066 1620 Dihedral : 4.627 52.497 1267 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.46 % Allowed : 19.35 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.25), residues: 1130 helix: 0.44 (0.26), residues: 440 sheet: -1.22 (0.33), residues: 241 loop : -1.18 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 317 TYR 0.020 0.001 TYR R 145 PHE 0.022 0.001 PHE A 376 TRP 0.015 0.001 TRP N 49 HIS 0.002 0.001 HIS B 188 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 9420) covalent geometry : angle 0.61046 (12770) SS BOND : bond 0.00329 ( 6) SS BOND : angle 1.03908 ( 12) hydrogen bonds : bond 0.03522 ( 399) hydrogen bonds : angle 4.47383 ( 1137) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 177 time to evaluate : 0.368 Fit side-chains TARDY: cannot create tardy model for: "GLU R 127 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: N 89 LYS cc_start: 0.8909 (mmmt) cc_final: 0.8122 (mtpt) REVERT: B 196 SER cc_start: 0.8871 (t) cc_final: 0.8651 (t) REVERT: B 222 MET cc_start: 0.7800 (OUTLIER) cc_final: 0.6746 (ppp) REVERT: B 231 GLU cc_start: 0.7944 (pt0) cc_final: 0.7499 (pt0) REVERT: B 239 PHE cc_start: 0.8761 (OUTLIER) cc_final: 0.8122 (m-80) REVERT: B 285 LYS cc_start: 0.7977 (pptt) cc_final: 0.7161 (mmmt) REVERT: A 284 ASP cc_start: 0.7696 (m-30) cc_final: 0.7268 (p0) REVERT: A 286 SER cc_start: 0.8917 (OUTLIER) cc_final: 0.8625 (m) REVERT: A 343 ASP cc_start: 0.8459 (m-30) cc_final: 0.7922 (m-30) REVERT: R 74 ASP cc_start: 0.6992 (t0) cc_final: 0.6547 (t0) REVERT: R 215 ASP cc_start: 0.7678 (m-30) cc_final: 0.6975 (p0) REVERT: R 293 ASP cc_start: 0.6230 (t0) cc_final: 0.5915 (t0) REVERT: R 336 LYS cc_start: 0.7118 (mmtt) cc_final: 0.6675 (mtmt) REVERT: R 397 MET cc_start: 0.7960 (mmp) cc_final: 0.7200 (mtt) REVERT: G 14 LYS cc_start: 0.8961 (ptpp) cc_final: 0.8754 (ptmt) REVERT: G 29 LYS cc_start: 0.8048 (tppt) cc_final: 0.7675 (mmmt) REVERT: P 3 GLU cc_start: 0.6896 (OUTLIER) cc_final: 0.6061 (mp0) REVERT: P 19 GLN cc_start: 0.8197 (mm-40) cc_final: 0.7625 (mt0) outliers start: 34 outliers final: 24 residues processed: 194 average time/residue: 0.0901 time to fit residues: 24.1277 Evaluate side-chains 197 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 169 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain R residue 72 TRP Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 161 ILE Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 182 ASN Chi-restraints excluded: chain R residue 328 ILE Chi-restraints excluded: chain R residue 330 ILE Chi-restraints excluded: chain R residue 389 SER Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain P residue 3 GLU Chi-restraints excluded: chain P residue 23 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 104 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 21 optimal weight: 0.2980 chunk 57 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 24 optimal weight: 0.0670 chunk 96 optimal weight: 0.7980 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 220 HIS A 292 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.158553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.122330 restraints weight = 13093.407| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.56 r_work: 0.3363 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9426 Z= 0.129 Angle : 0.583 10.745 12782 Z= 0.302 Chirality : 0.043 0.224 1410 Planarity : 0.004 0.065 1620 Dihedral : 4.542 53.898 1267 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.95 % Allowed : 20.57 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.25), residues: 1130 helix: 0.53 (0.26), residues: 441 sheet: -1.11 (0.33), residues: 234 loop : -1.14 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 317 TYR 0.018 0.001 TYR R 145 PHE 0.023 0.001 PHE A 376 TRP 0.015 0.001 TRP N 49 HIS 0.002 0.000 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 9420) covalent geometry : angle 0.58016 (12770) SS BOND : bond 0.00452 ( 6) SS BOND : angle 1.84970 ( 12) hydrogen bonds : bond 0.03273 ( 399) hydrogen bonds : angle 4.32769 ( 1137) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 175 time to evaluate : 0.321 Fit side-chains TARDY: cannot create tardy model for: "GLU R 127 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: N 122 GLN cc_start: 0.8327 (pt0) cc_final: 0.7943 (pm20) REVERT: B 177 GLU cc_start: 0.6727 (mm-30) cc_final: 0.6476 (mp0) REVERT: B 196 SER cc_start: 0.8837 (t) cc_final: 0.8604 (t) REVERT: B 222 MET cc_start: 0.7791 (OUTLIER) cc_final: 0.7486 (pmm) REVERT: B 231 GLU cc_start: 0.7863 (pt0) cc_final: 0.7166 (pt0) REVERT: B 239 PHE cc_start: 0.8756 (OUTLIER) cc_final: 0.8107 (m-80) REVERT: B 285 LYS cc_start: 0.7912 (pptt) cc_final: 0.7125 (mmmt) REVERT: A 284 ASP cc_start: 0.7661 (m-30) cc_final: 0.7276 (p0) REVERT: A 286 SER cc_start: 0.8880 (OUTLIER) cc_final: 0.8565 (m) REVERT: A 343 ASP cc_start: 0.8368 (m-30) cc_final: 0.7890 (m-30) REVERT: R 74 ASP cc_start: 0.7108 (t0) cc_final: 0.6635 (t0) REVERT: R 215 ASP cc_start: 0.7635 (m-30) cc_final: 0.7015 (p0) REVERT: R 336 LYS cc_start: 0.7094 (mmtt) cc_final: 0.6580 (mtmm) REVERT: R 397 MET cc_start: 0.7832 (mmp) cc_final: 0.7137 (mtt) REVERT: G 13 ARG cc_start: 0.8955 (mtp85) cc_final: 0.8353 (ptp-110) REVERT: P 19 GLN cc_start: 0.8241 (mm-40) cc_final: 0.7866 (mt0) outliers start: 29 outliers final: 23 residues processed: 193 average time/residue: 0.0914 time to fit residues: 24.5330 Evaluate side-chains 189 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 163 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 111 ASP Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain R residue 72 TRP Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 161 ILE Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 182 ASN Chi-restraints excluded: chain R residue 328 ILE Chi-restraints excluded: chain R residue 389 SER Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain P residue 3 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 52 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 102 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 59 optimal weight: 0.3980 chunk 110 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.154841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.119068 restraints weight = 13196.598| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.64 r_work: 0.3293 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.4724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 9426 Z= 0.245 Angle : 0.679 9.855 12782 Z= 0.352 Chirality : 0.046 0.207 1410 Planarity : 0.005 0.066 1620 Dihedral : 4.908 59.571 1267 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 4.07 % Allowed : 20.47 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.25), residues: 1130 helix: 0.42 (0.26), residues: 440 sheet: -1.54 (0.31), residues: 239 loop : -1.16 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 317 TYR 0.022 0.002 TYR R 145 PHE 0.023 0.002 PHE A 376 TRP 0.017 0.001 TRP N 49 HIS 0.004 0.001 HIS B 188 Details of bonding type rmsd covalent geometry : bond 0.00581 ( 9420) covalent geometry : angle 0.67283 (12770) SS BOND : bond 0.00331 ( 6) SS BOND : angle 2.97951 ( 12) hydrogen bonds : bond 0.03771 ( 399) hydrogen bonds : angle 4.57069 ( 1137) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 160 time to evaluate : 0.346 Fit side-chains TARDY: cannot create tardy model for: "GLU R 127 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: N 89 LYS cc_start: 0.8861 (mmmt) cc_final: 0.8110 (mtpt) REVERT: B 231 GLU cc_start: 0.7979 (pt0) cc_final: 0.7432 (pt0) REVERT: B 239 PHE cc_start: 0.8918 (OUTLIER) cc_final: 0.8290 (m-80) REVERT: B 285 LYS cc_start: 0.8142 (pptt) cc_final: 0.7331 (mmmt) REVERT: A 284 ASP cc_start: 0.7794 (m-30) cc_final: 0.7432 (p0) REVERT: A 286 SER cc_start: 0.8951 (OUTLIER) cc_final: 0.8614 (m) REVERT: A 393 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8505 (mp) REVERT: R 74 ASP cc_start: 0.6978 (t0) cc_final: 0.6515 (t0) REVERT: R 215 ASP cc_start: 0.7628 (m-30) cc_final: 0.7020 (p0) REVERT: R 293 ASP cc_start: 0.6510 (t0) cc_final: 0.6249 (t0) REVERT: R 336 LYS cc_start: 0.7057 (mmtt) cc_final: 0.6465 (mtmm) REVERT: R 397 MET cc_start: 0.7955 (mmp) cc_final: 0.7145 (mtt) REVERT: G 13 ARG cc_start: 0.8941 (mtp85) cc_final: 0.8740 (ptp-110) REVERT: G 14 LYS cc_start: 0.8620 (ptmt) cc_final: 0.8404 (pttt) REVERT: G 25 ILE cc_start: 0.7653 (OUTLIER) cc_final: 0.7411 (mp) REVERT: G 29 LYS cc_start: 0.8142 (tppt) cc_final: 