Starting phenix.real_space_refine on Sun Jul 27 17:15:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uy8_26867/07_2025/7uy8_26867.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uy8_26867/07_2025/7uy8_26867.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7uy8_26867/07_2025/7uy8_26867.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uy8_26867/07_2025/7uy8_26867.map" model { file = "/net/cci-nas-00/data/ceres_data/7uy8_26867/07_2025/7uy8_26867.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uy8_26867/07_2025/7uy8_26867.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 42 5.16 5 C 6123 2.51 5 N 1592 2.21 5 O 1794 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 9552 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 3187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3187 Classifications: {'peptide': 392} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 374} Chain breaks: 4 Chain: "A" Number of atoms: 1255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1255 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 1, 'TRANS': 154} Chain breaks: 1 Chain: "D" Number of atoms: 2007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 2007 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 5, 'TRANS': 235} Chain breaks: 2 Chain: "C" Number of atoms: 3102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 3102 Classifications: {'peptide': 372} Link IDs: {'PTRANS': 12, 'TRANS': 359} Chain breaks: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3324 SG CYS A1248 21.007 84.408 119.017 1.00104.84 S ATOM 3348 SG CYS A1251 17.659 85.381 117.384 1.00107.89 S ATOM 3474 SG CYS A1273 20.686 86.040 115.527 1.00116.42 S ATOM 3489 SG CYS A1275 20.080 88.042 118.795 1.00130.38 S Time building chain proxies: 6.04, per 1000 atoms: 0.63 Number of scatterers: 9552 At special positions: 0 Unit cell: (82.5, 100.1, 159.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 42 16.00 O 1794 8.00 N 1592 7.00 C 6123 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: 2.74 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1401 " pdb="ZN ZN A1401 " - pdb=" SG CYS A1251 " pdb="ZN ZN A1401 " - pdb=" SG CYS A1273 " pdb="ZN ZN A1401 " - pdb=" SG CYS A1248 " pdb="ZN ZN A1401 " - pdb=" SG CYS A1275 " Number of angles added : 6 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2266 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 10 sheets defined 47.5% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'B' and resid 161 through 167 Processing helix chain 'B' and resid 189 through 208 removed outlier: 3.993A pdb=" N ILE B 193 " --> pdb=" O ASN B 189 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU B 202 " --> pdb=" O GLU B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 212 Processing helix chain 'B' and resid 264 through 268 removed outlier: 3.897A pdb=" N ASN B 267 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASP B 268 " --> pdb=" O PHE B 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 264 through 268' Processing helix chain 'B' and resid 341 through 355 removed outlier: 4.019A pdb=" N ASP B 345 " --> pdb=" O TYR B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 375 removed outlier: 3.990A pdb=" N LYS B 374 " --> pdb=" O ASN B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 403 Processing helix chain 'B' and resid 461 through 470 removed outlier: 4.056A pdb=" N ILE B 465 " --> pdb=" O ASP B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 492 removed outlier: 3.862A pdb=" N GLN B 492 " --> pdb=" O ALA B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 520 removed outlier: 4.317A pdb=" N ASN B 520 " --> pdb=" O LEU B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 523 No H-bonds generated for 'chain 'B' and resid 521 through 523' Processing helix chain 'B' and resid 562 through 566 removed outlier: 3.759A pdb=" N GLY B 565 " --> pdb=" O ILE B 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 1234 through 1239 Processing helix chain 'A' and resid 1279 through 1300 removed outlier: 3.850A pdb=" N GLU A1300 " --> pdb=" O ARG A1296 " (cutoff:3.500A) Processing helix chain 'A' and resid 1328 through 1342 removed outlier: 3.723A pdb=" N LEU A1332 " --> pdb=" O SER A1328 " (cutoff:3.500A) Processing helix chain 'A' and resid 1346 through 1351 removed outlier: 3.738A pdb=" N GLU A1351 " --> pdb=" O LYS A1347 " (cutoff:3.500A) Processing helix chain 'A' and resid 1354 through 1374 removed outlier: 3.758A pdb=" N ILE A1358 " --> pdb=" O GLN A1354 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N THR A1367 " --> pdb=" O THR A1363 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU A1368 " --> pdb=" O ILE A1364 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU A1371 " --> pdb=" O THR A1367 " (cutoff:3.500A) Processing helix chain 'A' and resid 1382 through 1387 removed outlier: 4.100A pdb=" N PHE A1386 " --> pdb=" O LEU A1382 " (cutoff:3.500A) Processing helix chain 'A' and resid 1388 through 1390 No H-bonds generated for 'chain 'A' and resid 1388 through 1390' Processing helix chain 'D' and resid 32 through 45 Processing helix chain 'D' and resid 59 through 80 removed outlier: 3.749A pdb=" N ILE D 63 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL D 64 " --> pdb=" O ILE D 60 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN D 65 " --> pdb=" O GLN D 61 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG D 70 " --> pdb=" O LEU D 66 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N MET D 71 " --> pdb=" O ALA