Starting phenix.real_space_refine on Sun Apr 5 01:16:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dpd_47103/04_2026/9dpd_47103.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dpd_47103/04_2026/9dpd_47103.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dpd_47103/04_2026/9dpd_47103.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dpd_47103/04_2026/9dpd_47103.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dpd_47103/04_2026/9dpd_47103.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dpd_47103/04_2026/9dpd_47103.map" } resolution = 3.87 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= 0.109 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 P 2 5.49 5 S 43 5.16 5 C 4268 2.51 5 N 1116 2.21 5 O 1235 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6664 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1742 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 201} Chain breaks: 5 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "D" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2693 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 316} Chain breaks: 4 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 2, 'HIS:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "C" Number of atoms: 2193 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 280, 2185 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 264} Chain breaks: 1 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2, 'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 29 Conformer: "B" Number of residues, atoms: 280, 2185 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 264} Chain breaks: 1 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2, 'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 29 bond proxies already assigned to first conformer: 2224 Chain: "C" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.15, per 1000 atoms: 0.32 Number of scatterers: 6664 At special positions: 0 Unit cell: (77.05, 88.55, 117.3, 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) S 43 16.00 P 2 15.00 O 1235 8.00 N 1116 7.00 C 4268 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 148 " - pdb=" SG CYS C 324 " distance=2.04 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: 0.65 Conformation dependent library (CDL) restraints added in 372.1 milliseconds 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1580 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 9 sheets defined 41.9% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'B' and resid 169 through 177 removed outlier: 4.552A pdb=" N VAL B 175 " --> pdb=" O VAL B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 218 Processing helix chain 'B' and resid 275 through 279 Processing helix chain 'B' and resid 286 through 290 removed outlier: 3.574A pdb=" N LEU B 290 " --> pdb=" O PRO B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 355 removed outlier: 3.657A pdb=" N LEU B 355 " --> pdb=" O PHE B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 433 through 445 removed outlier: 3.643A pdb=" N GLN B 445 " --> pdb=" O LEU B 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 9 Processing helix chain 'D' and resid 15 through 26 removed outlier: 3.703A pdb=" N ILE D 19 " --> pdb=" O ASP D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 49 removed outlier: 3.959A pdb=" N GLU D 42 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE D 48 " --> pdb=" O ARG D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 133 removed outlier: 3.657A pdb=" N ALA D 126 " --> pdb=" O ILE D 122 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU D 127 " --> pdb=" O LYS D 123 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE D 129 " --> pdb=" O GLU D 125 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU D 130 " --> pdb=" O ALA D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 153 Processing helix chain 'D' and resid 169 through 177 removed outlier: 4.418A pdb=" N VAL D 175 " --> pdb=" O VAL D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 218 removed outlier: 3.628A pdb=" N PHE D 202 " --> pdb=" O GLY D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 335 through 355 removed outlier: 3.532A pdb=" N LEU D 355 " --> pdb=" O PHE D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 406 removed outlier: 3.631A pdb=" N ARG D 405 " --> pdb=" O TYR D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 445 removed outlier: 3.777A pdb=" N GLN D 445 " --> pdb=" O LEU D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 457 Processing helix chain 'C' and resid 63 through 73 Processing helix chain 'C' and resid 85 through 92 removed outlier: 3.866A pdb=" N SER C 88 " --> pdb=" O ALA C 85 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR C 89 " --> pdb=" O GLY C 86 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N SER C 90 " --> pdb=" O ILE C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 119 removed outlier: 4.185A pdb=" N ILE C 118 " --> pdb=" O PRO C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 125 Processing helix chain 'C' and resid 128 through 139 removed outlier: 3.793A pdb=" N LYS C 136 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N GLU C 137 " --> pdb=" O ALA C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 158 removed outlier: 3.728A pdb=" N TYR C 150 " --> pdb=" O THR C 146 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N MET C 152 " --> pdb=" O CYS C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 177 Processing helix chain 'C' and resid 205 through 214 removed outlier: 4.140A pdb=" N MET C 209 " --> pdb=" O PRO