Starting phenix.real_space_refine on Wed Feb 4 01:16:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lol_63249/02_2026/9lol_63249_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lol_63249/02_2026/9lol_63249.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lol_63249/02_2026/9lol_63249_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lol_63249/02_2026/9lol_63249_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lol_63249/02_2026/9lol_63249.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lol_63249/02_2026/9lol_63249.map" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.091 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 38 5.16 5 C 5190 2.51 5 N 1385 2.21 5 O 1471 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8084 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3500 Classifications: {'peptide': 422} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 403} Chain breaks: 4 Chain: "B" Number of atoms: 3314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3314 Classifications: {'peptide': 412} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 395} Chain: "C" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1270 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain breaks: 2 Time building chain proxies: 1.49, per 1000 atoms: 0.18 Number of scatterers: 8084 At special positions: 0 Unit cell: (78.736, 110.852, 131.572, 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 38 16.00 O 1471 8.00 N 1385 7.00 C 5190 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: 0.61 Conformation dependent library (CDL) restraints added in 281.9 milliseconds 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1908 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 7 sheets defined 44.8% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 40 through 43 Processing helix chain 'A' and resid 54 through 73 Processing helix chain 'A' and resid 130 through 150 removed outlier: 3.710A pdb=" N TYR A 134 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE A 148 " --> pdb=" O MET A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 176 removed outlier: 8.788A pdb=" N VAL A 161 " --> pdb=" O GLU A 157 " (cutoff:3.500A) removed outlier: 9.162A pdb=" N LYS A 162 " --> pdb=" O ASP A 158 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A 163 " --> pdb=" O GLY A 159 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ARG A 174 " --> pdb=" O LYS A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 185 through 191 Processing helix chain 'A' and resid 199 through 217 Processing helix chain 'A' and resid 237 through 251 removed outlier: 4.295A pdb=" N ILE A 243 " --> pdb=" O ASP A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 257 Processing helix chain 'A' and resid 335 through 365 Proline residue: A 348 - end of helix removed outlier: 3.970A pdb=" N GLU A 359 " --> pdb=" O SER A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 421 removed outlier: 4.269A pdb=" N LYS A 411 " --> pdb=" O PRO A 407 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE A 412 " --> pdb=" O ASP A 408 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 474 Processing helix chain 'B' and resid 242 through 250 Processing helix chain 'B' and resid 275 through 291 removed outlier: 3.650A pdb=" N LEU B 289 " --> pdb=" O LEU B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 345 removed outlier: 3.509A pdb=" N LEU B 343 " --> pdb=" O GLN B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 356 removed outlier: 3.534A pdb=" N LYS B 356 " --> pdb=" O ILE B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 364 Processing helix chain 'B' and resid 368 through 382 removed outlier: 3.688A pdb=" N THR B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 388 removed outlier: 4.434A pdb=" N LEU B 386 " --> pdb=" O ASP B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 410 Processing helix chain 'B' and resid 438 through 450 Processing helix chain 'B' and resid 453 through 458 removed outlier: 3.914A pdb=" N GLY B 458 " --> pdb=" O PHE B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 517 removed outlier: 3.614A pdb=" N PHE B 510 " --> pdb=" O CYS B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 529 removed outlier: 4.412A pdb=" N ALA B 522 " --> pdb=" O GLY B 518 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR B 529 " --> pdb=" O GLU B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 537 Processing helix chain 'B' and resid 566 through 585 Processing helix chain 'B' and resid 622 through 645 removed outlier: 5.922A pdb=" N ASP B 642 " --> pdb=" O ARG B 638 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ARG B 643 " --> pdb=" O LYS B 639 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 28 Processing helix chain 'C' and resid 67 through 72 removed outlier: 3.716A pdb=" N GLN C 71 " --> pdb=" O GLU C 68 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N SER C 72 " --> pdb=" O ARG C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 78 Processing helix chain 'C' and resid 94 through 111 removed outlier: 4.058A pdb=" N ASP C 100 " --> pdb=" O PHE C 96 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER C 101 " --> pdb=" O LYS C 97 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TRP C 102 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG C 103 " --> pdb=" O LEU