D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 100 Processing helix chain 'D' and resid 115 through 142 removed outlier: 3.946A pdb=" N LYS D 119 " --> pdb=" O GLU D 115 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASN D 120 " --> pdb=" O TYR D 116 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU D 127 " --> pdb=" O GLN D 123 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE D 132 " --> pdb=" O VAL D 128 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR D 138 " --> pdb=" O CYS D 134 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE D 140 " --> pdb=" O MET D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 146 Processing helix chain 'D' and resid 147 through 165 Processing helix chain 'D' and resid 168 through 179 removed outlier: 3.562A pdb=" N SER D 173 " --> pdb=" O ALA D 169 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ASP D 174 " --> pdb=" O ASN D 170 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU D 177 " --> pdb=" O SER D 173 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS D 178 " --> pdb=" O ASP D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 190 Processing helix chain 'D' and resid 190 through 198 removed outlier: 3.629A pdb=" N THR D 197 " --> pdb=" O LYS D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 234 removed outlier: 3.682A pdb=" N LEU D 232 " --> pdb=" O PRO D 229 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER D 233 " --> pdb=" O SER D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 249 No H-bonds generated for 'chain 'D' and resid 247 through 249' Processing helix chain 'D' and resid 250 through 276 removed outlier: 3.547A pdb=" N VAL D 255 " --> pdb=" O THR D 251 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N MET D 267 " --> pdb=" O LEU D 263 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG D 268 " --> pdb=" O LEU D 264 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN D 276 " --> pdb=" O LEU D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 292 removed outlier: 3.563A pdb=" N LEU D 286 " --> pdb=" O ASP D 282 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N PHE D 288 " --> pdb=" O ASP D 284 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ASP D 291 " --> pdb=" O SER D 287 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU D 292 " --> pdb=" O PHE D 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 30 removed outlier: 5.032A pdb=" N TYR C 27 " --> pdb=" O LEU C 23 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ARG C 28 " --> pdb=" O GLU C 24 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N TYR C 30 " --> pdb=" O TYR C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 42 Processing helix chain 'C' and resid 43 through 46 Processing helix chain 'C' and resid 73 through 84 Processing helix chain 'C' and resid 137 through 156 removed outlier: 4.298A pdb=" N MET C 141 " --> pdb=" O CYS C 137 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASP C 146 " --> pdb=" O ARG C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 183 Processing helix chain 'C' and resid 184 through 195 removed outlier: 3.509A pdb=" N LEU C 195 " --> pdb=" O ILE C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 215 removed outlier: 3.702A pdb=" N LYS C 214 " --> pdb=" O PRO C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 226 removed outlier: 3.647A pdb=" N ASN C 224 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 253 removed outlier: 5.168A pdb=" N VAL C 247 " --> pdb=" O GLU C 243 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N GLU C 248 " --> pdb=" O LYS C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 269 removed outlier: 4.027A pdb=" N PHE C 267 " --> pdb=" O ILE C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 287 removed outlier: 3.520A pdb=" N SER C 276 " --> pdb=" O SER C 272 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS C 284 " --> pdb=" O GLU C 280 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N THR C 285 " --> pdb=" O LYS C 281 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEU C 286 " --> pdb=" O GLU C 282 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS C 287 " --> pdb=" O TRP C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 302 removed outlier: 4.456A pdb=" N SER C 302 " --> pdb=" O GLU C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 321 removed outlier: 3.727A pdb=" N LEU C 315 " --> pdb=" O LEU C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 358 Processing helix chain 'C' and resid 374 through 399 removed outlier: 3.630A pdb=" N PHE C 391 " --> pdb=" O ILE C 387 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 171 through 172 removed outlier: 3.567A pdb=" N VAL B 171 " --> pdb=" O ASP B 449 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE B 536 " --> pdb=" O ARG B 454 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ILE B 537 " --> pdb=" O ILE B 556 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 260 through 262 removed outlier: 3.691A pdb=" N PHE B 261 " --> pdb=" O ILE B 253 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE B 253 " --> pdb=" O PHE B 261 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG B 252 " --> pdb=" O ILE B 239 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 407 through 411 removed outlier: 7.324A pdb=" N LEU B 325 " --> pdb=" O THR B 358 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N ILE B 360 " --> pdb=" O LEU B 325 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N MET B 327 " --> pdb=" O ILE B 360 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N