Starting phenix.real_space_refine on Sun Jul 27 12:04:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fim_31603/07_2025/7fim_31603.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fim_31603/07_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_31603/07_2025/7fim_31603.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fim_31603/07_2025/7fim_31603.map" model { file = "/net/cci-nas-00/data/ceres_data/7fim_31603/07_2025/7fim_31603.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fim_31603/07_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 5.72, per 1000 atoms: 0.62 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: 2.36 Conformation dependent library (CDL) restraints added in 985.8 milliseconds 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2176 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 11 sheets defined 41.3% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 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: 2.78 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: 1.640 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: 23.630 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 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:3.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6203 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9426 Z= 0.189 Angle : 0.835 9.816 12782 Z= 0.458 Chirality : 0.047 0.259 1410 Planarity : 0.005 0.080 1620 Dihedral : 13.919 87.284 3372 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 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 Details of bonding type rmsd hydrogen bonds : bond 0.21641 ( 399) hydrogen bonds : angle 7.68338 ( 1137) SS BOND : bond 0.00344 ( 6) SS BOND : angle 1.33496 ( 12) covalent geometry : bond 0.00351 ( 9420) covalent geometry : angle 0.83455 (12770) *********************** 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 : 1.040 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: 0.2650 time to fit residues: 109.6135 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 : 0.932 ------------------------------------------------------------------------------- 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 9426 Z= 0.190 Angle : 0.658 11.160 12782 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 Details of bonding type rmsd hydrogen bonds : bond 0.04621 ( 399) hydrogen bonds : angle 5.15298 ( 1137) SS BOND : bond 0.00558 ( 6) SS BOND : angle 1.00538 ( 12) covalent geometry : bond 0.00432 ( 9420) covalent geometry : angle 0.65766 (12770) *********************** 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 : 0.984 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: 0.2465 time to fit residues: 73.9214 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 : 0.981 ------------------------------------------------------------------------------- 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: 5.9990 chunk 92 optimal weight: 0.9980 chunk 10 optimal weight: 0.4980 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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** ** R 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.162283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.126234 restraints weight = 13214.881| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.54 r_work: 0.3412 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9426 Z= 0.127 Angle : 0.589 8.102 12782 Z= 0.306 Chirality : 0.043 0.177 1410 Planarity : 0.004 0.064 1620 Dihedral : 4.752 46.640 1269 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.55 % Allowed : 14.77 % Favored : 82.69 % 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: -1.22 (0.25), residues: 1130 helix: -0.09 (0.25), residues: 437 sheet: -1.09 (0.34), residues: 225 loop : -1.22 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 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 0.009 0.001 ARG A 333 Details of bonding type rmsd hydrogen bonds : bond 0.03855 ( 399) hydrogen bonds : angle 4.63851 ( 1137) SS BOND : bond 0.00244 ( 6) SS BOND : angle 0.64991 ( 12) covalent geometry : bond 0.00290 ( 9420) covalent geometry : angle 0.58859 (12770) *********************** 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 221 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 196 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU R 127 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: B 285 LYS cc_start: 0.7587 (pptt) cc_final: 0.6635 (mmpt) REVERT: A 343 ASP cc_start: 0.8474 (m-30) cc_final: 0.7899 (m-30) REVERT: R 74 ASP cc_start: 0.6812 (t0) cc_final: 0.6359 (t0) REVERT: R 215 ASP cc_start: 0.7633 (m-30) cc_final: 0.7108 (p0) REVERT: R 336 LYS cc_start: 0.7560 (mmtt) cc_final: 0.7140 (mtmt) REVERT: R 397 MET cc_start: 0.7868 (mmp) cc_final: 0.7222 (mtm) REVERT: G 9 ILE cc_start: 0.8629 (mt) cc_final: 0.8378 (mm) REVERT: G 14 LYS cc_start: 0.8865 (ptpp) cc_final: 0.8493 (pttt) REVERT: P 3 GLU cc_start: 0.6876 (OUTLIER) cc_final: 0.6153 (mp0) REVERT: P 19 GLN cc_start: 0.8284 (mm-40) cc_final: 0.8045 (mm-40) outliers start: 25 outliers final: 17 residues processed: 212 average time/residue: 0.2384 time to fit residues: 67.5536 Evaluate side-chains 188 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 170 time to evaluate : 1.088 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 14 optimal weight: 0.2980 chunk 76 optimal weight: 8.9990 chunk 74 optimal weight: 20.0000 chunk 95 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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** 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 = 0.156127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.120616 restraints weight = 13034.325| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.67 r_work: 0.3309 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9426 Z= 0.215 Angle : 0.647 9.613 12782 Z= 0.336 Chirality : 0.045 0.200 1410 Planarity : 0.004 0.065 1620 Dihedral : 4.942 52.364 1269 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 4.28 % Allowed : 17.01 % Favored : 78.72 % 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: -1.28 (0.25), residues: 1130 helix: 0.03 (0.25), residues: 439 sheet: -1.32 (0.33), residues: 233 loop : -1.33 (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 0.018 0.002 PHE N 110 TYR 0.021 0.002 TYR R 145 ARG 0.005 0.001 ARG R 44 Details of bonding type rmsd hydrogen bonds : bond 0.04011 ( 399) hydrogen bonds : angle 4.65749 ( 1137) SS BOND : bond 0.00429 ( 6) SS BOND : angle 0.94660 ( 12) covalent geometry : bond 0.00503 ( 9420) covalent geometry : angle 0.64651 (12770) *********************** 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 211 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 169 time to evaluate : 1.038 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: B 239 PHE cc_start: 0.8834 (OUTLIER) cc_final: 0.8251 (m-80) REVERT: B 264 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7950 (pm20) REVERT: B 285 LYS cc_start: 0.8052 (pptt) cc_final: 0.7333 (mmmt) REVERT: A 343 ASP cc_start: 0.8468 (m-30) cc_final: 0.7902 (m-30) REVERT: R 74 ASP cc_start: 0.6918 (t0) cc_final: 0.6499 (t0) REVERT: R 336 LYS cc_start: 0.7369 (mmtt) cc_final: 0.6955 (mtmt) REVERT: R 397 MET cc_start: 0.8028 (mmp) cc_final: 0.7332 (mtt) REVERT: G 9 ILE cc_start: 0.8722 (mt) cc_final: 0.8125 (mm) REVERT: G 13 ARG cc_start: 0.8501 (mtm-85) cc_final: 0.8030 (ptp-110) REVERT: G 14 LYS cc_start: 0.8876 (ptpp) cc_final: 0.8640 (ptmt) REVERT: P 3 GLU cc_start: 0.6892 (OUTLIER) cc_final: 0.5947 (mp0) REVERT: P 19 GLN cc_start: 0.8488 (mm-40) cc_final: 0.8284 (mm-40) outliers start: 42 outliers final: 29 residues processed: 195 average time/residue: 0.2160 time to fit residues: 58.2472 Evaluate side-chains 192 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 160 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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 239 PHE Chi-restraints excluded: chain B residue 264 GLN Chi-restraints excluded: chain B residue 268 THR 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 250 SER 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 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 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: 0.9980 chunk 18 optimal weight: 0.5980 chunk 45 optimal weight: 0.1980 chunk 83 optimal weight: 0.0970 chunk 31 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 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 = 0.4037 r_free = 0.4037 target = 0.159117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.123375 restraints weight = 12896.714| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.47 r_work: 0.3387 