Starting phenix.real_space_refine on Tue May 13 00:31:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j5d_35985/05_2025/8j5d_35985.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j5d_35985/05_2025/8j5d_35985.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j5d_35985/05_2025/8j5d_35985.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j5d_35985/05_2025/8j5d_35985.map" model { file = "/net/cci-nas-00/data/ceres_data/8j5d_35985/05_2025/8j5d_35985.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j5d_35985/05_2025/8j5d_35985.cif" } resolution = 3.0 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= 0.084 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 39 5.16 5 C 6088 2.51 5 N 1599 2.21 5 O 1805 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 9531 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3340 Classifications: {'peptide': 422} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 398} Chain breaks: 1 Chain: "B" Number of atoms: 2356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2356 Classifications: {'peptide': 316} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 300} Chain: "D" Number of atoms: 1488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1488 Classifications: {'peptide': 191} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 182} Chain breaks: 1 Chain: "C" Number of atoms: 2347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2347 Classifications: {'peptide': 315} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 299} Time building chain proxies: 5.50, per 1000 atoms: 0.58 Number of scatterers: 9531 At special positions: 0 Unit cell: (70.62, 92.02, 146.59, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 39 16.00 O 1805 8.00 N 1599 7.00 C 6088 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.35 Conformation dependent library (CDL) restraints added in 1.2 seconds 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2288 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 9 sheets defined 47.0% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 125 through 139 Processing helix chain 'A' and resid 163 through 176 Processing helix chain 'A' and resid 202 through 212 Processing helix chain 'A' and resid 243 through 259 Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 287 through 291 Processing helix chain 'A' and resid 304 through 318 removed outlier: 4.452A pdb=" N SER A 310 " --> pdb=" O TYR A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 341 removed outlier: 3.530A pdb=" N THR A 341 " --> pdb=" O PRO A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 352 Processing helix chain 'A' and resid 353 through 382 Processing helix chain 'A' and resid 405 through 411 Processing helix chain 'A' and resid 421 through 433 removed outlier: 4.251A pdb=" N ILE A 425 " --> pdb=" O GLY A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 471 Processing helix chain 'A' and resid 484 through 497 Processing helix chain 'A' and resid 519 through 523 Processing helix chain 'A' and resid 524 through 539 Processing helix chain 'B' and resid 94 through 104 Processing helix chain 'B' and resid 119 through 128 removed outlier: 3.789A pdb=" N HIS B 128 " --> pdb=" O ALA B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 148 removed outlier: 3.634A pdb=" N ALA B 145 " --> pdb=" O PRO B 141 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASP B 146 " --> pdb=" O SER B 142 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU B 148 " --> pdb=" O LEU B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 190 removed outlier: 4.165A pdb=" N GLU B 188 " --> pdb=" O GLU B 184 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASN B 189 " --> pdb=" O ALA B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 215 Proline residue: B 207 - end of helix Processing helix chain 'B' and resid 220 through 222 No H-bonds generated for 'chain 'B' and resid 220 through 222' Processing helix chain 'B' and resid 228 through 244 removed outlier: 3.663A pdb=" N VAL B 232 " --> pdb=" O THR B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 270 Processing helix chain 'B' and resid 277 through 282 Processing helix chain 'B' and resid 283 through 299 removed outlier: 5.363A pdb=" N GLY B 292 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N THR B 293 " --> pdb=" O GLN B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 325 Processing helix chain 'B' and resid 362 through 366 Processing helix chain 'B' and resid 369 through 396 removed outlier: 4.590A pdb=" N VAL B 381 " --> pdb=" O GLU B 377 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLU B 382 " --> pdb=" O ALA B 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 111 Processing helix chain 'D' and resid 136 through 146 removed outlier: 3.773A pdb=" N THR D 140 " --> pdb=" O ASP D 136 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS D 142 " --> pdb=" O GLY D 138 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N MET D 143 " --> pdb=" O ASP D 139 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU D 146 " --> pdb=" O LYS D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 170 removed outlier: 4.080A pdb=" N LEU D 167 " --> pdb=" O PRO D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 216 removed outlier: 3.642A pdb=" N