LEU B 362 " --> pdb=" O MET B 327 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ALA B 329 " --> pdb=" O LEU B 362 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE B 574 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA B 572 " --> pdb=" O VAL B 328 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N ALA B 330 " --> pdb=" O ASN B 570 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ASN B 570 " --> pdb=" O ALA B 330 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ARG B 587 " --> pdb=" O PHE B 577 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1245 through 1248 removed outlier: 3.502A pdb=" N GLN A1253 " --> pdb=" O VAL A1246 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N CYS A1251 " --> pdb=" O CYS A1248 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1303 through 1304 Processing sheet with id=AA6, first strand: chain 'D' and resid 223 through 224 removed outlier: 3.665A pdb=" N VAL D 238 " --> pdb=" O ILE D 245 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 65 through 67 removed outlier: 4.523A pdb=" N ALA C 93 " --> pdb=" O GLU C 55 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N SER C 57 " --> pdb=" O ILE C 91 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ILE C 91 " --> pdb=" O SER C 57 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N THR C 59 " --> pdb=" O ILE C 89 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ILE C 89 " --> pdb=" O THR C 59 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 65 through 67 removed outlier: 4.523A pdb=" N ALA C 93 " --> pdb=" O GLU C 55 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N SER C 57 " --> pdb=" O ILE C 91 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ILE C 91 " --> pdb=" O SER C 57 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N THR C 59 " --> pdb=" O ILE C 89 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ILE C 89 " --> pdb=" O THR C 59 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 113 through 115 removed outlier: 4.509A pdb=" N GLY C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL C 164 " --> pdb=" O HIS C 172 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 342 through 343 removed outlier: 4.322A pdb=" N HIS C 343 " --> pdb=" O ASN C 348 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ASN C 348 " --> pdb=" O HIS C 343 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 369 hydrogen bonds defined for protein. 1050 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.72 Time building geometry restraints manager: 3.25 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: 3063 1.34 - 1.46: 2016 1.46 - 1.58: 4570 1.58 - 1.70: 0 1.70 - 1.82: 70 Bond restraints: 9719 Sorted by residual: bond pdb=" N THR C 346 " pdb=" CA THR C 346 " ideal model delta sigma weight residual 1.456 1.481 -0.025 1.23e-02 6.61e+03 4.06e+00 bond pdb=" C ILE B 423 " pdb=" N PRO B 424 " ideal model delta sigma weight residual 1.339 1.399 -0.059 3.40e-02 8.65e+02 3.06e+00 bond pdb=" CA LEU B 173 " pdb=" C LEU B 173 " ideal model delta sigma weight residual 1.520 1.539 -0.019 1.39e-02 5.18e+03 1.83e+00 bond pdb=" N LYS A1272 " pdb=" CA LYS A1272 " ideal model delta sigma weight residual 1.454 1.472 -0.018 1.31e-02 5.83e+03 1.82e+00 bond pdb=" CA ILE A1270 " pdb=" CB ILE A1270 " ideal model delta sigma weight residual 1.540 1.526 0.014 1.23e-02 6.61e+03 1.33e+00 ... (remaining 9714 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 12762 1.70 - 3.39: 255 3.39 - 5.09: 40 5.09 - 6.78: 16 6.78 - 8.48: 6 Bond angle restraints: 13079 Sorted by residual: angle pdb=" N LYS A1272 " pdb=" CA LYS A1272 " pdb=" C LYS A1272 " ideal model delta sigma weight residual 110.48 118.52 -8.04 1.48e+00 4.57e-01 2.95e+01 angle pdb=" N LYS C 345 " pdb=" CA LYS C 345 " pdb=" C LYS C 345 " ideal model delta sigma weight residual 109.59 102.21 7.38 1.47e+00 4.63e-01 2.52e+01 angle pdb=" N LEU A1271 " pdb=" CA LEU A1271 " pdb=" C LEU A1271 " ideal model delta sigma weight residual 113.17 118.27 -5.10 1.26e+00 6.30e-01 1.64e+01 angle pdb=" N ILE A1270 " pdb=" CA ILE A1270 " pdb=" C ILE A1270 " ideal model delta sigma weight residual 108.11 113.62 -5.51 1.40e+00 5.10e-01 1.55e+01 angle pdb=" N ILE B 368 " pdb=" CA ILE B 368 " pdb=" C ILE B 368 " ideal model delta sigma weight residual 112.80 108.86 3.94 1.15e+00 7.56e-01 1.17e+01 ... (remaining 13074 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.85: 5352 16.85 - 33.70: 482 33.70 - 50.55: 117 50.55 - 67.39: 23 67.39 - 84.24: 17 Dihedral angle restraints: 5991 sinusoidal: 2531 harmonic: 3460 Sorted by residual: dihedral pdb=" CA SER B 460 " pdb=" C SER B 460 " pdb=" N ASP B 461 " pdb=" CA ASP B 461 " ideal model delta harmonic sigma weight residual 180.00 154.82 25.18 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" N THR C 346 " pdb=" C THR C 346 " pdb=" CA THR C 346 " pdb=" CB THR C 346 " ideal model delta harmonic sigma weight residual 123.40 134.67 -11.27 0 2.50e+00 1.60e-01 2.03e+01 dihedral pdb=" C THR C 346 " pdb=" N THR C 346 " pdb=" CA THR C 346 " pdb=" CB THR C 346 " ideal model delta harmonic sigma weight residual -122.00 -132.96 10.96 0 2.50e+00 1.60e-01 1.92e+01 ... (remaining 5988 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1351 0.082 - 0.165: 117 0.165 - 0.247: 4 0.247 - 0.329: 0 0.329 - 0.412: 1 Chirality restraints: 1473 Sorted by residual: chirality pdb=" CA THR C 346 " pdb=" N THR C 346 " pdb=" C THR C 346 " pdb=" CB THR C 346 " both_signs ideal model delta sigma weight residual