Starting phenix.real_space_refine on Fri Nov 15 19:41:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5d_35985/11_2024/8j5d_35985.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5d_35985/11_2024/8j5d_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5d_35985/11_2024/8j5d_35985.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5d_35985/11_2024/8j5d_35985.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5d_35985/11_2024/8j5d_35985.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5d_35985/11_2024/8j5d_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-5513/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: 5.67, per 1000 atoms: 0.59 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: 2.64 Conformation dependent library (CDL) restraints added in 1.1 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: 1.15 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: 2.78 Time building geometry restraints manager: 3.00 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: 0.860 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: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 24.260 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.510 ------------------------------------------------------------------------------- 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= 0.218 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 *********************** 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 : 1.148 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: 1.0183 time to fit residues: 158.2820 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 : 1.262 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 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= 0.464 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 *********************** 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 : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 TYR cc_start: 0.6900 (OUTLIER) cc_final: 0.5289 (m-80) REVERT: A 304 ASP cc_start: 0.6700 (OUTLIER) cc_final: 0.6446 (m-30) REVERT: B 180 LYS cc_start: 0.7834 (OUTLIER) cc_final: 0.7225 (mtmm) REVERT: B 337 GLU cc_start: 0.5962 (OUTLIER) cc_final: 0.5406 (pt0) REVERT: B 372 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7423 (mt-10) REVERT: C 362 GLU cc_start: 0.6572 (OUTLIER) cc_final: 0.5998 (pm20) outliers start: 57 outliers final: 24 residues processed: 164 average time/residue: 1.0391 time to fit residues: 185.2718 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 : 1.086 ------------------------------------------------------------------------------- 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 62 optimal weight: 0.7980 chunk 34 optimal weight: 8.9990 chunk 92 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 chunk 110 optimal weight: 0.7980 chunk 38 optimal weight: 9.9990 chunk 89 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 9727 Z= 0.220 Angle : 0.605 10.479 13191 Z= 0.306 Chirality : 0.043 0.178 1501 Planarity : 0.005 0.070 1699 Dihedral : 4.996 37.502 1326 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 4.66 % Allowed : 20.02 % Favored : 75.32 % 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: -0.61 (0.43), residues: 143 loop : -1.21 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 398 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 0.006 0.000 ARG A 126 *********************** 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 179 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 131 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.5244 (ppp) cc_final: 0.4972 (ppp) REVERT: A 129 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.7968 (mmp) REVERT: A 175 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7599 (ptmm) REVERT: A 285 TYR cc_start: 0.6936 (OUTLIER) cc_final: 0.5447 (m-80) REVERT: B 207 PRO cc_start: 0.7702 (Cg_endo) cc_final: 0.7493 (Cg_exo) REVERT: B 337 GLU cc_start: 0.6325 (OUTLIER) cc_final: 0.5603 (pt0) REVERT: B 372 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7167 (mt-10) REVERT: C 252 VAL cc_start: 0.7102 (OUTLIER) cc_final: 0.6850 (m) REVERT: C 263 ILE cc_start: 0.7980 (OUTLIER) cc_final: 0.7581 (mm) outliers start: 48 outliers final: 16 residues processed: 168 average time/residue: 1.0295 time to fit residues: 188.0134 Evaluate side-chains 143 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 1.129 ------------------------------------------------------------------------------- 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 170 ASP 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 348 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 12 optimal weight: 0.0980 chunk 53 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 118 optimal weight: 4.9990 chunk 106 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.1418 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= 0.255 Angle : 0.633 11.842 13191 Z= 0.318 Chirality : 0.044 0.178 1501 Planarity : 0.005 0.070 1699 Dihedral : 4.786 37.327 1322 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 5.05 % Allowed : 19.92 % Favored : 75.02 % 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: -0.20 (0.24), residues: 1232 helix: 1.19 (0.23), residues: 513 sheet: -0.63 (0.42), residues: 143 loop : -1.23 (0.26), residues: 576 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 0.016 0.002 PHE C 335 TYR 0.024 0.002 TYR A 363 ARG 0.007 0.001 ARG A 126 *********************** 