Starting phenix.real_space_refine on Wed Mar 4 05:28:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6sgx_10187/03_2026/6sgx_10187.cif Found real_map, /net/cci-nas-00/data/ceres_data/6sgx_10187/03_2026/6sgx_10187.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6sgx_10187/03_2026/6sgx_10187.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6sgx_10187/03_2026/6sgx_10187.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6sgx_10187/03_2026/6sgx_10187.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6sgx_10187/03_2026/6sgx_10187.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 28 5.16 5 C 7202 2.51 5 N 2016 2.21 5 O 1981 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11227 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 548 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain breaks: 1 Chain: "B" Number of atoms: 3042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3042 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 22, 'TRANS': 403} Chain breaks: 3 Chain: "C" Number of atoms: 3135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3135 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 27, 'TRANS': 410} Chain breaks: 4 Chain: "F" Number of atoms: 2673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2673 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 29, 'TRANS': 307} Chain breaks: 4 Chain: "G" Number of atoms: 1829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1829 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 15, 'TRANS': 225} Chain breaks: 7 Time building chain proxies: 2.38, per 1000 atoms: 0.21 Number of scatterers: 11227 At special positions: 0 Unit cell: (130.811, 105.287, 141.446, 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 28 16.00 O 1981 8.00 N 2016 7.00 C 7202 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 446.3 milliseconds 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2816 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 7 sheets defined 54.8% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 34 through 49 removed outlier: 3.649A pdb=" N VAL A 38 " --> pdb=" O THR A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 87 removed outlier: 3.704A pdb=" N THR A 66 " --> pdb=" O ASP A 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 46 Processing helix chain 'B' and resid 111 through 119 Processing helix chain 'B' and resid 127 through 156 removed outlier: 3.730A pdb=" N HIS B 131 " --> pdb=" O TRP B 127 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE B 132 " --> pdb=" O GLY B 128 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ALA B 133 " --> pdb=" O PRO B 129 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARG B 134 " --> pdb=" O THR B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 180 removed outlier: 3.561A pdb=" N PHE B 165 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 196 Processing helix chain 'B' and resid 198 through 205 removed outlier: 3.732A pdb=" N ALA B 205 " --> pdb=" O ALA B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 234 removed outlier: 4.260A pdb=" N LEU B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 263 removed outlier: 3.933A pdb=" N ALA B 260 " --> pdb=" O LEU B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 285 removed outlier: 4.350A pdb=" N CYS B 273 " --> pdb=" O ASP B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 294 removed outlier: 3.511A pdb=" N LEU B 289 " --> pdb=" O GLN B 285 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA B 294 " --> pdb=" O SER B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 351 removed outlier: 3.680A pdb=" N ARG B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG B 325 " --> pdb=" O PRO B 321 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL B 350 " --> pdb=" O SER B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 373 removed outlier: 3.923A pdb=" N VAL B 364 " --> pdb=" O TRP B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 377 removed outlier: 3.640A pdb=" N TRP B 377 " --> pdb=" O ALA B 374 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 374 through 377' Processing helix chain 'B' and resid 379 through 404 removed outlier: 3.785A pdb=" N LYS B 383 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N SER B 390 " --> pdb=" O LEU B 386 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N TYR B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 430 removed outlier: 3.893A pdb=" N ASN B 430 " --> pdb=" O VAL B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 466 removed outlier: 4.280A pdb=" N LEU B 458 " --> pdb=" O LEU B 454 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ILE B 459 " --> pdb=" O ASP B 455 " (cutoff:3.500A) Proline residue: B 460 - end of helix removed outlier: 3.574A pdb=" N ALA B 463 " --> pdb=" O ILE B 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 47 removed outlier: 3.778A pdb=" N ILE C 38 " --> pdb=" O PRO C 34 " (cutoff:3.500A) Proline residue: C 40 - end of helix Processing helix chain 'C' and resid 82 through 87 removed outlier: 3.520A pdb=" N VAL C 86 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY C 87 " --> pdb=" O LEU C 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 82 through 87' Processing helix chain 'C' and resid 115 through 124 removed outlier: 3.556A pdb=" N PHE C 119 " --> pdb=" O ALA C 115 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG C 124 " --> pdb=" O SER C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 157 removed outlier: 3.778A pdb=" N ALA C 133 " --> pdb=" O PRO C 129 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ARG C 134 " --> pdb=" O THR C 130 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER C 151 " --> pdb=" O GLY C 147 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ARG C 155 " --> pdb=" O SER C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 181 removed outlier: 3.638A pdb=" N PHE C 165 " --> pdb=" O