False 2.53 2.11 0.41 2.00e-01 2.50e+01 4.24e+00 chirality pdb=" CA LYS C 345 " pdb=" N LYS C 345 " pdb=" C LYS C 345 " pdb=" CB LYS C 345 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA LYS A1272 " pdb=" N LYS A1272 " pdb=" C LYS A1272 " pdb=" CB LYS A1272 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 1470 not shown) Planarity restraints: 1659 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS C 343 " -0.025 2.00e-02 2.50e+03 5.05e-02 2.55e+01 pdb=" C HIS C 343 " 0.087 2.00e-02 2.50e+03 pdb=" O HIS C 343 " -0.033 2.00e-02 2.50e+03 pdb=" N PRO C 344 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL C 351 " 0.069 5.00e-02 4.00e+02 1.05e-01 1.77e+01 pdb=" N PRO C 352 " -0.182 5.00e-02 4.00e+02 pdb=" CA PRO C 352 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO C 352 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A1268 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.14e+00 pdb=" C ALA A1268 " 0.043 2.00e-02 2.50e+03 pdb=" O ALA A1268 " -0.016 2.00e-02 2.50e+03 pdb=" N SER A1269 " -0.015 2.00e-02 2.50e+03 ... (remaining 1656 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 930 2.75 - 3.28: 10141 3.28 - 3.82: 14469 3.82 - 4.36: 16706 4.36 - 4.90: 28141 Nonbonded interactions: 70387 Sorted by model distance: nonbonded pdb=" OH TYR B 177 " pdb=" OD1 ASN B 518 " model vdw 2.207 3.040 nonbonded pdb=" O GLY C 347 " pdb=" OD1 ASN C 368 " model vdw 2.221 3.040 nonbonded pdb=" O VAL C 37 " pdb=" OG SER C 41 " model vdw 2.221 3.040 nonbonded pdb=" OG1 THR C 52 " pdb=" OD1 ASN C 72 " model vdw 2.244 3.040 nonbonded pdb=" OH TYR B 341 " pdb=" O PHE B 365 " model vdw 2.245 3.040 ... (remaining 70382 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 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: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 27.580 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6355 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 : 0.003 0.059 9723 Z= 0.131 Angle : 0.639 8.479 13085 Z= 0.342 Chirality : 0.046 0.412 1473 Planarity : 0.004 0.105 1659 Dihedral : 14.554 84.242 3725 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.25), residues: 1135 helix: 0.63 (0.26), residues: 418 sheet: -0.54 (0.46), residues: 131 loop : -1.20 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 318 HIS 0.006 0.001 HIS C 219 PHE 0.021 0.001 PHE B 174 TYR 0.034 0.002 TYR B 260 ARG 0.006 0.000 ARG B 252 Details of bonding type rmsd hydrogen bonds : bond 0.20847 ( 366) hydrogen bonds : angle 6.92554 ( 1050) metal coordination : bond 0.00271 ( 4) metal coordination : angle 3.91138 ( 6) covalent geometry : bond 0.00276 ( 9719) covalent geometry : angle 0.63384 (13079) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1306 ASP cc_start: 0.7482 (p0) cc_final: 0.7038 (p0) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.2670 time to fit residues: 44.4494 Evaluate side-chains 57 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 104 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1253 GLN A1315 GLN C 172 HIS C 228 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.038325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.031894 restraints weight = 135055.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.032697 restraints weight = 81953.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.033281 restraints weight = 56948.634| |-----------------------------------------------------------------------------| r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9723 Z= 0.165 Angle : 0.631 8.168 13085 Z= 0.334 Chirality : 0.044 0.154 1473 Planarity : 0.004 0.070 1659 Dihedral : 4.842 23.206 1235 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.18 % Allowed : 5.60 % Favored : 94.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.25), residues: 1135 helix: 0.61 (0.25), residues: 443 sheet: -0.75 (0.45), residues: 131 loop : -1.18 (0.27), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 174 HIS 0.006 0.001 HIS C 219 PHE 0.022 0.001 PHE C 31 TYR 0.021 0.002 TYR B 260 ARG 0.016 0.001 ARG A1243 Details of bonding type rmsd hydrogen bonds : bond 0.04478 ( 366) hydrogen bonds : angle 5.32198 ( 1050) metal coordination : bond 0.00361 ( 4) metal coordination : angle 4.39035 ( 6) covalent geometry : bond 0.00344 ( 9719) covalent geometry : angle 0.62423 (13079) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 283 MET cc_start: 0.9629 (ppp) cc_final: 0.9210 (ppp) REVERT: B 426 MET cc_start: 0.9223 (pmm) cc_final: 0.8893 (pmm) REVERT: B 464 MET cc_start: 0.9143 (mmm) cc_final: 0.8913 (mmm) REVERT: A 1306 ASP cc_start: 0.9057 (p0) cc_final: 0.8802 (p0) REVERT: A 1312 TYR cc_start: 0.9652 (p90) cc_final: 0.9088 (p90) REVERT: A 1327 MET cc_start: 0.8275 (pmm) cc_final: 0.7851 (pmm) REVERT: D 40 ARG cc_start: 0.9787 (tmt170) cc_final: 0.9579 (tpt90) REVERT: D 64 VAL cc_start: 0.9829 (t) cc_final: 0.9121 (t) REVERT: D 267 MET cc_start: 0.9736 (mtm) cc_final: 0.9354 (mtm) REVERT: C 118 MET cc_start: 0.8981 (ppp) cc_final: 0.8700 (ppp) REVERT: C 226 MET cc_start: 0.9494 (mmm) cc_final: 0.9189 (mmm) outliers start: 2 outliers final: 0 residues processed: 66 average time/residue: 0.2091 time to fit residues: 20.4462 Evaluate side-chains 50 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 8 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 80 optimal weight: 0.4980 chunk 89 optimal weight: 7.9990 chunk 10 optimal weight: 20.0000 chunk 37 optimal weight: 4.9990 chunk 67 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 75 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 chunk 99 optimal weight: 6.