PHE D 215 " --> pdb=" O SER D 212 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE D 216 " --> pdb=" O SER D 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 212 through 216' Processing helix chain 'D' and resid 217 through 225 Processing helix chain 'D' and resid 267 through 280 Processing helix chain 'C' and resid 94 through 104 Processing helix chain 'C' and resid 118 through 127 Processing helix chain 'C' and resid 140 through 148 removed outlier: 4.029A pdb=" N ASP C 146 " --> pdb=" O SER C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 190 Processing helix chain 'C' and resid 201 through 217 Proline residue: C 207 - end of helix Processing helix chain 'C' and resid 220 through 224 removed outlier: 3.883A pdb=" N LEU C 224 " --> pdb=" O PRO C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 243 removed outlier: 3.636A pdb=" N VAL C 232 " --> pdb=" O THR C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 270 Processing helix chain 'C' and resid 277 through 289 Processing helix chain 'C' and resid 291 through 299 Processing helix chain 'C' and resid 306 through 325 Processing helix chain 'C' and resid 362 through 366 Processing helix chain 'C' and resid 369 through 395 Processing sheet with id=AA1, first strand: chain 'A' and resid 108 through 111 removed outlier: 6.273A pdb=" N VAL A 108 " --> pdb=" O GLY A 143 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N MET A 145 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL A 110 " --> pdb=" O MET A 145 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N ASP A 147 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE A 144 " --> pdb=" O GLN A 181 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N VAL A 183 " --> pdb=" O ILE A 144 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE A 146 " --> pdb=" O VAL A 183 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N SER A 185 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL A 148 " --> pdb=" O SER A 185 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N VAL A 180 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU A 269 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL A 268 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N SER A 390 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE A 270 " --> pdb=" O SER A 390 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N LYS A 392 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N VAL A 272 " --> pdb=" O LYS A 392 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N ALA A 475 " --> pdb=" O ALA A 434 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N PHE A 436 " --> pdb=" O ALA A 475 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N GLU A 477 " --> pdb=" O PHE A 436 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N PHE A 438 " --> pdb=" O GLU A 477 " (cutoff:3.500A) removed outlier: 9.100A pdb=" N THR A 514 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLY A 476 " --> pdb=" O THR A 514 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 216 through 218 removed outlier: 3.737A pdb=" N TYR A 217 " --> pdb=" O ASN A 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 134 through 138 removed outlier: 6.543A pdb=" N SER B 109 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ARG B 136 " --> pdb=" O SER B 109 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU B 111 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N PHE B 138 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU B 113 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N TYR B 83 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR B 110 " --> pdb=" O TYR B 83 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL B 154 " --> pdb=" O HIS B 196 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ILE B 195 " --> pdb=" O PHE B 225 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL B 227 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE B 197 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ARG B 349 " --> pdb=" O VAL B 360 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N VAL B 360 " --> pdb=" O ARG B 349 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LYS B 351 " --> pdb=" O GLU B 358 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 254 through 256 Processing sheet with id=AA5, first strand: chain 'D' and resid 76 through 82 removed outlier: 6.395A pdb=" N SER D 152 " --> pdb=" O ALA D 123 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ALA D 123 " --> pdb=" O SER D 152 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL D 154 " --> pdb=" O LYS D 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 247 through 251 removed outlier: 6.582A pdb=" N ARG D 88 " --> pdb=" O HIS D 100 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 184 through 186 Processing sheet with id=AA8, first strand: chain 'C' and resid 134 through 139 removed outlier: 6.455A pdb=" N SER C 109 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N ARG C 136 " --> pdb=" O SER C 109 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU C 111 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N PHE C 138 " --> pdb=" O LEU C 111 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU C 113 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N