Starting phenix.real_space_refine on Fri Feb 14 00:14:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uy8_26867/02_2025/7uy8_26867.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uy8_26867/02_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_26867/02_2025/7uy8_26867.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uy8_26867/02_2025/7uy8_26867.map" model { file = "/net/cci-nas-00/data/ceres_data/7uy8_26867/02_2025/7uy8_26867.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uy8_26867/02_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.63, per 1000 atoms: 0.59 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: 2.33 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: 1.04 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: 2.61 Time building geometry restraints manager: 2.70 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: 1.260 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: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 24.730 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.640 ------------------------------------------------------------------------------- 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 9719 Z= 0.180 Angle : 0.634 8.479 13079 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 *********************** 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 : 1.147 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: 0.2590 time to fit residues: 43.1034 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 : 1.153 ------------------------------------------------------------------------------- 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 = 37)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.031893 restraints weight = 135055.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.032698 restraints weight = 81938.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.033277 restraints weight = 56952.324| |-----------------------------------------------------------------------------| r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 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 9719 Z= 0.222 Angle : 0.624 8.168 13079 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 *********************** 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 : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 283 MET cc_start: 0.9628 (ppp) cc_final: 0.9209 (ppp) REVERT: B 426 MET cc_start: 0.9221 (pmm) cc_final: 0.8892 (pmm) REVERT: B 464 MET cc_start: 0.9141 (mmm) cc_final: 0.8911 (mmm) REVERT: A 1306 ASP cc_start: 0.9054 (p0) cc_final: 0.8797 (p0) REVERT: A 1312 TYR cc_start: 0.9648 (p90) cc_final: 0.9083 (p90) REVERT: A 1327 MET cc_start: 0.8275 (pmm) cc_final: 0.7851 (pmm) REVERT: D 40 ARG cc_start: 0.9786 (tmt170) cc_final: 0.9578 (tpt90) REVERT: D 64 VAL cc_start: 0.9829 (t) cc_final: 0.9120 (t) REVERT: D 267 MET cc_start: 0.9736 (mtm) cc_final: 0.9355 (mtm) REVERT: C 70 MET cc_start: 0.9004 (mtt) cc_final: 0.8798 (tpp) REVERT: C 118 MET cc_start: 0.8982 (ppp) cc_final: 0.8702 (ppp) REVERT: C 226 MET cc_start: 0.9493 (mmm) cc_final: 0.9189 (mmm) outliers start: 2 outliers final: 0 residues processed: 66 average time/residue: 0.2126 time to fit residues: 20.6842 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 : 1.141 ------------------------------------------------------------------------------- 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: 8.9990 chunk 74 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 89 optimal weight: 8.9990 chunk 10 optimal weight: 20.0000 chunk 37 optimal weight: 8.9990 chunk 67 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 53 optimal weight: 10.0000 chunk 99 optimal weight: 6.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- 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 = 0.3005 r_free = 0.3005 target = 0.035941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.029779 restraints weight = 142288.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.030570 restraints weight = 87028.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.031128 restraints weight = 60536.955| |-----------------------------------------------------------------------------| r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9719 Z= 0.226 Angle : 0.601 5.842 13079 Z= 0.323 Chirality : 0.044 0.164 1473 Planarity : 0.004 0.056 1659 Dihedral : 4.934 22.561 1235 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.81 % Favored : 94.10 % Rotamer: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % 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: -0.58 (0.25), residues: 1135 helix: 0.75 (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 0.022 0.002 TRP C 283 HIS 0.007 0.002 HIS C 219 PHE 0.014 0.002 PHE B 174 TYR 0.019 0.002 TYR B 533 ARG 0.006 0.001 ARG C 188 *********************** 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 59 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 283 MET cc_start: 0.9693 (ppp) cc_final: 0.9254 (ppp) REVERT: B 426 MET cc_start: 0.9222 (pmm) cc_final: 0.8850 (pmm) REVERT: A 1306 ASP cc_start: 0.9090 (p0) cc_final: 0.8843 (p0) REVERT: A 1312 TYR cc_start: 0.9676 (p90) cc_final: 0.9113 (p90) REVERT: A 1327 MET cc_start: 0.8271 (pmm) cc_final: 0.8017 (pmm) REVERT: A 1369 ASP cc_start: 0.9699 (t0) cc_final: 0.9383 (m-30) REVERT: D 247 TYR cc_start: 0.9069 (t80) cc_final: 0.8652 (t80) REVERT: D 267 MET cc_start: 0.9728 (mtm) cc_final: 0.9333 (mtm) REVERT: C 70 MET cc_start: 0.9123 (mtt) cc_final: 0.8810 (mpp) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.2623 time to fit residues: 22.4067 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 : 1.073 ------------------------------------------------------------------------------- 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: 9.9990 chunk 78 optimal weight: 0.7980 chunk 83 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 43 optimal weight: 2.9990 chunk 90 optimal weight: 8.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 247 ASN B 391 GLN B 425 GLN B 469 ASN B 491 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.035099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.029064 restraints weight = 141188.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.029833 restraints weight = 86383.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.030387 restraints weight = 60163.537| |-----------------------------------------------------------------------------| r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.4275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9719 Z= 0.216 Angle : 0.605 7.192 13079 Z= 0.323 Chirality : 0.044 0.155 1473 Planarity : 0.004 0.062 1659 Dihedral : 4.951 24.590 1235 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.37 % Favored : 94.54 % Rotamer: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % 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: -0.53 (0.25), residues: 1135 helix: 0.87 (0.24), residues: 443 sheet: -1.22 (0.40), residues: 146 loop : -1.10 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 138 HIS 0.005 0.001 HIS C 219 PHE 0.014 0.002 PHE C 31 TYR 0.016 0.001 TYR B 533 ARG 0.005 0.001 ARG A1243 *********************** 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 59 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 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: 0.9147 (pmm) cc_final: 0.8779 (pmm) REVERT: A 1247 ASP cc_start: 0.9353 (p0) cc_final: 0.8978 (t0) REVERT: A 1277 ASN cc_start: 0.8120 (m-40) cc_final: 0.7573 (p0) REVERT: A 1306 ASP cc_start: 0.9146 (p0) cc_final: 0.8903 (p0) REVERT: A 1312 TYR cc_start: 0.9665 (p90) cc_final: 0.9112 (p90) REVERT: A 1369 ASP cc_start: 0.9713 (t0) cc_final: 0.9421 (m-30) REVERT: D 152 ARG cc_start: 0.9574 (ppt170) cc_final: 0.9245 (ttp80) REVERT: D 222 MET cc_start: 0.9149 (ppp) cc_final: 0.8936 (ppp) REVERT: D 247 TYR cc_start: 0.8965 (t80) cc_final: 0.8441 (t80) REVERT: D 267 MET cc_start: 0.9710 (mtm) cc_final: 0.9425 (mtp) REVERT: C 193 ASP cc_start: 0.9705 (t0) cc_final: 0.9348 (m-30) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.2263 time to fit residues: 19.7871 Evaluate side-chains 46 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 1.238 ------------------------------------------------------------------------------- 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: 4.9990 chunk 54 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 24 optimal weight: 20.0000 chunk 109 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 100 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 425 GLN D 102 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.026612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2496 r_free = 0.2496 target = 0.020266 restraints weight = 140402.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2516 r_free = 0.2516 target = 0.020737 restraints weight = 109444.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.2531 r_free = 0.2531 target = 0.021101 restraints weight = 90861.474| |-----------------------------------------------------------------------------| r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.4368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 9719 Z= 0.159 Angle : 0.559 7.148 13079 Z= 0.296 Chirality : 0.043 0.161 1473 Planarity : 0.004 0.052 1659 Dihedral : 4.680 22.460 1235 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % 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: -0.28 (0.26), residues: 1135 helix: 1.08 (0.25), residues: 443 sheet: -1.03 (0.40), residues: 150 loop : -0.98 (0.28), residues: 542 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 0.020 0.001 PHE B 486 TYR 0.014 0.001 TYR B 260 ARG 0.005 0.000 ARG D 40 *********************** 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 61 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 426 MET cc_start: 0.9107 (pmm) cc_final: 0.8721 (pmm) REVERT: A 1247 ASP cc_start: 0.9390 (p0) cc_final: 