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 HIS B 303 HIS B 391 GLN B 407 GLN B 425 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.036368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.030099 restraints weight = 141246.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.030878 restraints weight = 86580.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.031447 restraints weight = 60259.327| |-----------------------------------------------------------------------------| r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9723 Z= 0.163 Angle : 0.598 6.400 13085 Z= 0.319 Chirality : 0.044 0.161 1473 Planarity : 0.004 0.056 1659 Dihedral : 4.897 22.620 1235 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.64 % Favored : 94.27 % Rotamer: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.25), residues: 1135 helix: 0.77 (0.25), residues: 441 sheet: -1.05 (0.41), residues: 141 loop : -1.11 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 283 HIS 0.007 0.002 HIS B 196 PHE 0.014 0.001 PHE B 174 TYR 0.017 0.002 TYR B 533 ARG 0.005 0.001 ARG D 152 Details of bonding type rmsd hydrogen bonds : bond 0.03948 ( 366) hydrogen bonds : angle 5.10889 ( 1050) metal coordination : bond 0.00402 ( 4) metal coordination : angle 3.79475 ( 6) covalent geometry : bond 0.00339 ( 9719) covalent geometry : angle 0.59284 (13079) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 283 MET cc_start: 0.9672 (ppp) cc_final: 0.9217 (ppp) REVERT: B 426 MET cc_start: 0.9218 (pmm) cc_final: 0.8849 (pmm) REVERT: B 464 MET cc_start: 0.9144 (mmm) cc_final: 0.8790 (mmm) REVERT: A 1306 ASP cc_start: 0.9087 (p0) cc_final: 0.8843 (p0) REVERT: A 1312 TYR cc_start: 0.9676 (p90) cc_final: 0.9115 (p90) REVERT: A 1327 MET cc_start: 0.8265 (pmm) cc_final: 0.8007 (pmm) REVERT: A 1369 ASP cc_start: 0.9694 (t0) cc_final: 0.9379 (m-30) REVERT: D 247 TYR cc_start: 0.9088 (t80) cc_final: 0.8680 (t80) REVERT: D 267 MET cc_start: 0.9728 (mtm) cc_final: 0.9340 (mtm) REVERT: C 70 MET cc_start: 0.9212 (mmp) cc_final: 0.8970 (mmp) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.2523 time to fit residues: 21.6531 Evaluate side-chains 49 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 44 optimal weight: 8.9990 chunk 78 optimal weight: 0.0010 chunk 83 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 36 optimal weight: 0.0060 chunk 8 optimal weight: 7.9990 chunk 5 optimal weight: 9.9990 chunk 101 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 43 optimal weight: 0.8980 chunk 90 optimal weight: 9.9990 overall best weight: 2.9806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 391 GLN B 425 GLN B 491 ASN D 102 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.035603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.029471 restraints weight = 141048.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.030242 restraints weight = 85953.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.030794 restraints weight = 59962.765| |-----------------------------------------------------------------------------| r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 9723 Z= 0.154 Angle : 0.598 8.427 13085 Z= 0.315 Chirality : 0.043 0.162 1473 Planarity : 0.004 0.060 1659 Dihedral : 4.904 24.544 1235 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.29 % Favored : 94.63 % Rotamer: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.25), residues: 1135 helix: 0.90 (0.24), residues: 448 sheet: -1.06 (0.41), residues: 139 loop : -1.13 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 138 HIS 0.005 0.001 HIS C 219 PHE 0.015 0.001 PHE B 546 TYR 0.016 0.001 TYR B 533 ARG 0.006 0.001 ARG C 54 Details of bonding type rmsd hydrogen bonds : bond 0.03549 ( 366) hydrogen bonds : angle 4.89749 ( 1050) metal coordination : bond 0.00679 ( 4) metal coordination : angle 5.22814 ( 6) covalent geometry : bond 0.00318 ( 9719) covalent geometry : angle 0.58746 (13079) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 426 MET cc_start: 0.9133 (pmm) cc_final: 0.8773 (pmm) REVERT: A 1247 ASP cc_start: 0.9333 (p0) cc_final: 0.8974 (t0) REVERT: A 1277 ASN cc_start: 0.8155 (m-40) cc_final: 0.7605 (p0) REVERT: A 1306 ASP cc_start: 0.9132 (p0) cc_final: 0.8890 (p0) REVERT: A 1312 TYR cc_start: 0.9666 (p90) cc_final: 0.9101 (p90) REVERT: A 1369 ASP cc_start: 0.9708 (t0) cc_final: 0.9412 (m-30) REVERT: D 64 VAL cc_start: 0.9836 (t) cc_final: 0.9250 (t) REVERT: D 247 TYR cc_start: 0.8977 (t80) cc_final: 0.8462 (t80) REVERT: D 267 MET cc_start: 0.9713 (mtm) cc_final: 0.9438 (mtp) REVERT: C 70 MET cc_start: 0.9303 (mmp) cc_final: 0.8948 (mmp) REVERT: C 193 ASP cc_start: 0.9714 (t0) cc_final: 0.9372 (m-30) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.2427 time to fit residues: 21.0844 Evaluate side-chains 48 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 86 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 109 optimal weight: 7.9990 chunk 71 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 56 optimal weight: 9.9990 chunk 100 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.034046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.028101 restraints weight = 143718.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.028845 restraints weight = 88072.