Starting phenix.real_space_refine on Wed Jun 26 10:03:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r10_14226/06_2024/7r10_14226.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r10_14226/06_2024/7r10_14226.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r10_14226/06_2024/7r10_14226.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r10_14226/06_2024/7r10_14226.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r10_14226/06_2024/7r10_14226.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r10_14226/06_2024/7r10_14226.pdb" } resolution = 4.0 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 51 5.16 5 C 6286 2.51 5 N 1620 2.21 5 O 1865 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 9823 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 4801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4801 Classifications: {'peptide': 588} Link IDs: {'PTRANS': 25, 'TRANS': 562} Chain breaks: 1 Chain: "A" Number of atoms: 4923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 622, 4923 Classifications: {'peptide': 622} Link IDs: {'PTRANS': 32, 'TRANS': 589} Chain breaks: 4 Chain: "D" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 85 Unusual residues: {' ZN': 1, 'NAG': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.13, per 1000 atoms: 0.62 Number of scatterers: 9823 At special positions: 0 Unit cell: (94.864, 108.878, 164.934, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 51 16.00 O 1865 8.00 N 1620 7.00 C 6286 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.07 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 343 " " NAG D 902 " - " ASN D 53 " " NAG D 903 " - " ASN D 90 " " NAG D 904 " - " ASN D 322 " " NAG D 905 " - " ASN D 432 " " NAG D 906 " - " ASN D 546 " " NAG D 907 " - " ASN D 103 " Time building additional restraints: 3.65 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 901 " pdb="ZN ZN D 901 " - pdb=" NE2 HIS D 378 " pdb="ZN ZN D 901 " - pdb=" NE2 HIS D 374 " 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2272 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 13 sheets defined 36.7% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'D' and resid 20 through 53 removed outlier: 3.684A pdb=" N HIS D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N GLU D 35 " --> pdb=" O LYS D 31 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 Processing helix chain 'D' and resid 92 through 101 Processing helix chain 'D' and resid 103 through 108 Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 147 through 155 Processing helix chain 'D' and resid 157 through 173 Processing helix chain 'D' and resid 176 through 194 Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 218 through 224 removed outlier: 3.668A pdb=" N LEU D 222 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 218 through 224' Processing helix chain 'D' and resid 226 through 233 Processing helix chain 'D' and resid 233 through 249 Processing helix chain 'D' and resid 265 through 268 removed outlier: 4.357A pdb=" N GLY D 268 " --> pdb=" O HIS D 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 265 through 268' Processing helix chain 'D' and resid 275 through 281 removed outlier: 3.650A pdb=" N SER D 280 " --> pdb=" O ASN D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 301 Processing helix chain 'D' and resid 305 through 319 Processing helix chain 'D' and resid 326 through 331 removed outlier: 3.677A pdb=" N SER D 331 " --> pdb=" O PHE D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.799A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 399 through 413 removed outlier: 3.771A pdb=" N ALA D 403 " --> pdb=" O GLY D 399 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.940A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 466 Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 499 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 533 removed outlier: 4.651A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.584A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 599 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.887A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 removed outlier: 3.633A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.009A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.661A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'D' and resid 347 through 350 Processing sheet with id=AA3, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.939A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.471A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.229A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.847A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.815A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 