0.9069 (t0) REVERT: A 1312 TYR cc_start: 0.9722 (p90) cc_final: 0.9157 (p90) REVERT: A 1369 ASP cc_start: 0.9690 (t0) cc_final: 0.9418 (m-30) REVERT: D 64 VAL cc_start: 0.9852 (t) cc_final: 0.9298 (t) REVERT: D 152 ARG cc_start: 0.9583 (ppt170) cc_final: 0.9197 (ttp80) REVERT: D 247 TYR cc_start: 0.9070 (t80) cc_final: 0.8522 (t80) REVERT: D 267 MET cc_start: 0.9647 (mtm) cc_final: 0.9360 (mtp) REVERT: C 193 ASP cc_start: 0.9685 (t0) cc_final: 0.9357 (m-30) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.2350 time to fit residues: 20.4918 Evaluate side-chains 46 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 1.129 ------------------------------------------------------------------------------- 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: 4.9990 chunk 86 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 71 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 94 optimal weight: 0.0000 chunk 20 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 = 0.2734 r_free = 0.2734 target = 0.026485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2500 r_free = 0.2500 target = 0.020260 restraints weight = 140181.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 17)----------------| | r_work = 0.2521 r_free = 0.2521 target = 0.020747 restraints weight = 108532.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2536 r_free = 0.2536 target = 0.021110 restraints weight = 89450.624| |-----------------------------------------------------------------------------| r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.4567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 9719 Z= 0.162 Angle : 0.562 7.239 13079 Z= 0.293 Chirality : 0.044 0.192 1473 Planarity : 0.004 0.050 1659 Dihedral : 4.601 23.040 1235 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % 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: -0.24 (0.26), residues: 1135 helix: 1.16 (0.25), residues: 446 sheet: -0.99 (0.41), residues: 145 loop : -1.01 (0.28), residues: 544 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 0.011 0.001 PHE B 344 TYR 0.013 0.001 TYR B 260 ARG 0.008 0.000 ARG D 40 *********************** 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 56 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 426 MET cc_start: 0.9080 (pmm) cc_final: 0.8695 (pmm) REVERT: B 464 MET cc_start: 0.9147 (mmm) cc_final: 0.8838 (mmm) REVERT: A 1247 ASP cc_start: 0.9380 (p0) cc_final: 0.9037 (t0) REVERT: A 1312 TYR cc_start: 0.9704 (p90) cc_final: 0.9147 (p90) REVERT: A 1369 ASP cc_start: 0.9695 (t0) cc_final: 0.9424 (m-30) REVERT: D 152 ARG cc_start: 0.9588 (ppt170) cc_final: 0.9177 (ttp80) REVERT: D 222 MET cc_start: 0.9194 (ppp) cc_final: 0.8966 (ppp) REVERT: D 247 TYR cc_start: 0.9093 (t80) cc_final: 0.8502 (t80) REVERT: D 267 MET cc_start: 0.9640 (mtm) cc_final: 0.9329 (mtp) REVERT: C 193 ASP cc_start: 0.9706 (t0) cc_final: 0.9404 (m-30) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.2594 time to fit residues: 20.9018 Evaluate side-chains 45 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 1.120 ------------------------------------------------------------------------------- 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: 7.9990 chunk 2 optimal weight: 0.8980 chunk 63 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 40 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 59 optimal weight: 0.0870 chunk 109 optimal weight: 0.9990 overall best weight: 1.5964 ------------------------------------------------------------------------------- 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 = 0.2732 r_free = 0.2732 target = 0.026425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2492 r_free = 0.2492 target = 0.020052 restraints weight = 140667.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2513 r_free = 0.2513 target = 0.020544 restraints weight = 109335.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2528 r_free = 0.2528 target = 0.020912 restraints weight = 90204.249| |-----------------------------------------------------------------------------| r_work (final): 0.2520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.4765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 9719 Z= 0.156 Angle : 0.553 7.155 13079 Z= 0.288 Chirality : 0.043 0.172 1473 Planarity : 0.003 0.048 1659 Dihedral : 4.522 22.733 1235 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % 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: -0.19 (0.26), residues: 1135 helix: 1.26 (0.25), residues: 446 sheet: -0.93 (0.41), residues: 138 loop : -1.06 (0.28), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 163 HIS 0.006 0.001 HIS C 219 PHE 0.032 0.001 PHE B 395 TYR 0.013 0.001 TYR B 260 ARG 0.006 0.000 ARG D 40 *********************** 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 : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 426 MET cc_start: 0.9065 (pmm) cc_final: 0.8779 (pmm) REVERT: B 464 MET cc_start: 0.9270 (mmm) cc_final: 