C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 118 Processing helix chain 'C' and resid 136 through 146 Processing helix chain 'C' and resid 161 through 172 removed outlier: 4.051A pdb=" N ALA C 165 " --> pdb=" O ASN C 161 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE C 166 " --> pdb=" O VAL C 162 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 20 removed outlier: 3.589A pdb=" N LYS A 18 " --> pdb=" O GLU A 112 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ILE A 111 " --> pdb=" O ILE A 122 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE A 122 " --> pdb=" O ILE A 111 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LYS A 113 " --> pdb=" O PRO A 120 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 49 removed outlier: 6.348A pdb=" N LEU A 24 " --> pdb=" O ARG A 107 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ARG A 107 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N PHE A 100 " --> pdb=" O PRO A 96 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN A 89 " --> pdb=" O THR A 86 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N LYS A 82 " --> pdb=" O PHE A 93 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ARG B 297 " --> pdb=" O PHE B 308 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N SER B 259 " --> pdb=" O PRO B 264 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 193 through 194 removed outlier: 5.749A pdb=" N ILE A 193 " --> pdb=" O GLU A 388 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N SER A 390 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR B 593 " --> pdb=" O LYS A 432 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LYS B 592 " --> pdb=" O VAL B 607 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N HIS B 544 " --> pdb=" O CYS B 616 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU B 554 " --> pdb=" O SER B 549 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N ALA B 390 " --> pdb=" O PHE B 555 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 230 through 234 removed outlier: 6.760A pdb=" N PHE A 225 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N SER A 234 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N THR A 223 " --> pdb=" O SER A 234 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N VAL A 220 " --> pdb=" O ASP A 329 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ASP A 329 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL A 316 " --> pdb=" O LEU A 283 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 230 through 234 removed outlier: 6.760A pdb=" N PHE A 225 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N SER A 234 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N THR A 223 " --> pdb=" O SER A 234 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N VAL A 220 " --> pdb=" O ASP A 329 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ASP A 329 " --> pdb=" O VAL A 220 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 460 through 464 removed outlier: 3.740A pdb=" N PHE B 417 " --> pdb=" O VAL B 493 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA B 428 " --> pdb=" O LEU B 420 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ALA B 422 " --> pdb=" O LEU B 426 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N LEU B 426 " --> pdb=" O ALA B 422 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU B 650 " --> pdb=" O LEU B 429 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG B 431 " --> pdb=" O LEU B 650 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 36 through 37 removed outlier: 3.729A pdb=" N TYR C 37 " --> pdb=" O ALA C 43 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU C 9 " --> pdb=" O GLN C 60 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N TRP C 62 " --> pdb=" O LEU C 9 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL C 11 " --> pdb=" O TRP C 62 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N THR C 64 " --> pdb=" O VAL C 11 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ILE C 13 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 8.989A pdb=" N CYS C 83 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LYS C 10 " --> pdb=" O CYS C 83 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N VAL C 85 " --> pdb=" O LYS C 10 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE C 12 " --> pdb=" O VAL C 85 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N VAL C 87 " --> pdb=" O ILE C 12 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU C 14 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N ASP C 89 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N CYS C 84 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N LEU C 123 " --> pdb=" O CYS C 84 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU C 86 " --> pdb=" O LEU C 123 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ILE C 125 " --> pdb=" O LEU C 86 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N PHE C 88 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N PHE C 152 " --> pdb=" O PHE C 120 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL C 122 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N THR C 154 " --> pdb=" O VAL C 122 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N GLY C 124 " --> pdb=" O THR C 154 " (cutoff:3.500A) 454 hydrogen bonds defined for protein. 