LEU C 161 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE C 166 " --> pdb=" O LEU C 162 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL C 167 " --> pdb=" O GLY C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'C' and resid 196 through 204 removed outlier: 3.511A pdb=" N ALA C 201 " --> pdb=" O LEU C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 231 Processing helix chain 'C' and resid 241 through 263 removed outlier: 3.692A pdb=" N THR C 245 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR C 247 " --> pdb=" O VAL C 243 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA C 260 " --> pdb=" O LEU C 256 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA C 261 " --> pdb=" O VAL C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 285 removed outlier: 3.638A pdb=" N ILE C 271 " --> pdb=" O SER C 267 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N CYS C 273 " --> pdb=" O ASP C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 294 Processing helix chain 'C' and resid 313 through 318 Processing helix chain 'C' and resid 319 through 345 removed outlier: 3.783A pdb=" N ARG C 325 " --> pdb=" O PRO C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 350 removed outlier: 4.308A pdb=" N VAL C 350 " --> pdb=" O SER C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 373 removed outlier: 4.136A pdb=" N VAL C 364 " --> pdb=" O TRP C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 376 No H-bonds generated for 'chain 'C' and resid 374 through 376' Processing helix chain 'C' and resid 379 through 404 removed outlier: 3.683A pdb=" N HIS C 389 " --> pdb=" O TRP C 385 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N SER C 390 " --> pdb=" O LEU C 386 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N TYR C 391 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 430 removed outlier: 3.748A pdb=" N TRP C 412 " --> pdb=" O GLN C 408 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA C 427 " --> pdb=" O VAL C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 467 removed outlier: 4.252A pdb=" N ASP C 455 " --> pdb=" O ALA C 451 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ILE C 459 " --> pdb=" O ASP C 455 " (cutoff:3.500A) Proline residue: C 460 - end of helix removed outlier: 3.600A pdb=" N VAL C 466 " --> pdb=" O MET C 462 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY C 467 " --> pdb=" O ALA C 463 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 43 Processing helix chain 'F' and resid 93 through 130 removed outlier: 3.879A pdb=" N VAL F 97 " --> pdb=" O ARG F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 138 removed outlier: 3.630A pdb=" N ALA F 137 " --> pdb=" O GLU F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 197 removed outlier: 3.973A pdb=" N LEU F 190 " --> pdb=" O ALA F 186 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASP F 195 " --> pdb=" O ARG F 191 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL F 196 " --> pdb=" O GLY F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 212 No H-bonds generated for 'chain 'F' and resid 210 through 212' Processing helix chain 'F' and resid 224 through 239 removed outlier: 3.658A pdb=" N TRP F 238 " --> pdb=" O GLN F 234 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS F 239 " --> pdb=" O ALA F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 263 removed outlier: 3.569A pdb=" N LEU F 261 " --> pdb=" O TRP F 258 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TRP F 263 " --> pdb=" O TRP F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 293 Processing helix chain 'F' and resid 386 through 396 removed outlier: 3.560A pdb=" N ALA F 390 " --> pdb=" O SER F 386 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 17 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 49 through 64 Processing helix chain 'G' and resid 86 through 88 No H-bonds generated for 'chain 'G' and resid 86 through 88' Processing helix chain 'G' and resid 89 through 95 removed outlier: 3.523A pdb=" N VAL G 93 " --> pdb=" O GLN G 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 98 No H-bonds generated for 'chain 'G' and resid 96 through 98' Processing helix chain 'G' and resid 131 through 136 Processing helix chain 'G' and resid 143 through 162 removed outlier: 3.587A pdb=" N VAL G 150 " --> pdb=" O ASP G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 212 Processing helix chain 'G' and resid 265 through 269 Processing sheet with id=AA1, first strand: chain 'B' and resid 67 through 71 removed outlier: 8.375A pdb=" N LEU B 94 " --> pdb=" O ARG B 11 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ALA B 13 " --> pdb=" O LEU B 94 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N LEU B 96 " --> pdb=" O ALA B 13 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LEU B 15 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N ALA B 98 " --> pdb=" O LEU B 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.542A pdb=" N LEU C 94 " --> pdb=" O ARG C 11 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ALA C 13 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N LEU C 96 " --> pdb=" O ALA C 13 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LEU C 15 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 9.286A pdb=" N ALA C 98 " --> pdb=" O LEU C 15 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 23 through 24 Processing sheet with id=AA4, first strand: chain 'F' and resid 202 through 208 removed outlier: 4.787A pdb=" N ALA F 203 " --> pdb=" O ARG F 162 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG F 162 " --> pdb=" O ALA F 203 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N THR F 205 " --> pdb=" O ALA F 160 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL F 381 " --> pdb=" O ARG F 162 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 339 through 343 removed outlier: 5.908A pdb=" N ILE F 215 " --> pdb=" O