0.8962 (mmm) REVERT: A 1247 ASP cc_start: 0.9361 (p0) cc_final: 0.9038 (t0) REVERT: A 1312 TYR cc_start: 0.9698 (p90) cc_final: 0.9145 (p90) REVERT: A 1342 MET cc_start: 0.8300 (ppp) cc_final: 0.7636 (ppp) REVERT: A 1369 ASP cc_start: 0.9692 (t0) cc_final: 0.9454 (m-30) REVERT: D 152 ARG cc_start: 0.9579 (ppt170) cc_final: 0.9179 (ttp80) REVERT: D 247 TYR cc_start: 0.9095 (t80) cc_final: 0.8470 (t80) REVERT: D 267 MET cc_start: 0.9646 (mtm) cc_final: 0.9342 (mtp) REVERT: C 193 ASP cc_start: 0.9729 (t0) cc_final: 0.9420 (m-30) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.2538 time to fit residues: 20.4371 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 : 1.167 ------------------------------------------------------------------------------- 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: 7.9990 chunk 13 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 42 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 chunk 68 optimal weight: 0.6980 chunk 114 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 17 optimal weight: 0.3980 chunk 98 optimal weight: 0.7980 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.035244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.029177 restraints weight = 142340.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.029985 restraints weight = 85492.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.030536 restraints weight = 58627.744| |-----------------------------------------------------------------------------| r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.5047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9719 Z= 0.167 Angle : 0.571 7.545 13079 Z= 0.296 Chirality : 0.043 0.167 1473 Planarity : 0.003 0.046 1659 Dihedral : 4.526 23.220 1235 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % 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: -0.18 (0.25), residues: 1135 helix: 1.23 (0.25), residues: 447 sheet: -0.84 (0.41), residues: 140 loop : -1.06 (0.28), residues: 548 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 0.026 0.001 PHE B 395 TYR 0.013 0.001 TYR B 260 ARG 0.006 0.000 ARG A1243 *********************** 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 55 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 464 MET cc_start: 0.9288 (mmm) cc_final: 0.8953 (mmm) REVERT: A 1247 ASP cc_start: 0.9275 (p0) cc_final: 0.8874 (t0) REVERT: A 1306 ASP cc_start: 0.9135 (p0) cc_final: 0.8916 (p0) REVERT: A 1312 TYR cc_start: 0.9627 (p90) cc_final: 0.9050 (p90) REVERT: A 1369 ASP cc_start: 0.9708 (t0) cc_final: 0.9463 (m-30) REVERT: D 152 ARG cc_start: 0.9593 (ppt170) cc_final: 0.9188 (ttp80) REVERT: D 222 MET cc_start: 0.9181 (ppp) cc_final: 0.8949 (ppp) REVERT: D 247 TYR cc_start: 0.9043 (t80) cc_final: 0.8388 (t80) REVERT: D 267 MET cc_start: 0.9679 (mtm) cc_final: 0.9418 (mtp) REVERT: C 193 ASP cc_start: 0.9737 (t0) cc_final: 0.9435 (m-30) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.2565 time to fit residues: 20.2947 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 : 1.130 ------------------------------------------------------------------------------- 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: 10.0000 chunk 86 optimal weight: 8.9990 chunk 2 optimal weight: 0.0570 chunk 60 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 44 optimal weight: 9.9990 chunk 82 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 overall best weight: 2.4106 ------------------------------------------------------------------------------- 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 = 0.2701 r_free = 0.2701 target = 0.025497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2465 r_free = 0.2465 target = 0.019479 restraints weight = 147127.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2486 r_free = 0.2486 target = 0.019937 restraints weight = 114800.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2501 r_free = 0.2501 target = 0.020279 restraints weight = 94987.258| |-----------------------------------------------------------------------------| r_work (final): 0.2494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.5355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9719 Z= 0.186 Angle : 0.598 8.326 13079 Z= 0.308 Chirality : 0.044 0.181 1473 Planarity : 0.004 0.047 1659 Dihedral : 4.595 22.816 1235 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % 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: -0.19 (0.25), residues: 1135 helix: 1.22 (0.25), residues: 447 sheet: -0.84 (0.42), residues: 137 loop : -1.07 (0.28), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 163 HIS 0.006 0.001 HIS C 343 PHE 0.026 0.001 PHE B 395 TYR 0.013 0.001 TYR B 260 ARG 0.006 0.000 ARG A1243 *********************** 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 55 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 426 MET cc_start: 0.8847 (pmm) cc_final: 0.8631 (pmm) REVERT: B 464 MET cc_start: 0.9302 (mmm) cc_final: 0.8967 (mmm) REVERT: A 1247 ASP cc_start: 0.9365 (p0) cc_final: 0.9013 (t0) REVERT: A 1277 ASN cc_start: 0.8054 (m-40) cc_final: 0.7550 (p0) REVERT: A 1312 TYR cc_start: 0.9700 (p90) cc_final: 0.9166 (p90) REVERT: A 1369 ASP cc_start: 0.9695 (t0) cc_final: 0.9446 (m-30) REVERT: D 152 ARG cc_start: 0.9567 (ppt170) cc_final: 0.9150 (ttp80) REVERT: D 247 TYR cc_start: 0.9100 (t80) cc_final: 0.8455 (t80) REVERT: D 267 MET cc_start: 0.9648 (mtm) cc_final: 0.9393 (mtp) REVERT: C 193 ASP cc_start: 0.9724 (t0) cc_final: 0.9424 (m-30) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.2614 time to fit residues: 20.5853 Evaluate side-chains 46 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 1.269 ------------------------------------------------------------------------------- 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: 7.9990 chunk 7 optimal weight: 10.0000 chunk 108 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 103 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 chunk 83 optimal weight: 0.4980 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.2698 r_free = 0.2698 target = 0.025397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2456 r_free = 0.2456 target = 0.019294 restraints weight = 147821.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2478 r_free = 0.2478 target = 0.019774 restraints weight = 113341.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2492 r_free = 0.2492 target = 0.020106 restraints weight = 92750.327| |-----------------------------------------------------------------------------| r_work (final): 0.2488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.5563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9719 Z= 0.178 Angle : 0.588 7.814 13079 Z= 0.304 Chirality : 0.043 0.163 1473 Planarity : 0.003 0.046 1659 Dihedral : 4.588 23.288 1235 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % 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: -0.22 (0.25), residues: 1135 helix: 1.19 (0.25), residues: 448 sheet: -0.87 (0.41), residues: 140 loop : -1.06 (0.28), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 163 HIS 0.004 0.001 HIS C 219 PHE 0.026 0.001 PHE B 395 TYR 0.013 0.001 TYR B 260 ARG 0.006 0.000 ARG A1243 ********************** 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 56 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 361 LEU cc_start: 0.9855 (mp) cc_final: 0.9649 (pt) REVERT: B 464 MET cc_start: 0.9281 (mmm) cc_final: 0.9006 (mmm) REVERT: A 1247 ASP cc_start: 0.9351 (p0) cc_final: 0.9003 (t0) REVERT: A 1277 ASN cc_start: 0.8054 (m-40) cc_final: 0.7545 (p0) REVERT: A 1312 TYR cc_start: 0.9691 (p90) cc_final: 0.9155 (p90) REVERT: A 1369 ASP cc_start: 0.9694 (t0) cc_final: 0.9453 (m-30) REVERT: D 152 ARG cc_start: 0.9572 (ppt170) cc_final: 0.9156 (ttp80) REVERT: D 222 MET cc_start: 0.9235 (ppp) cc_final: 0.9008 (ppp) REVERT: D 247 TYR cc_start: 0.9135 (t80) cc_final: 0.8546 (t80) REVERT: D 267 MET cc_start: 0.9637 (mtm) cc_final: 0.9286 (mtm) REVERT: C 193 ASP cc_start: 0.9700 (t0) cc_final: 0.9399 (m-30) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.2360 time to fit residues: 19.0853 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 : 1.087 ------------------------------------------------------------------------------- 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: 0.9990 chunk 48 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 29 optimal weight: 9.9990 chunk 68 optimal weight: 7.9990 chunk 72 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 chunk 2 optimal weight: 0.0980 chunk 47 optimal weight: 10.0000 chunk 33 optimal weight: 0.2980 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 425 GLN B 557 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.026285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2490 r_free = 0.2490 target = 0.020123 restraints weight = 143158.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2511 r_free = 0.2511 target = 0.020622 restraints weight = 110045.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2525 r_free = 0.2525 target = 0.020960 restraints weight = 90017.142| |-----------------------------------------------------------------------------| r_work (final): 0.2517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.5553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 9719 Z= 0.150 Angle : 0.588 8.721 13079 Z= 0.296 Chirality : 0.044 0.163 1473 Planarity : 0.003 0.046 1659 Dihedral : 4.353 22.203 1235 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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: -0.10 (0.26), residues: 1135 helix: 1.26 (0.25), residues: 448 sheet: -0.69 (0.41), residues: 143 loop : -1.00 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 163 HIS 0.005 0.001 HIS C 219 PHE 0.023 0.001 PHE B 395 TYR 0.013 0.001 TYR B 478 ARG 0.005 0.000 ARG A1243 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2388.83 seconds wall clock time: 44 minutes 20.30 seconds (2660.30 seconds total)