C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 251 removed outlier: 3.874A pdb=" N PHE C 244 " --> pdb=" O PRO C 240 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 270 No H-bonds generated for 'chain 'C' and resid 268 through 270' Processing helix chain 'C' and resid 271 through 276 removed outlier: 3.534A pdb=" N LYS C 275 " --> pdb=" O SER C 271 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA C 276 " --> pdb=" O LEU C 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 271 through 276' Processing helix chain 'C' and resid 323 through 336 removed outlier: 4.117A pdb=" N GLY C 327 " --> pdb=" O GLU C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 355 Processing sheet with id=AA1, first strand: chain 'B' and resid 157 through 159 removed outlier: 3.576A pdb=" N ARG B 157 " --> pdb=" O ILE B 361 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL B 393 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ALA B 381 " --> pdb=" O GLU B 391 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLU B 391 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 9.230A pdb=" N LEU B 392 " --> pdb=" O CYS B 431 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N CYS B 431 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER B 394 " --> pdb=" O THR B 429 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN B 427 " --> pdb=" O SER B 396 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N CYS B 398 " --> pdb=" O MET B 425 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N MET B 425 " --> pdb=" O CYS B 398 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ASN B 427 " --> pdb=" O VAL B 328 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N VAL B 328 " --> pdb=" O ASN B 427 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N THR B 429 " --> pdb=" O GLN B 326 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLN B 326 " --> pdb=" O THR B 429 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE B 292 " --> pdb=" O TYR B 329 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 157 through 159 removed outlier: 3.576A pdb=" N ARG B 157 " --> pdb=" O ILE B 361 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL B 393 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ALA B 381 " --> pdb=" O GLU B 391 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLU B 391 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 9.230A pdb=" N LEU B 392 " --> pdb=" O CYS B 431 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N CYS B 431 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER B 394 " --> pdb=" O THR B 429 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN B 427 " --> pdb=" O SER B 396 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N CYS B 398 " --> pdb=" O MET B 425 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N MET B 425 " --> pdb=" O CYS B 398 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ASN B 427 " --> pdb=" O VAL B 328 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N VAL B 328 " --> pdb=" O ASN B 427 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N THR B 429 " --> pdb=" O GLN B 326 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLN B 326 " --> pdb=" O THR B 429 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AA4, first strand: chain 'D' and resid 154 through 159 removed outlier: 3.616A pdb=" N LYS D 154 " --> pdb=" O ASN D 363 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE D 361 " --> pdb=" O GLU D 156 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N ILE D 158 " --> pdb=" O TYR D 359 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N TYR D 359 " --> pdb=" O ILE D 158 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ALA D 381 " --> pdb=" O GLU D 391 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N GLU D 391 " --> pdb=" O ALA D 381 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N VAL D 393 " --> pdb=" O CYS D 431 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N CYS D 431 " --> pdb=" O VAL D 393 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N CYS D 395 " --> pdb=" O THR D 429 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N THR D 429 " --> pdb=" O CYS D 395 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ASN D 397 " --> pdb=" O ASN D 427 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ASN D 427 " --> pdb=" O ASN D 397 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N MET D 425 " --> pdb=" O SER D 330 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N SER D 330 " --> pdb=" O MET D 425 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ASN D 427 " --> pdb=" O VAL D 328 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N VAL D 328 " --> pdb=" O ASN D 427 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N THR D 429 " --> pdb=" O GLN D 326 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N GLN D 326 " --> pdb=" O THR D 429 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE D 327 " --> pdb=" O TYR D 294 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE D 292 " --> pdb=" O TYR D 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 409 through 410 removed outlier: 4.316A pdb=" N GLU D 421 " --> pdb=" O TYR D 410 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 449 through 451 removed outlier: 3.760A pdb=" N ILE D 450 " --> pdb=" O ILE D 468 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 183 through 185 removed outlier: 6.186A pdb=" N CYS C 164 " --> pdb=" O VAL C 184 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ILE C 80 " --> pdb=" O LEU C 258 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N MET C 260 " --> pdb=" O ILE C 80 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU C 82 " --> pdb=" O MET C 260 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 193 through 195 Processing sheet with id=AA9, first strand: chain 'C' and resid 285 through 286 260 hydrogen bonds defined for protein. 