HIS F 341 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N THR F 343 " --> pdb=" O ILE F 215 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL F 217 " --> pdb=" O THR F 343 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N LEU F 360 " --> pdb=" O ARG F 214 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N THR F 216 " --> pdb=" O LEU F 360 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL F 362 " --> pdb=" O THR F 216 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE F 218 " --> pdb=" O VAL F 362 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 282 through 283 removed outlier: 8.504A pdb=" N THR F 283 " --> pdb=" O VAL F 246 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU F 248 " --> pdb=" O THR F 283 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY F 245 " --> pdb=" O LEU F 315 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N VAL F 317 " --> pdb=" O GLY F 245 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ALA F 247 " --> pdb=" O VAL F 317 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 166 through 169 removed outlier: 4.762A pdb=" N VAL G 79 " --> pdb=" O VAL G 169 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER G 120 " --> pdb=" O VAL G 82 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS G 106 " --> pdb=" O THR G 125 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N VAL G 237 " --> pdb=" O VAL G 199 " (cutoff:3.500A) 600 hydrogen bonds defined for protein. 1776 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.50 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3712 1.34 - 1.46: 2306 1.46 - 1.58: 5369 1.58 - 1.70: 1 1.70 - 1.82: 48 Bond restraints: 11436 Sorted by residual: bond pdb=" C ILE F 139 " pdb=" N PRO F 140 " ideal model delta sigma weight residual 1.334 1.388 -0.054 2.34e-02 1.83e+03 5.33e+00 bond pdb=" C GLN G 19 " pdb=" N PRO G 20 " ideal model delta sigma weight residual 1.334 1.382 -0.049 2.34e-02 1.83e+03 4.31e+00 bond pdb=" C SER B 435 " pdb=" N PRO B 436 " ideal model delta sigma weight residual 1.334 1.379 -0.045 2.34e-02 1.83e+03 3.64e+00 bond pdb=" CA LEU B 441 " pdb=" C LEU B 441 " ideal model delta sigma weight residual 1.525 1.558 -0.033 2.10e-02 2.27e+03 2.49e+00 bond pdb=" CB PRO C 199 " pdb=" CG PRO C 199 " ideal model delta sigma weight residual 1.492 1.415 0.077 5.00e-02 4.00e+02 2.39e+00 ... (remaining 11431 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 14929 2.10 - 4.20: 578 4.20 - 6.30: 89 6.30 - 8.39: 49 8.39 - 10.49: 10 Bond angle restraints: 15655 Sorted by residual: angle pdb=" N VAL G 172 " pdb=" CA VAL G 172 " pdb=" C VAL G 172 " ideal model delta sigma weight residual 110.23 116.85 -6.62 1.04e+00 9.25e-01 4.06e+01 angle pdb=" N VAL G 129 " pdb=" CA VAL G 129 " pdb=" C VAL G 129 " ideal model delta sigma weight residual 112.96 108.12 4.84 1.00e+00 1.00e+00 2.35e+01 angle pdb=" C ASP C 319 " pdb=" N LEU C 320 " pdb=" CA LEU C 320 " ideal model delta sigma weight residual 120.09 125.76 -5.67 1.25e+00 6.40e-01 2.06e+01 angle pdb=" C ASP B 211 " pdb=" N PHE B 212 " pdb=" CA PHE B 212 " ideal model delta sigma weight residual 121.54 129.92 -8.38 1.91e+00 2.74e-01 1.93e+01 angle pdb=" C GLN G 22 " pdb=" N THR G 23 " pdb=" CA THR G 23 " ideal model delta sigma weight residual 122.08 128.41 -6.33 1.47e+00 4.63e-01 1.85e+01 ... (remaining 15650 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 6158 17.57 - 35.14: 592 35.14 - 52.71: 86 52.71 - 70.27: 7 70.27 - 87.84: 7 Dihedral angle restraints: 6850 sinusoidal: 2533 harmonic: 4317 Sorted by residual: dihedral pdb=" CA VAL C 282 " pdb=" C VAL C 282 " pdb=" N THR C 283 " pdb=" CA THR C 283 " ideal model delta harmonic sigma weight residual 180.00 146.28 33.72 0 5.00e+00 4.00e-02 4.55e+01 dihedral pdb=" CA GLY G 171 " pdb=" C GLY G 171 " pdb=" N VAL G 172 " pdb=" CA VAL G 172 " ideal model delta harmonic sigma weight residual -180.00 -147.28 -32.72 0 5.00e+00 4.00e-02 4.28e+01 dihedral pdb=" CA VAL B 99 " pdb=" C VAL B 99 " pdb=" N PRO B 100 " pdb=" CA PRO B 100 " ideal model delta harmonic sigma weight residual -180.00 -148.01 -31.99 0 5.00e+00 4.00e-02 4.09e+01 ... (remaining 6847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1600 0.069 - 0.137: 282 0.137 - 0.206: 53 0.206 - 0.274: 11 0.274 - 0.343: 5 Chirality restraints: 1951 Sorted by residual: chirality pdb=" CB VAL C 282 " pdb=" CA VAL C 282 " pdb=" CG1 VAL C 282 " pdb=" CG2 VAL C 282 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CG LEU C 143 " pdb=" CB LEU C 143 " pdb=" CD1 LEU C 143 " pdb=" CD2 LEU C 143 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CB ILE B 108 " pdb=" CA ILE B 108 " pdb=" CG1 ILE B 108 " pdb=" CG2 ILE B 108 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.54e+00 ... (remaining 1948 not shown) Planarity restraints: 1974 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU G 90 " 0.046 5.00e-02 4.00e+02 6.88e-02 7.57e+00 pdb=" N PRO G 91 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO G 91 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO G 91 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 459 " -0.045 5.00e-02 4.00e+02 6.79e-02 7.38e+00 pdb=" N PRO C 460 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO C 460 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 460 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 39 " -0.043 5.00e-02 4.00e+02 6.46e-02 6.67e+00 pdb=" N PRO B 40 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 40 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 40 " -0.037 5.00e-02 4.00e+02 ... (remaining 1971 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2930 2.80 - 3.33: 10147 3.33 - 3.85: 17898 3.85 - 4.38: 19373 4.38 - 4.90: 34555 Nonbonded interactions: 84903 Sorted by model distance: nonbonded pdb=" OG SER C 228 " pdb=" O PHE C 244 " model vdw 2.280 3.040 nonbonded pdb=" O GLY B 279 " pdb=" OG1 THR B 283 " model vdw 2.281 3.040 nonbonded pdb=" O SER