11.012A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.667A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.093A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 142 through 143 removed outlier: 5.622A pdb=" N LEU A 244 " --> pdb=" O VAL A 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 313 Processing sheet with id=AA8, first strand: chain 'A' and resid 324 through 328 removed outlier: 3.898A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ILE A 584 " --> pdb=" O SER A 555 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AB1, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'A' and resid 664 through 667 removed outlier: 6.534A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) 416 hydrogen bonds defined for protein. 1146 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: 2.90 Time building geometry restraints manager: 4.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3104 1.34 - 1.46: 2360 1.46 - 1.58: 4545 1.58 - 1.70: 0 1.70 - 1.82: 74 Bond restraints: 10083 Sorted by residual: bond pdb=" N CYS A 291 " pdb=" CA CYS A 291 " ideal model delta sigma weight residual 1.459 1.497 -0.039 1.24e-02 6.50e+03 9.76e+00 bond pdb=" N VAL A 320 " pdb=" CA VAL A 320 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.11e+00 bond pdb=" N ARG A 319 " pdb=" CA ARG A 319 " ideal model delta sigma weight residual 1.456 1.492 -0.037 1.22e-02 6.72e+03 9.01e+00 bond pdb=" N LYS A 529 " pdb=" CA LYS A 529 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.18e-02 7.18e+03 8.27e+00 bond pdb=" N ASP A 290 " pdb=" CA ASP A 290 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.24e-02 6.50e+03 7.73e+00 ... (remaining 10078 not shown) Histogram of bond angle deviations from ideal: 100.30 - 107.05: 319 107.05 - 113.79: 5504 113.79 - 120.54: 3867 120.54 - 127.29: 3889 127.29 - 134.03: 129 Bond angle restraints: 13708 Sorted by residual: angle pdb=" CA CYS A 291 " pdb=" C CYS A 291 " pdb=" O CYS A 291 " ideal model delta sigma weight residual 120.55 116.78 3.77 1.07e+00 8.73e-01 1.24e+01 angle pdb=" CA PHE A 318 " pdb=" C PHE A 318 " pdb=" O PHE A 318 " ideal model delta sigma weight residual 121.55 117.93 3.62 1.06e+00 8.90e-01 1.17e+01 angle pdb=" CA SER A 591 " pdb=" C SER A 591 " pdb=" O SER A 591 " ideal model delta sigma weight residual 121.55 118.37 3.18 1.06e+00 8.90e-01 9.00e+00 angle pdb=" CA ILE A 332 " pdb=" C ILE A 332 " pdb=" O ILE A 332 " ideal model delta sigma weight residual 121.09 117.94 3.15 1.06e+00 8.90e-01 8.82e+00 angle pdb=" CA ARG A 319 " pdb=" C ARG A 319 " pdb=" O ARG A 319 " ideal model delta sigma weight residual 121.16 117.98 3.18 1.12e+00 7.97e-01 8.06e+00 ... (remaining 13703 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 5491 17.52 - 35.04: 437 35.04 - 52.57: 83 52.57 - 70.09: 19 70.09 - 87.61: 10 Dihedral angle restraints: 6040 sinusoidal: 2502 harmonic: 3538 Sorted by residual: dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -153.14 67.14 1 1.00e+01 1.00e-02 5.87e+01 dihedral pdb=" CB CYS D 133 " pdb=" SG CYS D 133 " pdb=" SG CYS D 141 " pdb=" CB CYS D 141 " ideal model delta sinusoidal sigma weight residual 93.00 32.40 60.60 1 1.00e+01 1.00e-02 4.89e+01 dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual -86.00 -38.84 -47.16 1 1.00e+01 1.00e-02 3.07e+01 ... (remaining 6037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1147 0.044 - 0.087: 233 0.087 - 0.131: 103 0.131 - 0.174: 9 0.174 - 0.218: 2 Chirality restraints: 1494 Sorted by residual: chirality pdb=" CA ILE A 332 " pdb=" N ILE A 332 " pdb=" C ILE A 332 " pdb=" CB ILE A 332 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA VAL A 143 " pdb=" N VAL A 143 " pdb=" C VAL A 143 " pdb=" CB VAL A 143 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 7.70e-01 chirality pdb=" CA VAL A 320 " pdb=" N VAL A 320 " pdb=" C VAL A 320 " pdb=" CB VAL A 320 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.42e-01 ... (remaining 1491 not shown) Planarity restraints: 1767 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU D 35 " 0.016 2.00e-02 2.50e+03 3.13e-02 9.82e+00 pdb=" C GLU D 35 " -0.054 2.00e-02 2.50e+03 pdb=" O GLU D 35 " 0.020 2.00e-02 2.50e+03 pdb=" N ALA D 36 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 478 " 0.036 5.00e-02 4.00e+02 5.45e-02 4.75e+00 pdb=" N PRO A 479 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 479 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 479 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 289 " -0.011 2.00e-02 2.50e+03 2.13e-02 4.54e+00 pdb=" C VAL A 289 " 0.037 2.00e-02 