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 176 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 124 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.8058 (mmp) REVERT: A 175 LYS cc_start: 0.7858 (OUTLIER) cc_final: 0.7565 (ptmm) REVERT: A 285 TYR cc_start: 0.7121 (OUTLIER) cc_final: 0.5581 (m-80) REVERT: A 304 ASP cc_start: 0.6239 (OUTLIER) cc_final: 0.4864 (m-30) REVERT: B 337 GLU cc_start: 0.6275 (OUTLIER) cc_final: 0.5530 (pt0) REVERT: B 372 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7212 (mt-10) REVERT: D 143 MET cc_start: 0.7184 (ttt) cc_final: 0.6762 (ttp) REVERT: C 252 VAL cc_start: 0.7129 (OUTLIER) cc_final: 0.6859 (m) REVERT: C 263 ILE cc_start: 0.8010 (OUTLIER) cc_final: 0.7602 (mm) outliers start: 52 outliers final: 19 residues processed: 164 average time/residue: 1.0599 time to fit residues: 188.6548 Evaluate side-chains 143 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 116 time to evaluate : 1.146 ------------------------------------------------------------------------------- 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 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 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 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 67 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.113 9727 Z= 0.301 Angle : 0.674 12.120 13191 Z= 0.336 Chirality : 0.045 0.178 1501 Planarity : 0.005 0.070 1699 Dihedral : 4.826 37.024 1321 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 5.83 % Allowed : 19.63 % Favored : 74.54 % 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: -0.32 (0.24), residues: 1232 helix: 1.08 (0.23), residues: 513 sheet: -0.73 (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 0.005 0.001 HIS A 405 PHE 0.018 0.002 PHE C 335 TYR 0.025 0.002 TYR A 363 ARG 0.009 0.001 ARG A 126 *********************** 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 187 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 127 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.4874 (ppp) cc_final: 0.4664 (ppp) REVERT: A 129 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.7967 (mmp) REVERT: A 175 LYS cc_start: 0.7832 (OUTLIER) cc_final: 0.7541 (ptmm) REVERT: A 184 MET cc_start: 0.7871 (OUTLIER) cc_final: 0.7120 (tpp) REVERT: A 285 TYR cc_start: 0.7209 (OUTLIER) cc_final: 0.5506 (m-80) REVERT: B 337 GLU cc_start: 0.5957 (OUTLIER) cc_final: 0.5288 (pt0) REVERT: B 372 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7166 (mt-10) REVERT: D 143 MET cc_start: 0.7200 (ttt) cc_final: 0.6621 (ttp) REVERT: C 252 VAL cc_start: 0.7161 (OUTLIER) cc_final: 0.6891 (m) REVERT: C 263 ILE cc_start: 0.8121 (OUTLIER) cc_final: 0.7697 (mm) REVERT: C 379 LEU cc_start: 0.6937 (OUTLIER) cc_final: 0.6703 (tt) outliers start: 60 outliers final: 25 residues processed: 171 average time/residue: 0.9968 time to fit residues: 186.7332 Evaluate side-chains 152 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 118 time to evaluate : 1.235 ------------------------------------------------------------------------------- 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 184 MET Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 285 TYR 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 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 341 THR 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 Chi-restraints excluded: chain C residue 377 GLU 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 107 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 69 optimal weight: 0.5980 chunk 29 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 98 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.125 9727 Z= 0.339 Angle : 0.705 12.329 13191 Z= 0.352 Chirality : 0.046 0.183 1501 Planarity : 0.005 0.071 1699 Dihedral : 4.953 37.401 1321 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 5.73 % Allowed : 20.89 % Favored : 73.37 % 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: -0.52 (0.23), residues: 1232 helix: 0.94 (0.22), residues: 511 sheet: -1.05 (0.41), residues: 151 loop : -1.33 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 163 HIS 0.005 0.001 HIS A 405 PHE 0.020 0.002 PHE C 335 TYR 0.027 0.002 TYR A 363 ARG 0.012 0.001 ARG A 126 *********************** 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 185 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 126 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 LYS cc_start: 0.7844 (OUTLIER) cc_final: 0.7573 (ptmm) REVERT: A 184 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.7104 (tpp) REVERT: A 227 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7377 (mm-30) REVERT: A 285 TYR cc_start: 0.7276 (OUTLIER) cc_final: 0.5523 (m-80) REVERT: B 337 GLU cc_start: 0.5779 (OUTLIER) cc_final: 0.5161 (pt0) REVERT: B 372 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7205 (mt-10) REVERT: C 252 VAL cc_start: 0.7192 (OUTLIER) cc_final: 0.6911 (m) REVERT: C 263 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7818 (mm) REVERT: C 362 GLU cc_start: 0.6340 (OUTLIER) cc_final: 0.5845 (pm20) REVERT: C 379 LEU cc_start: 0.7023 (OUTLIER) cc_final: 0.6796 (tt) outliers start: 59 outliers final: 24 residues processed: 169 average time/residue: 0.9917 time to fit residues: 182.6741 Evaluate side-chains 151 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 118 time to evaluate : 1.166 ------------------------------------------------------------------------------- 