TYR C 83 " --> pdb=" O SER C 109 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N LEU C 111 " --> pdb=" O TYR C 83 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL C 85 " --> pdb=" O LEU C 111 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N LEU C 113 " --> pdb=" O VAL C 85 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL C 87 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ASP C 115 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N ILE C 195 " --> pdb=" O PHE C 225 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL C 227 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE C 197 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N ARG C 349 " --> pdb=" O VAL C 360 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N VAL C 360 " --> pdb=" O ARG C 349 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LYS C 351 " --> pdb=" O GLU C 358 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 254 through 256 451 hydrogen bonds defined for protein. 1281 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: 2.68 Time building geometry restraints manager: 2.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3109 1.35 - 1.47: 2180 1.47 - 1.59: 4374 1.59 - 1.71: 0 1.71 - 1.83: 64 Bond restraints: 9727 Sorted by residual: bond pdb=" C MET A 111 " pdb=" N MET A 112 " ideal model delta sigma weight residual 1.328 1.360 -0.032 1.44e-02 4.82e+03 4.79e+00 bond pdb=" CG PRO B 207 " pdb=" CD PRO B 207 " ideal model delta sigma weight residual 1.503 1.447 0.056 3.40e-02 8.65e+02 2.73e+00 bond pdb=" C MET A 112 " pdb=" N PRO A 113 " ideal model delta sigma weight residual 1.331 1.350 -0.019 1.21e-02 6.83e+03 2.36e+00 bond pdb=" C CYS A 189 " pdb=" N GLY A 190 " ideal model delta sigma weight residual 1.335 1.324 0.011 7.50e-03 1.78e+04 2.07e+00 bond pdb=" CB ASP B 342 " pdb=" CG ASP B 342 " ideal model delta sigma weight residual 1.516 1.552 -0.036 2.50e-02 1.60e+03 2.04e+00 ... (remaining 9722 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.00: 13084 3.00 - 6.00: 93 6.00 - 9.01: 7 9.01 - 12.01: 3 12.01 - 15.01: 4 Bond angle restraints: 13191 Sorted by residual: angle pdb=" N PRO B 207 " pdb=" CD PRO B 207 " pdb=" CG PRO B 207 " ideal model delta sigma weight residual 103.20 95.04 8.16 1.50e+00 4.44e-01 2.96e+01 angle pdb=" C SER A 196 " pdb=" CA SER A 196 " pdb=" CB SER A 196 " ideal model delta sigma weight residual 116.54 110.70 5.84 1.15e+00 7.56e-01 2.58e+01 angle pdb=" CA PRO B 207 " pdb=" N PRO B 207 " pdb=" CD PRO B 207 " ideal model delta sigma weight residual 112.00 104.99 7.01 1.40e+00 5.10e-01 2.51e+01 angle pdb=" CB MET A 112 " pdb=" CG MET A 112 " pdb=" SD MET A 112 " ideal model delta sigma weight residual 112.70 127.71 -15.01 3.00e+00 1.11e-01 2.50e+01 angle pdb=" CB PRO B 207 " pdb=" CG PRO B 207 " pdb=" CD PRO B 207 " ideal model delta sigma weight residual 106.10 92.52 13.58 3.20e+00 9.77e-02 1.80e+01 ... (remaining 13186 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.19: 5185 17.19 - 34.38: 454 34.38 - 51.57: 140 51.57 - 68.76: 43 68.76 - 85.96: 12 Dihedral angle restraints: 5834 sinusoidal: 2270 harmonic: 3564 Sorted by residual: dihedral pdb=" CA ALA D 198 " pdb=" C ALA D 198 " pdb=" N SER D 199 " pdb=" CA SER D 199 " ideal model delta harmonic sigma weight residual 180.00 159.94 20.06 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA ARG D 179 " pdb=" C ARG D 179 " pdb=" N GLY D 180 " pdb=" CA GLY D 180 " ideal model delta harmonic sigma weight residual 180.00 163.48 16.52 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA SER D 194 " pdb=" C SER D 194 " pdb=" N ASN D 195 " pdb=" CA ASN D 195 " ideal model delta harmonic sigma weight residual 180.00 163.49 16.51 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 5831 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1052 0.039 - 0.077: 308 0.077 - 0.116: 122 0.116 - 0.154: 15 0.154 - 0.193: 4 Chirality restraints: 1501 Sorted by residual: chirality pdb=" CB VAL B 286 " pdb=" CA VAL B 286 " pdb=" CG1 VAL B 286 " pdb=" CG2 VAL B 286 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.27e-01 chirality pdb=" CB THR B 285 " pdb=" CA THR B 285 " pdb=" OG1 THR B 285 " pdb=" CG2 THR B 285 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.56e-01 chirality pdb=" CB VAL B 391 " pdb=" CA VAL B 391 " pdb=" CG1 VAL B 391 " pdb=" CG2 VAL B 391 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.16 2.00e-01 2.50e+01 6.77e-01 ... (remaining 1498 not shown) Planarity restraints: 1699 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 283 " -0.020 2.00e-02 2.50e+03 4.01e-02 1.61e+01 pdb=" C GLU B 283 " 0.069 2.00e-02 2.50e+03 pdb=" O GLU B 283 " -0.026 2.00e-02 2.50e+03 pdb=" N LEU B 284 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE D 266 " -0.043 5.00e-02 4.00e+02 6.60e-02 6.96e+00 pdb=" N PRO D 267 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO D 267 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 267 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 200 " 0.034 5.00e-02 4.00e+02 5.18e-02 4.29e+00 pdb=" N PRO C 201 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO C 201 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 201 " 0.026 5.00e-02 4.00e+02 ... (remaining 1696 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 