729 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: 1.00 Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2148 1.35 - 1.47: 1581 1.47 - 1.59: 3023 1.59 - 1.71: 4 1.71 - 1.83: 61 Bond restraints: 6817 Sorted by residual: bond pdb=" N THR C 171 " pdb=" CA THR C 171 " ideal model delta sigma weight residual 1.457 1.477 -0.019 1.29e-02 6.01e+03 2.21e+00 bond pdb=" CB MET D 417 " pdb=" CG MET D 417 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.29e+00 bond pdb=" CB CYS C 324 " pdb=" SG CYS C 324 " ideal model delta sigma weight residual 1.808 1.772 0.036 3.30e-02 9.18e+02 1.22e+00 bond pdb=" CB ARG C 201 " pdb=" CG ARG C 201 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.07e+00 bond pdb=" C GLU D 466 " pdb=" O GLU D 466 " ideal model delta sigma weight residual 1.243 1.234 0.010 9.50e-03 1.11e+04 1.01e+00 ... (remaining 6812 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 9015 1.99 - 3.97: 179 3.97 - 5.96: 21 5.96 - 7.94: 12 7.94 - 9.93: 4 Bond angle restraints: 9231 Sorted by residual: angle pdb=" C GLU D 466 " pdb=" CA GLU D 466 " pdb=" CB GLU D 466 " ideal model delta sigma weight residual 117.23 110.48 6.75 1.36e+00 5.41e-01 2.46e+01 angle pdb=" CA MET D 417 " pdb=" CB MET D 417 " pdb=" CG MET D 417 " ideal model delta sigma weight residual 114.10 121.61 -7.51 2.00e+00 2.50e-01 1.41e+01 angle pdb=" CA ARG C 201 " pdb=" CB ARG C 201 " pdb=" CG ARG C 201 " ideal model delta sigma weight residual 114.10 121.60 -7.50 2.00e+00 2.50e-01 1.41e+01 angle pdb=" CA CYS C 324 " pdb=" CB CYS C 324 " pdb=" SG CYS C 324 " ideal model delta sigma weight residual 114.40 122.67 -8.27 2.30e+00 1.89e-01 1.29e+01 angle pdb=" CA GLU D 466 " pdb=" C GLU D 466 " pdb=" N LEU D 467 " ideal model delta sigma weight residual 119.98 116.95 3.03 8.50e-01 1.38e+00 1.27e+01 ... (remaining 9226 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.49: 3739 24.49 - 48.97: 375 48.97 - 73.46: 32 73.46 - 97.94: 10 97.94 - 122.43: 2 Dihedral angle restraints: 4158 sinusoidal: 1724 harmonic: 2434 Sorted by residual: dihedral pdb=" CA CYS C 324 " pdb=" C CYS C 324 " pdb=" N ASP C 325 " pdb=" CA ASP C 325 " ideal model delta harmonic sigma weight residual -180.00 -154.42 -25.58 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA LYS C 126 " pdb=" C LYS C 126 " pdb=" N HIS C 127 " pdb=" CA HIS C 127 " ideal model delta harmonic sigma weight residual 180.00 158.66 21.34 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" O1A AR6 C 401 " pdb=" O3A AR6 C 401 " pdb=" PA AR6 C 401 " pdb=" PB AR6 C 401 " ideal model delta sinusoidal sigma weight residual -82.51 39.92 -122.43 1 3.00e+01 1.11e-03 1.64e+01 ... (remaining 4155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 745 0.044 - 0.088: 207 0.088 - 0.132: 61 0.132 - 0.176: 5 0.176 - 0.220: 3 Chirality restraints: 1021 Sorted by residual: chirality pdb=" CB ILE D 408 " pdb=" CA ILE D 408 " pdb=" CG1 ILE D 408 " pdb=" CG2 ILE D 408 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CB THR D 429 " pdb=" CA THR D 429 " pdb=" OG1 THR D 429 " pdb=" CG2 THR D 429 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CB ILE B 408 " pdb=" CA ILE B 408 " pdb=" CG1 ILE B 408 " pdb=" CG2 ILE B 408 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.18 2.00e-01 2.50e+01 7.99e-01 ... (remaining 1018 not shown) Planarity restraints: 1177 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS C 127 " 0.047 5.00e-02 4.00e+02 7.19e-02 8.27e+00 pdb=" N PRO C 128 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO C 128 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 128 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET D 417 " 0.009 2.00e-02 2.50e+03 1.85e-02 3.44e+00 pdb=" C MET D 417 " -0.032 2.00e-02 2.50e+03 pdb=" O MET D 417 " 0.012 2.00e-02 2.50e+03 pdb=" N ASP D 418 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 321 " 0.008 2.00e-02 2.50e+03 1.71e-02 2.93e+00 pdb=" C PHE D 321 " -0.030 2.00e-02 2.50e+03 pdb=" O PHE D 321 " 0.011 2.00e-02 2.50e+03 pdb=" N GLU D 322 " 0.010 2.00e-02 2.50e+03 ... (remaining 1174 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 2752 2.93 - 3.42: 6730 3.42 - 3.91: 10922 3.91 - 4.41: 12382 4.41 - 4.90: 20084 Nonbonded interactions: 52870 Sorted by model distance: nonbonded pdb=" O ASP D 152 " pdb=" OD1 ASP D 152 " model vdw 2.436 3.040 nonbonded pdb=" N GLN D 320 " pdb=" NE2 GLN D 320 " model vdw 2.449 3.200 nonbonded pdb=" O THR C 171 " pdb=" OG1 THR C 171 " model vdw 2.539 3.040 nonbonded pdb=" N GLN C 326 " pdb=" OE1 GLN C 326 " model vdw 2.552 3.120 nonbonded pdb=" N ASP B 400 " pdb=" OD1 ASP B 400 " model vdw 2.558 3.120 ... (remaining 52865 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=0.09 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: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.810 Find NCS groups from input model: 0.020 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: 0.000 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 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 0.036 6818 Z= 0.138 Angle : 0.717 9.928 9233 Z= 0.377 Chirality : 0.045 0.220 1021 Planarity : 0.005 0.072 1177 Dihedral : 17.801 122.430 2575 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.67 % Allowed : 26.22 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % 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: -0.80 (0.29), residues: 807 helix: 0.09 (0.30), residues: 309 sheet: -1.68 (0.46), residues: 130 loop : -0.46 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 75 TYR 0.013 0.001 TYR C 114 PHE 0.011 0.001 PHE C 235 TRP 0.016 0.001 TRP C 337 HIS 0.006 0.001 HIS C 187 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 6817) covalent geometry : angle 0.71426 ( 9231) SS BOND : bond 0.00625 ( 1) SS BOND : angle 4.43259 ( 2) hydrogen bonds : bond 0.18921 ( 246) hydrogen bonds : angle 7.66450 ( 729) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 225 THR cc_start: 0.4115 (OUTLIER) cc_final: 0.3604 (p) REVERT: B 343 GLU cc_start: 0.7622 (tm-30) cc_final: 0.7183 (tm-30) REVERT: D 405 ARG cc_start: 0.8305 (ttm110) cc_final: 0.7801 (tmt170) REVERT: D 456 LEU cc_start: 0.9089 (tp) cc_final: 0.8870 (tp) REVERT: C 93 ILE cc_start: 0.7581 (OUTLIER) cc_final: 0.7050 (tp) REVERT: C 278 LEU cc_start: 0.8300 (pp) cc_final: 0.7763 (mp) outliers start: 12 outliers final: 8 residues processed: 116 average time/residue: 0.0833 time to fit residues: 12.7426 Evaluate side-chains 107 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 267 GLN Chi-restraints excluded: chain C residue 337 TRP Chi-restraints excluded: chain C residue 341 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.0270 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.0980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.0870 chunk 74 optimal weight: 1.9990 overall best weight: 0.3016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 205 GLN D 320 GLN C 167 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.176032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.169766 restraints weight = 13088.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.159404 restraints weight = 21645.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.158374 restraints weight = 17781.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.158704 restraints weight = 16183.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.159167 restraints weight = 11736.015| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3699 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3699 r_free = 0.3699 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3699 r_free = 0.3699 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3699 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.0948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6818 Z= 0.115 Angle : 0.615 8.489 9233 Z= 0.307 Chirality : 0.045 0.175 1021 Planarity : 0.005 0.062 1177 Dihedral : 8.904 121.869 970 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.91 % Allowed : 25.52 % Favored : 70.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % 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: -0.70 (0.30), residues: 807 helix: 0.17 (0.30), residues: 315 sheet: -1.59 (0.45), residues: 140 loop : -0.37 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 407 TYR 0.011 0.001 TYR D 352 PHE 0.016 0.001 PHE C 269 TRP 0.006 0.001 TRP D 43 HIS 0.005 0.001 HIS D 140 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 6817) covalent geometry : angle 0.61280 ( 9231) SS BOND : bond 0.00424 ( 1) SS BOND : angle 3.55304 ( 2) hydrogen bonds : bond 0.04315 ( 246) hydrogen bonds : angle 5.71961 ( 729) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 204 GLU cc_start: 0.7004 (OUTLIER) cc_final: 0.6516 (tt0) REVERT: B 343 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7467 (tm-30) REVERT: D 420 VAL cc_start: 0.8035 (OUTLIER) cc_final: 0.7781 (m) REVERT: C 93 ILE cc_start: 0.7536 (OUTLIER) cc_final: 0.7031 (tp) outliers start: 28 outliers final: 16 residues processed: 128 average time/residue: 0.0731 time to fit residues: 12.8796 Evaluate side-chains 116 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 341 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 0 optimal weight: 4.9990 chunk 5 optimal weight: 0.0980 chunk 54 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 53 optimal weight: 0.0370 chunk 29 optimal weight: 1.9990 overall best weight: 0.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 131 ASN D 320 GLN D 326 GLN D 363 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.169845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.163136 restraints weight = 15938.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.157471 restraints weight = 23820.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.152906 restraints weight = 16157.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.154236 restraints weight = 15420.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.154170 restraints weight = 11445.258| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3653 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3653 r_free = 0.3653 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3653 r_free = 0.3653 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3653 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6818 Z= 0.151 Angle : 0.624 8.726 9233 Z= 0.312 Chirality : 0.046 0.230 1021 Planarity : 0.004 0.057 1177 Dihedral : 8.372 117.748 961 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 6.14 % Allowed : 23.71 % Favored : 70.