B 231 " pdb=" OG SER B 235 " model vdw 2.292 3.040 nonbonded pdb=" OG1 THR C 82 " pdb=" OG1 THR C 85 " model vdw 2.342 3.040 nonbonded pdb=" O ILE F 139 " pdb=" OG1 THR F 142 " model vdw 2.348 3.040 ... (remaining 84898 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 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 8 through 16 or resid 21 through 47 or resid 65 through 21 \ 1 or resid 214 through 436 or resid 441 through 471)) selection = (chain 'C' and (resid 8 through 294 or resid 316 through 471)) } 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=0.91 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.590 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.450 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 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 : 0.006 0.077 11436 Z= 0.265 Angle : 1.028 10.492 15655 Z= 0.545 Chirality : 0.059 0.343 1951 Planarity : 0.008 0.069 1974 Dihedral : 13.905 87.842 4034 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.90 % Favored : 90.03 % Rotamer: Outliers : 0.26 % Allowed : 11.63 % Favored : 88.11 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.09 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.82 (0.16), residues: 1464 helix: -2.87 (0.12), residues: 806 sheet: -2.38 (0.36), residues: 143 loop : -3.72 (0.22), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 108 TYR 0.013 0.002 TYR F 104 PHE 0.023 0.002 PHE G 48 TRP 0.032 0.002 TRP F 231 HIS 0.007 0.001 HIS F 118 Details of bonding type rmsd covalent geometry : bond 0.00613 (11436) covalent geometry : angle 1.02804 (15655) hydrogen bonds : bond 0.13601 ( 600) hydrogen bonds : angle 6.48735 ( 1776) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 247 time to evaluate : 0.422 Fit side-chains REVERT: B 97 GLN cc_start: 0.7997 (mt0) cc_final: 0.7761 (mt0) REVERT: B 118 ILE cc_start: 0.9143 (mm) cc_final: 0.8832 (mt) REVERT: B 443 MET cc_start: 0.6726 (mtt) cc_final: 0.6233 (mtm) REVERT: C 184 ARG cc_start: 0.6290 (ttp80) cc_final: 0.5518 (mmm-85) REVERT: C 278 LEU cc_start: 0.9038 (mt) cc_final: 0.8834 (mt) REVERT: C 443 MET cc_start: 0.6863 (mmm) cc_final: 0.6439 (mmm) REVERT: C 471 LEU cc_start: 0.7870 (mt) cc_final: 0.7572 (mt) REVERT: F 151 ARG cc_start: 0.8170 (mtm110) cc_final: 0.7905 (mtm110) REVERT: F 337 VAL cc_start: 0.9078 (t) cc_final: 0.8873 (t) REVERT: G 26 GLN cc_start: 0.6384 (mm-40) cc_final: 0.6142 (mp10) outliers start: 3 outliers final: 0 residues processed: 249 average time/residue: 0.1141 time to fit residues: 39.2243 Evaluate side-chains 187 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.1980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 GLN B 97 GLN B 285 GLN C 131 HIS C 331 GLN C 389 HIS F 122 GLN F 163 HIS F 266 HIS G 74 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.133430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.118076 restraints weight = 16852.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.119768 restraints weight = 12791.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.120994 restraints weight = 10403.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.121804 restraints weight = 8996.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.122496 restraints weight = 8024.591| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3313 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3312 r_free = 0.3312 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3312 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 11436 Z= 0.146 Angle : 0.666 9.045 15655 Z= 0.337 Chirality : 0.042 0.192 1951 Planarity : 0.006 0.056 1974 Dihedral : 5.469 37.293 1620 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.70 % Favored : 90.30 % Rotamer: Outliers : 2.60 % Allowed : 16.75 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.70 (0.21), residues: 1464 helix: -0.86 (0.17), residues: 809 sheet: -1.81 (0.40), residues: 147 loop : -3.25 (0.25), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 66 TYR 0.015 0.001 TYR B 361 PHE 0.018 0.001 PHE A 88 TRP 0.025 0.001 TRP F 231 HIS 0.007 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00342 (11436) covalent geometry : angle 0.66557 (15655) hydrogen bonds : bond 0.03733 ( 600) hydrogen bonds : angle 4.31311 ( 1776) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 200 time to evaluate : 0.267 Fit side-chains REVERT: B 97 GLN cc_start: 0.8131 (mt0) cc_final: 0.7861 (mt0) REVERT: B 118 ILE cc_start: 0.9190 (mm) cc_final: 0.8896 (mt) REVERT: B 443 MET cc_start: 0.6534 (mtt) cc_final: 0.6203 (mtm) REVERT: C 184 ARG cc_start: 0.6405 (ttp80) cc_final: 0.5524 (mmm-85) REVERT: C 278 LEU cc_start: 0.9040 (mt) cc_final: 0.8795 (mt) REVERT: C 443 MET cc_start: 0.6941 (mmm) cc_final: 0.6461 (mmm) REVERT: F 151 ARG cc_start: 0.8139 (mtm110) cc_final: 0.7838 (mtm110) REVERT: G 4 ARG cc_start: 0.6485 (mmt180) cc_final: 0.4869 (mmt180) REVERT: G 26 GLN cc_start: 0.6287 (mm-40) cc_final: 0.5883 (mp10) REVERT: G 123 SER cc_start: 0.9068 (m) cc_final: 0.8669 (t) REVERT: G 207 GLU cc_start: 0.8020 (tm-30) cc_final: 0.7801 (tm-30) outliers start: 30 outliers final: 21 residues processed: 214 average time/residue: 0.0950 time to fit residues: 29.2675 Evaluate side-chains 198 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 177 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 243 MET Chi-restraints excluded: chain F residue 344 THR Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 281 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 55 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 102 optimal weight: 0.0670 chunk 101 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 143 optimal weight: 0.0980 chunk 138 optimal weight: 0.6980 chunk 11 optimal weight: 0.1980 chunk 106 optimal weight: 0.0980 overall best weight: 0.2118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 ASN C 164 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.141044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.128044 restraints weight = 16372.