Starting phenix.real_space_refine on Thu Mar 13 23:21:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fim_31603/03_2025/7fim_31603.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fim_31603/03_2025/7fim_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7fim_31603/03_2025/7fim_31603.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fim_31603/03_2025/7fim_31603.map" model { file = "/net/cci-nas-00/data/ceres_data/7fim_31603/03_2025/7fim_31603.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fim_31603/03_2025/7fim_31603.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} 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: 9.28, per 1000 atoms: 1.01 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: 2.45 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.92 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: 2.65 Time building geometry restraints manager: 2.92 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: 1.650 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 28.160 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.590 ------------------------------------------------------------------------------- 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 9420 Z= 0.234 Angle : 0.835 9.816 12770 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 : 7.19 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.018 0.001 TRP R 72 HIS 0.003 0.001 HIS A 357 PHE 0.017 0.001 PHE N 110 TYR 0.015 0.001 TYR P 10 ARG 0.016 0.001 ARG G 13 *********************** 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 : 1.098 Fit side-chains 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 34 TYR cc_start: 0.6826 (m-10) cc_final: 0.6184 (m-80) REVERT: N 48 GLU cc_start: 0.8312 (pp20) cc_final: 0.7945 (pp20) REVERT: N 111 ASP cc_start: 0.7222 (m-30) cc_final: 0.6950 (t0) REVERT: N 114 SER cc_start: 0.8260 (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: 0.6571 (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: 0.7542 (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: 0.6703 (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: 0.6531 (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: 0.5786 (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: 0.2643 time to fit residues: 109.4208 Evaluate side-chains 195 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 192 time to evaluate : 1.012 ------------------------------------------------------------------------------- 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 94 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 47 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.4065 r_free = 0.4065 target = 0.161639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.126579 restraints weight = 12999.854| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.72 r_work: 0.3393 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9420 Z= 0.280 Angle : 0.658 11.160 12770 Z= 0.344 Chirality : 0.045 0.194 1410 Planarity : 0.005 0.067 1620 Dihedral : 5.352 56.805 1273 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.85 % Allowed : 11.30 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.24), residues: 1130 helix: -0.62 (0.24), residues: 437 sheet: -1.34 (0.34), residues: 229 loop : -1.31 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP N 49 HIS 0.009 0.001 HIS R 212 PHE 0.018 0.002 PHE N 110 TYR 0.018 0.002 TYR R 145 ARG 0.007 0.001 ARG N 40 *********************** 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 234 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 206 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU R 127 " (corrupted residue). Skipping it. REVERT: N 114 SER cc_start: 0.8210 (t) cc_final: 0.7751 (t) REVERT: N 116 THR cc_start: 0.8241 (p) cc_final: 0.7841 (t) REVERT: B 285 LYS cc_start: 0.7571 (pptt) cc_final: 0.6623 (mmpt) REVERT: A 230 GLU cc_start: 0.7139 (mt-10) cc_final: 0.6881 (mt-10) REVERT: R 74 ASP cc_start: 0.6856 (t0) cc_final: 0.6403 (t0) REVERT: R 82 ASN cc_start: 0.6285 (t0) cc_final: 0.5907 (m-40) REVERT: R 182 ASN cc_start: 0.8680 (t0) cc_final: 0.8448 (t0) REVERT: R 189 LEU cc_start: 0.8573 (tt) cc_final: 0.8339 (tp) REVERT: R 215 ASP cc_start: 0.7691 (m-30) cc_final: 0.7113 (p0) REVERT: R 304 ASN cc_start: 0.7866 (m-40) cc_final: 0.6884 (t0) REVERT: R 336 LYS cc_start: 0.7420 (mmtt) cc_final: 0.7056 (mtmm) REVERT: R 397 MET cc_start: 0.7801 (mmp) cc_final: 0.7287 (mtm) REVERT: G 9 ILE cc_start: 0.8522 (mt) cc_final: 0.7975 (mm) REVERT: G 13 ARG cc_start: 0.8417 (mtm-85) cc_final: 0.7959 (ptp-110) REVERT: G 14 LYS cc_start: 0.8827 (ptpp) cc_final: 0.8501 (pttt) REVERT: P 19 GLN cc_start: 0.8480 (mm-40) cc_final: 0.8159 (mm-40) outliers start: 28 outliers final: 21 residues processed: 225 average time/residue: 0.2516 time to fit residues: 75.2154 Evaluate side-chains 201 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 180 time to evaluate : 1.078 ------------------------------------------------------------------------------- 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 152 SER Chi-restraints excluded: chain B residue 276 CYS 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 A residue 375 VAL Chi-restraints excluded: chain R residue 72 TRP 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 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 42 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 20 optimal weight: 0.1980 chunk 6 optimal weight: 0.0870 chunk 70 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 ** R 320 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 = 0.4065 r_free = 0.4065 target = 0.161664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.126559 restraints weight = 13224.376| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.55 r_work: 0.3407 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9420 Z= 0.199 Angle : 0.594 8.875 12770 Z= 0.309 Chirality : 0.043 0.180 1410 Planarity : 0.004 0.065 1620 Dihedral : 4.777 47.281 1269 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.75 % Allowed : 14.87 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.25), residues: 1130 helix: -0.02 (0.25), residues: 431 sheet: -1.15 (0.35), residues: 219 loop : -1.29 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 174 HIS 0.003 0.001 HIS B 59 PHE 0.015 0.001 PHE A 376 TYR 0.016 0.001 TYR R 148 ARG 0.010 0.001 ARG A 333 *********************** 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 223 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 196 time to evaluate : 0.975 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLU R 127 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: B 285 LYS cc_start: 0.7630 (pptt) cc_final: 0.6669 (mmpt) REVERT: A 343 ASP cc_start: 0.8505 (m-30) cc_final: 0.7919 (m-30) REVERT: R 74 ASP cc_start: 0.6856 (t0) cc_final: 0.6405 (t0) REVERT: R 215 ASP cc_start: 0.7662 (m-30) cc_final: 0.7122 (p0) REVERT: R 336 LYS cc_start: 0.7599 (mmtt) cc_final: 0.7162 (mtmt) REVERT: R 397 MET cc_start: 0.7864 (mmp) cc_final: 0.7205 (mtm) REVERT: G 9 ILE cc_start: 0.8635 (mt) cc_final: 0.8409 (mm) REVERT: G 14 LYS cc_start: 0.8888 (ptpp) cc_final: 0.8534 (pttt) REVERT: P 3 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6092 (mp0) REVERT: P 19 GLN cc_start: 0.8268 (mm-40) cc_final: 0.8028 (mm-40) outliers start: 27 outliers final: 18 residues processed: 213 average time/residue: 0.2433 time to fit residues: 69.1170 Evaluate side-chains 185 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 166 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 33 ASN 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 152 SER 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 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 372 ILE 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 P residue 3 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 54 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 74 optimal weight: 30.0000 chunk 95 optimal weight: 3.9990 chunk 73 optimal weight: 0.0670 chunk 5 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 overall best weight: 1.5322 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 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 = 0.4002 r_free = 0.4002 target = 0.156080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.120724 restraints weight = 13030.799| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.66 r_work: 0.3304 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9420 Z= 0.343 Angle : 0.654 9.332 12770 Z= 0.341 Chirality : 0.045 0.201 1410 Planarity : 0.005 0.065 1620 Dihedral : 4.963 52.281 1269 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 4.48 % Allowed : 16.60 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.25), residues: 1130 helix: 0.05 (0.25), residues: 439 sheet: -1.37 (0.33), residues: 233 loop : -1.37 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP N 49 HIS 0.004 0.001 HIS B 188 PHE 0.017 0.002 PHE N 110 TYR 0.020 0.002 TYR R 145 ARG 0.014 0.001 ARG A 317 *********************** 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 212 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 168 time to evaluate : 1.048 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 239 PHE cc_start: 0.8811 (OUTLIER) cc_final: 0.8213 (m-80) REVERT: B 285 LYS cc_start: 0.8050 (pptt) cc_final: 0.7322 (mmmt) REVERT: A 343 ASP cc_start: 0.8454 (m-30) cc_final: 0.7930 (m-30) REVERT: R 74 ASP cc_start: 0.6882 (t0) cc_final: 0.6457 (t0) REVERT: R 336 LYS cc_start: 0.7453 (mmtt) cc_final: 0.6999 (mtmt) REVERT: R 397 MET cc_start: 0.7974 (mmp) cc_final: 0.7274 (mtt) REVERT: G 14 LYS cc_start: 0.8881 (ptpp) cc_final: 0.8619 (ptmt) REVERT: P 3 GLU cc_start: 0.6898 (OUTLIER) cc_final: 0.5947 (mp0) REVERT: P 19 GLN cc_start: 0.8459 (mm-40) cc_final: 0.8253 (mm-40) outliers start: 44 outliers final: 30 residues processed: 195 average time/residue: 0.2229 time to fit residues: 60.2550 Evaluate side-chains 190 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 158 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 24 CYS Chi-restraints excluded: chain N residue 33 ASN 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 152 SER Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 327 ASP 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 161 ILE Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 182 ASN Chi-restraints excluded: chain R residue 319 VAL Chi-restraints excluded: chain R residue 389 SER Chi-restraints excluded: chain R residue 400 ILE Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain P residue 3 GLU Chi-restraints excluded: chain P residue 14 LEU 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 20 optimal weight: 0.2980 chunk 18 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 83 optimal weight: 0.0980 chunk 31 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 86 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- 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 ** B 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4031 r_free = 0.4031 target = 0.158726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.123082 restraints weight = 12943.691| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.57 r_work: 0.3361 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9420 Z= 0.193 Angle : 0.589 9.677 12770 Z= 0.305 Chirality : 0.043 0.180 1410 Planarity : 0.004 0.065 1620 Dihedral : 4.676 53.844 1267 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.26 % Allowed : 20.16 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.25), residues: 1130 helix: 0.37 (0.26), residues: 432 sheet: -1.14 (0.33), residues: 238 loop : -1.22 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP N 49 HIS 0.002 0.000 HIS B 59 PHE 0.011 0.001 PHE B 246 TYR 0.016 0.001 TYR R 145 ARG 0.010 0.000 ARG A 317 *********************** 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 205 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 173 time to evaluate : 1.288 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: 0.8901 (mmmt) cc_final: 0.8158 (mtpt) REVERT: B 222 MET cc_start: 0.7751 (OUTLIER) cc_final: 0.6707 (ppp) REVERT: B 239 PHE cc_start: 0.8832 (OUTLIER) cc_final: 0.8304 (m-80) REVERT: B 285 LYS cc_start: 0.7905 (pptt) cc_final: 0.7136 (mmmt) REVERT: A 284 ASP cc_start: 0.7634 (m-30) cc_final: 0.7355 (p0) REVERT: A 286 SER cc_start: 0.8929 (OUTLIER) cc_final: 0.8525 (m) REVERT: A 343 ASP cc_start: 0.8401 (m-30) cc_final: 0.7906 (m-30) REVERT: R 74 ASP cc_start: 0.6867 (t0) cc_final: 0.6424 (t0) REVERT: R 215 ASP cc_start: 0.7670 (m-30) cc_final: 0.6929 (p0) REVERT: R 293 ASP cc_start: 0.5689 (t0) cc_final: 0.5031 (t0) REVERT: R 336 LYS cc_start: 0.7293 (mmtt) cc_final: 0.6855 (mtmt) REVERT: R 397 MET cc_start: 0.7906 (mmp) cc_final: 0.7151 (mtt) REVERT: G 14 LYS cc_start: 0.8908 (ptpp) cc_final: 0.8637 (ptmt) REVERT: P 3 GLU cc_start: 0.6907 (OUTLIER) cc_final: 0.6119 (mp0) outliers start: 32 outliers final: 21 residues processed: 190 average time/residue: 0.2585 time to fit residues: 67.9460 Evaluate side-chains 187 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 162 time to evaluate : 1.