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.029380 restraints weight = 61495.439| |-----------------------------------------------------------------------------| r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.4762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9723 Z= 0.174 Angle : 0.620 7.990 13085 Z= 0.329 Chirality : 0.043 0.178 1473 Planarity : 0.004 0.073 1659 Dihedral : 5.021 21.876 1235 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.20 % Favored : 94.71 % Rotamer: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.25), residues: 1135 helix: 0.82 (0.24), residues: 449 sheet: -1.28 (0.40), residues: 149 loop : -1.14 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 138 HIS 0.005 0.001 HIS B 585 PHE 0.015 0.002 PHE C 31 TYR 0.015 0.002 TYR B 533 ARG 0.005 0.001 ARG A1243 Details of bonding type rmsd hydrogen bonds : bond 0.03723 ( 366) hydrogen bonds : angle 5.12892 ( 1050) metal coordination : bond 0.00372 ( 4) metal coordination : angle 4.79639 ( 6) covalent geometry : bond 0.00358 ( 9719) covalent geometry : angle 0.61206 (13079) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 2.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 426 MET cc_start: 0.9154 (pmm) cc_final: 0.8779 (pmm) REVERT: B 464 MET cc_start: 0.9235 (mmm) cc_final: 0.8923 (mmm) REVERT: A 1247 ASP cc_start: 0.9332 (p0) cc_final: 0.8944 (t0) REVERT: A 1306 ASP cc_start: 0.9181 (p0) cc_final: 0.8952 (p0) REVERT: A 1312 TYR cc_start: 0.9666 (p90) cc_final: 0.9116 (p90) REVERT: A 1369 ASP cc_start: 0.9719 (t0) cc_final: 0.9446 (m-30) REVERT: D 152 ARG cc_start: 0.9576 (ppt170) cc_final: 0.9237 (ttp80) REVERT: D 222 MET cc_start: 0.9170 (ppp) cc_final: 0.8949 (ppp) REVERT: D 267 MET cc_start: 0.9705 (mtm) cc_final: 0.9412 (mtp) REVERT: C 70 MET cc_start: 0.9368 (mmp) cc_final: 0.9034 (mmp) REVERT: C 193 ASP cc_start: 0.9697 (t0) cc_final: 0.9368 (m-30) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.3719 time to fit residues: 30.6668 Evaluate side-chains 42 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 31 optimal weight: 0.1980 chunk 86 optimal weight: 10.0000 chunk 105 optimal weight: 0.0040 chunk 76 optimal weight: 7.9990 chunk 72 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 36 optimal weight: 0.0370 chunk 94 optimal weight: 7.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.8272 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 425 GLN C 348 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.034412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.029577 restraints weight = 137652.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.030361 restraints weight = 82923.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.030896 restraints weight = 57432.811| |-----------------------------------------------------------------------------| r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.4690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 9723 Z= 0.106 Angle : 0.581 8.778 13085 Z= 0.297 Chirality : 0.044 0.181 1473 Planarity : 0.003 0.050 1659 Dihedral : 4.659 23.437 1235 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.26), residues: 1135 helix: 1.13 (0.25), residues: 452 sheet: -1.03 (0.42), residues: 140 loop : -1.04 (0.28), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 163 HIS 0.004 0.001 HIS C 219 PHE 0.013 0.001 PHE B 174 TYR 0.014 0.001 TYR B 260 ARG 0.006 0.000 ARG D 40 Details of bonding type rmsd hydrogen bonds : bond 0.03238 ( 366) hydrogen bonds : angle 4.81090 ( 1050) metal coordination : bond 0.00322 ( 4) metal coordination : angle 4.86065 ( 6) covalent geometry : bond 0.00229 ( 9719) covalent geometry : angle 0.57187 (13079) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 2.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 426 MET cc_start: 0.9092 (pmm) cc_final: 0.8699 (pmm) REVERT: B 464 MET cc_start: 0.9200 (mmm) cc_final: 0.8908 (mmm) REVERT: A 1247 ASP cc_start: 0.9315 (p0) cc_final: 0.8915 (t0) REVERT: A 1306 ASP cc_start: 0.9174 (p0) cc_final: 0.8940 (p0) REVERT: A 1312 TYR cc_start: 0.9622 (p90) cc_final: 0.9036 (p90) REVERT: A 1369 ASP cc_start: 0.9697 (t0) cc_final: 0.9436 (m-30) REVERT: D 152 ARG cc_start: 0.9591 (ppt170) cc_final: 0.9200 (ttp80) REVERT: D 222 MET cc_start: 0.9213 (ppp) cc_final: 0.9003 (ppp) REVERT: D 247 TYR cc_start: 0.9041 (t80) cc_final: 0.8438 (t80) REVERT: D 267 MET cc_start: 0.9674 (mtm) cc_final: 0.9381 (mtp) REVERT: C 70 MET cc_start: 0.9368 (mmp) cc_final: 0.9085 (mmp) REVERT: C 193 ASP cc_start: 0.9706 (t0) cc_final: 0.9398 (m-30) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.2291 time to fit residues: 20.6068 Evaluate side-chains 44 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 110 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 1 optimal weight: 0.9990 chunk 101 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 chunk 40 optimal weight: 8.9990 chunk 70 optimal weight: 9.9990 chunk 91 optimal weight: 0.7980 chunk 59 optimal weight: 0.0970 chunk 109 optimal weight: 0.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 425 GLN B 469 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.035232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.029171 restraints weight = 140498.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.029959 restraints weight = 84920.