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.128930 restraints weight = 13891.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.129428 restraints weight = 11667.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.129899 restraints weight = 10415.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.130256 restraints weight = 9639.758| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3386 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3386 r_free = 0.3386 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3386 r_free = 0.3386 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3386 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 11436 Z= 0.113 Angle : 0.612 9.459 15655 Z= 0.303 Chirality : 0.041 0.184 1951 Planarity : 0.005 0.055 1974 Dihedral : 4.866 36.270 1620 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 3.12 % Allowed : 18.49 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.22), residues: 1464 helix: 0.14 (0.19), residues: 807 sheet: -1.40 (0.41), residues: 151 loop : -3.03 (0.26), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 108 TYR 0.009 0.001 TYR B 361 PHE 0.006 0.001 PHE G 48 TRP 0.026 0.001 TRP F 231 HIS 0.005 0.001 HIS B 389 Details of bonding type rmsd covalent geometry : bond 0.00257 (11436) covalent geometry : angle 0.61248 (15655) hydrogen bonds : bond 0.03262 ( 600) hydrogen bonds : angle 3.88660 ( 1776) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 198 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: B 97 GLN cc_start: 0.8120 (mt0) cc_final: 0.7837 (mt0) REVERT: B 443 MET cc_start: 0.6715 (mtt) cc_final: 0.6469 (mtm) REVERT: B 446 MET cc_start: 0.5817 (tmm) cc_final: 0.5250 (tmm) REVERT: C 72 ILE cc_start: 0.8267 (mm) cc_final: 0.7964 (mm) REVERT: C 184 ARG cc_start: 0.6332 (ttp80) cc_final: 0.5534 (mmm-85) REVERT: C 278 LEU cc_start: 0.9058 (mt) cc_final: 0.8801 (mt) REVERT: C 443 MET cc_start: 0.6912 (mmm) cc_final: 0.6381 (mmm) REVERT: G 4 ARG cc_start: 0.6622 (mmt180) cc_final: 0.5182 (mmt180) REVERT: G 26 GLN cc_start: 0.6324 (mm-40) cc_final: 0.5795 (mp10) REVERT: G 40 LEU cc_start: 0.8330 (mm) cc_final: 0.8117 (mm) outliers start: 36 outliers final: 25 residues processed: 220 average time/residue: 0.0984 time to fit residues: 31.1978 Evaluate side-chains 197 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 172 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 164 GLN Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 243 MET Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 344 THR Chi-restraints excluded: chain F residue 354 ASP Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 199 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 13 optimal weight: 0.0670 chunk 75 optimal weight: 0.7980 chunk 20 optimal weight: 0.0770 chunk 49 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 78 optimal weight: 0.3980 chunk 105 optimal weight: 0.4980 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 164 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.137592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.122486 restraints weight = 16721.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.123360 restraints weight = 13451.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.124119 restraints weight = 11239.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.125247 restraints weight = 9946.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.125607 restraints weight = 8517.061| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11436 Z= 0.116 Angle : 0.610 9.023 15655 Z= 0.300 Chirality : 0.041 0.178 1951 Planarity : 0.005 0.055 1974 Dihedral : 4.720 37.052 1620 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 3.47 % Allowed : 18.92 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.23), residues: 1464 helix: 0.57 (0.19), residues: 802 sheet: -1.31 (0.42), residues: 148 loop : -2.89 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 66 TYR 0.009 0.001 TYR F 104 PHE 0.006 0.001 PHE G 226 TRP 0.022 0.001 TRP F 231 HIS 0.004 0.001 HIS B 389 Details of bonding type rmsd covalent geometry : bond 0.00267 (11436) covalent geometry : angle 0.61012 (15655) hydrogen bonds : bond 0.03160 ( 600) hydrogen bonds : angle 3.77132 ( 1776) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 191 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: B 97 GLN cc_start: 0.8210 (mt0) cc_final: 0.7925 (mt0) REVERT: B 443 MET cc_start: 0.6617 (mtt) cc_final: 0.6296 (mtm) REVERT: B 446 MET cc_start: 0.5766 (tmm) cc_final: 0.5151 (tmm) REVERT: C 72 ILE cc_start: 0.8295 (mm) cc_final: 0.7936 (mm) REVERT: C 184 ARG cc_start: 0.6377 (ttp80) cc_final: 0.5530 (mmm-85) REVERT: C 278 LEU cc_start: 0.8990 (mt) cc_final: 0.8735 (mt) REVERT: C 443 MET cc_start: 0.7031 (mmm) cc_final: 0.6407 (mmm) REVERT: F 223 GLU cc_start: 0.6919 (mt-10) cc_final: 0.6678 (tm-30) REVERT: G 4 ARG cc_start: 0.6499 (mmt180) cc_final: 0.5276 (mmt180) REVERT: G 123 SER cc_start: 0.9043 (m) cc_final: 0.8574 (t) outliers start: 40 outliers final: 30 residues processed: 217 average time/residue: 0.0925 time to fit residues: 29.4893 Evaluate side-chains 207 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 177 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 164 GLN Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 344 THR Chi-restraints excluded: chain F residue 354 ASP Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 199 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 86 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 HIS C 164 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.131959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.116349 restraints weight = 16775.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.117977 restraints weight = 12891.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.119052 restraints weight = 10555.