2.50e+03 pdb=" O VAL A 289 " -0.014 2.00e-02 2.50e+03 pdb=" N ASP A 290 " -0.012 2.00e-02 2.50e+03 ... (remaining 1764 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 176 2.68 - 3.24: 9263 3.24 - 3.79: 14875 3.79 - 4.35: 19540 4.35 - 4.90: 32679 Nonbonded interactions: 76533 Sorted by model distance: nonbonded pdb=" OE2 GLU D 402 " pdb="ZN ZN D 901 " model vdw 2.131 2.230 nonbonded pdb=" O PRO A 85 " pdb=" OH TYR A 269 " model vdw 2.277 2.440 nonbonded pdb=" O ASN A 81 " pdb=" NE2 GLN A 239 " model vdw 2.292 2.520 nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.296 2.440 nonbonded pdb=" O ASN D 53 " pdb=" ND2 ASN D 58 " model vdw 2.334 2.520 ... (remaining 76528 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.520 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: 9.210 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 30.260 Find NCS groups from input model: 0.310 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 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 0.039 10083 Z= 0.207 Angle : 0.516 6.545 13708 Z= 0.291 Chirality : 0.043 0.218 1494 Planarity : 0.003 0.054 1760 Dihedral : 13.309 87.611 3729 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.47 % Allowed : 0.19 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.25), residues: 1196 helix: 2.25 (0.28), residues: 388 sheet: 0.80 (0.38), residues: 182 loop : -0.87 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 353 HIS 0.005 0.001 HIS A 146 PHE 0.010 0.001 PHE D 512 TYR 0.012 0.001 TYR A 265 ARG 0.002 0.000 ARG D 245 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 65 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 190 MET cc_start: 0.9308 (ttp) cc_final: 0.9053 (tmm) REVERT: D 270 MET cc_start: 0.8684 (tpp) cc_final: 0.8244 (tpp) REVERT: A 177 MET cc_start: 0.4589 (ttm) cc_final: 0.4307 (mtm) outliers start: 5 outliers final: 3 residues processed: 70 average time/residue: 0.2502 time to fit residues: 25.3171 Evaluate side-chains 41 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 319 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 3.9990 chunk 90 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 31 optimal weight: 0.0470 chunk 61 optimal weight: 8.9990 chunk 48 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 70 optimal weight: 8.9990 chunk 108 optimal weight: 0.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 101 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10083 Z= 0.162 Angle : 0.499 10.699 13708 Z= 0.252 Chirality : 0.042 0.178 1494 Planarity : 0.004 0.068 1760 Dihedral : 6.143 56.680 1463 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.84 % Allowed : 4.12 % Favored : 95.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.25), residues: 1196 helix: 2.20 (0.27), residues: 388 sheet: 0.85 (0.38), residues: 167 loop : -0.86 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.003 0.001 HIS D 378 PHE 0.010 0.001 PHE A 79 TYR 0.011 0.001 TYR A 265 ARG 0.008 0.000 ARG A 646 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 39 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 190 MET cc_start: 0.9305 (ttp) cc_final: 0.9071 (tmm) REVERT: D 270 MET cc_start: 0.8748 (tpp) cc_final: 0.8165 (tpp) REVERT: D 303 ASP cc_start: 0.6653 (p0) cc_final: 0.6441 (p0) REVERT: D 332 MET cc_start: 0.8364 (ppp) cc_final: 0.8132 (tmm) REVERT: A 266 TYR cc_start: 0.9733 (OUTLIER) cc_final: 0.8837 (m-80) outliers start: 9 outliers final: 4 residues processed: 47 average time/residue: 0.2654 time to fit residues: 18.0122 Evaluate side-chains 37 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 32 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 338 ASN Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 646 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 9.9990 chunk 33 optimal weight: 0.4980 chunk 90 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 30 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 chunk 117 optimal weight: 20.0000 chunk 97 optimal weight: 0.7980 chunk 108 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 87 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10083 Z= 0.145 Angle : 0.469 7.292 13708 Z= 0.238 Chirality : 0.041 0.170 1494 Planarity : 0.003 0.056 1760 Dihedral : 5.413 56.753 1458 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.84 % Allowed : 6.74 % Favored : 92.