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.030512 restraints weight = 58907.527| |-----------------------------------------------------------------------------| r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.4961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9723 Z= 0.121 Angle : 0.569 8.349 13085 Z= 0.294 Chirality : 0.043 0.176 1473 Planarity : 0.004 0.048 1659 Dihedral : 4.614 21.892 1235 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.26), residues: 1135 helix: 1.17 (0.25), residues: 453 sheet: -0.89 (0.42), residues: 133 loop : -1.04 (0.28), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 163 HIS 0.004 0.001 HIS C 219 PHE 0.012 0.001 PHE B 344 TYR 0.013 0.001 TYR B 260 ARG 0.005 0.000 ARG A1243 Details of bonding type rmsd hydrogen bonds : bond 0.03239 ( 366) hydrogen bonds : angle 4.77390 ( 1050) metal coordination : bond 0.00275 ( 4) metal coordination : angle 4.73530 ( 6) covalent geometry : bond 0.00259 ( 9719) covalent geometry : angle 0.56035 (13079) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 426 MET cc_start: 0.9051 (pmm) cc_final: 0.8696 (pmm) REVERT: B 464 MET cc_start: 0.9293 (mmm) cc_final: 0.8968 (mmm) REVERT: A 1247 ASP cc_start: 0.9321 (p0) cc_final: 0.8929 (t0) REVERT: A 1306 ASP cc_start: 0.9194 (p0) cc_final: 0.8960 (p0) REVERT: A 1312 TYR cc_start: 0.9628 (p90) cc_final: 0.9045 (p90) REVERT: A 1369 ASP cc_start: 0.9707 (t0) cc_final: 0.9469 (m-30) REVERT: D 64 VAL cc_start: 0.9844 (t) cc_final: 0.9243 (t) REVERT: D 152 ARG cc_start: 0.9589 (ppt170) cc_final: 0.9183 (ttp80) REVERT: D 222 MET cc_start: 0.9273 (ppp) cc_final: 0.9063 (ppp) REVERT: D 247 TYR cc_start: 0.9069 (t80) cc_final: 0.8462 (t80) REVERT: D 267 MET cc_start: 0.9684 (mtm) cc_final: 0.9435 (mtp) REVERT: C 70 MET cc_start: 0.9505 (mmp) cc_final: 0.9103 (mmp) REVERT: C 155 ASP cc_start: 0.9454 (m-30) cc_final: 0.9242 (m-30) REVERT: C 193 ASP cc_start: 0.9713 (t0) cc_final: 0.9404 (m-30) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.2404 time to fit residues: 19.5554 Evaluate side-chains 48 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 3 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 65 optimal weight: 10.0000 chunk 42 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 84 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 chunk 114 optimal weight: 9.9990 chunk 50 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 overall best weight: 4.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 GLN ** B 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.024172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2421 r_free = 0.2421 target = 0.018335 restraints weight = 155195.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2442 r_free = 0.2442 target = 0.018789 restraints weight = 119714.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2457 r_free = 0.2457 target = 0.019123 restraints weight = 98744.193| |-----------------------------------------------------------------------------| r_work (final): 0.2450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.5731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9723 Z= 0.201 Angle : 0.679 9.724 13085 Z= 0.356 Chirality : 0.045 0.204 1473 Planarity : 0.004 0.048 1659 Dihedral : 5.189 24.314 1235 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 19.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.25), residues: 1135 helix: 0.87 (0.24), residues: 446 sheet: -0.91 (0.42), residues: 133 loop : -1.21 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 138 HIS 0.008 0.002 HIS C 343 PHE 0.019 0.002 PHE B 522 TYR 0.020 0.002 TYR B 533 ARG 0.007 0.001 ARG A1243 Details of bonding type rmsd hydrogen bonds : bond 0.03775 ( 366) hydrogen bonds : angle 5.17987 ( 1050) metal coordination : bond 0.00548 ( 4) metal coordination : angle 5.86147 ( 6) covalent geometry : bond 0.00402 ( 9719) covalent geometry : angle 0.66732 (13079) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 464 MET cc_start: 0.9309 (mmm) cc_final: 0.8953 (mmm) REVERT: A 1247 ASP cc_start: 0.9361 (p0) cc_final: 0.9089 (t0) REVERT: A 1312 TYR cc_start: 0.9712 (p90) cc_final: 0.9206 (p90) REVERT: A 1369 ASP cc_start: 0.9701 (t0) cc_final: 0.9435 (m-30) REVERT: D 152 ARG cc_start: 0.9573 (ppt170) cc_final: 0.9197 (ttp80) REVERT: D 267 MET cc_start: 0.9658 (mtm) cc_final: 0.9440 (mtp) REVERT: C 70 MET cc_start: 0.9491 (mmp) cc_final: 0.9116 (mmp) REVERT: C 193 ASP cc_start: 0.9741 (t0) cc_final: 0.9442 (m-30) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.2454 time to fit residues: 17.9595 Evaluate side-chains 41 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 56 optimal weight: 9.9990 chunk 86 optimal weight: 0.0010 chunk 2 optimal weight: 0.0170 chunk 60 optimal weight: 6.9990 chunk 74 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 82 optimal weight: 0.0980 chunk 67 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 28 optimal weight: 0.4980 overall best weight: 0.2824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 425 GLN B 440 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.035763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.029660 restraints weight = 139082.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.030466 restraints weight = 82485.