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % 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: -0.67 (0.30), residues: 807 helix: 0.17 (0.30), residues: 317 sheet: -1.66 (0.44), residues: 138 loop : -0.29 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 69 TYR 0.012 0.002 TYR C 114 PHE 0.015 0.002 PHE C 269 TRP 0.010 0.001 TRP C 337 HIS 0.007 0.001 HIS C 187 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 6817) covalent geometry : angle 0.62036 ( 9231) SS BOND : bond 0.00798 ( 1) SS BOND : angle 4.65954 ( 2) hydrogen bonds : bond 0.04085 ( 246) hydrogen bonds : angle 5.22783 ( 729) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 104 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 172 ASP cc_start: 0.7690 (t70) cc_final: 0.7397 (t70) REVERT: B 204 GLU cc_start: 0.7048 (OUTLIER) cc_final: 0.6582 (tt0) REVERT: B 343 GLU cc_start: 0.7733 (tm-30) cc_final: 0.7372 (tm-30) REVERT: B 400 ASP cc_start: 0.5878 (p0) cc_final: 0.5662 (p0) REVERT: D 131 ASN cc_start: 0.8603 (OUTLIER) cc_final: 0.8226 (t0) REVERT: D 221 ILE cc_start: 0.8620 (OUTLIER) cc_final: 0.8370 (tt) REVERT: D 431 CYS cc_start: 0.8668 (OUTLIER) cc_final: 0.7749 (p) REVERT: C 93 ILE cc_start: 0.7977 (OUTLIER) cc_final: 0.7447 (tp) outliers start: 44 outliers final: 24 residues processed: 130 average time/residue: 0.0708 time to fit residues: 12.9947 Evaluate side-chains 129 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 100 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 320 GLN Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 344 MET Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 431 CYS Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 341 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 78 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 131 ASN D 320 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.169767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.163552 restraints weight = 11316.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.152855 restraints weight = 19792.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.151336 restraints weight = 19822.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.151420 restraints weight = 17135.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.151786 restraints weight = 14241.629| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3612 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3612 r_free = 0.3612 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3612 r_free = 0.3612 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3612 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6818 Z= 0.156 Angle : 0.627 9.172 9233 Z= 0.312 Chirality : 0.045 0.169 1021 Planarity : 0.004 0.055 1177 Dihedral : 8.380 116.936 961 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 6.28 % Allowed : 24.55 % Favored : 69.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % 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: -0.67 (0.29), residues: 807 helix: 0.19 (0.29), residues: 317 sheet: -1.74 (0.44), residues: 133 loop : -0.30 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 69 TYR 0.012 0.001 TYR C 114 PHE 0.012 0.001 PHE C 269 TRP 0.010 0.001 TRP C 337 HIS 0.007 0.001 HIS C 187 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 6817) covalent geometry : angle 0.62400 ( 9231) SS BOND : bond 0.00990 ( 1) SS BOND : angle 4.53030 ( 2) hydrogen bonds : bond 0.03758 ( 246) hydrogen bonds : angle 5.09533 ( 729) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 106 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 204 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6557 (tt0) REVERT: B 285 LEU cc_start: 0.5752 (mt) cc_final: 0.5547 (mp) REVERT: B 400 ASP cc_start: 0.5795 (p0) cc_final: 0.5538 (p0) REVERT: D 221 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8473 (tt) REVERT: D 431 CYS cc_start: 0.8634 (OUTLIER) cc_final: 0.7736 (p) REVERT: C 93 ILE cc_start: 0.8066 (OUTLIER) cc_final: 0.7629 (tp) outliers start: 45 outliers final: 28 residues processed: 133 average time/residue: 0.0726 time to fit residues: 13.5396 Evaluate side-chains 135 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 103 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 300 CYS Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 416 MET Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 431 CYS Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 341 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 2 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 320 GLN ** C 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.167950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.160609 restraints weight = 10869.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.152822 restraints weight = 18917.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.151617 restraints weight = 13860.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.151600 restraints weight = 13335.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.151801 restraints weight = 11049.406| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3624 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3624 r_free = 0.3624 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3624 r_free = 0.3624 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3624 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6818 Z= 0.145 Angle : 0.624 8.496 9233 Z= 0.310 Chirality : 0.045 0.165 1021 Planarity : 0.004 0.053 1177 Dihedral : 8.375 115.472 961 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 5.58 % Allowed : 25.94 % Favored : 68.