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9426 Z= 0.121 Angle : 0.575 9.679 12782 Z= 0.298 Chirality : 0.042 0.174 1410 Planarity : 0.004 0.065 1620 Dihedral : 4.617 53.513 1267 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.36 % Allowed : 20.16 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.94 (0.25), residues: 1130 helix: 0.38 (0.26), residues: 432 sheet: -1.08 (0.34), residues: 228 loop : -1.24 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP N 49 HIS 0.002 0.000 HIS B 59 PHE 0.010 0.001 PHE B 246 TYR 0.021 0.001 TYR P 10 ARG 0.004 0.000 ARG R 44 Details of bonding type rmsd hydrogen bonds : bond 0.03387 ( 399) hydrogen bonds : angle 4.39723 ( 1137) SS BOND : bond 0.00275 ( 6) SS BOND : angle 0.87901 ( 12) covalent geometry : bond 0.00278 ( 9420) covalent geometry : angle 0.57494 (12770) *********************** 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 212 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 179 time to evaluate : 0.992 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: 0.7729 (OUTLIER) cc_final: 0.6723 (ppp) REVERT: B 239 PHE cc_start: 0.8791 (OUTLIER) cc_final: 0.8290 (m-80) REVERT: B 285 LYS cc_start: 0.7875 (pptt) cc_final: 0.7145 (mmmt) REVERT: A 284 ASP cc_start: 0.7559 (m-30) cc_final: 0.7341 (p0) REVERT: A 286 SER cc_start: 0.8816 (OUTLIER) cc_final: 0.8470 (m) REVERT: A 343 ASP cc_start: 0.8375 (m-30) cc_final: 0.7880 (m-30) REVERT: R 74 ASP cc_start: 0.6975 (t0) cc_final: 0.6520 (t0) REVERT: R 215 ASP cc_start: 0.7668 (m-30) cc_final: 0.7052 (p0) REVERT: R 293 ASP cc_start: 0.5626 (t0) cc_final: 0.4930 (t0) REVERT: R 336 LYS cc_start: 0.7225 (mmtt) cc_final: 0.6843 (mtmt) REVERT: R 397 MET cc_start: 0.7924 (mmp) cc_final: 0.7245 (mtt) REVERT: G 9 ILE cc_start: 0.8721 (mt) cc_final: 0.8455 (mm) REVERT: G 14 LYS cc_start: 0.8886 (ptpp) cc_final: 0.8643 (ptmt) REVERT: P 3 GLU cc_start: 0.6835 (OUTLIER) cc_final: 0.6177 (mp0) outliers start: 33 outliers final: 20 residues processed: 197 average time/residue: 0.2252 time to fit residues: 61.5560 Evaluate side-chains 187 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 1.129 ------------------------------------------------------------------------------- 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 266 LEU Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain A residue 250 SER 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 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 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: 0.7980 chunk 34 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 56 optimal weight: 0.0070 chunk 108 optimal weight: 2.9990 overall best weight: 1.3402 ------------------------------------------------------------------------------- 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** A 29 GLN A 59 GLN A 220 HIS ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.155410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.119454 restraints weight = 13000.955| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.55 r_work: 0.3307 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9426 Z= 0.198 Angle : 0.622 9.783 12782 Z= 0.322 Chirality : 0.044 0.200 1410 Planarity : 0.004 0.066 1620 Dihedral : 4.757 58.272 1267 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 4.18 % Allowed : 20.16 % Favored : 75.66 % 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: -1.05 (0.25), residues: 1130 helix: 0.37 (0.26), residues: 439 sheet: -1.40 (0.32), residues: 235 loop : -1.23 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP N 49 HIS 0.003 0.001 HIS B 188 PHE 0.022 0.002 PHE A 376 TYR 0.019 0.001 TYR R 145 ARG 0.014 0.001 ARG A 317 Details of bonding type rmsd hydrogen bonds : bond 0.03692 ( 399) hydrogen bonds : angle 4.49474 ( 1137) SS BOND : bond 0.00398 ( 6) SS BOND : angle 1.21257 ( 12) covalent geometry : bond 0.00464 ( 9420) covalent geometry : angle 0.62137 (12770) *********************** 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 201 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 160 time to evaluate : 1.057 Fit side-chains 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: 0.8879 (mmmt) cc_final: 0.8125 (mtpt) REVERT: B 94 LYS cc_start: 0.8408 (mttp) cc_final: 0.8047 (mttt) REVERT: B 193 MET cc_start: 0.8498 (mmm) cc_final: 0.8209 (mmt) REVERT: B 222 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.6910 (ppp) REVERT: B 239 PHE cc_start: 0.8956 (OUTLIER) cc_final: 0.8337 (m-80) REVERT: B 285 LYS cc_start: 0.8032 (pptt) cc_final: 0.7288 (mmmt) REVERT: A 284 ASP cc_start: 0.7724 (m-30) cc_final: 0.7328 (p0) REVERT: A 286 SER cc_start: 0.8917 (OUTLIER) cc_final: 0.8604 (m) REVERT: A 343 ASP cc_start: 0.8395 (m-30) cc_final: 0.7919 (m-30) REVERT: R 74 ASP cc_start: 0.7011 (t0) cc_final: 0.6571 (t0) REVERT: R 215 ASP cc_start: 0.7570 (m-30) cc_final: 0.6934 (p0) REVERT: R 293 ASP cc_start: 0.5640 (t0) cc_final: 0.4958 (t0) REVERT: R 336 LYS cc_start: 0.7083 (mmtt) cc_final: 0.6565 (mtmm) REVERT: R 397 MET cc_start: 0.7969 (mmp) cc_final: 0.7230 (mtt) REVERT: G 9 ILE cc_start: 0.8723 (mt) cc_final: 0.8004 (tp) REVERT: G 13 ARG cc_start: 0.8517 (mtm-85) cc_final: 0.8064 (ptp-110) REVERT: P 3 GLU cc_start: 0.6898 (OUTLIER) cc_final: 0.5949 (mp0) REVERT: P 19 GLN cc_start: 0.8363 (mm-40) cc_final: 0.7906 (mt0) outliers start: 41 outliers final: 31 residues processed: 184 average time/residue: 0.2187 time to fit residues: 55.3011 Evaluate side-chains 191 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 156 time to evaluate : 1.099 ------------------------------------------------------------------------------- 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 109 CYS 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 222 MET Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 268 THR 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 250 SER 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 330 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 66 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 1 optimal weight: 0.2980 chunk 73 optimal weight: 0.5980 chunk 14 optimal weight: 0.3980 chunk 106 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.4011 r_free = 0.4011 target = 0.156948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.121350 restraints weight = 13221.441| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.78 r_work: 0.3314 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9426 Z= 0.149 Angle : 0.605 10.217 12782 Z= 0.311 Chirality : 0.044 0.222 1410 Planarity : 0.004 0.066 1620 Dihedral : 4.685 59.200 1267 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 4.48 % Allowed : 20.67 % Favored : 74.85 % 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: -0.91 (0.25), residues: 1130 helix: 0.47 (0.26), residues: 440 sheet: -1.37 (0.31), residues: 248 loop : -1.09 (0.29), residues: 442 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 0.018 0.001 TYR R 145 ARG 0.012 0.000 ARG A 317 Details of bonding type rmsd hydrogen bonds : bond 0.03398 ( 399) hydrogen bonds : angle 4.38258 ( 1137) SS BOND : bond 0.00325 ( 6) SS BOND : angle 1.11062 ( 12) covalent geometry : bond 0.00350 ( 9420) covalent geometry : angle 0.60389 (12770) *********************** 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 205 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 161 time to evaluate : 0.931 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: 0.8863 (mmmt) cc_final: 0.8070 (mtpt) REVERT: B 222 MET cc_start: 0.7964 (OUTLIER) cc_final: 0.7666 (pmm) REVERT: B 239 PHE cc_start: 0.8972 (OUTLIER) cc_final: 0.8274 (m-80) REVERT: B 285 LYS cc_start: 0.8051 (pptt) cc_final: 0.7211 (mmmt) REVERT: A 20 ARG cc_start: 0.8136 (mtm110) cc_final: 0.7814 (mtm110) REVERT: A 221 MET cc_start: 0.8296 (mmm) cc_final: 0.8075 (tpp) REVERT: A 284 ASP cc_start: 0.7734 (m-30) cc_final: 0.7377 (p0) REVERT: A 286 SER cc_start: 0.8895 (OUTLIER) cc_final: 0.8568 (m) REVERT: A 343 ASP cc_start: 0.8455 (m-30) cc_final: 0.7956 (m-30) REVERT: R 74 ASP cc_start: 0.7103 (t0) cc_final: 0.6643 (t0) REVERT: R 215 ASP cc_start: 0.7561 (m-30) cc_final: 0.6916 (p0) REVERT: R 293 ASP cc_start: 0.5816 (t0) cc_final: 0.4968 (t0) REVERT: R 336 LYS cc_start: 0.7070 (mmtt) cc_final: 0.6528 (mtmm) REVERT: R 397 MET cc_start: 0.7926 (mmp) cc_final: 0.7146 (mtt) REVERT: G 9 ILE cc_start: 0.8715 (mt) cc_final: 0.8507 (tp) REVERT: G 25 ILE cc_start: 0.7702 (OUTLIER) cc_final: 0.7460 (mt) REVERT: P 3 GLU cc_start: 0.6887 (OUTLIER) cc_final: 0.6030 (mp0) REVERT: P 19 GLN cc_start: 0.8249 (mm-40) cc_final: 0.7871 (mt0) outliers start: 44 outliers final: 29 residues processed: 187 average time/residue: 