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.031034 restraints weight = 56546.203| |-----------------------------------------------------------------------------| r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.5505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 9723 Z= 0.116 Angle : 0.607 8.655 13085 Z= 0.307 Chirality : 0.045 0.168 1473 Planarity : 0.003 0.050 1659 Dihedral : 4.587 22.463 1235 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.26), residues: 1135 helix: 1.04 (0.25), residues: 454 sheet: -0.89 (0.42), residues: 134 loop : -1.07 (0.28), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 163 HIS 0.007 0.001 HIS C 219 PHE 0.032 0.001 PHE B 486 TYR 0.013 0.001 TYR B 260 ARG 0.004 0.000 ARG D 40 Details of bonding type rmsd hydrogen bonds : bond 0.03157 ( 366) hydrogen bonds : angle 4.81246 ( 1050) metal coordination : bond 0.00302 ( 4) metal coordination : angle 4.94377 ( 6) covalent geometry : bond 0.00248 ( 9719) covalent geometry : angle 0.59750 (13079) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 426 MET cc_start: 0.8833 (pmm) cc_final: 0.8564 (pmm) REVERT: B 464 MET cc_start: 0.9286 (mmm) cc_final: 0.8970 (mmm) REVERT: A 1247 ASP cc_start: 0.9287 (p0) cc_final: 0.8874 (t0) REVERT: A 1306 ASP cc_start: 0.9210 (p0) cc_final: 0.9003 (p0) REVERT: A 1312 TYR cc_start: 0.9597 (p90) cc_final: 0.8950 (p90) REVERT: A 1369 ASP cc_start: 0.9694 (t0) cc_final: 0.9434 (m-30) REVERT: D 152 ARG cc_start: 0.9602 (ppt170) cc_final: 0.9194 (ttp80) REVERT: D 222 MET cc_start: 0.9140 (ppp) cc_final: 0.8905 (ppp) REVERT: D 247 TYR cc_start: 0.9063 (t80) cc_final: 0.8398 (t80) REVERT: D 267 MET cc_start: 0.9644 (mtm) cc_final: 0.9313 (mtm) REVERT: C 70 MET cc_start: 0.9544 (mmp) cc_final: 0.9157 (mmp) REVERT: C 155 ASP cc_start: 0.9603 (m-30) cc_final: 0.9382 (m-30) REVERT: C 193 ASP cc_start: 0.9709 (t0) cc_final: 0.9373 (m-30) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.2700 time to fit residues: 22.6603 Evaluate side-chains 47 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 114 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 GLN ** B 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.024732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2434 r_free = 0.2434 target = 0.018772 restraints weight = 152174.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2456 r_free = 0.2456 target = 0.019252 restraints weight = 115716.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2472 r_free = 0.2472 target = 0.019615 restraints weight = 94341.763| |-----------------------------------------------------------------------------| r_work (final): 0.2467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.5888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9723 Z= 0.154 Angle : 0.615 9.076 13085 Z= 0.318 Chirality : 0.043 0.172 1473 Planarity : 0.004 0.047 1659 Dihedral : 4.784 23.452 1235 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.26), residues: 1135 helix: 1.07 (0.25), residues: 453 sheet: -0.96 (0.41), residues: 134 loop : -1.13 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 163 HIS 0.006 0.001 HIS B 585 PHE 0.015 0.001 PHE B 522 TYR 0.014 0.001 TYR B 260 ARG 0.006 0.000 ARG A1243 Details of bonding type rmsd hydrogen bonds : bond 0.03307 ( 366) hydrogen bonds : angle 4.92146 ( 1050) metal coordination : bond 0.00311 ( 4) metal coordination : angle 5.32918 ( 6) covalent geometry : bond 0.00314 ( 9719) covalent geometry : angle 0.60475 (13079) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2270 Ramachandran restraints generated. 1135 Oldfield, 0 Emsley, 1135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 426 MET cc_start: 0.8923 (pmm) cc_final: 0.8649 (pmm) REVERT: B 464 MET cc_start: 0.9347 (mmm) cc_final: 0.9036 (mmm) REVERT: A 1247 ASP cc_start: 0.9293 (p0) cc_final: 0.8968 (t0) REVERT: A 1312 TYR cc_start: 0.9703 (p90) cc_final: 0.9192 (p90) REVERT: A 1369 ASP cc_start: 0.9703 (t0) cc_final: 0.9439 (m-30) REVERT: D 152 ARG cc_start: 0.9565 (ppt170) cc_final: 0.9162 (ttp80) REVERT: D 222 MET cc_start: 0.9274 (ppp) cc_final: 0.9042 (ppp) REVERT: D 267 MET cc_start: 0.9651 (mtm) cc_final: 0.9386 (mtp) REVERT: C 70 MET cc_start: 0.9537 (mmp) cc_final: 0.9147 (mmp) REVERT: C 155 ASP cc_start: 0.9646 (m-30) cc_final: 0.9418 (m-30) REVERT: C 193 ASP cc_start: 0.9702 (t0) cc_final: 0.9399 (m-30) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.2477 time to fit residues: 19.0595 Evaluate side-chains 44 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 69 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 68 optimal weight: 6.9990 chunk 72 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 425 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.025096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2446 r_free = 0.2446 target = 0.019088 restraints weight = 148693.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2469 r_free = 0.2469 target = 0.019579 restraints weight = 113427.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 16)----------------| | r_work = 0.2485 r_free = 0.2485 target = 0.019956 restraints weight = 92201.012| |-----------------------------------------------------------------------------| r_work (final): 0.2479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.5942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 9723 Z= 0.111 Angle : 0.592 9.392 13085 Z= 0.299 Chirality : 0.044 0.159 1473 Planarity : 0.003 0.048 1659 Dihedral : 4.622 22.751 1235 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.26), residues: 1135 helix: 1.09 (0.25), residues: 454 sheet: -0.89 (0.41), residues: 133 loop : -1.10 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 163 HIS 0.006 0.001 HIS C 219 PHE 0.013 0.001 PHE B 344 TYR 0.013 0.001 TYR B 260 ARG 0.012 0.001 ARG D 285 Details of bonding type rmsd hydrogen bonds : bond 0.03122 ( 366) hydrogen bonds : angle 4.81679 ( 1050) metal coordination : bond 0.00270 ( 4) metal coordination : angle 5.39057 ( 6) covalent geometry : bond 0.00239 ( 9719) covalent geometry : angle 0.58030 (13079) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2891.26 seconds wall clock time: 53 minutes 22.34 seconds (3202.34 seconds total)