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 33 ASN 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 152 SER 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 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 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 172 LEU Chi-restraints excluded: chain R residue 182 ASN Chi-restraints excluded: chain R residue 330 ILE Chi-restraints excluded: chain P residue 3 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 90 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 12 optimal weight: 8.9990 chunk 104 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 109 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 56 optimal weight: 0.0470 chunk 108 optimal weight: 1.9990 overall best weight: 0.9282 ------------------------------------------------------------------------------- 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 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 GLN A 220 HIS ** 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 = 0.4011 r_free = 0.4011 target = 0.156816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.121023 restraints weight = 12964.060| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.79 r_work: 0.3327 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9420 Z= 0.241 Angle : 0.593 9.992 12770 Z= 0.308 Chirality : 0.043 0.198 1410 Planarity : 0.004 0.065 1620 Dihedral : 4.679 56.787 1267 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.87 % Allowed : 20.06 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.25), residues: 1130 helix: 0.51 (0.26), residues: 434 sheet: -1.35 (0.32), residues: 233 loop : -1.28 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 49 HIS 0.003 0.001 HIS B 188 PHE 0.022 0.001 PHE A 376 TYR 0.020 0.001 TYR R 145 ARG 0.011 0.000 ARG A 317 *********************** 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 207 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 169 time to evaluate : 0.986 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 222 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.6761 (ppp) REVERT: B 239 PHE cc_start: 0.8940 (OUTLIER) cc_final: 0.8276 (m-80) REVERT: B 285 LYS cc_start: 0.8002 (pptt) cc_final: 0.7220 (mmmt) REVERT: A 20 ARG cc_start: 0.8157 (mtm110) cc_final: 0.7829 (mtm110) REVERT: A 284 ASP cc_start: 0.7748 (m-30) cc_final: 0.7335 (p0) REVERT: A 286 SER cc_start: 0.8859 (OUTLIER) cc_final: 0.8459 (m) REVERT: A 343 ASP cc_start: 0.8445 (m-30) cc_final: 0.7930 (m-30) REVERT: R 74 ASP cc_start: 0.7133 (t0) cc_final: 0.6698 (t0) REVERT: R 173 HIS cc_start: 0.8426 (m90) cc_final: 0.8077 (m90) REVERT: R 215 ASP cc_start: 0.7692 (m-30) cc_final: 0.7030 (p0) REVERT: R 293 ASP cc_start: 0.5619 (t0) cc_final: 0.4925 (t0) REVERT: R 336 LYS cc_start: 0.7098 (mmtt) cc_final: 0.6572 (mtmm) REVERT: R 397 MET cc_start: 0.7939 (mmp) cc_final: 0.7124 (mtt) REVERT: G 14 LYS cc_start: 0.8965 (ptpp) cc_final: 0.8764 (ptmt) REVERT: P 3 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6052 (mp0) REVERT: P 19 GLN cc_start: 0.8238 (mm-40) cc_final: 0.7658 (mt0) outliers start: 38 outliers final: 26 residues processed: 191 average time/residue: 0.2203 time to fit residues: 57.6596 Evaluate side-chains 194 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 164 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 33 ASN 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 152 SER 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 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 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 5 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 66 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 1 optimal weight: 0.3980 chunk 73 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 106 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- 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 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3981 r_free = 0.3981 target = 0.154553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.119072 restraints weight = 13365.511| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.69 r_work: 0.3276 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.4655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 9420 Z= 0.369 Angle : 0.660 9.869 12770 Z= 0.343 Chirality : 0.046 0.220 1410 Planarity : 0.005 0.065 1620 Dihedral : 4.955 56.029 1267 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 