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % 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: -0.62 (0.30), residues: 807 helix: 0.27 (0.30), residues: 316 sheet: -1.77 (0.45), residues: 129 loop : -0.31 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 69 TYR 0.014 0.002 TYR D 352 PHE 0.011 0.001 PHE C 151 TRP 0.010 0.001 TRP C 337 HIS 0.007 0.001 HIS C 187 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 6817) covalent geometry : angle 0.62045 ( 9231) SS BOND : bond 0.00411 ( 1) SS BOND : angle 4.83246 ( 2) hydrogen bonds : bond 0.03612 ( 246) hydrogen bonds : angle 4.92756 ( 729) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 102 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 172 ASP cc_start: 0.7723 (t70) cc_final: 0.7344 (t70) REVERT: B 204 GLU cc_start: 0.7003 (OUTLIER) cc_final: 0.6607 (tt0) REVERT: B 382 TRP cc_start: 0.7826 (t-100) cc_final: 0.6846 (t-100) REVERT: B 400 ASP cc_start: 0.5998 (p0) cc_final: 0.5652 (p0) REVERT: D 410 TYR cc_start: 0.9015 (OUTLIER) cc_final: 0.8453 (t80) REVERT: D 431 CYS cc_start: 0.8617 (OUTLIER) cc_final: 0.7811 (p) REVERT: C 93 ILE cc_start: 0.8111 (OUTLIER) cc_final: 0.7755 (tp) outliers start: 40 outliers final: 27 residues processed: 129 average time/residue: 0.0648 time to fit residues: 11.9149 Evaluate side-chains 130 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 99 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 320 GLN Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 410 TYR Chi-restraints excluded: chain D residue 416 MET Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 431 CYS Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 341 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 63 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 66 optimal weight: 0.4980 chunk 2 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.167520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.161017 restraints weight = 12897.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.150955 restraints weight = 20789.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.149806 restraints weight = 20663.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.149736 restraints weight = 19333.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.150017 restraints weight = 14341.174| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3625 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3625 r_free = 0.3625 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3625 r_free = 0.3625 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3625 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6818 Z= 0.145 Angle : 0.625 8.667 9233 Z= 0.309 Chirality : 0.044 0.162 1021 Planarity : 0.004 0.052 1177 Dihedral : 8.332 114.354 961 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 5.44 % Allowed : 26.08 % Favored : 68.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % 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: -0.65 (0.30), residues: 807 helix: 0.27 (0.30), residues: 316 sheet: -1.82 (0.44), residues: 135 loop : -0.30 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 69 TYR 0.012 0.001 TYR C 114 PHE 0.011 0.001 PHE C 151 TRP 0.010 0.001 TRP C 337 HIS 0.006 0.001 HIS C 187 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 6817) covalent geometry : angle 0.62141 ( 9231) SS BOND : bond 0.00034 ( 1) SS BOND : angle 4.67435 ( 2) hydrogen bonds : bond 0.03588 ( 246) hydrogen bonds : angle 4.86909 ( 729) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 104 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 204 GLU cc_start: 0.7033 (OUTLIER) cc_final: 0.6644 (tt0) REVERT: B 382 TRP cc_start: 0.7843 (t-100) cc_final: 0.6892 (t-100) REVERT: B 400 ASP cc_start: 0.5959 (p0) cc_final: 0.5661 (p0) REVERT: D 410 TYR cc_start: 0.9003 (OUTLIER) cc_final: 0.8434 (t80) REVERT: D 431 CYS cc_start: 0.8636 (OUTLIER) cc_final: 0.7890 (p) REVERT: C 93 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7815 (tp) REVERT: C 278 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7289 (mp) outliers start: 39 outliers final: 30 residues processed: 130 average time/residue: 0.0701 time to fit residues: 12.7994 Evaluate side-chains 135 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 100 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 300 CYS Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 410 TYR Chi-restraints excluded: chain D residue 416 MET Chi-restraints excluded: chain D residue 431 CYS Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 267 GLN Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 341 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 21 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 59 optimal weight: 0.0670 chunk 33 optimal weight: 0.7980 chunk 52 optimal weight: 0.0470 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 0.0170 overall best weight: 0.3854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.169462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.162241 restraints weight = 17226.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.154738 restraints weight = 28014.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.152100 restraints weight = 17779.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.152344 restraints weight = 15109.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.152839 restraints weight = 11406.085| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3625 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3625 r_free = 0.3625 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3625 r_free = 0.3625 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3625 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6818 Z= 0.114 Angle : 0.598 8.716 9233 Z= 0.296 Chirality : 0.044 0.217 1021 Planarity : 0.004 0.050 1177 Dihedral : 8.023 113.805 959 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 4.18 % Allowed : 27.48 % Favored : 68.