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.25), residues: 1196 helix: 2.24 (0.27), residues: 384 sheet: 0.93 (0.40), residues: 159 loop : -0.82 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.002 0.001 HIS D 378 PHE 0.009 0.001 PHE D 230 TYR 0.013 0.001 TYR A 612 ARG 0.005 0.000 ARG A 646 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 33 time to evaluate : 1.085 Fit side-chains revert: symmetry clash REVERT: D 190 MET cc_start: 0.9297 (ttp) cc_final: 0.9070 (tmm) REVERT: D 270 MET cc_start: 0.8697 (tpp) cc_final: 0.8103 (tpp) REVERT: D 303 ASP cc_start: 0.6725 (p0) cc_final: 0.6461 (p0) REVERT: D 376 MET cc_start: 0.9092 (tpp) cc_final: 0.8852 (mmm) REVERT: A 79 PHE cc_start: 0.7770 (OUTLIER) cc_final: 0.7437 (m-80) REVERT: A 177 MET cc_start: 0.6299 (mtm) cc_final: 0.5921 (mtp) REVERT: A 266 TYR cc_start: 0.9695 (OUTLIER) cc_final: 0.9018 (m-80) outliers start: 9 outliers final: 4 residues processed: 40 average time/residue: 0.2122 time to fit residues: 13.3917 Evaluate side-chains 39 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 33 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 338 ASN Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 277 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 73 optimal weight: 7.9990 chunk 109 optimal weight: 0.9990 chunk 115 optimal weight: 6.9990 chunk 57 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 31 optimal weight: 8.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 450 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10083 Z= 0.282 Angle : 0.521 5.790 13708 Z= 0.271 Chirality : 0.042 0.181 1494 Planarity : 0.003 0.033 1760 Dihedral : 5.436 58.066 1458 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.03 % Allowed : 8.52 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.25), residues: 1196 helix: 2.01 (0.27), residues: 389 sheet: 0.89 (0.38), residues: 170 loop : -0.80 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.005 0.001 HIS D 378 PHE 0.013 0.001 PHE D 230 TYR 0.021 0.002 TYR A 453 ARG 0.004 0.000 ARG A 646 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 32 time to evaluate : 1.114 Fit side-chains revert: symmetry clash REVERT: D 190 MET cc_start: 0.9340 (ttp) cc_final: 0.8914 (tmm) REVERT: D 248 LEU cc_start: 0.9248 (tp) cc_final: 0.9019 (tp) REVERT: D 270 MET cc_start: 0.8812 (tpp) cc_final: 0.8155 (tpp) REVERT: D 332 MET cc_start: 0.8271 (ppp) cc_final: 0.8037 (tmm) REVERT: A 79 PHE cc_start: 0.7937 (OUTLIER) cc_final: 0.7583 (m-80) REVERT: A 177 MET cc_start: 0.6488 (mtm) cc_final: 0.6202 (mtp) REVERT: A 266 TYR cc_start: 0.9654 (OUTLIER) cc_final: 0.9013 (m-80) outliers start: 11 outliers final: 6 residues processed: 41 average time/residue: 0.1991 time to fit residues: 13.0115 Evaluate side-chains 40 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 32 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 338 ASN Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 277 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 0.0030 chunk 65 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 80 optimal weight: 9.9990 chunk 0 optimal weight: 3.9990 chunk 59 optimal weight: 0.0070 chunk 104 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.9812 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10083 Z= 0.193 Angle : 0.477 8.068 13708 Z= 0.244 Chirality : 0.041 0.177 1494 Planarity : 0.003 0.032 1760 Dihedral : 5.215 58.933 1458 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.12 % Allowed : 9.46 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.25), residues: 1196 helix: 2.07 (0.27), residues: 389 sheet: 0.97 (0.39), residues: 166 loop : -0.78 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.003 0.001 HIS D 378 PHE 0.011 0.001 PHE D 369 TYR 0.014 0.001 TYR D 207 ARG 0.003 0.000 ARG A 646 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 32 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 190 MET cc_start: 0.9329 (ttp) cc_final: 0.8943 (tmm) REVERT: D 248 LEU cc_start: 0.9244 (tp) cc_final: 0.9044 (tp) REVERT: D 270 MET cc_start: 0.8747 (tpp) cc_final: 0.8111 (tpp) REVERT: D 332 MET cc_start: 0.8128 (ppp) cc_final: 0.7918 (tmm) REVERT: A 79 PHE cc_start: 0.7974 (OUTLIER) cc_final: 0.7676 (m-80) REVERT: A 177 MET cc_start: 0.6460 (mtm) cc_final: 0.6146 (mtp) REVERT: A 266 TYR cc_start: 0.9595 (OUTLIER) cc_final: 0.8934 (m-80) outliers start: 12 outliers final: 6 residues processed: 42 average time/residue: 0.2293 time to fit residues: 14.8845 Evaluate side-chains 40 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 32 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 338 ASN Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 646 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 68 optimal weight: 8.9990 chunk 28 optimal weight: 0.8980 chunk 116 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 53 optimal weight: 0.0870 chunk 9 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 60 optimal weight: 9.