4.79 % Allowed : 19.96 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.25), residues: 1130 helix: 0.37 (0.26), residues: 439 sheet: -1.68 (0.31), residues: 239 loop : -1.24 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP N 49 HIS 0.007 0.001 HIS A 220 PHE 0.023 0.002 PHE A 376 TYR 0.020 0.002 TYR R 145 ARG 0.008 0.001 ARG A 317 *********************** 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 209 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 162 time to evaluate : 3.141 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: 0.8875 (mmmt) cc_final: 0.8115 (mtpt) REVERT: B 231 GLU cc_start: 0.8040 (pt0) cc_final: 0.7784 (pt0) REVERT: B 239 PHE cc_start: 0.9022 (OUTLIER) cc_final: 0.8357 (m-80) REVERT: B 285 LYS cc_start: 0.8189 (pptt) cc_final: 0.7367 (mmmt) REVERT: A 15 GLU cc_start: 0.8054 (mp0) cc_final: 0.7779 (mp0) REVERT: A 284 ASP cc_start: 0.7812 (m-30) cc_final: 0.7348 (p0) REVERT: A 286 SER cc_start: 0.8949 (OUTLIER) cc_final: 0.8597 (m) REVERT: R 74 ASP cc_start: 0.7090 (t0) cc_final: 0.6641 (t0) REVERT: R 215 ASP cc_start: 0.7559 (m-30) cc_final: 0.6926 (p0) REVERT: R 293 ASP cc_start: 0.5918 (t0) cc_final: 0.5079 (t0) REVERT: R 336 LYS cc_start: 0.7067 (mmtt) cc_final: 0.6497 (mtmm) REVERT: R 397 MET cc_start: 0.8019 (mmp) cc_final: 0.7132 (mtm) REVERT: R 407 ASN cc_start: 0.8542 (m-40) cc_final: 0.8097 (t0) REVERT: G 25 ILE cc_start: 0.7705 (OUTLIER) cc_final: 0.7453 (mt) REVERT: P 3 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.5940 (mp0) REVERT: P 19 GLN cc_start: 0.8307 (mm-40) cc_final: 0.7759 (mt0) outliers start: 47 outliers final: 29 residues processed: 191 average time/residue: 0.3461 time to fit residues: 89.6273 Evaluate side-chains 188 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 155 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 33 ASN 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 281 VAL 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 296 LEU 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 265 ILE Chi-restraints excluded: chain R residue 330 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 72 optimal weight: 8.9990 chunk 15 optimal weight: 7.9990 chunk 111 optimal weight: 0.7980 chunk 55 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 109 optimal weight: 0.0060 chunk 76 optimal weight: 0.2980 chunk 37 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 41 HIS 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 = 0.4011 r_free = 0.4011 target = 0.157075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.121017 restraints weight = 13217.126| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.56 r_work: 0.3336 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.4664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9420 Z= 0.192 Angle : 0.611 10.821 12770 Z= 0.313 Chirality : 0.043 0.232 1410 Planarity : 0.004 0.067 1620 Dihedral : 4.791 54.848 1267 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.26 % Allowed : 21.49 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.25), residues: 1130 helix: 0.57 (0.26), residues: 437 sheet: -1.47 (0.32), residues: 231 loop : -1.18 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP N 49 HIS 0.002 0.001 HIS A 220 PHE 0.024 0.001 PHE A 376 TYR 0.020 0.001 TYR R 145 ARG 0.005 0.000 ARG A 317 *********************** 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 199 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 167 time to evaluate : 1.069 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: N 89 LYS cc_start: 0.8846 (mmmt) cc_final: 0.8079 (mtpt) REVERT: N 110 PHE cc_start: 0.8591 (OUTLIER) cc_final: 0.8323 (t80) REVERT: B 239 PHE cc_start: 0.8933 (OUTLIER) cc_final: 0.8262 (m-80) REVERT: B 285 LYS cc_start: 0.8075 (pptt) cc_final: 0.7213 (mmmt) REVERT: A 20 ARG cc_start: 0.8082 (mtm110) cc_final: 0.7694 (mtm110) REVERT: A 284 ASP cc_start: 0.7690 (m-30) cc_final: 0.7339 (p0) REVERT: A 286 SER cc_start: 0.8818 (OUTLIER) cc_final: 0.8475 (m) REVERT: A 343 ASP cc_start: 0.8452 (m-30) cc_final: 0.7908 (m-30) REVERT: R 74 ASP cc_start: 0.7137 (t0) cc_final: 0.6677 (t0) REVERT: R 215 ASP cc_start: 0.7577 (m-30) cc_final: 0.6993 (p0) REVERT: R 293 ASP cc_start: 0.5834 (t0) cc_final: 0.4920 (t0) REVERT: R 336 LYS cc_start: 0.6937 (mmtt) cc_final: 0.6394 (mtmm) REVERT: R 397 MET cc_start: 0.7852 (mmp) cc_final: 0.7134 (mtt) REVERT: G 14 LYS cc_start: 0.8650 (ptmt) cc_final: 0.8398 (pttt) REVERT: G 25 ILE cc_start: 0.7724 (OUTLIER) cc_final: 0.7483 (mp) REVERT: P 19 GLN cc_start: 0.8318 (mm-40) cc_final: 0.7823 (mt0) outliers start: 32 outliers final: 22 residues processed: 184 average time/residue: 0.2521 time to fit residues: 62.4060 Evaluate side-chains 185 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 159 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 33 ASN Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 110 PHE Chi-restraints excluded: chain N residue 111 ASP Chi-restraints excluded: chain N residue 119 TYR 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 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 265 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 27 optimal weight: 0.0980 chunk 38 optimal weight: 0.9990 chunk 105 optimal weight: 9.9990 chunk 79 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 83 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 74 optimal weight: 30.0000 chunk 93 optimal weight: 0.9980 chunk 109 optimal weight: 0.0870 chunk 106 optimal weight: 3.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 GLN ** B 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4013 r_free = 0.4013 target = 0.157352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.121610 restraints weight = 12980.300| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.80 r_work: 0.3324 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 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 0.047 9420 Z= 0.203 Angle : 0.610 10.186 12770 Z= 0.314 Chirality : 0.043 0.258 1410 Planarity : 0.004 0.067 1620 Dihedral : 4.648 53.660 1267 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.95 % Allowed : 21.79 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.25), residues: 1130 helix: 0.62 (0.26), residues: 438 sheet: -1.45 (0.32), residues: 230 loop : -1.11 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 49 HIS 0.003 0.001 HIS A 220 PHE 0.023 0.001 PHE A 376 TYR 0.021 0.001 TYR R 145 ARG 0.005 0.000 ARG A 317 *********************** 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 189 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 160 time to evaluate : 1.010 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: N 89 LYS cc_start: 0.8846 (mmmt) cc_final: 0.8034 (mtpt) REVERT: B 64 TYR cc_start: 0.8822 (OUTLIER) cc_final: 0.8189 (t80) REVERT: B 94 LYS cc_start: 0.8186 (mttp) cc_final: 0.7930 (mttt) REVERT: B 177 GLU cc_start: 0.6903 (mm-30) cc_final: 0.6613 (mp0) REVERT: B 239 PHE cc_start: 0.8939 (OUTLIER) cc_final: 0.8234 (m-80) REVERT: B 285 LYS cc_start: 0.8101 (pptt) cc_final: 0.7197 (mmmt) REVERT: A 20 ARG cc_start: 0.8118 (mtm110) cc_final: 0.7699 (mtm110) REVERT: A 27 GLU cc_start: 0.8415 (mm-30) cc_final: 0.8157 (mm-30) REVERT: A 218 ASN cc_start: 0.8163 (p0) cc_final: 0.7762 (m-40) REVERT: A 284 ASP cc_start: 0.7710 (m-30) cc_final: 0.7340 (p0) REVERT: A 286 SER cc_start: 0.8851 (OUTLIER) cc_final: 0.8508 (m) REVERT: A 343 ASP cc_start: 0.8473 (m-30) cc_final: 0.7925 (m-30) REVERT: R 74 ASP cc_start: 0.7179 (t0) cc_final: 0.6737 (t0) REVERT: R 173 HIS cc_start: 0.8578 (m90) cc_final: 0.8321 (m-70) REVERT: R 198 ASP cc_start: 0.7575 (p0) cc_final: 0.7349 (p0) REVERT: R 215 ASP cc_start: 0.7592 (m-30) cc_final: 0.6997 (p0) REVERT: R 336 LYS cc_start: 0.7046 (mmtt) cc_final: 0.6457 (mtmm) REVERT: R 397 MET cc_start: 0.7673 (mmp) cc_final: 0.7089 (mtt) REVERT: R 407 ASN cc_start: 0.8476 (m-40) cc_final: 0.8010 (t0) REVERT: G 13 ARG cc_start: 0.8967 (mtp85) cc_final: 0.8766 (ptp-110) REVERT: G 25 ILE cc_start: 0.7726 (OUTLIER) cc_final: 0.7491 (mp) REVERT: P 19 GLN cc_start: 0.8313 (mm-40) cc_final: 0.7997 (tt0) outliers start: 29 outliers final: 23 residues processed: 176 average time/residue: 0.2250 time to fit residues: 54.3421 Evaluate side-chains 186 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 159 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 33 ASN Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 111 ASP Chi-restraints excluded: chain N residue 119 TYR Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 64 TYR 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 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 R residue 265 ILE Chi-restraints excluded: chain R residue 372 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 