Starting phenix.real_space_refine on Thu Mar 14 19:26:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uy8_26867/03_2024/7uy8_26867.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uy8_26867/03_2024/7uy8_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_26867/03_2024/7uy8_26867.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uy8_26867/03_2024/7uy8_26867.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uy8_26867/03_2024/7uy8_26867.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uy8_26867/03_2024/7uy8_26867.pdb" } 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 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-5265/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: 5.43, per 1000 atoms: 0.57 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: 3.53 Conformation dependent library (CDL) restraints added in 1.5 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: 0.97 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: 2.46 Time building geometry restraints manager: 3.87 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 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: 0.720 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: 0.000 Extract box with map and model: 3.920 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 28.630 Find NCS groups from input model: 0.260 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:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.250 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 1.169 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: 0.2496 time to fit residues: 41.4731 Evaluate side-chains 57 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 1.124 ------------------------------------------------------------------------------- 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: 0.6589 moved from start: 0.2241 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= 0.183 Angle : 0.588 9.900 13079 Z= 0.312 Chirality : 0.043 0.162 1473 Planarity : 0.004 0.071 1659 Dihedral : 4.742 23.460 1235 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 0.37 % Allowed : 5.23 % Favored : 94.40 % 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: -0.62 (0.25), residues: 1135 helix: 0.66 (0.25), residues: 441 sheet: -0.78 (0.45), residues: 134 loop : -1.17 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 174 HIS 0.005 0.001 HIS B 349 PHE 0.019 0.001 PHE C 31 TYR 0.018 0.001 TYR B 260 ARG 0.010 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 70 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 66 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1306 ASP cc_start: 0.7638 (p0) cc_final: 0.7205 (p0) outliers start: 4 outliers final: 0 residues processed: 70 average time/residue: 0.2064 time to fit residues: 21.5004 Evaluate side-chains 50 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 1.129 ------------------------------------------------------------------------------- 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: 0.9990 chunk 32 optimal weight: 4.9990 chunk 86 optimal weight: 0.0570 chunk 71 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 104 optimal weight: 7.9990 chunk 113 optimal weight: 9.9990 chunk 93 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 83 optimal weight: 9.9990 overall best weight: 2.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 407 GLN D 94 ASN ** D 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6672 moved from start: 0.3059 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= 0.179 Angle : 0.551 5.956 13079 Z= 0.293 Chirality : 0.043 0.149 1473 Planarity : 0.004 0.075 1659 Dihedral : 4.631 22.445 1235 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.73 % Favored : 94.19 % Rotamer: Outliers : 0.09 % Allowed : 4.50 % Favored : 95.41 % 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: -0.54 (0.25), residues: 1135 helix: 0.83 (0.25), residues: 438 sheet: -0.91 (0.43), residues: 128 loop : -1.16 (0.27), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 283 HIS 0.006 0.001 HIS C 219 PHE 0.012 0.001 PHE B 174 TYR 0.017 0.001 TYR D 247 ARG 0.008 0.001 ARG D 152 *********************** 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 64 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 63 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1306 ASP cc_start: 0.7863 (p0) cc_final: 0.7513 (p0) REVERT: C 70 MET cc_start: 0.6374 (mmp) cc_final: 0.5908 (mmp) REVERT: C 155 ASP cc_start: 0.8346 (m-30) cc_final: 0.8065 (m-30) outliers start: 1 outliers final: 0 residues processed: 64 average time/residue: 0.2241 time to fit residues: 20.9942 Evaluate side-chains 49 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 1.144 ------------------------------------------------------------------------------- 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: 10.0000 chunk 78 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 11 optimal weight: 20.0000 chunk 49 optimal weight: 9.9990 chunk 70 optimal weight: 9.9990 chunk 104 optimal weight: 7.9990 chunk 111 optimal weight: 0.0060 chunk 99 optimal weight: 0.9980 chunk 29 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 391 GLN B 425 GLN B 491 ASN ** A1314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6672 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 9719 Z= 0.162 Angle : 0.537 5.718 13079 Z= 0.284 Chirality : 0.043 0.152 1473 Planarity : 0.004 0.051 1659 Dihedral : 4.561 24.335 1235 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.46 % Favored : 94.45 % Rotamer: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % 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: -0.51 (0.25), residues: 1135 helix: 0.93 (0.25), residues: 441 sheet: -1.01 (0.41), residues: 128 loop : -1.20 (0.27), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 147 HIS 0.004 0.001 HIS C 219 PHE 0.013 