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 184 MET Chi-restraints excluded: chain A residue 197 VAL 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 341 THR 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 232 VAL 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 134 ILE 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 262 THR 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 13 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 66 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 73 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 B 128 HIS ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 9727 Z= 0.242 Angle : 0.679 13.028 13191 Z= 0.337 Chirality : 0.044 0.184 1501 Planarity : 0.005 0.070 1699 Dihedral : 4.770 37.283 1321 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 4.66 % Allowed : 21.87 % Favored : 73.47 % 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: -0.29 (0.24), residues: 1232 helix: 1.17 (0.23), residues: 512 sheet: -0.70 (0.41), residues: 154 loop : -1.33 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 163 HIS 0.004 0.001 HIS A 370 PHE 0.014 0.001 PHE C 335 TYR 0.022 0.002 TYR A 363 ARG 0.010 0.001 ARG A 126 *********************** 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 172 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 124 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.4717 (ppp) cc_final: 0.4046 (ppp) REVERT: A 129 MET cc_start: 0.8217 (mmp) cc_final: 0.7865 (mmt) REVERT: A 184 MET cc_start: 0.7747 (OUTLIER) cc_final: 0.7048 (tpp) REVERT: A 227 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7365 (mm-30) REVERT: A 285 TYR cc_start: 0.7307 (OUTLIER) cc_final: 0.5871 (m-80) REVERT: B 337 GLU cc_start: 0.6118 (OUTLIER) cc_final: 0.5443 (pt0) REVERT: B 372 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7100 (mt-10) REVERT: C 252 VAL cc_start: 0.7090 (OUTLIER) cc_final: 0.6816 (m) REVERT: C 263 ILE cc_start: 0.8058 (OUTLIER) cc_final: 0.7691 (mm) outliers start: 48 outliers final: 24 residues processed: 162 average time/residue: 1.0168 time to fit residues: 179.8530 Evaluate side-chains 145 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 115 time to evaluate : 1.186 ------------------------------------------------------------------------------- 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 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 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 140 THR Chi-restraints excluded: chain D residue 196 LEU 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 218 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain C residue 339 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 23 optimal weight: 0.0770 chunk 22 optimal weight: 0.0570 chunk 75 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 overall best weight: 0.5856 ------------------------------------------------------------------------------- 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 ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 9727 Z= 0.202 Angle : 0.670 15.992 13191 Z= 0.331 Chirality : 0.044 0.187 1501 Planarity : 0.005 0.070 1699 Dihedral : 4.602 36.971 1321 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 4.08 % Allowed : 22.45 % Favored : 73.47 % 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: 1.31 (0.23), residues: 511 sheet: -0.70 (0.43), residues: 143 loop : -1.23 (0.25), residues: 578 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 0.020 0.001 TYR A 363 ARG 0.012 0.001 ARG A 126 *********************** 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: 42 poor density : 132 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.4625 (ppp) cc_final: 0.3886 (ppp) REVERT: A 125 ARG cc_start: 0.6567 (mtm110) cc_final: 0.5890 (ptt90) REVERT: A 184 MET cc_start: 0.7736 (OUTLIER) cc_final: 0.7001 (tpp) REVERT: A 227 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7307 (mm-30) REVERT: A 285 TYR cc_start: 0.7155 (OUTLIER) cc_final: 0.5796 (m-80) REVERT: A 304 ASP cc_start: 0.6163 (OUTLIER) cc_final: 0.5695 (m-30) REVERT: B 231 ASP cc_start: 0.7722 (OUTLIER) cc_final: 0.7401 (t0) REVERT: B 337 GLU cc_start: 0.6158 (OUTLIER) cc_final: 0.5383 (pt0) REVERT: B 372 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7016 (mt-10) REVERT: C 252 VAL cc_start: 0.7074 (OUTLIER) cc_final: 0.6797 (m) REVERT: C 263 ILE cc_start: 0.7975 (OUTLIER) cc_final: 0.7620 (mm) outliers start: 42 outliers final: 19 residues processed: 163 average time/residue: 0.8915 time to fit residues: 160.4445 Evaluate side-chains 147 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 1.106 ------------------------------------------------------------------------------- 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 514 THR Chi-restraints excluded: chain A residue 538 MET 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 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 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 155 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 263 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 113 optimal weight: 8.9990 chunk 66 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 116 optimal weight: 0.0060 overall best weight: 0.7798 ------------------------------------------------------------------------------- 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** C 236 