1266 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: 1.21 Time building geometry restraints manager: 0.83 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: 2618 1.34 - 1.46: 1871 1.46 - 1.58: 3712 1.58 - 1.70: 0 1.70 - 1.82: 60 Bond restraints: 8261 Sorted by residual: bond pdb=" CB VAL B 283 " pdb=" CG2 VAL B 283 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.74e+00 bond pdb=" CB PRO B 530 " pdb=" CG PRO B 530 " ideal model delta sigma weight residual 1.492 1.564 -0.072 5.00e-02 4.00e+02 2.09e+00 bond pdb=" CA ASP A 445 " pdb=" CB ASP A 445 " ideal model delta sigma weight residual 1.527 1.547 -0.020 1.70e-02 3.46e+03 1.43e+00 bond pdb=" CG PRO B 530 " pdb=" CD PRO B 530 " ideal model delta sigma weight residual 1.503 1.539 -0.036 3.40e-02 8.65e+02 1.14e+00 bond pdb=" CG LEU B 258 " pdb=" CD1 LEU B 258 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.12e+00 ... (remaining 8256 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 10949 1.84 - 3.69: 182 3.69 - 5.53: 23 5.53 - 7.37: 5 7.37 - 9.22: 1 Bond angle restraints: 11160 Sorted by residual: angle pdb=" N VAL C 162 " pdb=" CA VAL C 162 " pdb=" C VAL C 162 " ideal model delta sigma weight residual 113.22 106.50 6.72 1.23e+00 6.61e-01 2.98e+01 angle pdb=" N ILE C 41 " pdb=" CA ILE C 41 " pdb=" C ILE C 41 " ideal model delta sigma weight residual 112.96 108.18 4.78 1.00e+00 1.00e+00 2.28e+01 angle pdb=" CG ARG B 528 " pdb=" CD ARG B 528 " pdb=" NE ARG B 528 " ideal model delta sigma weight residual 112.00 118.67 -6.67 2.20e+00 2.07e-01 9.19e+00 angle pdb=" CA TYR A 142 " pdb=" CB TYR A 142 " pdb=" CG TYR A 142 " ideal model delta sigma weight residual 113.90 108.93 4.97 1.80e+00 3.09e-01 7.63e+00 angle pdb=" CA ASP A 445 " pdb=" CB ASP A 445 " pdb=" CG ASP A 445 " ideal model delta sigma weight residual 112.60 115.29 -2.69 1.00e+00 1.00e+00 7.23e+00 ... (remaining 11155 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 4211 17.72 - 35.45: 524 35.45 - 53.17: 204 53.17 - 70.90: 32 70.90 - 88.62: 19 Dihedral angle restraints: 4990 sinusoidal: 2056 harmonic: 2934 Sorted by residual: dihedral pdb=" CA ALA C 173 " pdb=" C ALA C 173 " pdb=" N LEU C 174 " pdb=" CA LEU C 174 " ideal model delta harmonic sigma weight residual 180.00 161.48 18.52 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA LYS A 318 " pdb=" C LYS A 318 " pdb=" N ALA A 319 " pdb=" CA ALA A 319 " ideal model delta harmonic sigma weight residual 180.00 162.21 17.79 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CG ARG B 528 " pdb=" CD ARG B 528 " pdb=" NE ARG B 528 " pdb=" CZ ARG B 528 " ideal model delta sinusoidal sigma weight residual -90.00 -40.33 -49.67 2 1.50e+01 4.44e-03 1.24e+01 ... (remaining 4987 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 845 0.037 - 0.074: 276 0.074 - 0.112: 90 0.112 - 0.149: 21 0.149 - 0.186: 1 Chirality restraints: 1233 Sorted by residual: chirality pdb=" CA ASP A 445 " pdb=" N ASP A 445 " pdb=" C ASP A 445 " pdb=" CB ASP A 445 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.67e-01 chirality pdb=" CA VAL C 29 " pdb=" N VAL C 29 " pdb=" C VAL C 29 " pdb=" CB VAL C 29 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.43e-01 chirality pdb=" CA ILE A 29 " pdb=" N ILE A 29 " pdb=" C ILE A 29 " pdb=" CB ILE A 29 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.93e-01 ... (remaining 1230 not shown) Planarity restraints: 1427 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 529 " -0.040 5.00e-02 4.00e+02 5.87e-02 5.51e+00 pdb=" N PRO B 530 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO B 530 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 530 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 589 " 0.028 5.00e-02 4.00e+02 4.24e-02 2.87e+00 pdb=" N PRO B 590 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 590 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 590 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 505 " -0.007 2.00e-02 2.50e+03 1.50e-02 2.24e+00 pdb=" C ASP B 505 " 0.026 2.00e-02 2.50e+03 pdb=" O ASP B 505 " -0.010 2.00e-02 2.50e+03 pdb=" N CYS B 506 " -0.009 2.00e-02 2.50e+03 ... (remaining 1424 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 246 2.71 - 3.26: 7675 3.26 - 3.80: 13045 3.80 - 4.35: 16978 4.35 - 4.90: 28883 Nonbonded interactions: 66827 Sorted by model distance: nonbonded pdb=" N ASP B 487 " pdb=" OD1 ASP B 487 " model vdw 2.161 3.120 nonbonded pdb=" OG1 THR A 86 " pdb=" O ASN A 89 " model vdw 2.202 3.040 nonbonded pdb=" OE2 GLU A 427 " pdb=" OH TYR B 596 " model vdw 2.219 3.040 nonbonded pdb=" O SER A 435 " pdb=" OG SER A 435 " model vdw 2.233 3.040 nonbonded pdb=" OH TYR A 48 " pdb=" ND2 ASN A 61 " model vdw 2.248 3.120 ... (remaining 66822 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 ========== 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 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: 1.060 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.850 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:6.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 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 : 0.004 0.072 8261 Z= 0.155 Angle : 0.591 9.215 11160 Z= 0.328 Chirality : 0.043 0.186 1233 Planarity : 0.004 0.059 1427 Dihedral : 18.608 88.624 3082 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.31 % Allowed : 3.69 % Favored : 96.00 % Rotamer: Outliers : 3.84 % Allowed : 29.01 % Favored : 67.