0.001 PHE B 546 TYR 0.014 0.001 TYR B 260 ARG 0.008 0.001 ARG C 54 *********************** 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 61 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1306 ASP cc_start: 0.7963 (p0) cc_final: 0.7588 (p0) REVERT: C 70 MET cc_start: 0.6450 (mmp) cc_final: 0.5856 (mmp) REVERT: C 155 ASP cc_start: 0.8229 (m-30) cc_final: 0.7912 (m-30) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.2100 time to fit residues: 19.2360 Evaluate side-chains 49 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 1.130 ------------------------------------------------------------------------------- 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: 10.0000 chunk 1 optimal weight: 4.9990 chunk 82 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 94 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 chunk 99 optimal weight: 0.2980 chunk 28 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 overall best weight: 5.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 HIS ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 GLN B 469 ASN ** B 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.4863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9719 Z= 0.321 Angle : 0.708 7.229 13079 Z= 0.383 Chirality : 0.045 0.173 1473 Planarity : 0.005 0.057 1659 Dihedral : 5.395 21.054 1235 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 26.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.99 % Favored : 93.92 % Rotamer: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % 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: -0.87 (0.25), residues: 1135 helix: 0.49 (0.24), residues: 442 sheet: -1.26 (0.40), residues: 133 loop : -1.26 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP C 138 HIS 0.008 0.002 HIS B 196 PHE 0.027 0.002 PHE B 395 TYR 0.028 0.002 TYR B 533 ARG 0.011 0.001 ARG B 587 *********************** 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 : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1306 ASP cc_start: 0.7883 (p0) cc_final: 0.7517 (p0) REVERT: D 71 MET cc_start: 0.8297 (ttt) cc_final: 0.7699 (tpp) REVERT: C 70 MET cc_start: 0.6707 (mmp) cc_final: 0.6173 (mmp) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.2047 time to fit residues: 16.5910 Evaluate side-chains 39 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 1.058 ------------------------------------------------------------------------------- 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: 4.9990 chunk 21 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 111 optimal weight: 0.3980 chunk 92 optimal weight: 10.0000 chunk 51 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- 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 65 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: 0.6924 moved from start: 0.5069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9719 Z= 0.213 Angle : 0.588 6.616 13079 Z= 0.313 Chirality : 0.044 0.196 1473 Planarity : 0.004 0.045 1659 Dihedral : 5.096 22.984 1235 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 19.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.02 % Favored : 94.89 % Rotamer: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % 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: -0.66 (0.25), residues: 1135 helix: 0.79 (0.25), residues: 444 sheet: -1.47 (0.40), residues: 137 loop : -1.16 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 138 HIS 0.008 0.001 HIS C 219 PHE 0.026 0.002 PHE B 395 TYR 0.014 0.001 TYR C 30 ARG 0.006 0.001 ARG A1243 *********************** 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 52 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1306 ASP cc_start: 0.7801 (p0) cc_final: 0.7418 (p0) REVERT: D 71 MET cc_start: 0.8200 (ttt) cc_final: 0.7757 (tpp) REVERT: C 70 MET cc_start: 0.6285 (mmp) cc_final: 0.5552 (mmp) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.2100 time to fit residues: 16.9627 Evaluate side-chains 41 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 1.223 ------------------------------------------------------------------------------- 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: 9.9990 chunk 63 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 62 optimal weight: 0.8980 chunk 93 optimal weight: 10.0000 chunk 110 optimal weight: 4.9990 chunk 69 optimal weight: 0.0030 chunk 67 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 44 optimal weight: 10.0000 overall best weight: 2.5794 ------------------------------------------------------------------------------- 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 440 HIS ** D 65 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: 0.6927 moved from start: 0.5319 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= 0.192 Angle : 0.575 6.680 13079 Z= 0.305 Chirality : 0.043 0.177 1473 Planarity : 0.004 0.045 1659 Dihedral : 4.983 20.882 1235 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 19.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.37 % Favored : 94.54 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % 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: -0.63 (0.25), residues: 1135 helix: 0.85 (0.25), residues: 443 sheet: -1.40 (0.41), residues: 131 loop : -1.20 (0.27), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 138 HIS 0.006 0.001 HIS C 219 PHE 0.023 0.002 PHE B 395 TYR 0.014 0.001 TYR C 30 ARG 0.005 0.001 ARG A1243 *********************** 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 : 1.083 Fit side-chains revert: symmetry clash REVERT: A 1306 ASP cc_start: 0.7760 (p0) cc_final: 0.7405 (p0) REVERT: C 70 MET cc_start: 0.6315 (mmp) cc_final: 0.5572 (mmp) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1996 time to fit residues: 15.8871 Evaluate side-chains 38 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 1.156 ------------------------------------------------------------------------------- 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: 6.9990 chunk 21 optimal weight: 20.0000 chunk 70 optimal weight: 9.9990 chunk 75 optimal weight: 8.9990 chunk 54 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 100 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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** ** A1304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.5741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9719 Z= 0.220 Angle : 0.597 7.365 13079 Z= 0.318 Chirality : 0.044 0.179 1473 Planarity : 0.004 0.044 1659 Dihedral : 5.091 22.709 1235 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 21.