0.7749 (mmmt) REVERT: P 3 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.5924 (mp0) REVERT: P 19 GLN cc_start: 0.8334 (mm-40) cc_final: 0.7953 (tt0) outliers start: 40 outliers final: 28 residues processed: 189 average time/residue: 0.0951 time to fit residues: 24.4835 Evaluate side-chains 190 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 157 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 111 ASP Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain N residue 119 TYR Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain R residue 72 TRP Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 161 ILE Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 182 ASN Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 330 ILE Chi-restraints excluded: chain R residue 389 SER Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain P residue 3 GLU Chi-restraints excluded: chain P residue 5 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 6 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 56 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 98 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 21 optimal weight: 0.1980 chunk 54 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.157363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.121375 restraints weight = 12920.569| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.52 r_work: 0.3340 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.4746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9426 Z= 0.137 Angle : 0.632 11.765 12782 Z= 0.324 Chirality : 0.044 0.245 1410 Planarity : 0.004 0.068 1620 Dihedral : 4.878 58.393 1267 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.44 % Allowed : 22.10 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: -0.85 (0.25), residues: 1130 helix: 0.52 (0.26), residues: 443 sheet: -1.33 (0.32), residues: 238 loop : -1.09 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 20 TYR 0.021 0.001 TYR R 145 PHE 0.024 0.001 PHE A 376 TRP 0.018 0.001 TRP N 49 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 9420) covalent geometry : angle 0.62853 (12770) SS BOND : bond 0.00347 ( 6) SS BOND : angle 2.11726 ( 12) hydrogen bonds : bond 0.03327 ( 399) hydrogen bonds : angle 4.36800 ( 1137) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU R 127 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: N 89 LYS cc_start: 0.8816 (mmmt) cc_final: 0.8045 (mtpt) REVERT: B 231 GLU cc_start: 0.7959 (pt0) cc_final: 0.7496 (pt0) REVERT: B 239 PHE cc_start: 0.8832 (OUTLIER) cc_final: 0.8180 (m-80) REVERT: B 285 LYS cc_start: 0.8048 (pptt) cc_final: 0.7225 (mmmt) REVERT: A 284 ASP cc_start: 0.7633 (m-30) cc_final: 0.7323 (p0) REVERT: A 286 SER cc_start: 0.8811 (OUTLIER) cc_final: 0.8477 (m) REVERT: A 343 ASP cc_start: 0.8389 (m-30) cc_final: 0.7850 (m-30) REVERT: R 74 ASP cc_start: 0.7087 (t0) cc_final: 0.6623 (t0) REVERT: R 189 LEU cc_start: 0.8617 (tt) cc_final: 0.8290 (tp) REVERT: R 215 ASP cc_start: 0.7527 (m-30) cc_final: 0.6956 (p0) REVERT: R 293 ASP cc_start: 0.6540 (t0) cc_final: 0.6057 (t70) REVERT: R 336 LYS cc_start: 0.6935 (mmtt) cc_final: 0.6385 (mtmm) REVERT: R 397 MET cc_start: 0.7659 (mmp) cc_final: 0.7111 (mtt) REVERT: R 407 ASN cc_start: 0.8389 (m-40) cc_final: 0.8044 (t0) REVERT: G 13 ARG cc_start: 0.8856 (mtp85) cc_final: 0.8246 (ptp-110) REVERT: P 19 GLN cc_start: 0.8380 (mm-40) cc_final: 0.8058 (tt0) outliers start: 24 outliers final: 18 residues processed: 187 average time/residue: 0.0988 time to fit residues: 25.1421 Evaluate side-chains 185 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 165 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 111 ASP Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain R residue 72 TRP Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 182 ASN Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain P residue 3 GLU Chi-restraints excluded: chain P residue 5 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 13 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 25 optimal weight: 0.4980 chunk 0 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 98 optimal weight: 0.0470 chunk 86 