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.120038 restraints weight = 9177.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.120408 restraints weight = 8201.126| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 11436 Z= 0.195 Angle : 0.680 8.578 15655 Z= 0.337 Chirality : 0.044 0.207 1951 Planarity : 0.005 0.058 1974 Dihedral : 4.991 38.223 1620 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 4.08 % Allowed : 19.62 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.22), residues: 1464 helix: 0.55 (0.19), residues: 807 sheet: -1.01 (0.47), residues: 129 loop : -2.97 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 148 TYR 0.014 0.002 TYR F 104 PHE 0.011 0.001 PHE G 226 TRP 0.020 0.001 TRP B 264 HIS 0.006 0.001 HIS F 118 Details of bonding type rmsd covalent geometry : bond 0.00464 (11436) covalent geometry : angle 0.67956 (15655) hydrogen bonds : bond 0.03603 ( 600) hydrogen bonds : angle 3.95602 ( 1776) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 182 time to evaluate : 0.389 Fit side-chains REVERT: B 97 GLN cc_start: 0.8297 (mt0) cc_final: 0.8022 (mt0) REVERT: B 443 MET cc_start: 0.6528 (mtt) cc_final: 0.6242 (mtm) REVERT: B 446 MET cc_start: 0.5827 (tmm) cc_final: 0.5216 (tmm) REVERT: C 72 ILE cc_start: 0.8487 (mm) cc_final: 0.8142 (mm) REVERT: C 184 ARG cc_start: 0.6449 (ttp80) cc_final: 0.5552 (mmm-85) REVERT: C 278 LEU cc_start: 0.9086 (mt) cc_final: 0.8766 (mt) REVERT: C 443 MET cc_start: 0.7055 (mmm) cc_final: 0.6459 (mmm) REVERT: G 4 ARG cc_start: 0.6671 (mmt180) cc_final: 0.5372 (mmt180) REVERT: G 26 GLN cc_start: 0.6327 (mm-40) cc_final: 0.5635 (mp10) REVERT: G 123 SER cc_start: 0.9149 (m) cc_final: 0.8695 (t) outliers start: 47 outliers final: 42 residues processed: 208 average time/residue: 0.0909 time to fit residues: 27.6577 Evaluate side-chains 219 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 177 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 164 GLN Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 344 THR Chi-restraints excluded: chain F residue 354 ASP Chi-restraints excluded: chain F residue 401 ASP Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain G residue 281 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 23 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 148 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 134 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 164 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.133405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.117633 restraints weight = 16955.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.119239 restraints weight = 12931.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.120588 restraints weight = 10584.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.121385 restraints weight = 9081.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.122126 restraints weight = 8143.928| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11436 Z= 0.145 Angle : 0.640 8.866 15655 Z= 0.316 Chirality : 0.043 0.229 1951 Planarity : 0.005 0.056 1974 Dihedral : 4.861 37.730 1620 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 4.86 % Allowed : 20.49 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.23), residues: 1464 helix: 0.74 (0.19), residues: 805 sheet: -1.05 (0.44), residues: 141 loop : -2.84 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 116 TYR 0.011 0.001 TYR F 104 PHE 0.015 0.001 PHE A 88 TRP 0.021 0.001 TRP F 231 HIS 0.004 0.001 HIS F 163 Details of bonding type rmsd covalent geometry : bond 0.00344 (11436) covalent geometry : angle 0.64010 (15655) hydrogen bonds : bond 0.03369 ( 600) hydrogen bonds : angle 3.84459 ( 1776) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 176 time to evaluate : 0.454 Fit side-chains revert: symmetry clash REVERT: B 97 GLN cc_start: 0.8272 (mt0) cc_final: 0.7987 (mt0) REVERT: B 443 MET cc_start: 0.6659 (mtt) cc_final: 0.6341 (mtm) REVERT: B 446 MET cc_start: 0.5819 (tmm) cc_final: 0.5213 (tmm) REVERT: C 72 ILE cc_start: 0.8444 (mm) cc_final: 0.8087 (mm) REVERT: C 184 ARG cc_start: 0.6406 (ttp80) cc_final: 0.5530 (mmm-85) REVERT: C 278 LEU cc_start: 0.9065 (mt) cc_final: 0.8743 (mt) REVERT: C 443 MET cc_start: 0.7042 (mmm) cc_final: 0.6517 (mmm) REVERT: F 92 MET cc_start: 0.7843 (tpp) cc_final: 0.7625 (ttt) REVERT: G 4 ARG cc_start: 0.6624 (mmt180) cc_final: 0.5298 (mmt180) REVERT: G 79 VAL cc_start: 0.9100 (OUTLIER) cc_final: 0.8864 (p) REVERT: G 123 SER cc_start: 0.9111 (m) cc_final: 0.8609 (t) outliers start: 56 outliers final: 46 residues processed: 215 average time/residue: 0.0874 time to fit residues: 28.2371 Evaluate side-chains 218 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 171 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 164 GLN Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 344 THR Chi-restraints excluded: chain F residue 354 ASP Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 197 TYR Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain G residue 281 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 52 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 120 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 14 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 53 optimal weight: 0.1980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 164 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.134578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.119037 restraints weight = 16605.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.120729 restraints weight = 12612.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.121899 restraints weight = 10368.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.122864 restraints weight = 8914.