Starting phenix.real_space_refine (version: dev) on Sun Dec 18 12:38:17 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uy8_26867/12_2022/7uy8_26867.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uy8_26867/12_2022/7uy8_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uy8_26867/12_2022/7uy8_26867.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uy8_26867/12_2022/7uy8_26867.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uy8_26867/12_2022/7uy8_26867.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uy8_26867/12_2022/7uy8_26867.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "C TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 5.71, per 1000 atoms: 0.60 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 - 3.50 Amino acid : False - 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: 3.34 Conformation dependent library (CDL) restraints added in 1.4 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: 0.46 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: 2.40 Time building geometry restraints manager: 3.68 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: 99.49 - 106.39: 192 106.39 - 113.30: 5291 113.30 - 120.21: 3524 120.21 - 127.12: 4007 127.12 - 134.03: 65 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 2.440 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 2.440 nonbonded pdb=" OG1 THR C 52 " pdb=" OD1 ASN C 72 " model vdw 2.244 2.440 nonbonded pdb=" OH TYR B 341 " pdb=" O PHE B 365 " model vdw 2.245 2.440 ... (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 ========== 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 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. 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: 0.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.190 Check model and map are aligned: 0.130 Convert atoms to be neutral: 0.080 Process input model: 27.900 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6026 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 : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer Outliers : 0.00 % 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.2443 time to fit residues: 40.7100 Evaluate side-chains 57 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 1.208 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6820 ------------------------------------------------------------------------------- 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: 6.9990 chunk 87 optimal weight: 8.9990 chunk 48 optimal weight: 9.9990 chunk 29 optimal weight: 7.9990 chunk 58 optimal weight: 0.9990 chunk 46 optimal weight: 9.9990 chunk 90 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 104 optimal weight: 10.0000 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1253 GLN A1315 GLN A1352 ASN D 94 ASN ** D 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6256 moved from start: 0.2237 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= 0.185 Angle : 0.589 9.546 13079 Z= 0.312 Chirality : 0.043 0.165 1473 Planarity : 0.004 0.071 1659 Dihedral : 4.740 23.471 1235 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer Outliers : 0.37 % 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: -0.61 (0.25), residues: 1135 helix: 0.67 (0.25), residues: 441 sheet: -0.77 (0.45), residues: 134 loop : -1.17 (0.27), residues: 560 *********************** 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 69 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 65 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 69 average time/residue: 0.2092 time to fit residues: 21.6606 Evaluate side-chains 49 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 1.227 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 104 optimal weight: 6.9990 chunk 113 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 83 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 B 444 ASN B 585 HIS D 94 ASN ** D 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6450 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 9719 Z= 0.236 Angle : 0.596 6.013 13079 Z= 0.321 Chirality : 0.043 0.158 1473 Planarity : 0.005 0.090 1659 Dihedral : 4.869 21.635 1235 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.17 % Favored : 93.74 % Rotamer Outliers : 0.09 % 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: 0.71 (0.25), residues: 438 sheet: -1.07 (0.41), residues: 136 loop : -1.16 (0.27), residues: 561 *********************** 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 61 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 61 average time/residue: 0.2242 time to fit residues: 20.3740 Evaluate side-chains 44 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 1.261 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 9.9990 chunk 78 optimal weight: 0.0570 chunk 54 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 99 optimal weight: 0.0970 chunk 29 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 overall best weight: 2.4302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 425 GLN B 491 ASN ** A1314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6445 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 9719 Z= 0.188 Angle : 0.562 5.714 13079 Z= 0.299 Chirality : 0.043 0.160 1473 Planarity : 0.004 0.059 1659 Dihedral : 4.826 24.114 1235 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.46 % Favored : 94.45 % Rotamer Outliers : 0.00 % 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: 0.82 (0.25), residues: 443 sheet: -1.18 (0.41), residues: 139 loop : -1.16 (0.27), residues: 553 *********************** 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 54 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.2049 time to fit residues: 17.3527 Evaluate side-chains 44 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 1.208 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 82 optimal weight: 8.9990 chunk 45 optimal weight: 8.9990 chunk 94 optimal weight: 0.8980 chunk 76 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 56 optimal weight: 8.9990 chunk 99 optimal weight: 0.0870 chunk 28 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 overall best weight: 3.5964 ------------------------------------------------------------------------------- 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 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 GLN B 469 ASN ** A1304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6602 moved from start: 0.4734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 9719 Z= 0.240 Angle : 0.613 5.539 13079 Z= 0.331 Chirality : 0.043 0.179 1473 Planarity : 0.004 0.048 1659 Dihedral : 5.087 20.714 1235 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 22.