254 2.69 - 3.25: 9598 3.25 - 3.80: 15723 3.80 - 4.35: 21185 4.35 - 4.90: 34873 Nonbonded interactions: 81633 Sorted by model distance: nonbonded pdb=" OH TYR D 177 " pdb=" OD1 ASN D 225 " model vdw 2.144 3.040 nonbonded pdb=" OE1 GLN A 220 " pdb=" OH TYR A 303 " model vdw 2.153 3.040 nonbonded pdb=" OH TYR A 400 " pdb=" OE1 GLN A 462 " model vdw 2.156 3.040 nonbonded pdb=" OH TYR D 77 " pdb=" OD2 ASP D 118 " model vdw 2.162 3.040 nonbonded pdb=" OE1 GLU A 372 " pdb=" NE2 HIS A 432 " model vdw 2.168 3.120 ... (remaining 81628 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and resid 81 through 395) selection = chain 'C' } 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 individual isotropic 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: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.520 Find NCS groups from input model: 0.200 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:12.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 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 0.058 9727 Z= 0.151 Angle : 0.709 15.012 13191 Z= 0.365 Chirality : 0.043 0.193 1501 Planarity : 0.005 0.066 1699 Dihedral : 15.673 85.956 3546 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.43 % Allowed : 20.51 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.08 % 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: 0.07 (0.24), residues: 1232 helix: 1.35 (0.22), residues: 513 sheet: -0.08 (0.45), residues: 142 loop : -1.12 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 163 HIS 0.005 0.001 HIS A 370 PHE 0.010 0.001 PHE A 359 TYR 0.033 0.002 TYR B 219 ARG 0.015 0.001 ARG A 126 Details of bonding type rmsd hydrogen bonds : bond 0.05900 ( 451) hydrogen bonds : angle 5.22108 ( 1281) covalent geometry : bond 0.00332 ( 9727) covalent geometry : angle 0.70863 (13191) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 143 MET cc_start: 0.7255 (ttt) cc_final: 0.6810 (ttp) outliers start: 25 outliers final: 16 residues processed: 142 average time/residue: 0.9104 time to fit residues: 141.6852 Evaluate side-chains 133 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain B residue 258 HIS Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 190 ASN Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 306 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 96 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN A 271 GLN A 352 ASN A 397 HIS A 427 GLN D 205 ASN C 128 HIS ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.173025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.134695 restraints weight = 11587.486| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.51 r_work: 0.3576 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.179 9727 Z= 0.289 Angle : 0.740 10.299 13191 Z= 0.376 Chirality : 0.048 0.176 1501 Planarity : 0.006 0.073 1699 Dihedral : 6.115 50.672 1340 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 5.54 % Allowed : 17.69 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.08 % 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: -0.67 (0.23), residues: 1232 helix: 0.67 (0.22), residues: 509 sheet: -0.85 (0.41), residues: 152 loop : -1.33 (0.25), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 398 HIS 0.008 0.001 HIS A 405 PHE 0.024 0.002 PHE D 266 TYR 0.030 0.003 TYR A 363 ARG 0.005 0.001 ARG B 234 Details of bonding type rmsd hydrogen bonds : bond 0.04652 ( 451) hydrogen bonds : angle 5.46201 ( 1281) covalent geometry : bond 0.00704 ( 9727) covalent geometry : angle 0.73955 (13191) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 120 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 TYR cc_start: 0.6875 (OUTLIER) cc_final: 0.5108 (m-80) REVERT: A 304 ASP cc_start: 0.6402 (OUTLIER) cc_final: 0.6130 (m-30) REVERT: B 180 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7250 (mtmm) REVERT: B 337 GLU cc_start: 0.5872 (OUTLIER) cc_final: 0.5311 (pt0) REVERT: B 372 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7391 (mt-10) REVERT: C 137 ASP cc_start: 0.6911 (p0) cc_final: 0.6693 (p0) REVERT: C 362 GLU cc_start: 0.6690 (OUTLIER) cc_final: 0.6176 (pm20) outliers start: 57 outliers final: 24 residues processed: 164 average time/residue: 0.9950 time to fit residues: 177.4296 Evaluate side-chains 141 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 111 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 443 MET Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 536 LYS Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 269 LYS Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain C residue 362 GLU Chi-restraints excluded: chain C residue 379 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 88 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 95 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 27 optimal weight: 0.0970 chunk 83 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 ASN A 427 GLN B 189 ASN C 134 GLN ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.178627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.140437 restraints weight = 11345.507| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 2.57 r_work: 0.3676 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 9727 Z= 0.137 Angle : 0.602 10.454 13191 Z= 0.304 Chirality : 0.043 