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.123453 restraints weight = 7958.125| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11436 Z= 0.133 Angle : 0.629 8.952 15655 Z= 0.311 Chirality : 0.042 0.244 1951 Planarity : 0.005 0.054 1974 Dihedral : 4.785 37.867 1620 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 4.34 % Allowed : 21.35 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.23), residues: 1464 helix: 0.91 (0.19), residues: 804 sheet: -0.99 (0.44), residues: 145 loop : -2.72 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 116 TYR 0.011 0.001 TYR F 104 PHE 0.007 0.001 PHE G 226 TRP 0.023 0.001 TRP F 231 HIS 0.004 0.001 HIS B 389 Details of bonding type rmsd covalent geometry : bond 0.00314 (11436) covalent geometry : angle 0.62875 (15655) hydrogen bonds : bond 0.03269 ( 600) hydrogen bonds : angle 3.77011 ( 1776) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 182 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: B 97 GLN cc_start: 0.8245 (mt0) cc_final: 0.7957 (mt0) REVERT: B 443 MET cc_start: 0.6595 (mtt) cc_final: 0.6321 (mtm) REVERT: B 446 MET cc_start: 0.5821 (tmm) cc_final: 0.5217 (tmm) REVERT: C 72 ILE cc_start: 0.8373 (mm) cc_final: 0.7984 (mm) REVERT: C 184 ARG cc_start: 0.6303 (ttp80) cc_final: 0.5522 (mmm-85) REVERT: C 278 LEU cc_start: 0.9006 (mt) cc_final: 0.8729 (mt) REVERT: C 443 MET cc_start: 0.7009 (mmm) cc_final: 0.6479 (mmm) REVERT: G 59 MET cc_start: 0.6758 (ptt) cc_final: 0.6459 (tpt) REVERT: G 79 VAL cc_start: 0.9107 (OUTLIER) cc_final: 0.8889 (p) REVERT: G 123 SER cc_start: 0.9095 (m) cc_final: 0.8589 (t) outliers start: 50 outliers final: 45 residues processed: 217 average time/residue: 0.0889 time to fit residues: 28.5497 Evaluate side-chains 218 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 172 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 164 GLN Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 344 THR Chi-restraints excluded: chain F residue 354 ASP Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 197 TYR Chi-restraints excluded: chain G residue 199 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 2 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 111 optimal weight: 0.3980 chunk 24 optimal weight: 0.5980 chunk 108 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 1 optimal weight: 0.2980 chunk 45 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 93 optimal weight: 3.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 164 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.135346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.119675 restraints weight = 16599.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.121406 restraints weight = 12610.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.122640 restraints weight = 10277.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.123584 restraints weight = 8814.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.124264 restraints weight = 7820.007| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11436 Z= 0.130 Angle : 0.627 8.956 15655 Z= 0.310 Chirality : 0.042 0.250 1951 Planarity : 0.005 0.052 1974 Dihedral : 4.714 38.027 1620 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 4.69 % Allowed : 21.61 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.23), residues: 1464 helix: 1.05 (0.19), residues: 803 sheet: -0.94 (0.45), residues: 135 loop : -2.63 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 116 TYR 0.010 0.001 TYR F 104 PHE 0.029 0.001 PHE A 88 TRP 0.023 0.001 TRP F 231 HIS 0.004 0.001 HIS B 389 Details of bonding type rmsd covalent geometry : bond 0.00306 (11436) covalent geometry : angle 0.62671 (15655) hydrogen bonds : bond 0.03214 ( 600) hydrogen bonds : angle 3.71694 ( 1776) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 173 time to evaluate : 0.499 Fit side-chains REVERT: B 443 MET cc_start: 0.6575 (mtt) cc_final: 0.6326 (mtm) REVERT: B 446 MET cc_start: 0.5804 (tmm) cc_final: 0.5190 (tmm) REVERT: C 72 ILE cc_start: 0.8308 (mm) cc_final: 0.7905 (mm) REVERT: C 184 ARG cc_start: 0.6293 (ttp80) cc_final: 0.5540 (mmm-85) REVERT: C 278 LEU cc_start: 0.8998 (mt) cc_final: 0.8725 (mt) REVERT: C 443 MET cc_start: 0.7019 (mmm) cc_final: 0.6465 (mmm) REVERT: G 59 MET cc_start: 0.6826 (ptt) cc_final: 0.6465 (tpt) REVERT: G 79 VAL cc_start: 0.9081 (OUTLIER) cc_final: 0.8855 (p) REVERT: G 123 SER cc_start: 0.9085 (m) cc_final: 0.8591 (t) outliers start: 54 outliers final: 48 residues processed: 210 average time/residue: 0.0909 time to fit residues: 28.2893 Evaluate side-chains 218 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 169 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 164 GLN Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 344 THR Chi-restraints excluded: chain F residue 354 ASP Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 197 TYR Chi-restraints excluded: chain G residue 199 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 125 optimal weight: 5.9990 chunk 113 optimal weight: 0.5980 chunk 71 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 88 optimal weight: 0.0970 chunk 126 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 164 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.134420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.118726 restraints weight = 16576.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.120448 restraints weight = 12632.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.121516 restraints weight = 10362.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.122517 restraints weight = 8970.