0.2069 time to fit residues: 53.0956 Evaluate side-chains 192 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 158 time to evaluate : 0.930 ------------------------------------------------------------------------------- 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 109 CYS 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 222 MET 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 266 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain A residue 250 SER 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 72 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 chunk 111 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.3979 r_free = 0.3979 target = 0.154034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.119190 restraints weight = 13370.415| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.82 r_work: 0.3269 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.4689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9426 Z= 0.224 Angle : 0.667 10.329 12782 Z= 0.344 Chirality : 0.046 0.226 1410 Planarity : 0.005 0.066 1620 Dihedral : 4.835 56.302 1267 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.38 % Allowed : 20.77 % Favored : 74.85 % 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: -1.11 (0.25), residues: 1130 helix: 0.38 (0.25), residues: 440 sheet: -1.68 (0.31), residues: 244 loop : -1.17 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP N 49 HIS 0.004 0.001 HIS A 220 PHE 0.023 0.002 PHE A 376 TYR 0.017 0.002 TYR R 145 ARG 0.014 0.001 ARG A 317 Details of bonding type rmsd hydrogen bonds : bond 0.03780 ( 399) hydrogen bonds : angle 4.54088 ( 1137) SS BOND : bond 0.00472 ( 6) SS BOND : angle 1.79500 ( 12) covalent geometry : bond 0.00530 ( 9420) covalent geometry : angle 0.66536 (12770) *********************** 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 205 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 162 time to evaluate : 1.034 Fit side-chains TARDY: cannot create tardy model for: "GLU R 127 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: N 34 TYR cc_start: 0.8445 (m-80) cc_final: 0.8100 (m-80) REVERT: N 89 LYS cc_start: 0.8867 (mmmt) cc_final: 0.8065 (mtpt) REVERT: B 94 LYS cc_start: 0.8538 (mttp) cc_final: 0.8107 (mttt) REVERT: B 177 GLU cc_start: 0.6905 (mm-30) cc_final: 0.6667 (mp0) REVERT: B 231 GLU cc_start: 0.8084 (pt0) cc_final: 0.7836 (pt0) REVERT: B 239 PHE cc_start: 0.9002 (OUTLIER) cc_final: 0.8320 (m-80) REVERT: B 285 LYS cc_start: 0.8209 (pptt) cc_final: 0.7338 (mmmt) REVERT: A 15 GLU cc_start: 0.8082 (mp0) cc_final: 0.7839 (mp0) REVERT: A 218 ASN cc_start: 0.8175 (p0) cc_final: 0.7749 (m-40) REVERT: A 284 ASP cc_start: 0.7803 (m-30) cc_final: 0.7343 (p0) REVERT: A 286 SER cc_start: 0.8951 (OUTLIER) cc_final: 0.8617 (m) REVERT: R 74 ASP cc_start: 0.7210 (t0) cc_final: 0.6817 (t0) REVERT: R 215 ASP cc_start: 0.7640 (m-30) cc_final: 0.7006 (p0) REVERT: R 293 ASP cc_start: 0.5791 (t0) cc_final: 0.4974 (t0) REVERT: R 336 LYS cc_start: 0.6966 (mmtt) cc_final: 0.6382 (mtmm) REVERT: R 397 MET cc_start: 0.7996 (mmp) cc_final: 0.7150 (mtt) REVERT: R 407 ASN cc_start: 0.8502 (m-40) cc_final: 0.8023 (t0) REVERT: G 9 ILE cc_start: 0.8664 (mt) cc_final: 0.8360 (mm) REVERT: G 25 ILE cc_start: 0.7705 (OUTLIER) cc_final: 0.7450 (mt) REVERT: P 3 GLU cc_start: 0.6943 (OUTLIER) cc_final: 0.5956 (mp0) REVERT: P 19 GLN cc_start: 0.8336 (mm-40) cc_final: 0.7958 (mt0) outliers start: 43 outliers final: 34 residues processed: 191 average time/residue: 0.2272 time to fit residues: 59.2297 Evaluate side-chains 194 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 156 time to evaluate : 0.985 ------------------------------------------------------------------------------- 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 110 PHE 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 266 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 281 VAL 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 224 VAL Chi-restraints excluded: chain A residue 250 SER 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 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: 0.7980 chunk 38 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 83 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 chunk 74 optimal weight: 20.0000 chunk 93 optimal weight: 2.9990 chunk 109 