0.187 1501 Planarity : 0.005 0.070 1699 Dihedral : 4.981 38.602 1326 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 4.47 % Allowed : 20.02 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.08 % 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: -0.16 (0.24), residues: 1232 helix: 1.21 (0.23), residues: 512 sheet: -0.60 (0.43), residues: 143 loop : -1.19 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 163 HIS 0.005 0.001 HIS A 370 PHE 0.012 0.001 PHE D 137 TYR 0.021 0.001 TYR A 363 ARG 0.006 0.000 ARG A 126 Details of bonding type rmsd hydrogen bonds : bond 0.03805 ( 451) hydrogen bonds : angle 4.98876 ( 1281) covalent geometry : bond 0.00324 ( 9727) covalent geometry : angle 0.60210 (13191) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 129 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.5034 (ppp) cc_final: 0.4705 (ppp) REVERT: A 129 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.7855 (mmp) REVERT: A 175 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7700 (ptmm) REVERT: A 285 TYR cc_start: 0.6933 (OUTLIER) cc_final: 0.5169 (m-80) REVERT: B 337 GLU cc_start: 0.6295 (OUTLIER) cc_final: 0.5577 (pt0) REVERT: B 372 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7091 (mt-10) REVERT: C 137 ASP cc_start: 0.6899 (p0) cc_final: 0.6599 (p0) REVERT: C 252 VAL cc_start: 0.7034 (OUTLIER) cc_final: 0.6781 (m) REVERT: C 263 ILE cc_start: 0.7962 (OUTLIER) cc_final: 0.7550 (mm) REVERT: C 379 LEU cc_start: 0.6676 (OUTLIER) cc_final: 0.6475 (tt) outliers start: 46 outliers final: 14 residues processed: 164 average time/residue: 0.9799 time to fit residues: 174.9511 Evaluate side-chains 139 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 536 LYS Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain B residue 258 HIS Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 379 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 37 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 69 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 ASN A 427 GLN A 448 GLN ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.175471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.137612 restraints weight = 11375.805| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.51 r_work: 0.3610 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 9727 Z= 0.181 Angle : 0.646 10.576 13191 Z= 0.325 Chirality : 0.044 0.179 1501 Planarity : 0.005 0.070 1699 Dihedral : 4.858 38.790 1322 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 5.05 % Allowed : 20.12 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.08 % 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 (0.24), residues: 1232 helix: 1.11 (0.23), residues: 513 sheet: -0.71 (0.42), residues: 144 loop : -1.27 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 398 HIS 0.004 0.001 HIS A 405 PHE 0.018 0.002 PHE C 335 TYR 0.025 0.002 TYR A 363 ARG 0.008 0.001 ARG A 126 Details of bonding type rmsd hydrogen bonds : bond 0.03972 ( 451) hydrogen bonds : angle 5.11672 ( 1281) covalent geometry : bond 0.00437 ( 9727) covalent geometry : angle 0.64610 (13191) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 125 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.4780 (OUTLIER) cc_final: 0.4493 (ppp) REVERT: A 129 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7981 (mmp) REVERT: A 175 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7691 (ptmm) REVERT: A 285 TYR cc_start: 0.7078 (OUTLIER) cc_final: 0.5302 (m-80) REVERT: A 304 ASP cc_start: 0.6137 (OUTLIER) cc_final: 0.4680 (m-30) REVERT: B 337 GLU cc_start: 0.5928 (OUTLIER) cc_final: 0.5223 (pt0) REVERT: B 372 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7212 (mt-10) REVERT: D 143 MET cc_start: 0.7248 (ttt) cc_final: 0.6758 (ttp) REVERT: C 137 ASP cc_start: 0.6840 (p0) cc_final: 0.6492 (p0) REVERT: C 252 VAL cc_start: 0.7068 (OUTLIER) cc_final: 0.6783 (m) REVERT: C 263 ILE cc_start: 0.8042 (OUTLIER) cc_final: 0.7631 (mm) outliers start: 52 outliers final: 22 residues processed: 163 average time/residue: 0.9807 time to fit residues: 173.7223 Evaluate side-chains 148 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 117 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 258 HIS Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 348 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 42 optimal weight: 3.9990 chunk 111 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 104 optimal weight: 0.5980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 ASN A 427 GLN ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.175282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.137330 restraints weight = 11425.566| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.49 r_work: 0.3617 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 9727 Z= 0.186 Angle : 0.666 12.089 13191 Z= 0.334 Chirality : 0.045 0.178 1501 Planarity : 0.005 0.070 1699 Dihedral : 4.889 39.081 1322 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 5.73 % Allowed : 19.63 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.08 % 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: -0.35 (0.24), residues: 1232 helix: 1.06 (0.23), residues: 513 sheet: -0.78 (0.42), residues: 143 loop : -1.28 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 