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.123123 restraints weight = 8018.309| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11436 Z= 0.150 Angle : 0.644 8.780 15655 Z= 0.320 Chirality : 0.043 0.263 1951 Planarity : 0.005 0.053 1974 Dihedral : 4.752 38.374 1620 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 4.69 % Allowed : 21.88 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.23), residues: 1464 helix: 1.04 (0.19), residues: 806 sheet: -0.90 (0.44), residues: 145 loop : -2.73 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 116 TYR 0.011 0.001 TYR F 104 PHE 0.008 0.001 PHE B 244 TRP 0.037 0.001 TRP B 264 HIS 0.005 0.001 HIS B 389 Details of bonding type rmsd covalent geometry : bond 0.00357 (11436) covalent geometry : angle 0.64415 (15655) hydrogen bonds : bond 0.03308 ( 600) hydrogen bonds : angle 3.76938 ( 1776) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 171 time to evaluate : 0.372 Fit side-chains REVERT: B 97 GLN cc_start: 0.8047 (mt0) cc_final: 0.7690 (mt0) REVERT: B 443 MET cc_start: 0.6594 (mtt) cc_final: 0.6331 (mtm) REVERT: B 446 MET cc_start: 0.5811 (tmm) cc_final: 0.5197 (tmm) REVERT: C 72 ILE cc_start: 0.8367 (mm) cc_final: 0.7967 (mm) REVERT: C 184 ARG cc_start: 0.6307 (ttp80) cc_final: 0.5562 (mmm-85) REVERT: C 278 LEU cc_start: 0.9020 (mt) cc_final: 0.8743 (mt) REVERT: C 443 MET cc_start: 0.7061 (mmm) cc_final: 0.6491 (mmm) REVERT: G 59 MET cc_start: 0.6803 (ptt) cc_final: 0.6465 (tpt) REVERT: G 79 VAL cc_start: 0.9103 (OUTLIER) cc_final: 0.8870 (p) REVERT: G 123 SER cc_start: 0.9105 (m) cc_final: 0.8605 (t) outliers start: 54 outliers final: 49 residues processed: 207 average time/residue: 0.0888 time to fit residues: 27.3787 Evaluate side-chains 219 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 169 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 164 GLN Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 344 THR Chi-restraints excluded: chain F residue 354 ASP Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 197 TYR Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain G residue 281 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 19 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 145 optimal weight: 0.0970 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 164 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.134376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.119211 restraints weight = 16712.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.120798 restraints weight = 12873.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.121882 restraints weight = 10663.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.122788 restraints weight = 9274.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.123170 restraints weight = 8285.480| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11436 Z= 0.150 Angle : 0.650 8.776 15655 Z= 0.323 Chirality : 0.043 0.273 1951 Planarity : 0.005 0.053 1974 Dihedral : 4.769 38.236 1620 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 4.60 % Allowed : 21.96 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.23), residues: 1464 helix: 1.09 (0.19), residues: 805 sheet: -0.87 (0.44), residues: 145 loop : -2.70 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 107 TYR 0.012 0.002 TYR F 104 PHE 0.014 0.001 PHE A 88 TRP 0.036 0.001 TRP B 264 HIS 0.005 0.001 HIS B 389 Details of bonding type rmsd covalent geometry : bond 0.00359 (11436) covalent geometry : angle 0.65039 (15655) hydrogen bonds : bond 0.03330 ( 600) hydrogen bonds : angle 3.77782 ( 1776) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 175 time to evaluate : 0.381 Fit side-chains REVERT: B 97 GLN cc_start: 0.8019 (mt0) cc_final: 0.7680 (mt0) REVERT: B 443 MET cc_start: 0.6603 (mtt) cc_final: 0.6364 (mtm) REVERT: B 446 MET cc_start: 0.5820 (tmm) cc_final: 0.5212 (tmm) REVERT: C 72 ILE cc_start: 0.8369 (mm) cc_final: 0.7962 (mm) REVERT: C 184 ARG cc_start: 0.6351 (ttp80) cc_final: 0.5603 (mmm-85) REVERT: C 278 LEU cc_start: 0.9032 (mt) cc_final: 0.8775 (mt) REVERT: C 443 MET cc_start: 0.7030 (mmm) cc_final: 0.6476 (mmm) REVERT: G 59 MET cc_start: 0.6761 (ptt) cc_final: 0.6465 (tpt) REVERT: G 79 VAL cc_start: 0.9113 (OUTLIER) cc_final: 0.8880 (p) REVERT: G 123 SER cc_start: 0.9099 (m) cc_final: 0.8593 (t) outliers start: 53 outliers final: 49 residues processed: 209 average time/residue: 0.0831 time to fit residues: 26.1612 Evaluate side-chains 223 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 173 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 164 GLN Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 344 THR Chi-restraints excluded: chain F residue 354 ASP Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 197 TYR Chi-restraints excluded: chain G residue 281 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 31 optimal weight: 3.9990 chunk 115 optimal weight: 0.5980 chunk 112 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 164 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.133631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.117941 restraints weight = 16733.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.119660 restraints weight = 12749.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.120863 restraints weight = 10397.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.121789 restraints weight = 8970.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.122261 restraints weight = 7988.145| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11436 Z= 0.162 Angle : 0.662 8.719 15655 Z= 0.329 Chirality : 0.044 0.275 1951 Planarity : 0.005 0.054 1974 Dihedral : 4.812 38.259 1620 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 4.69 % Allowed : 21.79 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.23), residues: 1464 helix: 1.09 (0.19), residues: 804 sheet: -0.84 (0.44), residues: 145 loop : -2.71 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 116 TYR 0.012 0.002 TYR F 104 PHE 0.014 0.001 PHE A 88 TRP 0.034 0.001 TRP B 264 HIS 0.005 0.001 HIS B 389 Details of bonding type rmsd covalent geometry : bond 0.00390 (11436) covalent geometry : angle 0.66188 (15655) hydrogen bonds : bond 0.03418 ( 600) hydrogen bonds : angle 3.80934 ( 1776) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1845.19 seconds wall clock time: 32 minutes 29.56 seconds (1949.56 seconds total)