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.99 % Favored : 93.92 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % 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: -0.75 (0.25), residues: 1135 helix: 0.65 (0.25), residues: 436 sheet: -1.31 (0.42), residues: 128 loop : -1.19 (0.27), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 283 HIS 0.007 0.002 HIS C 219 PHE 0.028 0.002 PHE B 395 TYR 0.016 0.002 TYR C 30 ARG 0.006 0.001 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 51 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 1.254 Fit side-chains revert: symmetry clash REVERT: A 1306 ASP cc_start: 0.7826 (p0) cc_final: 0.7462 (p0) REVERT: C 70 MET cc_start: 0.6398 (mmp) cc_final: 0.5544 (mmp) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1919 time to fit residues: 15.4168 Evaluate side-chains 42 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.9990 chunk 106 optimal weight: 0.4980 chunk 62 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 chunk 102 optimal weight: 0.0770 chunk 67 optimal weight: 10.0000 chunk 109 optimal weight: 0.8980 overall best weight: 1.8942 ------------------------------------------------------------------------------- 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** ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.5819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9719 Z= 0.175 Angle : 0.585 11.492 13079 Z= 0.303 Chirality : 0.044 0.159 1473 Planarity : 0.003 0.042 1659 Dihedral : 4.868 20.819 1235 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.55 % Favored : 94.36 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % 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: -0.51 (0.25), residues: 1135 helix: 0.82 (0.25), residues: 444 sheet: -1.09 (0.42), residues: 129 loop : -1.07 (0.28), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 163 HIS 0.006 0.001 HIS C 219 PHE 0.023 0.001 PHE B 395 TYR 0.014 0.001 TYR B 478 ARG 0.006 0.001 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 51 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1306 ASP cc_start: 0.7849 (p0) cc_final: 0.7504 (p0) REVERT: C 70 MET cc_start: 0.6312 (mmp) cc_final: 0.5490 (mmp) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.2131 time to fit residues: 16.7513 Evaluate side-chains 39 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 75 optimal weight: 9.9990 chunk 114 optimal weight: 8.9990 chunk 105 optimal weight: 0.5980 chunk 91 optimal weight: 0.6980 chunk 9 optimal weight: 0.4980 chunk 70 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 391 GLN D 41 ASN ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.5777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 9719 Z= 0.156 Angle : 0.590 9.025 13079 Z= 0.299 Chirality : 0.044 0.149 1473 Planarity : 0.003 0.043 1659 Dihedral : 4.620 22.770 1235 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.76 % Favored : 95.15 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.26), residues: 1135 helix: 0.89 (0.25), residues: 450 sheet: -0.93 (0.43), residues: 129 loop : -1.07 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 163 HIS 0.006 0.001 HIS C 219 PHE 0.022 0.001 PHE B 395 TYR 0.016 0.001 TYR B 478 ARG 0.005 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 53 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 327 MET cc_start: 0.6529 (ppp) cc_final: 0.5504 (ppp) REVERT: A 1306 ASP cc_start: 0.7680 (p0) cc_final: 0.7337 (p0) REVERT: C 70 MET cc_start: 0.6105 (mmp) cc_final: 0.5302 (mmp) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.2121 time to fit residues: 17.1224 Evaluate side-chains 45 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 0.4980 chunk 84 optimal weight: 0.9990 chunk 13 optimal weight: 0.0970 chunk 25 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 391 GLN D 41 ASN ** D 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.025863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2474 r_free = 0.2474 target = 0.019763 restraints weight = 144092.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2494 r_free = 0.2494 target = 0.020235 restraints weight = 111200.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2509 r_free = 0.2509 target = 0.020598 restraints weight = 91411.583| |-----------------------------------------------------------------------------| r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.5902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 9719 Z= 0.157 Angle : 0.566 8.833 13079 Z= 0.290 Chirality : 0.043 0.153 1473 Planarity : 0.003 0.042 1659 Dihedral : 4.510 20.627 1235 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.85 % Favored : 95.07 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % 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: -0.30 (0.26), residues: 1135 helix: 1.02 (0.25), residues: 450 sheet: -0.89 (0.42), residues: 135 loop : -1.03 (0.28), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 163 HIS 0.006 0.001 HIS C 219 PHE 0.022 0.001 PHE B 395 TYR 0.016 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: 1604.27 seconds wall clock time: 30 minutes 22.71 seconds (1822.71 seconds total)