398 HIS 0.004 0.001 HIS A 405 PHE 0.018 0.002 PHE C 335 TYR 0.024 0.002 TYR A 363 ARG 0.008 0.001 ARG A 126 Details of bonding type rmsd hydrogen bonds : bond 0.03984 ( 451) hydrogen bonds : angle 5.16404 ( 1281) covalent geometry : bond 0.00452 ( 9727) covalent geometry : angle 0.66586 (13191) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 126 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 LYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7644 (ptmm) REVERT: A 285 TYR cc_start: 0.7214 (OUTLIER) cc_final: 0.5342 (m-80) REVERT: B 216 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.8200 (mmmt) REVERT: B 337 GLU cc_start: 0.5777 (OUTLIER) cc_final: 0.5102 (pt0) REVERT: B 372 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7148 (mt-10) REVERT: D 143 MET cc_start: 0.7320 (ttt) cc_final: 0.6537 (ttp) REVERT: C 137 ASP cc_start: 0.6795 (p0) cc_final: 0.6446 (p0) REVERT: C 252 VAL cc_start: 0.7112 (OUTLIER) cc_final: 0.6832 (m) REVERT: C 263 ILE cc_start: 0.8093 (OUTLIER) cc_final: 0.7711 (mm) REVERT: C 379 LEU cc_start: 0.6811 (OUTLIER) cc_final: 0.6589 (tt) outliers start: 59 outliers final: 24 residues processed: 168 average time/residue: 0.9454 time to fit residues: 173.2101 Evaluate side-chains 150 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 118 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 258 HIS Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain C residue 379 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 12 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 101 optimal weight: 8.9990 chunk 60 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 27 optimal weight: 0.0570 chunk 117 optimal weight: 0.9990 overall best weight: 0.7704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 427 GLN ** C 196 HIS ** 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 = 0.4196 r_free = 0.4196 target = 0.177569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.139850 restraints weight = 11334.281| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 2.51 r_work: 0.3637 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 9727 Z= 0.137 Angle : 0.649 14.424 13191 Z= 0.322 Chirality : 0.043 0.183 1501 Planarity : 0.005 0.070 1699 Dihedral : 4.672 39.202 1321 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 4.76 % Allowed : 20.89 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.08 % 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: -0.14 (0.24), residues: 1232 helix: 1.30 (0.23), residues: 513 sheet: -0.67 (0.43), residues: 143 loop : -1.24 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 163 HIS 0.005 0.001 HIS A 370 PHE 0.012 0.001 PHE C 335 TYR 0.021 0.001 TYR A 363 ARG 0.010 0.001 ARG A 126 Details of bonding type rmsd hydrogen bonds : bond 0.03727 ( 451) hydrogen bonds : angle 4.98045 ( 1281) covalent geometry : bond 0.00323 ( 9727) covalent geometry : angle 0.64905 (13191) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 131 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.4603 (ppp) cc_final: 0.3681 (ppp) REVERT: A 129 MET cc_start: 0.7598 (mmt) cc_final: 0.7188 (mmp) REVERT: A 184 MET cc_start: 0.7820 (OUTLIER) cc_final: 0.7158 (tpp) REVERT: A 227 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7621 (mm-30) REVERT: A 285 TYR cc_start: 0.7136 (OUTLIER) cc_final: 0.5437 (m-80) REVERT: A 304 ASP cc_start: 0.6048 (OUTLIER) cc_final: 0.4637 (m-30) REVERT: B 309 MET cc_start: 0.7016 (tpp) cc_final: 0.6746 (tpp) REVERT: B 337 GLU cc_start: 0.6096 (OUTLIER) cc_final: 0.5372 (pt0) REVERT: B 372 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7025 (mt-10) REVERT: C 137 ASP cc_start: 0.6779 (p0) cc_final: 0.6410 (p0) REVERT: C 252 VAL cc_start: 0.7048 (OUTLIER) cc_final: 0.6742 (m) REVERT: C 263 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7668 (mm) REVERT: C 362 GLU cc_start: 0.6513 (OUTLIER) cc_final: 0.6136 (pm20) REVERT: C 379 LEU cc_start: 0.6675 (OUTLIER) cc_final: 0.6268 (tt) outliers start: 49 outliers final: 19 residues processed: 167 average time/residue: 0.9224 time to fit residues: 168.8173 Evaluate side-chains 146 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 230 SER Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 246 LYS Chi-restraints excluded: chain B residue 258 HIS Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 362 GLU Chi-restraints excluded: chain C residue 379 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 77 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 89 optimal weight: 0.0980 chunk 33 optimal weight: 3.9990 chunk 45 optimal weight: 0.0370 chunk 60 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 46 optimal weight: 5.