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % 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: -0.49 (0.30), residues: 807 helix: 0.37 (0.30), residues: 316 sheet: -1.70 (0.45), residues: 131 loop : -0.23 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 69 TYR 0.012 0.001 TYR C 204 PHE 0.011 0.001 PHE D 389 TRP 0.009 0.001 TRP C 337 HIS 0.005 0.001 HIS D 140 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 6817) covalent geometry : angle 0.59531 ( 9231) SS BOND : bond 0.00015 ( 1) SS BOND : angle 4.23298 ( 2) hydrogen bonds : bond 0.03266 ( 246) hydrogen bonds : angle 4.75152 ( 729) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 107 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 204 GLU cc_start: 0.7072 (OUTLIER) cc_final: 0.6674 (tt0) REVERT: B 382 TRP cc_start: 0.7875 (t-100) cc_final: 0.6808 (t-100) REVERT: B 400 ASP cc_start: 0.5813 (p0) cc_final: 0.5527 (p0) REVERT: D 410 TYR cc_start: 0.8943 (OUTLIER) cc_final: 0.8599 (t80) REVERT: D 431 CYS cc_start: 0.8710 (OUTLIER) cc_final: 0.7867 (p) REVERT: C 93 ILE cc_start: 0.8137 (OUTLIER) cc_final: 0.7748 (tp) REVERT: C 278 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7208 (mp) outliers start: 30 outliers final: 20 residues processed: 130 average time/residue: 0.0694 time to fit residues: 12.6202 Evaluate side-chains 124 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 410 TYR Chi-restraints excluded: chain D residue 431 CYS Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 267 GLN Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 341 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 35 optimal weight: 0.0980 chunk 58 optimal weight: 0.4980 chunk 38 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 397 ASN ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.169520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.162843 restraints weight = 13177.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.152801 restraints weight = 22307.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.152116 restraints weight = 16473.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.152157 restraints weight = 15244.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.152468 restraints weight = 11803.343| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3618 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3618 r_free = 0.3618 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3618 r_free = 0.3618 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3618 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6818 Z= 0.128 Angle : 0.619 10.787 9233 Z= 0.307 Chirality : 0.044 0.211 1021 Planarity : 0.004 0.048 1177 Dihedral : 7.997 112.019 959 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.91 % Allowed : 28.45 % Favored : 67.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % 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: -0.51 (0.30), residues: 807 helix: 0.39 (0.30), residues: 316 sheet: -1.80 (0.43), residues: 137 loop : -0.20 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 69 TYR 0.011 0.001 TYR C 204 PHE 0.011 0.001 PHE D 389 TRP 0.010 0.001 TRP C 337 HIS 0.005 0.001 HIS C 187 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 6817) covalent geometry : angle 0.61570 ( 9231) SS BOND : bond 0.00047 ( 1) SS BOND : angle 4.12643 ( 2) hydrogen bonds : bond 0.03338 ( 246) hydrogen bonds : angle 4.74033 ( 729) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 382 TRP cc_start: 0.7892 (t-100) cc_final: 0.6877 (t-100) REVERT: B 400 ASP cc_start: 0.5793 (p0) cc_final: 0.5537 (p0) REVERT: D 410 TYR cc_start: 0.8966 (OUTLIER) cc_final: 0.8578 (t80) REVERT: D 431 CYS cc_start: 0.8721 (OUTLIER) cc_final: 0.7906 (p) REVERT: C 93 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7770 (tp) REVERT: C 278 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7082 (mp) outliers start: 28 outliers final: 20 residues processed: 125 average time/residue: 0.0732 time to fit residues: 12.8544 Evaluate side-chains 125 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 410 TYR Chi-restraints excluded: chain D residue 431 CYS Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 267 GLN Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 341 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 80 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 42 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 397 ASN ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.165519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.158338 restraints weight = 16100.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.151021 restraints weight = 26220.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.147681 restraints weight = 17047.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.148301 restraints weight = 13709.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.148326 restraints weight = 11334.865| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3567 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3567 r_free = 0.3567 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3567 r_free = 0.3567 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3567 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 6818 Z= 0.197 Angle : 0.691 10.197 9233 Z= 0.345 Chirality : 0.047 0.206 1021 Planarity : 0.004 0.044 1177 Dihedral : 8.287 111.449 959 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 4.74 % Allowed : 27.89 % Favored : 67.