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.27), residues: 975 helix: 0.92 (0.26), residues: 393 sheet: 0.27 (0.34), residues: 237 loop : -1.01 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 528 TYR 0.018 0.001 TYR A 142 PHE 0.015 0.001 PHE A 172 TRP 0.009 0.001 TRP B 606 HIS 0.004 0.001 HIS B 520 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 8261) covalent geometry : angle 0.59141 (11160) hydrogen bonds : bond 0.16110 ( 437) hydrogen bonds : angle 6.67818 ( 1266) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 105 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 356 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.7582 (ptmm) outliers start: 34 outliers final: 29 residues processed: 137 average time/residue: 0.4151 time to fit residues: 60.9517 Evaluate side-chains 131 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 101 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 396 LYS Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 474 PHE Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 618 SER Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 140 GLN Chi-restraints excluded: chain C residue 178 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 140 GLN ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.206784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.170125 restraints weight = 8457.735| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 2.15 r_work: 0.3717 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3587 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.0842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8261 Z= 0.151 Angle : 0.565 6.859 11160 Z= 0.302 Chirality : 0.043 0.176 1233 Planarity : 0.004 0.037 1427 Dihedral : 7.626 71.023 1139 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.38 % Favored : 96.41 % Rotamer: Outliers : 5.53 % Allowed : 25.40 % Favored : 69.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.27), residues: 975 helix: 1.11 (0.26), residues: 394 sheet: 0.12 (0.33), residues: 242 loop : -0.93 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 370 TYR 0.015 0.001 TYR C 78 PHE 0.014 0.001 PHE A 172 TRP 0.009 0.001 TRP C 62 HIS 0.003 0.001 HIS A 393 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 8261) covalent geometry : angle 0.56466 (11160) hydrogen bonds : bond 0.04111 ( 437) hydrogen bonds : angle 5.21810 ( 1266) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 108 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: A 52 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7690 (pm20) REVERT: A 420 PHE cc_start: 0.7529 (OUTLIER) cc_final: 0.6890 (m-10) REVERT: B 559 GLU cc_start: 0.6649 (tp30) cc_final: 0.6397 (tt0) REVERT: C 67 GLN cc_start: 0.7348 (OUTLIER) cc_final: 0.6887 (mp10) outliers start: 49 outliers final: 16 residues processed: 147 average time/residue: 0.5286 time to fit residues: 82.1659 Evaluate side-chains 120 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 396 LYS Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain B residue 474 PHE Chi-restraints excluded: chain B residue 625 SER Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 83 CYS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 178 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 83 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 140 GLN A 313 HIS A 464 ASN B 354 GLN B 447 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.202214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.165540 restraints weight = 8437.242| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 2.01 r_work: 0.3649 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 8261 Z= 0.238 Angle : 0.645 7.169 11160 Z= 0.340 Chirality : 0.046 0.175 1233 Planarity : 0.004 0.037 1427 Dihedral : 6.124 51.789 1107 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.31 % Favored : 95.49 % Rotamer: Outliers : 5.87 % Allowed : 24.49 % Favored : 69.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.27), residues: 975 helix: 0.85 (0.26), residues: 393 sheet: 0.04 (0.33), residues: 242 loop : -1.05 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 370 TYR 0.025 0.002 TYR C 78 PHE 0.018 0.002 PHE A 28 TRP 0.010 0.002 TRP B 606 HIS 0.005 0.001 HIS B 631 Details of bonding type rmsd covalent geometry : bond 0.00562 ( 8261) covalent geometry : angle 0.64492 (11160) hydrogen bonds : bond 0.04628 ( 437) hydrogen bonds : angle 5.22925 ( 1266) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 110 time to evaluate : 0.223 Fit side-chains REVERT: A 52 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7094 (pm20) REVERT: A 420 PHE cc_start: 0.7883 (OUTLIER) cc_final: 0.7260 (m-10) REVERT: A 447 ARG cc_start: 0.6401 (OUTLIER) cc_final: 0.5562 (tmm-80) REVERT: B 293 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7524 (mppt) REVERT: C 67 GLN cc_start: 0.7492 (OUTLIER) cc_final: 0.6991 (mp10) REVERT: C 144 TYR cc_start: 0.7126 (OUTLIER) cc_final: 0.6924 (m-10) REVERT: C 164 GLN cc_start: 0.6890 (OUTLIER) cc_final: 0.6672 (mm-40) outliers start: 52 outliers final: 23 residues processed: 153 average time/residue: 0.4648 time to fit residues: 75.7648 Evaluate side-chains 132 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 102 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 293 LYS Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain B residue 474 PHE Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 83 CYS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 164 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 71 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 94 optimal weight: 6.9990 chunk 80 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 464 ASN B 354 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.203748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.167042 restraints weight = 8538.012| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 2.05 r_work: 0.3715 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3590 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8261 Z= 0.155 Angle : 0.568 6.623 11160 Z= 0.302 Chirality : 0.043 0.172 1233 Planarity : 0.004 0.037 1427 Dihedral : 5.693 52.680 1102 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.79 % Favored : 96.00 % Rotamer: Outliers : 5.30 % Allowed : 26.19 % Favored : 68.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.27), residues: 975 helix: 1.09 (0.26), residues: 391 sheet: 0.00 (0.33), residues: 243 loop : -0.98 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 446 TYR 0.020 0.001 TYR C 78 PHE 0.015 0.001 PHE A 172 TRP 0.015 0.002 TRP A 233 HIS 0.003 0.001 HIS B 631 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 8261) covalent geometry : angle 0.56760 (11160) hydrogen bonds : bond 0.03976 ( 437) hydrogen bonds : angle 5.10101 ( 1266) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 107 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: A 52 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7208 (pm20) REVERT: A 420 PHE cc_start: 0.7816 (OUTLIER) cc_final: 0.7237 (m-10) REVERT: A 421 THR cc_start: 0.4539 (OUTLIER) cc_final: 0.4329 (m) REVERT: A 465 GLU cc_start: 0.7095 (tp30) cc_final: 0.6659 (tt0) REVERT: C 144 TYR cc_start: 0.7198 (OUTLIER) cc_final: 0.6997 (m-10) outliers start: 47 outliers final: 20 residues processed: 144 average time/residue: 0.5708 time to fit residues: 87.1610 Evaluate side-chains 125 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 433 LYS Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain B residue 474 PHE Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 83 CYS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 140 GLN Chi-restraints excluded: chain C residue 144 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 46 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 91 optimal weight: 0.0870 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 140 GLN A 464 ASN B 354 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.204505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.167302 restraints weight = 8389.457| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 2.21 r_work: 0.3736 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3607 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8261 Z= 0.130 Angle : 0.550 8.716 11160 Z= 0.291 Chirality : 0.042 0.170 1233 Planarity : 0.003 0.035 1427 Dihedral : 5.511 52.993 1102 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.90 % Favored : 95.90 % Rotamer: Outliers : 4.85 % Allowed : 26.98 % Favored : 68.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.27), residues: 975 helix: 1.27 (0.26), residues: 395 sheet: 0.10 (0.33), residues: 239 loop : -0.99 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 528 TYR 0.017 0.001 TYR C 78 PHE 0.014 0.001 PHE A 172 TRP 0.009 0.001 TRP C 62 HIS 0.004 0.001 HIS B 520 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 8261) covalent geometry : angle 0.54983 (11160) hydrogen bonds : bond 0.03660 ( 437) hydrogen bonds : angle 4.94961 ( 1266) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 111 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: A 52 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7120 (pm20) REVERT: A 174 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.7273 (ptm-80) REVERT: A 237 GLU cc_start: 0.7361 (tp30) cc_final: 0.7075 (tp30) REVERT: A 406 HIS cc_start: 0.7374 (t70) cc_final: 0.7138 (t70) REVERT: A 420 PHE cc_start: 0.7736 (OUTLIER) cc_final: 0.7158 (m-10) REVERT: A 447 ARG cc_start: 0.6599 (OUTLIER) cc_final: 0.5864 (ttp-170) REVERT: A 465 GLU cc_start: 0.7219 (tp30) cc_final: 0.6737 (tt0) REVERT: B 293 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7680 (mppt) REVERT: B 498 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7421 (mp0) REVERT: B 559 GLU cc_start: 0.6896 (tp30) cc_final: 0.6615 (tt0) REVERT: C 144 TYR cc_start: 0.7280 (OUTLIER) cc_final: 0.7073 (m-10) outliers start: 43 outliers final: 20 residues processed: 144 average time/residue: 0.5312 time to fit residues: 81.3848 Evaluate side-chains 130 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 293 LYS Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 433 LYS Chi-restraints excluded: chain B residue 474 PHE Chi-restraints excluded: chain B residue 625 SER Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 28 TYR Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 83 CYS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 140 GLN Chi-restraints excluded: chain C residue 144 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 87 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 30 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 47 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 140 GLN A 464 ASN B 447 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.199407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.161657 restraints weight = 8385.510| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 2.16 r_work: 0.3679 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3548 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 8261 Z= 0.235 Angle : 0.646 7.395 11160 Z= 0.338 Chirality : 0.045 0.200 1233 Planarity : 0.004 0.035 1427 Dihedral : 5.654 54.268 1099 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.31 % Favored : 95.49 % Rotamer: Outliers : 5.42 % Allowed : 26.07 % Favored : 68.