optimal weight: 0.1980 chunk 106 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4009 r_free = 0.4009 target = 0.156865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.120850 restraints weight = 13000.416| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.54 r_work: 0.3340 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.4722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9426 Z= 0.138 Angle : 0.624 10.654 12782 Z= 0.320 Chirality : 0.044 0.247 1410 Planarity : 0.004 0.065 1620 Dihedral : 4.626 55.065 1267 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.67 % Allowed : 21.38 % Favored : 74.95 % 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: -0.89 (0.25), residues: 1130 helix: 0.54 (0.26), residues: 438 sheet: -1.44 (0.32), residues: 237 loop : -1.10 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP N 49 HIS 0.003 0.001 HIS A 220 PHE 0.023 0.001 PHE A 376 TYR 0.022 0.001 TYR R 145 ARG 0.008 0.000 ARG A 317 Details of bonding type rmsd hydrogen bonds : bond 0.03319 ( 399) hydrogen bonds : angle 4.32364 ( 1137) SS BOND : bond 0.00515 ( 6) SS BOND : angle 2.12867 ( 12) covalent geometry : bond 0.00327 ( 9420) covalent geometry : angle 0.62097 (12770) *********************** 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 204 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 168 time to evaluate : 1.093 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: 0.8834 (mmmt) cc_final: 0.8039 (mtpt) REVERT: B 64 TYR cc_start: 0.8831 (OUTLIER) cc_final: 0.8227 (t80) REVERT: B 177 GLU cc_start: 0.6830 (mm-30) cc_final: 0.6596 (mp0) REVERT: B 222 MET cc_start: 0.7883 (pmm) cc_final: 0.7645 (pmm) REVERT: B 239 PHE cc_start: 0.8953 (OUTLIER) cc_final: 0.8271 (m-80) REVERT: B 285 LYS cc_start: 0.8093 (pptt) cc_final: 0.7169 (mmmt) REVERT: A 218 ASN cc_start: 0.8140 (p0) cc_final: 0.7765 (m-40) REVERT: A 284 ASP cc_start: 0.7670 (m-30) cc_final: 0.7326 (p0) REVERT: A 286 SER cc_start: 0.8824 (OUTLIER) cc_final: 0.8479 (m) REVERT: A 343 ASP cc_start: 0.8425 (m-30) cc_final: 0.7878 (m-30) REVERT: R 74 ASP cc_start: 0.7172 (t0) cc_final: 0.6722 (t0) REVERT: R 198 ASP cc_start: 0.7574 (p0) cc_final: 0.7370 (p0) REVERT: R 215 ASP cc_start: 0.7572 (m-30) cc_final: 0.6988 (p0) REVERT: R 293 ASP cc_start: 0.5917 (t0) cc_final: 0.5006 (t0) REVERT: R 336 LYS cc_start: 0.7010 (mmtt) cc_final: 0.6454 (mtmm) REVERT: R 397 MET cc_start: 0.7695 (mmp) cc_final: 0.7039 (mtm) REVERT: R 407 ASN cc_start: 0.8508 (m-40) cc_final: 0.8065 (t0) REVERT: G 9 ILE cc_start: 0.8678 (mt) cc_final: 0.7999 (tp) REVERT: G 13 ARG cc_start: 0.8514 (mtm-85) cc_final: 0.8175 (ptp-110) REVERT: G 25 ILE cc_start: 0.7723 (OUTLIER) cc_final: 0.7493 (mp) REVERT: P 19 GLN cc_start: 0.8330 (mm-40) cc_final: 0.8010 (tt0) outliers start: 36 outliers final: 28 residues processed: 191 average time/residue: 0.2410 time to fit residues: 62.2179 Evaluate side-chains 192 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 160 time to evaluate : 1.086 ------------------------------------------------------------------------------- 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 110 PHE 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 64 TYR 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 226 THR Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 268 THR 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 250 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain R residue 72 TRP Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 182 ASN Chi-restraints excluded: chain R residue 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 9 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 39 optimal weight: 0.4980 chunk 60 optimal weight: 2.9990 chunk 84 optimal weight: 0.0270 chunk 76 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 GLN A 59 GLN ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.157969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.121978 restraints weight = 13232.162| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.74 r_work: 0.3337 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.4837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9426 Z= 0.137 Angle : 0.621 10.321 12782 Z= 0.319 Chirality : 0.043 0.232 1410 Planarity : 0.004 0.061 1620 Dihedral : 4.550 53.809 1267 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.36 % Allowed : 21.28 % Favored : 75.36 % 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: -0.84 (0.25), residues: 1130 helix: 0.55 (0.26), residues: 441 sheet: -1.42 (0.32), residues: 232 loop : -1.06 (0.29), residues: 457 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 0.022 0.001 TYR R 145 ARG 0.008 0.000 ARG A 317 Details of bonding type rmsd hydrogen bonds : bond 0.03293 ( 399) hydrogen bonds : angle 4.24294 ( 1137) SS BOND : bond 0.00452 ( 6) SS BOND : angle 2.01564 ( 12) covalent geometry : bond 0.00328 ( 9420) covalent geometry : angle 0.61793 (12770) ********************** 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 199 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 166 time to evaluate : 0.984 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: 0.8862 (mmmt) cc_final: 0.8059 (mtpt) REVERT: B 64 TYR cc_start: 0.8833 (OUTLIER) cc_final: 0.8223 (t80) REVERT: B 177 GLU cc_start: 0.7074 (mm-30) cc_final: 0.6785 (mp0) REVERT: B 222 MET cc_start: 0.7934 (pmm) cc_final: 0.7693 (pmm) REVERT: B 239 PHE cc_start: 0.8961 (OUTLIER) cc_final: 0.8253 (m-80) REVERT: B 285 LYS cc_start: 0.8097 (pptt) cc_final: 0.7146 (mmmt) REVERT: A 218 ASN cc_start: 0.8097 (p0) cc_final: 0.7773 (m-40) REVERT: A 284 ASP cc_start: 0.7691 (m-30) cc_final: 0.7335 (p0) REVERT: A 286 SER cc_start: 0.8857 (OUTLIER) cc_final: 0.8506 (m) REVERT: A 343 ASP cc_start: 0.8455 (m-30) cc_final: 0.7893 (m-30) REVERT: A 392 GLU cc_start: 0.8208 (pm20) cc_final: 0.7978 (mm-30) REVERT: R 74 ASP cc_start: 0.7174 (t0) cc_final: 0.6723 (t0) REVERT: R 215 ASP cc_start: 0.7596 (m-30) cc_final: 0.6999 (p0) REVERT: R 336 LYS cc_start: 0.6960 (mmtt) cc_final: 0.6373 (mtmm) REVERT: R 397 MET cc_start: 0.7680 (mmp) cc_final: 0.7074 (mtt) REVERT: R 407 ASN cc_start: 0.8471 (m-40) cc_final: 0.8027 (t0) REVERT: G 9 ILE cc_start: 0.8788 (mt) cc_final: 0.8017 (tp) REVERT: G 13 ARG cc_start: 0.8562 (mtm-85) cc_final: 0.8191 (ptp-110) REVERT: G 25 ILE cc_start: 0.7763 (OUTLIER) cc_final: 0.7528 (mp) REVERT: P 19 GLN cc_start: 0.8301 (mm-40) cc_final: 0.7983 (tt0) outliers start: 33 outliers final: 28 residues processed: 189 average time/residue: 0.2201 time to fit residues: 57.5194 Evaluate side-chains 195 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 163 time to evaluate : 1.111 ------------------------------------------------------------------------------- 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 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 64 TYR 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 226 THR Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain R residue 72 TRP Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 182 ASN Chi-restraints excluded: chain R residue 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 31 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 86 optimal weight: 0.3980 chunk 45 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 chunk 101 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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** A 371 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.155231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.119749 restraints weight = 13256.803| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.83 r_work: 0.3295 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.4960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9426 Z= 0.187 Angle : 0.647 9.929 12782 Z= 0.334 Chirality : 0.044 0.215 1410 Planarity : 0.004 0.060 1620 Dihedral : 4.646 51.657 1267 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.67 % Allowed : 21.18 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.94 (0.25), residues: 1130 helix: 0.50 (0.26), residues: 442 sheet: -1.52 (0.32), residues: 232 loop : -1.13 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP N 49 HIS 0.004 0.001 HIS A 220 PHE 0.023 0.001 PHE A 376 TYR 0.022 0.002 TYR R 145 ARG 0.008 0.001 ARG A 20 Details of bonding type rmsd hydrogen bonds : bond 0.03536 ( 399) hydrogen bonds : angle 4.35873 ( 1137) SS BOND : bond 0.00604 ( 6) SS BOND : angle 2.05439 ( 12) covalent geometry : bond 0.00442 ( 9420) covalent geometry : angle 0.64444 (12770) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4863.33 seconds wall clock time: 84 minutes 11.13 seconds (5051.13 seconds total)