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10083 Z= 0.154 Angle : 0.459 8.483 13708 Z= 0.233 Chirality : 0.040 0.178 1494 Planarity : 0.003 0.032 1760 Dihedral : 5.021 59.459 1458 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.22 % Allowed : 9.83 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.25), residues: 1196 helix: 2.13 (0.27), residues: 390 sheet: 1.01 (0.38), residues: 166 loop : -0.76 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.002 0.000 HIS D 378 PHE 0.009 0.001 PHE D 369 TYR 0.015 0.001 TYR A 612 ARG 0.003 0.000 ARG A 646 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 32 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 152 MET cc_start: 0.8935 (tpp) cc_final: 0.8560 (tpt) REVERT: D 190 MET cc_start: 0.9308 (ttp) cc_final: 0.9105 (tmm) REVERT: D 270 MET cc_start: 0.8701 (tpp) cc_final: 0.8055 (tpp) REVERT: D 332 MET cc_start: 0.8087 (ppp) cc_final: 0.7881 (tmm) REVERT: A 79 PHE cc_start: 0.7994 (OUTLIER) cc_final: 0.7741 (m-80) REVERT: A 177 MET cc_start: 0.6166 (mtm) cc_final: 0.5802 (mtp) REVERT: A 266 TYR cc_start: 0.9571 (OUTLIER) cc_final: 0.8900 (m-80) outliers start: 13 outliers final: 7 residues processed: 42 average time/residue: 0.2086 time to fit residues: 13.6196 Evaluate side-chains 41 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 32 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 338 ASN Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 646 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 84 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 chunk 64 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 chunk 53 optimal weight: 0.0010 overall best weight: 2.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 117 ASN D 159 ASN D 239 HIS A 49 HIS A 52 GLN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 10083 Z= 0.430 Angle : 0.620 10.288 13708 Z= 0.322 Chirality : 0.044 0.191 1494 Planarity : 0.004 0.032 1760 Dihedral : 5.549 59.017 1458 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.40 % Allowed : 10.02 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.25), residues: 1196 helix: 1.58 (0.27), residues: 389 sheet: 0.80 (0.39), residues: 168 loop : -0.90 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.005 0.001 HIS D 378 PHE 0.016 0.002 PHE D 369 TYR 0.027 0.002 TYR D 207 ARG 0.005 0.001 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 34 time to evaluate : 1.116 Fit side-chains revert: symmetry clash REVERT: D 152 MET cc_start: 0.9068 (tpp) cc_final: 0.8674 (tpt) REVERT: D 190 MET cc_start: 0.9360 (ttp) cc_final: 0.8991 (tmm) REVERT: D 270 MET cc_start: 0.8837 (tpp) cc_final: 0.8189 (tpp) REVERT: D 332 MET cc_start: 0.8196 (ppp) cc_final: 0.7990 (tmm) REVERT: D 338 ASN cc_start: 0.8817 (OUTLIER) cc_final: 0.8588 (p0) REVERT: A 79 PHE cc_start: 0.8117 (OUTLIER) cc_final: 0.7832 (m-80) REVERT: A 266 TYR cc_start: 0.9538 (OUTLIER) cc_final: 0.8867 (m-80) outliers start: 15 outliers final: 7 residues processed: 44 average time/residue: 0.2302 time to fit residues: 15.2282 Evaluate side-chains 42 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 32 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 338 ASN Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 646 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 8.9990 chunk 46 optimal weight: 0.9980 chunk 69 optimal weight: 9.9990 chunk 34 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10083 Z= 0.183 Angle : 0.502 9.779 13708 Z= 0.254 Chirality : 0.041 0.180 1494 Planarity : 0.003 0.033 1760 Dihedral : 5.274 59.447 1458 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.31 % Allowed : 10.86 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.25), residues: 1196 helix: 1.89 (0.27), residues: 389 sheet: 0.86 (0.39), residues: 168 loop : -0.83 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 436 HIS 0.003 0.001 HIS D 378 PHE 0.010 0.001 PHE D 369 TYR 0.013 0.001 TYR D 207 ARG 0.002 0.000 ARG A 646 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 32 time to evaluate : 1.024 Fit side-chains revert: symmetry clash REVERT: D 152 MET cc_start: 0.9032 (tpp) cc_final: 0.8629 (tpt) REVERT: D 190 MET cc_start: 0.9326 (ttp) cc_final: 0.8947 (tmm) REVERT: D 270 MET cc_start: 0.8737 (tpp) cc_final: 0.8110 (tpp) REVERT: D 338 ASN cc_start: 0.8787 (OUTLIER) cc_final: 0.8569 (p0) REVERT: A 79 PHE cc_start: 0.8046 (OUTLIER) cc_final: 0.7777 (m-80) REVERT: A 266 TYR cc_start: 0.9544 (OUTLIER) cc_final: 0.8863 (m-80) outliers start: 14 outliers final: 7 residues processed: 42 average time/residue: 0.2231 time to fit residues: 14.5126 Evaluate