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.73 % Favored : 94.19 % Rotamer Outliers : 0.00 % 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: -0.72 (0.25), residues: 1135 helix: 0.68 (0.24), residues: 448 sheet: -1.14 (0.42), residues: 133 loop : -1.26 (0.27), residues: 554 *********************** 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 52 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 1.312 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1920 time to fit residues: 16.1514 Evaluate side-chains 41 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 1.187 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 111 optimal weight: 0.3980 chunk 92 optimal weight: 7.9990 chunk 51 optimal weight: 8.9990 chunk 9 optimal weight: 0.0670 chunk 36 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 107 optimal weight: 9.9990 overall best weight: 1.4922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 425 GLN ** D 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6494 moved from start: 0.4760 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= 0.161 Angle : 0.554 5.987 13079 Z= 0.291 Chirality : 0.043 0.188 1473 Planarity : 0.003 0.046 1659 Dihedral : 4.767 22.415 1235 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.11 % Favored : 94.80 % Rotamer Outliers : 0.00 % 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: -0.50 (0.25), residues: 1135 helix: 0.91 (0.25), residues: 450 sheet: -1.13 (0.42), residues: 134 loop : -1.17 (0.27), residues: 551 *********************** 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 55 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.2204 time to fit residues: 18.4355 Evaluate side-chains 43 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 1.157 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 81 optimal weight: 0.2980 chunk 62 optimal weight: 10.0000 chunk 93 optimal weight: 9.9990 chunk 110 optimal weight: 2.9990 chunk 69 optimal weight: 0.2980 chunk 67 optimal weight: 8.9990 chunk 51 optimal weight: 8.9990 chunk 68 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 GLN ** D 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6554 moved from start: 0.5100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 9719 Z= 0.183 Angle : 0.560 8.617 13079 Z= 0.294 Chirality : 0.043 0.174 1473 Planarity : 0.003 0.043 1659 Dihedral : 4.732 20.265 1235 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 19.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.29 % Favored : 94.63 % Rotamer Outliers : 0.00 % 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: -0.39 (0.25), residues: 1135 helix: 0.98 (0.25), residues: 449 sheet: -1.08 (0.42), residues: 133 loop : -1.06 (0.28), residues: 553 *********************** 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 51 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 1.302 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1945 time to fit residues: 15.8449 Evaluate side-chains 41 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 1.229 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 70 optimal weight: 9.9990 chunk 75 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 87 optimal weight: 10.0000 chunk 100 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 440 HIS ** A1304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6678 moved from start: 0.5791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 9719 Z= 0.240 Angle : 0.625 7.978 13079 Z= 0.333 Chirality : 0.044 0.193 1473 Planarity : 0.004 0.042 1659 Dihedral : 5.133 23.326 1235 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 23.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.90 % Favored : 94.01 % Rotamer Outliers : 0.00 % 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: -0.68 (0.25), residues: 1135 helix: 0.71 (0.25), residues: 437 sheet: -1.33 (0.40), residues: 137 loop : -1.13 (0.27), residues: 561 *********************** 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 51 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 1.151 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1931 time to fit residues: 15.8143 Evaluate side-chains 39 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 1.187 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/iotbx/cli_parser.py", line 864, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.9973 > 50: distance: 66 - 71: 25.792 distance: 71 - 72: 33.082 distance: 72 - 73: 47.960 distance: 72 - 75: 18.296 distance: 73 - 80: 46.035 distance: 75 - 76: 12.735 distance: 76 - 77: 52.352 distance: 80 - 81: 31.400 distance: 81 - 82: 55.366 distance: 82 - 83: 40.842 distance: 82 - 86: 38.844 distance: 84 - 85: 40.032 distance: 86 - 87: 56.990 distance: 87 - 88: 18.733 distance: 87 - 90: 40.320 distance: 88 - 89: 28.777 distance: 88 - 93: 17.461 distance: 91 - 92: 40.750 distance: 94 - 95: 40.562 distance: 94 - 97: 20.380 distance: 95 - 96: 26.988 distance: 98 - 99: 46.014 distance: 98 - 100: 44.199 distance: 101 - 103: 56.548 distance: 102 - 103: 39.539 distance: 104 - 105: 40.391 distance: 105 - 108: 27.546 distance: 106 - 107: 39.040 distance: 106 - 110: 41.292 distance: 108 - 109: 30.054 distance: 110 - 111: 39.425 distance: 111 - 112: 57.021 distance: 111 - 114: 12.780 distance: 112 - 113: 38.946 distance: 112 - 118: 70.490 distance: 114 - 115: 18.494 distance: 114 - 116: 58.111 distance: 115 - 117: 44.105 distance: 118 - 119: 39.057 distance: 119 - 120: 38.604 distance: 119 - 122: 57.929 distance: 120 - 121: 37.428 distance: 120 - 128: 50.829 distance: 122 - 123: 55.351 distance: 123 - 124: 40.459 distance: 123 - 125: 38.925 distance: 124 - 126: 39.746 distance: 126 - 127: 39.028 distance: 128 - 129: 50.416 distance: 128 - 134: 51.106 distance: 129 - 130: 9.645 distance: 129 - 132: 4.525 distance: 130 - 131: 34.116 distance: 130 - 135: 48.902 distance: 132 - 133: 55.114 distance: 135 - 136: 22.322 distance: 136 - 139: 11.579 distance: 137 - 144: 39.992 distance: 139 - 140: 27.843 distance: 142 - 143: 4.873 distance: 144 - 145: 41.191 distance: 145 - 146: 69.190 distance: 145 - 148: 40.356 distance: 146 - 151: 33.838 distance: 148 - 149: 39.486 distance: 148 - 150: 41.167