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.27), residues: 975 helix: 1.02 (0.26), residues: 393 sheet: -0.00 (0.33), residues: 242 loop : -1.12 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 528 TYR 0.024 0.002 TYR C 78 PHE 0.017 0.002 PHE A 28 TRP 0.012 0.002 TRP B 606 HIS 0.005 0.001 HIS B 631 Details of bonding type rmsd covalent geometry : bond 0.00557 ( 8261) covalent geometry : angle 0.64607 (11160) hydrogen bonds : bond 0.04456 ( 437) hydrogen bonds : angle 5.14245 ( 1266) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 109 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 40 GLN cc_start: 0.7294 (mm-40) cc_final: 0.7076 (mm110) REVERT: A 52 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7127 (pm20) REVERT: A 128 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8469 (mm-30) REVERT: A 174 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.7418 (ptm-80) REVERT: A 237 GLU cc_start: 0.7422 (tp30) cc_final: 0.7118 (tp30) REVERT: A 420 PHE cc_start: 0.7994 (OUTLIER) cc_final: 0.7347 (m-10) REVERT: B 293 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7744 (mppt) REVERT: B 411 ARG cc_start: 0.7685 (OUTLIER) cc_final: 0.7071 (pmm-80) REVERT: B 559 GLU cc_start: 0.6899 (tp30) cc_final: 0.6609 (tt0) REVERT: C 38 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8460 (tttp) REVERT: C 144 TYR cc_start: 0.7227 (OUTLIER) cc_final: 0.6991 (m-10) outliers start: 48 outliers final: 27 residues processed: 147 average time/residue: 0.4933 time to fit residues: 77.3423 Evaluate side-chains 137 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 102 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 293 LYS Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 411 ARG Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain B residue 474 PHE Chi-restraints excluded: chain B residue 625 SER Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 83 CYS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 140 GLN Chi-restraints excluded: chain C residue 144 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 74 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 140 GLN A 464 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.202682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.165383 restraints weight = 8373.877| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 2.15 r_work: 0.3717 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3588 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8261 Z= 0.149 Angle : 0.569 6.989 11160 Z= 0.302 Chirality : 0.043 0.182 1233 Planarity : 0.004 0.034 1427 Dihedral : 5.410 54.624 1097 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.59 % Favored : 96.21 % Rotamer: Outliers : 4.51 % Allowed : 27.77 % Favored : 67.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.27), residues: 975 helix: 1.22 (0.26), residues: 394 sheet: 0.02 (0.34), residues: 240 loop : -1.03 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 528 TYR 0.018 0.001 TYR C 78 PHE 0.015 0.001 PHE A 172 TRP 0.011 0.002 TRP A 233 HIS 0.004 0.001 HIS B 520 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 8261) covalent geometry : angle 0.56945 (11160) hydrogen bonds : bond 0.03827 ( 437) hydrogen bonds : angle 5.00243 ( 1266) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 106 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8326 (mm-30) REVERT: A 174 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.7306 (ptm-80) REVERT: A 237 GLU cc_start: 0.7418 (tp30) cc_final: 0.7138 (tp30) REVERT: A 406 HIS cc_start: 0.7255 (t70) cc_final: 0.6991 (t70) REVERT: A 420 PHE cc_start: 0.7831 (OUTLIER) cc_final: 0.7276 (m-10) REVERT: B 411 ARG cc_start: 0.7583 (OUTLIER) cc_final: 0.6973 (pmm-80) REVERT: B 498 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7431 (mp0) REVERT: B 559 GLU cc_start: 0.6859 (tp30) cc_final: 0.6527 (pt0) REVERT: C 96 PHE cc_start: 0.7662 (OUTLIER) cc_final: 0.7390 (t80) outliers start: 40 outliers final: 24 residues processed: 139 average time/residue: 0.5399 time to fit residues: 79.9528 Evaluate side-chains 129 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 100 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 411 ARG Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 474 PHE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 625 SER Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 83 CYS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 96 PHE Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 140 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 41 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 92 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 140 GLN A 464 ASN B 447 ASN C 26 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.199115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.161474 restraints weight = 8363.869| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 2.09 r_work: 0.3680 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3554 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 8261 Z= 0.232 Angle : 0.645 6.863 11160 Z= 0.339 Chirality : 0.045 0.179 1233 Planarity : 0.004 0.042 1427 Dihedral : 5.621 54.984 1097 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.31 % Favored : 95.49 % Rotamer: Outliers : 5.76 % Allowed : 26.86 % Favored : 67.