side-chains 41 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 31 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 338 ASN Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 646 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 chunk 46 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 33 optimal weight: 0.6980 chunk 97 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10083 Z= 0.314 Angle : 0.557 10.867 13708 Z= 0.286 Chirality : 0.042 0.189 1494 Planarity : 0.003 0.033 1760 Dihedral : 5.437 59.453 1458 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.94 % Allowed : 11.05 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.25), residues: 1196 helix: 1.68 (0.27), residues: 389 sheet: 0.81 (0.39), residues: 168 loop : -0.91 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.003 0.001 HIS D 378 PHE 0.013 0.001 PHE D 369 TYR 0.021 0.002 TYR D 207 ARG 0.004 0.000 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 31 time to evaluate : 1.109 Fit side-chains revert: symmetry clash REVERT: D 152 MET cc_start: 0.8992 (tpp) cc_final: 0.8541 (tpt) REVERT: D 190 MET cc_start: 0.9351 (ttp) cc_final: 0.8964 (tmm) REVERT: D 270 MET cc_start: 0.8803 (tpp) cc_final: 0.8145 (tpp) REVERT: D 338 ASN cc_start: 0.8860 (OUTLIER) cc_final: 0.8613 (p0) REVERT: D 366 MET cc_start: 0.7594 (tmm) cc_final: 0.7135 (tmm) REVERT: A 79 PHE cc_start: 0.8078 (OUTLIER) cc_final: 0.7811 (m-80) REVERT: A 266 TYR cc_start: 0.9529 (OUTLIER) cc_final: 0.8853 (m-80) outliers start: 10 outliers final: 6 residues processed: 39 average time/residue: 0.2272 time to fit residues: 13.7041 Evaluate side-chains 40 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 31 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 338 ASN Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 646 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 119 optimal weight: 0.7980 chunk 110 optimal weight: 4.9990 chunk 95 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 58 optimal weight: 40.0000 chunk 75 optimal weight: 0.9990 chunk 101 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10083 Z= 0.175 Angle : 0.495 9.697 13708 Z= 0.250 Chirality : 0.041 0.183 1494 Planarity : 0.003 0.033 1760 Dihedral : 5.239 58.819 1458 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.94 % Allowed : 11.14 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.25), residues: 1196 helix: 1.89 (0.27), residues: 388 sheet: 0.87 (0.39), residues: 168 loop : -0.84 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 436 HIS 0.003 0.001 HIS D 378 PHE 0.010 0.001 PHE D 369 TYR 0.012 0.001 TYR A 453 ARG 0.002 0.000 ARG A 646 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 31 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 152 MET cc_start: 0.9011 (tpp) cc_final: 0.8607 (tpt) REVERT: D 190 MET cc_start: 0.9324 (ttp) cc_final: 0.8940 (tmm) REVERT: D 270 MET cc_start: 0.8733 (tpp) cc_final: 0.8080 (tpp) REVERT: A 79 PHE cc_start: 0.8041 (OUTLIER) cc_final: 0.7804 (m-80) REVERT: A 177 MET cc_start: 0.6324 (mtm) cc_final: 0.5922 (mtp) REVERT: A 266 TYR cc_start: 0.9534 (OUTLIER) cc_final: 0.8871 (m-80) outliers start: 10 outliers final: 6 residues processed: 38 average time/residue: 0.2268 time to fit residues: 13.2146 Evaluate side-chains 39 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 31 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 646 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 0.0870 chunk 14 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 68 optimal weight: 7.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.074644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.044891 restraints weight = 44850.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.046682 restraints weight = 28864.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.046903 restraints weight = 17468.056| |-----------------------------------------------------------------------------| r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10083 Z= 0.159 Angle : 0.474 9.517 13708 Z= 0.238 Chirality : 0.040 0.183 1494 Planarity : 0.003 0.032 1760 Dihedral : 5.011 58.474 1458 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.03 % Allowed : 10.86 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.25), residues: 1196 helix: 2.04 (0.27), residues: 386 sheet: 0.97 (0.39), residues: 168 loop : -0.77 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.002 0.000 HIS D 378 PHE 0.011 0.001 PHE D 327 TYR 0.014 0.001 TYR A 612 ARG 0.002 0.000 ARG A 646 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1760.52 seconds wall clock time: 32 minutes 25.02 seconds (1945.02 seconds total)