9 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 1 optimal weight: 7.9990 chunk 57 optimal weight: 0.6980 chunk 110 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3988 r_free = 0.3988 target = 0.154997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.119151 restraints weight = 13180.326| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.58 r_work: 0.3299 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.4881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9420 Z= 0.271 Angle : 0.649 11.741 12770 Z= 0.334 Chirality : 0.044 0.234 1410 Planarity : 0.004 0.064 1620 Dihedral : 4.732 51.281 1267 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.85 % Allowed : 21.89 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.25), residues: 1130 helix: 0.57 (0.26), residues: 438 sheet: -1.58 (0.32), residues: 227 loop : -1.15 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 49 HIS 0.004 0.001 HIS A 220 PHE 0.023 0.001 PHE A 376 TYR 0.021 0.002 TYR R 145 ARG 0.004 0.000 ARG A 317 ********************** 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 190 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 162 time to evaluate : 1.001 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 34 TYR cc_start: 0.8321 (m-80) cc_final: 0.7784 (m-80) REVERT: N 89 LYS cc_start: 0.8860 (mmmt) cc_final: 0.8068 (mtpt) REVERT: B 64 TYR cc_start: 0.8832 (OUTLIER) cc_final: 0.8224 (t80) REVERT: B 231 GLU cc_start: 0.8054 (pt0) cc_final: 0.7663 (pt0) REVERT: B 239 PHE cc_start: 0.8970 (OUTLIER) cc_final: 0.8307 (m-80) REVERT: B 285 LYS cc_start: 0.8139 (pptt) cc_final: 0.7242 (mmmt) REVERT: A 20 ARG cc_start: 0.8048 (mtm110) cc_final: 0.7749 (mtm110) REVERT: A 218 ASN cc_start: 0.8142 (p0) cc_final: 0.7810 (m-40) REVERT: A 284 ASP cc_start: 0.7727 (m-30) cc_final: 0.7326 (p0) REVERT: A 286 SER cc_start: 0.8879 (OUTLIER) cc_final: 0.8560 (m) REVERT: A 343 ASP cc_start: 0.8453 (m-30) cc_final: 0.7921 (m-30) REVERT: R 74 ASP cc_start: 0.7124 (t0) cc_final: 0.6650 (t0) REVERT: R 173 HIS cc_start: 0.8574 (m90) cc_final: 0.8341 (m-70) REVERT: R 189 LEU cc_start: 0.8696 (tt) cc_final: 0.8287 (tp) REVERT: R 215 ASP cc_start: 0.7580 (m-30) cc_final: 0.6987 (p0) REVERT: R 293 ASP cc_start: 0.5605 (t0) cc_final: 0.4902 (t70) REVERT: R 336 LYS cc_start: 0.6980 (mmtt) cc_final: 0.6437 (mtmm) REVERT: R 397 MET cc_start: 0.7755 (mmp) cc_final: 0.7176 (mtt) REVERT: R 407 ASN cc_start: 0.8507 (m-40) cc_final: 0.8052 (t0) REVERT: G 13 ARG cc_start: 0.8908 (mtp85) cc_final: 0.8345 (ptp-110) REVERT: G 25 ILE cc_start: 0.7699 (OUTLIER) cc_final: 0.7451 (mp) REVERT: P 19 GLN cc_start: 0.8459 (mm-40) cc_final: 0.8130 (tt0) outliers start: 28 outliers final: 23 residues processed: 180 average time/residue: 0.2229 time to fit residues: 54.9947 Evaluate side-chains 183 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 33 ASN Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 111 ASP Chi-restraints excluded: chain N residue 119 TYR Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 64 TYR 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 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 R residue 265 ILE Chi-restraints excluded: chain R residue 372 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 31 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 85 optimal weight: 0.0970 chunk 17 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3997 r_free = 0.3997 target = 0.156001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.120627 restraints weight = 13222.003| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.59 r_work: 0.3321 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.4956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9420 Z= 0.250 Angle : 0.643 11.198 12770 Z= 0.331 Chirality : 0.044 0.212 1410 Planarity : 0.004 0.060 1620 Dihedral : 4.722 49.963 1267 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.16 % Allowed : 22.00 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.25), residues: 1130 helix: 0.57 (0.26), residues: 441 sheet: -1.52 (0.32), residues: 231 loop : -1.17 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP N 49 HIS 0.003 0.001 HIS A 220 PHE 0.023 0.001 PHE A 376 TYR 0.020 0.001 TYR R 145 ARG 0.004 0.000 ARG A 317 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5006.97 seconds wall clock time: 88 minutes 40.34 seconds (5320.34 seconds total)