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.27), residues: 975 helix: 0.99 (0.26), residues: 394 sheet: -0.04 (0.34), residues: 242 loop : -1.12 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 528 TYR 0.027 0.002 TYR C 78 PHE 0.018 0.002 PHE A 28 TRP 0.020 0.002 TRP A 233 HIS 0.005 0.001 HIS B 631 Details of bonding type rmsd covalent geometry : bond 0.00553 ( 8261) covalent geometry : angle 0.64486 (11160) hydrogen bonds : bond 0.04424 ( 437) hydrogen bonds : angle 5.15382 ( 1266) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 105 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 GLN cc_start: 0.7238 (mm-40) cc_final: 0.6981 (mm110) REVERT: A 52 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7121 (pm20) REVERT: A 128 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8464 (mm-30) REVERT: A 174 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7428 (ptm-80) REVERT: A 237 GLU cc_start: 0.7467 (tp30) cc_final: 0.7188 (tp30) REVERT: A 406 HIS cc_start: 0.7417 (t70) cc_final: 0.7194 (t70) REVERT: A 420 PHE cc_start: 0.8047 (OUTLIER) cc_final: 0.7430 (m-10) REVERT: A 447 ARG cc_start: 0.6680 (OUTLIER) cc_final: 0.5878 (tmm160) REVERT: B 293 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7718 (mppt) REVERT: B 411 ARG cc_start: 0.7670 (OUTLIER) cc_final: 0.7049 (pmm-80) REVERT: C 13 ILE cc_start: 0.8431 (OUTLIER) cc_final: 0.7852 (mm) REVERT: C 26 ASN cc_start: 0.7394 (OUTLIER) cc_final: 0.6622 (m110) REVERT: C 38 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8413 (tttp) REVERT: C 144 TYR cc_start: 0.7224 (OUTLIER) cc_final: 0.6991 (m-10) outliers start: 51 outliers final: 31 residues processed: 148 average time/residue: 0.5616 time to fit residues: 88.4947 Evaluate side-chains 145 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 103 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 293 LYS Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 411 ARG Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain B residue 474 PHE Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 625 SER Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 26 ASN Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 83 CYS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 96 PHE Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 140 GLN Chi-restraints excluded: chain C residue 144 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 39 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 84 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 90 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 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 19 GLN A 140 GLN A 464 ASN C 26 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.203920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.167291 restraints weight = 8349.370| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 2.09 r_work: 0.3696 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3561 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8261 Z= 0.150 Angle : 0.578 6.467 11160 Z= 0.306 Chirality : 0.043 0.176 1233 Planarity : 0.004 0.045 1427 Dihedral : 5.441 55.161 1097 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.69 % Favored : 96.10 % Rotamer: Outliers : 4.40 % Allowed : 28.44 % Favored : 67.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.27), residues: 975 helix: 1.07 (0.26), residues: 400 sheet: -0.02 (0.34), residues: 240 loop : -1.04 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 528 TYR 0.019 0.001 TYR C 78 PHE 0.015 0.001 PHE A 172 TRP 0.025 0.002 TRP A 233 HIS 0.005 0.001 HIS A 406 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 8261) covalent geometry : angle 0.57802 (11160) hydrogen bonds : bond 0.03882 ( 437) hydrogen bonds : angle 5.03153 ( 1266) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 102 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: A 40 GLN cc_start: 0.7246 (mm-40) cc_final: 0.7012 (mm110) REVERT: A 174 ARG cc_start: 0.7810 (OUTLIER) cc_final: 0.7380 (ptm-80) REVERT: A 237 GLU cc_start: 0.7406 (tp30) cc_final: 0.7124 (tp30) REVERT: A 356 ASP cc_start: 0.6117 (t0) cc_final: 0.5832 (t0) REVERT: A 406 HIS cc_start: 0.7321 (t70) cc_final: 0.7024 (t70) REVERT: A 420 PHE cc_start: 0.7838 (OUTLIER) cc_final: 0.7295 (m-10) REVERT: A 447 ARG cc_start: 0.6576 (OUTLIER) cc_final: 0.5708 (tmm160) REVERT: B 293 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.7776 (mppt) REVERT: B 411 ARG cc_start: 0.7509 (OUTLIER) cc_final: 0.6821 (pmm-80) REVERT: C 26 ASN cc_start: 0.7182 (OUTLIER) cc_final: 0.6373 (m110) REVERT: C 96 PHE cc_start: 0.7792 (OUTLIER) cc_final: 0.7484 (t80) REVERT: C 144 TYR cc_start: 0.7217 (OUTLIER) cc_final: 0.6970 (m-10) REVERT: C 164 GLN cc_start: 