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % 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: -0.75 (0.29), residues: 807 helix: 0.18 (0.29), residues: 316 sheet: -1.87 (0.42), residues: 130 loop : -0.39 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 409 TYR 0.016 0.002 TYR D 352 PHE 0.018 0.002 PHE C 151 TRP 0.014 0.002 TRP C 337 HIS 0.011 0.001 HIS C 187 Details of bonding type rmsd covalent geometry : bond 0.00475 ( 6817) covalent geometry : angle 0.68680 ( 9231) SS BOND : bond 0.00319 ( 1) SS BOND : angle 5.05739 ( 2) hydrogen bonds : bond 0.03844 ( 246) hydrogen bonds : angle 4.87804 ( 729) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 100 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 410 TYR cc_start: 0.8980 (OUTLIER) cc_final: 0.8429 (t80) REVERT: D 431 CYS cc_start: 0.8770 (OUTLIER) cc_final: 0.7912 (p) REVERT: C 278 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7211 (mp) outliers start: 34 outliers final: 25 residues processed: 125 average time/residue: 0.0729 time to fit residues: 12.6833 Evaluate side-chains 128 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 410 TYR Chi-restraints excluded: chain D residue 431 CYS Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 267 GLN Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 341 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 0.9980 chunk 36 optimal weight: 0.0020 chunk 31 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.167251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.159924 restraints weight = 8816.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.158890 restraints weight = 17605.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.152029 restraints weight = 17540.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.150684 restraints weight = 19337.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.150580 restraints weight = 19703.113| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3638 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3638 r_free = 0.3638 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3638 r_free = 0.3638 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3638 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6818 Z= 0.134 Angle : 0.653 10.347 9233 Z= 0.323 Chirality : 0.045 0.231 1021 Planarity : 0.004 0.041 1177 Dihedral : 8.200 113.704 959 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.35 % Allowed : 29.85 % Favored : 66.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % 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: -0.62 (0.30), residues: 807 helix: 0.27 (0.30), residues: 316 sheet: -1.85 (0.43), residues: 130 loop : -0.28 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 281 TYR 0.011 0.001 TYR C 114 PHE 0.012 0.001 PHE B 180 TRP 0.010 0.001 TRP C 337 HIS 0.005 0.001 HIS C 187 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 6817) covalent geometry : angle 0.64949 ( 9231) SS BOND : bond 0.00093 ( 1) SS BOND : angle 4.46875 ( 2) hydrogen bonds : bond 0.03450 ( 246) hydrogen bonds : angle 4.79818 ( 729) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 431 CYS cc_start: 0.8684 (OUTLIER) cc_final: 0.7850 (p) REVERT: C 278 LEU cc_start: 0.7540 (OUTLIER) cc_final: 0.7102 (mp) outliers start: 24 outliers final: 19 residues processed: 116 average time/residue: 0.0674 time to fit residues: 11.1431 Evaluate side-chains 114 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 431 CYS Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 267 GLN Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 341 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 10.0000 chunk 14 optimal weight: 0.7980 chunk 66 optimal weight: 0.4980 chunk 47 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 70 optimal weight: 7.9990 chunk 37 optimal weight: 0.3980 chunk 16 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 131 ASN D 402 GLN ** C 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.167192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.160480 restraints weight = 12526.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.149036 restraints weight = 22019.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.147544 restraints weight = 24371.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.147893 restraints weight = 21438.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.148276 restraints weight = 15142.139| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3592 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3592 r_free = 0.3592 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3592 r_free = 0.3592 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3592 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6818 Z= 0.138 Angle : 0.640 10.117 9233 Z= 0.316 Chirality : 0.044 0.194 1021 Planarity : 0.004 0.040 1177 Dihedral : 8.129 112.523 959 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.91 % Allowed : 29.01 % Favored : 67.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.38 % 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: -0.57 (0.30), residues: 807 helix: 0.28 (0.30), residues: 316 sheet: -1.77 (0.44), residues: 131 loop : -0.24 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 281 TYR 0.012 0.001 TYR D 352 PHE 0.013 0.001 PHE B 180 TRP 0.010 0.001 TRP C 337 HIS 0.006 0.001 HIS C 187 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 6817) covalent geometry : angle 0.63648 ( 9231) SS BOND : bond 0.00106 ( 1) SS BOND : angle 4.33378 ( 2) hydrogen bonds : bond 0.03369 ( 246) hydrogen bonds : angle 4.68394 ( 729) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1231.83 seconds wall clock time: 22 minutes 2.81 seconds (1322.81 seconds total)