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 9727 Z= 0.211 Angle : 0.670 14.914 13191 Z= 0.333 Chirality : 0.044 0.189 1501 Planarity : 0.005 0.070 1699 Dihedral : 4.359 24.851 1316 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.69 % Allowed : 23.42 % 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: -0.12 (0.24), residues: 1232 helix: 1.28 (0.23), residues: 512 sheet: -0.65 (0.44), residues: 143 loop : -1.19 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 163 HIS 0.004 0.001 HIS A 370 PHE 0.029 0.001 PHE D 137 TYR 0.023 0.002 TYR C 114 ARG 0.010 0.001 ARG A 126 *********************** 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 164 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 126 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.4693 (ppp) cc_final: 0.4261 (ppp) REVERT: A 125 ARG cc_start: 0.6496 (mtm110) cc_final: 0.5557 (ptt90) REVERT: A 129 MET cc_start: 0.8472 (tpp) cc_final: 0.8195 (mmp) REVERT: A 184 MET cc_start: 0.7747 (OUTLIER) cc_final: 0.7021 (tpp) REVERT: A 227 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7301 (mm-30) REVERT: A 285 TYR cc_start: 0.7155 (OUTLIER) cc_final: 0.5796 (m-80) REVERT: A 522 LEU cc_start: 0.7321 (tt) cc_final: 0.7103 (tp) REVERT: B 231 ASP cc_start: 0.7742 (OUTLIER) cc_final: 0.7416 (t0) REVERT: B 337 GLU cc_start: 0.6157 (OUTLIER) cc_final: 0.5354 (pt0) REVERT: B 372 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7034 (mt-10) REVERT: C 263 ILE cc_start: 0.7995 (OUTLIER) cc_final: 0.7648 (mm) outliers start: 38 outliers final: 21 residues processed: 156 average time/residue: 0.9155 time to fit residues: 158.3877 Evaluate side-chains 145 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 1.146 ------------------------------------------------------------------------------- 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 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 465 LEU 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 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 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 218 VAL Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 263 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 7.9990 chunk 55 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 122 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 ** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 9727 Z= 0.232 Angle : 0.687 15.360 13191 Z= 0.341 Chirality : 0.044 0.182 1501 Planarity : 0.005 0.069 1699 Dihedral : 4.379 24.369 1316 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 3.40 % Allowed : 23.91 % Favored : 72.69 % 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: 1.25 (0.23), residues: 512 sheet: -0.68 (0.43), residues: 143 loop : -1.20 (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 0.032 0.002 PHE D 137 TYR 0.022 0.001 TYR A 363 ARG 0.009 0.001 ARG A 126 ********************** 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 158 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 123 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.4716 (ppp) cc_final: 0.3959 (ppp) REVERT: A 125 ARG cc_start: 0.6537 (mtm110) cc_final: 0.5735 (ptt90) REVERT: A 184 MET cc_start: 0.7744 (OUTLIER) cc_final: 0.7014 (tpp) REVERT: A 227 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7283 (mm-30) REVERT: A 285 TYR cc_start: 0.7166 (OUTLIER) cc_final: 0.5771 (m-80) REVERT: B 231 ASP cc_start: 0.7715 (OUTLIER) cc_final: 0.7392 (t0) REVERT: B 337 GLU cc_start: 0.6127 (OUTLIER) cc_final: 0.5337 (pt0) REVERT: B 372 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7035 (mt-10) REVERT: D 125 ASP cc_start: 0.5090 (p0) cc_final: 0.4866 (p0) REVERT: C 263 ILE cc_start: 0.7971 (OUTLIER) cc_final: 0.7638 (mm) outliers start: 35 outliers final: 20 residues processed: 150 average time/residue: 0.8802 time to fit residues: 145.8712 Evaluate side-chains 145 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 1.171 ------------------------------------------------------------------------------- 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 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 465 LEU 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 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 27 optimal weight: 0.0370 chunk 97 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 overall best weight: 0.7060 ------------------------------------------------------------------------------- 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 B 196 HIS ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.179756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.142152 restraints weight = 11038.637| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 2.53 r_work: 0.3699 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 9727 Z= 0.208 Angle : 0.670 15.377 13191 Z= 0.333 Chirality : 0.044 0.181 1501 Planarity : 0.005 0.069 1699 Dihedral : 4.274 19.096 1315 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 3.11 % Allowed : 23.91 % 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: -0.09 (0.24), residues: 1232 helix: 1.33 (0.23), residues: 512 sheet: -0.66 (0.43), residues: 143 loop : -1.19 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 163 HIS 0.006 0.001 HIS A 370 PHE 0.019 0.001 PHE B 316 TYR 0.021 0.002 TYR B 371 ARG 0.009 0.001 ARG A 126 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3431.92 seconds wall clock time: 62 minutes 38.08 seconds (3758.08 seconds total)