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.2882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.154859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.119213 restraints weight = 13167.204| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.65 r_work: 0.3297 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.4941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 9426 Z= 0.200 Angle : 0.672 11.055 12782 Z= 0.348 Chirality : 0.046 0.222 1410 Planarity : 0.004 0.067 1620 Dihedral : 4.937 56.482 1267 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.34 % Allowed : 22.51 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: -0.95 (0.25), residues: 1130 helix: 0.46 (0.26), residues: 444 sheet: -1.52 (0.32), residues: 234 loop : -1.10 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 20 TYR 0.020 0.002 TYR R 145 PHE 0.023 0.002 PHE A 376 TRP 0.017 0.001 TRP N 49 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00478 ( 9420) covalent geometry : angle 0.66878 (12770) SS BOND : bond 0.00311 ( 6) SS BOND : angle 2.13863 ( 12) hydrogen bonds : bond 0.03568 ( 399) hydrogen bonds : angle 4.47450 ( 1137) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 164 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU R 127 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: N 89 LYS cc_start: 0.8850 (mmmt) cc_final: 0.8058 (mtpt) REVERT: B 231 GLU cc_start: 0.7967 (pt0) cc_final: 0.7600 (pt0) REVERT: B 239 PHE cc_start: 0.8916 (OUTLIER) cc_final: 0.8196 (m-80) REVERT: B 285 LYS cc_start: 0.8102 (pptt) cc_final: 0.7223 (mmmt) REVERT: A 284 ASP cc_start: 0.7706 (m-30) cc_final: 0.7389 (p0) REVERT: A 286 SER cc_start: 0.8932 (OUTLIER) cc_final: 0.8607 (m) REVERT: A 343 ASP cc_start: 0.8431 (m-30) cc_final: 0.7938 (m-30) REVERT: R 74 ASP cc_start: 0.7109 (t0) cc_final: 0.6646 (t0) REVERT: R 198 ASP cc_start: 0.7648 (p0) cc_final: 0.7420 (p0) REVERT: R 215 ASP cc_start: 0.7593 (m-30) cc_final: 0.6994 (p0) REVERT: R 293 ASP cc_start: 0.6605 (t0) cc_final: 0.6144 (t70) REVERT: R 336 LYS cc_start: 0.6964 (mmtt) cc_final: 0.6394 (mtmm) REVERT: R 397 MET cc_start: 0.7691 (mmp) cc_final: 0.7134 (mtt) REVERT: R 407 ASN cc_start: 0.8476 (m-40) cc_final: 0.8125 (t0) REVERT: G 13 ARG cc_start: 0.8896 (mtp85) cc_final: 0.8308 (ptp-110) REVERT: P 19 GLN cc_start: 0.8451 (mm-40) cc_final: 0.8094 (tt0) outliers start: 23 outliers final: 19 residues processed: 181 average time/residue: 0.1018 time to fit residues: 25.2082 Evaluate side-chains 184 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 163 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain R residue 72 TRP Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 182 ASN Chi-restraints excluded: chain R residue 233 MET Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain P residue 3 GLU Chi-restraints excluded: chain P residue 5 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 95 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 99 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 98 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 GLN A 59 GLN ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.156294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.119910 restraints weight = 12883.991| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.48 r_work: 0.3333 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.4960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9426 Z= 0.151 Angle : 0.637 11.051 12782 Z= 0.328 Chirality : 0.044 0.207 1410 Planarity : 0.004 0.063 1620 Dihedral : 4.820 55.079 1267 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.34 % Allowed : 22.71 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: -0.82 (0.25), residues: 1130 helix: 0.55 (0.26), residues: 444 sheet: -1.34 (0.32), residues: 238 loop : -1.06 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 20 TYR 0.020 0.001 TYR R 145 PHE 0.023 0.001 PHE A 376 TRP 0.016 0.001 TRP N 49 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 9420) covalent geometry : angle 0.63466 (12770) SS BOND : bond 0.00252 ( 6) SS BOND : angle 1.76755 ( 12) hydrogen bonds : bond 0.03326 ( 399) hydrogen bonds : angle 4.36826 ( 1137) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2259.40 seconds wall clock time: 39 minutes 22.90 seconds (2362.90 seconds total)