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 427 GLN A 437 ASN C 173 ASN C 196 HIS C 236 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.179075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.141503 restraints weight = 11415.718| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 2.51 r_work: 0.3658 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9727 Z= 0.128 Angle : 0.652 13.084 13191 Z= 0.321 Chirality : 0.043 0.185 1501 Planarity : 0.005 0.069 1699 Dihedral : 4.605 39.131 1321 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 4.66 % Allowed : 21.77 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.08 % 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: -0.04 (0.24), residues: 1232 helix: 1.40 (0.23), residues: 511 sheet: -0.59 (0.44), residues: 143 loop : -1.20 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 163 HIS 0.006 0.001 HIS A 370 PHE 0.036 0.001 PHE D 137 TYR 0.020 0.001 TYR B 371 ARG 0.012 0.000 ARG A 126 Details of bonding type rmsd hydrogen bonds : bond 0.03636 ( 451) hydrogen bonds : angle 4.91132 ( 1281) covalent geometry : bond 0.00299 ( 9727) covalent geometry : angle 0.65249 (13191) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 125 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.4440 (ppp) cc_final: 0.3461 (ppp) REVERT: A 184 MET cc_start: 0.7747 (OUTLIER) cc_final: 0.7053 (tpp) REVERT: A 227 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7595 (mm-30) REVERT: A 285 TYR cc_start: 0.7125 (OUTLIER) cc_final: 0.5527 (m-80) REVERT: A 304 ASP cc_start: 0.5989 (OUTLIER) cc_final: 0.4571 (m-30) REVERT: B 231 ASP cc_start: 0.7932 (OUTLIER) cc_final: 0.7635 (t0) REVERT: B 337 GLU cc_start: 0.6051 (OUTLIER) cc_final: 0.5263 (pt0) REVERT: B 372 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.6977 (mt-10) REVERT: C 137 ASP cc_start: 0.6780 (p0) cc_final: 0.6400 (p0) REVERT: C 263 ILE cc_start: 0.7947 (OUTLIER) cc_final: 0.7551 (mm) REVERT: C 362 GLU cc_start: 0.6513 (OUTLIER) cc_final: 0.6139 (pm20) outliers start: 48 outliers final: 19 residues processed: 159 average time/residue: 0.9031 time to fit residues: 157.6669 Evaluate side-chains 146 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 246 LYS Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain C residue 362 GLU Chi-restraints excluded: chain C residue 379 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 3 optimal weight: 0.4980 chunk 13 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 5 optimal weight: 0.1980 chunk 39 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 ASN A 427 GLN A 437 ASN B 128 HIS ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.176434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.139047 restraints weight = 11539.065| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 2.48 r_work: 0.3628 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 9727 Z= 0.175 Angle : 0.696 15.522 13191 Z= 0.344 Chirality : 0.045 0.175 1501 Planarity : 0.005 0.069 1699 Dihedral : 4.697 39.148 1320 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 4.37 % Allowed : 22.74 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.24), residues: 1232 helix: 1.22 (0.23), residues: 512 sheet: -0.62 (0.43), residues: 143 loop : -1.22 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 163 HIS 0.004 0.001 HIS A 405 PHE 0.016 0.002 PHE C 335 TYR 0.024 0.002 TYR A 363 ARG 0.010 0.001 ARG A 126 Details of bonding type rmsd hydrogen bonds : bond 0.03864 ( 451) hydrogen bonds : angle 5.08337 ( 1281) covalent geometry : bond 0.00425 ( 9727) covalent geometry : angle 0.69641 (13191) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 129 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ARG cc_start: 0.5821 (OUTLIER) cc_final: 0.4996 (ppt170) REVERT: A 129 MET cc_start: 0.8481 (tpp) cc_final: 0.8203 (mmt) REVERT: A 184 MET cc_start: 0.7806 (OUTLIER) cc_final: 0.7111 (tpp) REVERT: A 227 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7547 (mm-30) REVERT: A 285 TYR cc_start: 0.7180 (OUTLIER) cc_final: 0.5464 (m-80) REVERT: B 231 ASP cc_start: 0.7959 (OUTLIER) cc_final: 0.7681 (t0) REVERT: B 337 GLU cc_start: 0.6001 (OUTLIER) cc_final: 0.5245 (pt0) REVERT: B 372 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7089 (mt-10) REVERT: C 137 ASP cc_start: 0.6737 (p0) cc_final: 0.6350 (p0) REVERT: C 263 ILE cc_start: 0.8064 (OUTLIER) cc_final: 0.7717 (mm) outliers start: 45 outliers final: 24 residues processed: 161 average time/residue: 0.9460 time to fit residues: 166.3453 Evaluate side-chains 152 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 121 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 230 SER Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 443 MET Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 246 LYS Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain C residue 379 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 64 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 100 optimal weight: 8.9990 chunk 16 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 121 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 30 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 427 GLN ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.177785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.140683 restraints weight = 11364.384| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 2.46 r_work: 0.3645 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 9727 Z= 0.147 Angle : 0.674 15.105 13191 Z= 0.332 Chirality : 0.044 0.189 1501 Planarity : 0.005 0.069 1699 Dihedral : 4.632 39.417 1320 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.69 % Allowed : 23.32 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.08 % 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: -0.14 (0.24), residues: 1232 helix: 1.27 (0.23), residues: 511 sheet: -0.59 (0.44), residues: 143 loop : -1.22 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 163 HIS 0.005 0.001 HIS A 370 PHE 0.030 0.001 PHE D 137 TYR 0.021 0.002 TYR A 363 ARG 0.012 0.001 ARG A 126 Details of bonding type rmsd hydrogen bonds : bond 0.03750 ( 451) hydrogen bonds : angle 5.00038 ( 1281) covalent geometry : bond 0.00352 ( 9727) covalent geometry : angle 0.67427 (13191) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 129 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.4545 (ppp) cc_final: 0.3749 (ppp) REVERT: A 184 MET cc_start: 0.7784 (OUTLIER) cc_final: 0.7084 (tpp) REVERT: A 227 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7560 (mm-30) REVERT: A 285 TYR cc_start: 0.7278 (OUTLIER) cc_final: 0.5597 (m-80) REVERT: B 231 ASP cc_start: 0.7976 (OUTLIER) cc_final: 0.7682 (t0) REVERT: B 337 GLU cc_start: 0.6050 (OUTLIER) cc_final: 0.5251 (pt0) REVERT: B 372 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7015 (mt-10) REVERT: C 137 ASP cc_start: 0.6645 (p0) cc_final: 0.6276 (p0) REVERT: C 263 ILE cc_start: 0.8007 (OUTLIER) cc_final: 0.7657 (mm) outliers start: 38 outliers final: 25 residues processed: 157 average time/residue: 0.8456 time to fit residues: 146.3540 Evaluate side-chains 150 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 119 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 230 SER Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain C residue 379 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 113 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 40 optimal weight: 0.0870 chunk 31 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 70 optimal weight: 5.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 ASN A 427 GLN ** C 196 HIS ** 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 = 0.4266 r_free = 0.4266 target = 0.181297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.143702 restraints weight = 11396.504| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 2.55 r_work: 0.3717 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 9727 Z= 0.130 Angle : 0.661 14.601 13191 Z= 0.327 Chirality : 0.043 0.188 1501 Planarity : 0.005 0.069 1699 Dihedral : 4.523 39.456 1320 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.40 % Allowed : 23.71 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.08 % 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: -0.04 (0.24), residues: 1232 helix: 1.34 (0.22), residues: 512 sheet: -0.55 (0.44), residues: 143 loop : -1.15 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 163 HIS 0.005 0.001 HIS A 370 PHE 0.011 0.001 PHE C 335 TYR 0.021 0.001 TYR A 363 ARG 0.013 0.001 ARG A 126 Details of bonding type rmsd hydrogen bonds : bond 0.03578 ( 451) hydrogen bonds : angle 4.89838 ( 1281) covalent geometry : bond 0.00303 ( 9727) covalent geometry : angle 0.66127 (13191) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 128 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.4480 (ppp) cc_final: 0.3689 (ppp) REVERT: A 184 MET cc_start: 0.7749 (OUTLIER) cc_final: 0.7056 (tpp) REVERT: A 227 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7610 (mm-30) REVERT: B 231 ASP cc_start: 0.7858 (OUTLIER) cc_final: 0.7557 (t0) REVERT: B 337 GLU cc_start: 0.6071 (OUTLIER) cc_final: 0.5318 (pt0) REVERT: B 372 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.6907 (mt-10) REVERT: D 125 ASP cc_start: 0.5350 (p0) cc_final: 0.5049 (p0) REVERT: C 137 ASP cc_start: 0.6795 (p0) cc_final: 0.6431 (p0) REVERT: C 263 ILE cc_start: 0.7931 (OUTLIER) cc_final: 0.7559 (mm) outliers start: 35 outliers final: 24 residues processed: 156 average time/residue: 0.8212 time to fit residues: 141.6352 Evaluate side-chains 154 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 230 SER Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain C residue 379 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 61 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 78 optimal weight: 7.9990 chunk 9 optimal weight: 0.7980 chunk 34 optimal weight: 7.9990 chunk 70 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 ASN A 427 GLN ** C 196 HIS ** 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 = 0.4239 r_free = 0.4239 target = 0.178495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.140678 restraints weight = 11435.426| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 2.57 r_work: 0.3675 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 9727 Z= 0.174 Angle : 0.686 13.708 13191 Z= 0.341 Chirality : 0.045 0.181 1501 Planarity : 0.005 0.068 1699 Dihedral : 4.665 39.600 1320 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.40 % Allowed : 23.71 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.24), residues: 1232 helix: 1.19 (0.23), residues: 512 sheet: -0.62 (0.43), residues: 143 loop : -1.21 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 163 HIS 0.004 0.001 HIS A 405 PHE 0.027 0.002 PHE B 316 TYR 0.025 0.002 TYR C 114 ARG 0.013 0.001 ARG A 126 Details of bonding type rmsd hydrogen bonds : bond 0.03832 ( 451) hydrogen bonds : angle 5.07641 ( 1281) covalent geometry : bond 0.00423 ( 9727) covalent geometry : angle 0.68645 (13191) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5693.12 seconds wall clock time: 99 minutes 8.91 seconds (5948.91 seconds total)