0.6996 (mt0) cc_final: 0.6747 (mp10) outliers start: 39 outliers final: 20 residues processed: 136 average time/residue: 0.5605 time to fit residues: 81.1498 Evaluate side-chains 128 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 293 LYS Chi-restraints excluded: chain B residue 411 ARG Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 474 PHE Chi-restraints excluded: chain B residue 625 SER Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 26 ASN Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 83 CYS Chi-restraints excluded: chain C residue 96 PHE Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 140 GLN Chi-restraints excluded: chain C residue 144 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 63 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 73 optimal weight: 0.0470 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 140 GLN A 464 ASN C 26 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.203589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.167732 restraints weight = 8502.888| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 2.13 r_work: 0.3677 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3546 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 8261 Z= 0.180 Angle : 0.612 6.681 11160 Z= 0.322 Chirality : 0.044 0.176 1233 Planarity : 0.004 0.034 1427 Dihedral : 5.301 54.666 1094 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.21 % Favored : 95.59 % Rotamer: Outliers : 4.63 % Allowed : 28.44 % Favored : 66.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.27), residues: 975 helix: 1.04 (0.26), residues: 400 sheet: -0.05 (0.34), residues: 240 loop : -1.02 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 528 TYR 0.022 0.002 TYR C 78 PHE 0.018 0.002 PHE A 209 TRP 0.035 0.002 TRP A 233 HIS 0.005 0.001 HIS A 406 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 8261) covalent geometry : angle 0.61239 (11160) hydrogen bonds : bond 0.04091 ( 437) hydrogen bonds : angle 5.06124 ( 1266) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 103 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: A 40 GLN cc_start: 0.7273 (mm-40) cc_final: 0.7024 (mm110) REVERT: A 52 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7205 (pm20) REVERT: A 174 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7385 (ptm-80) REVERT: A 237 GLU cc_start: 0.7507 (tp30) cc_final: 0.7229 (tp30) REVERT: A 420 PHE cc_start: 0.7953 (OUTLIER) cc_final: 0.7321 (m-10) REVERT: A 447 ARG cc_start: 0.6661 (OUTLIER) cc_final: 0.5782 (tmm160) REVERT: B 293 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.7816 (mppt) REVERT: B 411 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.6913 (pmm-80) REVERT: B 559 GLU cc_start: 0.6842 (tp30) cc_final: 0.6603 (tt0) REVERT: C 26 ASN cc_start: 0.7214 (OUTLIER) cc_final: 0.6430 (m110) REVERT: C 67 GLN cc_start: 0.7507 (OUTLIER) cc_final: 0.6977 (mp10) REVERT: C 144 TYR cc_start: 0.7223 (OUTLIER) cc_final: 0.6978 (m-10) REVERT: C 164 GLN cc_start: 0.7070 (mt0) cc_final: 0.6830 (mp10) outliers start: 41 outliers final: 24 residues processed: 138 average time/residue: 0.5694 time to fit residues: 83.7454 Evaluate side-chains 135 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 102 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 293 LYS Chi-restraints excluded: chain B residue 411 ARG Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 474 PHE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 625 SER Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 26 ASN Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 83 CYS Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 140 GLN Chi-restraints excluded: chain C residue 144 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 3 optimal weight: 0.0570 chunk 33 optimal weight: 2.9990 chunk 25 optimal weight: 0.3980 chunk 28 optimal weight: 0.7980 chunk 92 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 63 optimal weight: 7.9990 chunk 17 optimal weight: 0.3980 chunk 75 optimal weight: 0.5980 chunk 96 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 140 GLN A 464 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.203711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.167837 restraints weight = 8423.267| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 2.00 r_work: 0.3689 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3554 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.196 8261 Z= 0.269 Angle : 1.016 59.184 11160 Z= 0.612 Chirality : 0.049 0.692 1233 Planarity : 0.006 0.143 1427 Dihedral : 5.296 54.691 1094 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.10 % Favored : 95.69 % Rotamer: Outliers : 3.84 % Allowed : 29.12 % Favored : 67.04 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.27), residues: 975 helix: 1.06 (0.26), residues: 400 sheet: -0.05 (0.34), residues: 240 loop : -1.03 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 370 TYR 0.020 0.001 TYR C 78 PHE 0.042 0.002 PHE A 209 TRP 0.029 0.002 TRP A 233 HIS 0.007 0.001 HIS A 406 Details of bonding type rmsd covalent geometry : bond 0.00558 ( 8261) covalent geometry : angle 1.01599 (11160) hydrogen bonds : bond 0.04108 ( 437) hydrogen bonds : angle 5.08201 ( 1266) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3162.21 seconds wall clock time: 54 minutes 32.64 seconds (3272.64 seconds total)